Oxford Dictionary of Biochemistry and Molecular Biology

OXFORD DICTIONARY OF

BIOCHEMISTRY AND MOLECULAR BIOLOGY

Editors

General Editors

Subject Editors

Dr A. D. Smith (Managing Editor) Emeritus Reader in Biochemistry, and Honorary Research Fellow, Department of Molecular Pathology, University College London Medical School Professor S. P. Datta Emeritus Professor of Medical Biochemistry, and Honorary Research Fellow, Department ofBiochemistry and Molecular Biology, University College London Dr G. Howard Smith Honorary Research Fellow, Department of Biochemistry and Molecular Biology, University College London Professor P. N. Campbell Emeritus Professor of Biochemistry, and Honorary Research Fellow, Department ofBiochemistry and Molecular Biology, University College London Professor R. Bentley Professor Emeritus ofBiochemistry, Department of Biological Sciences, University of Pittsburgh Dr H. A. McKenzie Fellow, School of Chemistry, University of New South Wales, Australian Defence Force Academy, and Visitor, Molecular Medicine, John Curtin School of Medical Research, The Australian National University, Canberra

Dr D. A. Bender Senior Lecturer, Department of Biochemistry and Molecular Biology, University College London Dr A. J. Carozzi NH and MRC Research Officer, Centre for Molecular and Cellular Biology, University of Queensland Professor T. W. Goodwin FRS Emeritus Johnson Professor ofBiochemistry, University of Liverpool Dr J. H. Parish Senior Lecturer, School ofBiochemistry and Molecular Biology, University ofLeeds Dr S. C. Stanford Senior Lecturer, Department of Pharmacology, University College London

OXFORD DICTIONARY OF

BIOCHEMISTRY AND MOLECULAR BIOLOGY REVISED EDITION Managing Editor Dr A DSmith University College London General Editors Professor SPDatta University College London Dr GHSmith University College London Professor PN Campbell (Chairman) University College London Dr RBentley University of Pittsburgh Dr HAMcKenzie Australian Defence Force Ac. Subject Editors Dr DABender University College London Dr A J Harris University of Queensland Professor TW Goodwin University of Liverpool Dr HAMcKenzie Australian Defence Force Ac. Dr J HParish University of Leeds Dr CStanford University College London

OXFORD UNIVERSITY PRESS

OXFORD UNIVERSITY PRESS

Great Clarendon Street, Oxford OX2 6np Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research. scholarship, and education by publishing worldwide in Oxford New York Athens Auckland Bangkok Bogota Buenos Aires Calcutta Cape Town Chennai Dar es Salaam Delhi Florence Hong Kong Istanbul Karachi Kuala Lumpur Madrid Melbourne Mexico City Mumbai Nairobi Paris Sao Paulo Singapore Taipei Tokyo Toronto Warsaw with associated companies in Berlin Ibadan Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York

© The General Editors. 1997 The authors have asserted their right under the Copyright. Designs and Patents Act, 1988, to be identified as authors of this work First published 1997 Revised edition 2000 All rights reserved. No part of this publication may be reproduced. stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law. or under terms agreed with the appropriate reprographics rights organization. Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose this same condition on any acquirer A catalogue record for this book is available from the British Library Library of Congress Cataloging in Publication Data (Data applied for) ISBN 0 19 850673 2 Typeset by Market House Books Ltd, Aylesbury Printed in Great Britain by Butler & Tanner Ltd. Frome

Preface

Nearly twenty years ago one of us (S. P. D., soon joined by G. H. S.), began a distillation of the elements of biochemistry into an alphabetical arrangement. The task was formidable and eventually other editors were recruited, an editorial board was established, and now the work is offered as the Oxford Dictionary ofBiochemistry and Molecular Biology. It is hoped that the dictionary will serve the needs of the research biochemist or molecular biologist, as well as teachers of the subject and their students. In addition, it should prove of value to practitioners of other fields of study or work seeking the meaning of a biochemical term. An important function of a dictionary is to provide guidance on current usage in the field within its scope. The original 12-volume Oxford English Dictionary was compiled from about five million slips of paper bearing sentences or phrases extracted by some thousands of 'readers' from classical works of literature and those of the best contemporary authors. It was thus firmly based on good usage. In scientific subjects, specialist terminology is often codified in sets of recommendations regarding nomenclature, meaning, abbreviations, symbols, and so on. These have been agreed by international commissions (e.g. those of The International Union of Pure and Applied Chemistry and The International Union of Biochemistry and Molecular Biology) as a means of preserving order and facilitating communication between scientists. We have striven to conform as far as possible to the relevant international recommendations, but in some cases, where usage so frequently diverges from a recommendation that adherence to it would seriously detract from ease of use of the dictionary, we have kept to the principle that the dictionary should reflect usage (see the definitions of lexicographer). This does not extend, of course, to cases where usage, however widespread, contradicts sound scientific principles. The internationally agreed recommendation is always also listed. The various compilations of these recommendations that have been drawn upon are listed in Appendix B, together with a number of other sources of information on nomenclature. Biochemistry is the discipline that embraces the study of the structure and function of life-forms at the molecular level.

Molecular biology is a closely related discipline that originates in the study of DNA and its metabolism, and now embraces all those investigations that exploit the technology that has resulted from this work. Both disciplines aim to explain the behaviour of life-forms in molecular terms, and are so closely interrelated that separation is barely possible. It is inevitable that the content of this dictionary is to a degree arbitrary, but it is hoped that all important aspects of these subjects have received consideration. The compilers have attempted to offer a broad coverage of terms encountered in the literature of biochemistry and molecular biology by including an appreciable number from cognate sciences. Although the compilation is designed primarily to serve readers of contemporary material, the needs of those who tum to older literature have also been borne in mind. Some of the entries thus have a historical flavour, some obsolete terms are included (e.g. zymase), and in some cases a historical approach has been used as the best means of presenting an explanation of a term, as for example in the case of the entry for gene. The value of a scientific dictionary is enhanced by inclusion of contextual information as well as mere explanations ofmeaning or terminology. This dictionary will be found to have some of the attributes of an encyclopedia, although the extent to which it veers in this direction has varied with the whim of its compilers. It is our hope that in a single volume the reader has easy access to basic definitions as well as a generous helping of other information. In the present-day world, we are assailed by floods of 'information'. It has been suggested that the average weekday edition of a newspaper of record (e.g. The New York Times) provides more information than Shakespeare and his contemporaries would have acquired in a lifetime. With the availability of much information through the Internet, it may be asked whether a dictionary in paper form is actually necessary. In answer, we note that the Internet can be slow, and is not readily accessible in some parts of the world; the databases may be inadequate, and although usually very up-to-date, the high cost of their maintenance restricts them to specialized knowledge in a limited number of fields. Moreover, books have a

vi Preface

quality of their own, which is enabling them to maintain their popularity. It appears that the increasing use of the Internet is actually paralleled by the rate of publication of printed dictionaries; in an information-hungry age, there cannot be too many sources of good-quality information. We are deeply indebted to the Leverhulme Trust for the award of an emeritus fellowship to one of us (A. D. S.), to University College London, which has provided us with friends and expert colleagues, and to Dr O. Theodor Benfey, Dr Mary Ellen Bowden, and Professor Arnold Thackray, The Beckman Center for History of Chemistry, Chemical Heritage Foundation, Philadelphia, and Dr John Edsall, Harvard University for assistance with biographical data. Particular thanks are due to Dr H. B. F. Dixon for much advice on nomenclature and related matters. Help on questions of nomenclature from Dr G. P. Moss and Dr A. D. McNaught is also acknowledged. We are grateful to Dr D. H. Jenkinson for his help with the recommendations of the International Committee on Nomenclature in Pharmacology. We are also grateful for the valuable advice of Professor K. W. Taylor and Dr J. L. Crammer, on clinical topics, and Professor M. C. W. Evans, on plant biochemistry, and to Dr Margaret McKenzie, for reading the proofs. During the earlier stages of the project, Mrs S. Gove gave much valuable assistance and Miss A. Straker was most helpful in suggesting terms for inclusion. We also wish to thank all those other friends and colleagues, in addition to those separately listed, who have unstintingly given us help and advice.

We are pleased to acknowledge the collaboration and material support given to us by Oxford University Press. We also acknowledge the very friendly cooperation of Market House Books, especially the patience and good humour of Dr John Daintith through all the complications of the production. The copy editors, Robert Hine and Jane Cavell, made a number of helpful suggestions. The compilers offer no apology for their failure to include many deserving terms in the dictionary, but would be pleased to have their attention drawn to errors and to receive suggestions for additional entries in any future edition. Correspondence concerning the dictionary is best addressed to the Managing Editor, Oxford Dictionary of Biochemistry and Molecular Biology, c/o Oxford University Press, Great Clarendon Street, Oxford OX2 6DP January 1997

A. D. Smith S. P. Datta G. H. Smith P. N. Campbell R. Bentley H. A. McKenzie

This whole book is but a draught-nay, but the draught of a draught. Oh, Time, Strength, Cash, and Patience.

Herman Melville (1851) Moby Dick, or The Whale (ed. T. Tanner, 1988, p. 147, Oxford University Press).

Preface to the revised edition It must be inevitable with any work of this nature that a number of imperfections and errors occur. So the opportunity provided by the need to reprint this dictionary has been taken to effect some improvements within the limitation imposed by retention of the original pagination. As well as the correction of a variety of minor misprints and other minor defects, over four hundred entries been either revised or completely rewritten, and fifty or so new entries have been provided, some to remedy deficiencies and others to provide additional terms that have become of topical interest. To help make way for the new ones, about half as many original entries have been

deleted. In addition, Appendices B, C, and D have been updated, and Appendix B has been expanded and provided with all the relevant Internet addresses available at the time of writing. Valuable comments on the original edition by a number of readers are gratefully acknowledged, and thanks are again due to Dr. H. B. F. Dixon for advice on aspects of nomenclature as well as to Oxford University Press and Market House Books for their much appreciated cooperation. September 1999

A. D. S.

Note on proprietary status This dictionary includes some words which are, or are asserted to be, proprietary names or trade marks. Their inclusion does not imply that they have acquired for legal purposes a non-proprietary or general significance, nor is any other judgement implied concerning their legal status. In cases where the editor has some evidence that a word is used as a proprietary name or trade mark this is indicated by the designation proprietary name, but no judgement concerning the legal status of such words is made or implied thereby.

Guide to the Dictionary

1. Alphabetical order

1 .4 Secondary order involving locants

1 .1 Main order of headwords

When such modifiers constitute the only difference between two headwords, they determine the alphabetical order of the entries:

Alphabetical order is determined on a letter-by-letter basis, not word by word; spaces are disregarded: acid acid anhydride acid-base balance acid-base catalysis acid dissociation constant acid dye acidemia

1.2 Nonalphabetic characters Numbers, hyphens, primes, and subscript/superscript text are ignored for the purpose of indexing; an example is the following sequence of entries: FSH·RH

F1 sphere F'strain F-type penton phosphate pathway ftz

1.3 Locants and modifiers In chemical names, any locants and other hyphenated modifiers such as cis-, trans-, PO, and alphabetic Greek characters are not used to determine primary alphabetical order; hence the following entries all appear under the letter A: N-acetylgalactosamine p-aminobenzoic acid y-aminobutyrate shunt 6-aminohexanoic acid

However, the unhyphenated letters 'c' in 'cDNA' and 'd' in 'dCTP', for example, are treated as integral parts of the word and are used to determine alphabetical order.

benzodiazepine o-benzoquinone p-benzoquinone benzoyl

encephalitis 3'-end 5'-end end+

1.5 Format differences in headwords The order for entries where the headword is identical except for format is b, b, b-, b-, -b, -b, B, B, B-, 8-, -B, -B

1.6 Subscripts and superscripts Single letters with subscripts or superscripts are treated as single letters for the purposes of indexing, so entries for k eet and Km will both be found in the list of single-letter entries at the beginning of the letter K. The primary order of these single-letter entries is determined by their format (see section 1.5); where there is more than one entry with a given format (e.g. italic, lower case k), these are arranged by alphabetical order of their subscripts/superscripts.

1 .7 Greek letters • Where Greek letters form part of a chemical name, they are not used to determine alphabetical order (see section 1.3). Otherwise they are written out in full in the headword, e.g. nu body, beta strand. • The names of the letters of the Greek alphabet, together with their English transliterations used in etymologies, are listed in Appendix A. The meanings assigned to Greek alphabetic characters used as symbols are also given in Appendix A. • Greek characters are set in italic type when the character represents a variable or locant and in roman type when it represents a unit or subtype e.g. of a protein or particle.

viii Guide to the Dictionary

2. Format of entries 2.1 Summary of typefaces • The following distinguishing typefaces are employed in addition to the text light serif typeface used for definitions: large bold sans serif headwords alternative terms for and varitext bold serif ant spellings of headwords; hidden entries; run-ons text bold sans serif cross-references text italic serif usage notes and field labels; parts of speech; foreign language terms (including scientific and medical Latin); symbols for physical quantities and fundamental physical constants; stereochemical prefixes and alphabetical locants 2.2 Headwords • For each entry, the headword is in bold, sans serif type. • Upper-case (capital) initial letters are used only for proper names (or terms derived from them) and for proprietary names. Abbreviations and symbols are printed in upper and/or lower case as appropriate. • If a term would normally be set in bold type, this is indicated in the entry: B symbol for 1 Napierian absorbance (see absorbance). 2 magnetic flux density (bold italic). • Where the same basic term is used in different typefaces, such as roman/italic, or upper case/lower case, or as a prefix or suffix, each usage is given as a separate headword. For example, h, h, H, and Heach have a separate entry. • The order in which such entries are given is listed in section 1.5. 2.3 Alternative terms and variant spellings 2.3.1 Choice of headword Where alternative terms for a headword, or variant spellings of it, exist (see section 1.3), the headword selected for the main entry is generally the recommended or preferred term, or the one judged to be the commonest. Exceptions to this generalization are those instances where the name of a Greek alphabetic character is written out for convenience of indexing: beta globulin or ~ globulin.... 2.3.2 General Any alternative terms and alternative spellings are listed following the headword in bold, serif type: retrovirus or ribodeoxyvirus or RNA-DNA virus any virus belonging to the family Retroviridae .... Notes regarding the usage of these alternatives may be given in brackets and in italics; for example DNA glycosylase or (sometimes) DNA glycosidase any of a group of enzymes.... bacteremia or (esp. Brit.) bacteraemia the presence of live bacteria in the blood.

bilirubin or (formerly) bilirubin IXa the recommended trivial name for the linear tetrapyrrole.... • These alternative terms and spellings also appear as entries in the alphabetical sequence, with a cross-reference to the main entry where the term is defined, unless the variant would appear close to the main entry. Additional information is given where appropriate: demoxytocin an alternative name for deaminooxytocin. fructose-1,6-diphosphatase a former name for fructose-bisphosphatase. lipide a variant spelling of lipid. molecular exclusion chromatography a less common name for gel-permeation chromatography. oleomargarine an alternative name (esp. US) for margarine. penatin an obsolete name for glucose oxidase. 2.3.3 Chemical names • Synonyms may be given following the headword, in the order: other trivial names (if any); the semi-systematic or semi-trivial name(s); older systematic name in style, if still in widespread use; the systematic name in currently recommended style. • The headword used to represent a chemical compound that can exist in ionized form(s) is in most cases the name of its physiologically predominant form. So, for example, an entry is headed 'succinate' rather that 'succinic acid'. 2.3.4 Enzyme names Alternative names may be listed following the headword, which is normally the recommended name; otherwise alternative names include the recommended name (if the headword is the common name), the systematic name, and other names. The EC number is also given.

2.4 Multiple definitions • Where a term has more than one meaning, the different senses are numbered with bold Arabic numerals. blockade 1 (in pharmacology) the saturation of a specific type of receptor with an antagonist to its normal agonist. 2 (in immunology) the overloading or saturation of the reticuloendothelial system with inert particles, such as carbon particles. 3 to impose any such blockade. • The order of the numbered entries is generally determined by their biochemical significance. • The different senses may be further subdivided into def. la, def. 1b, etc. di+ comb. form 1 (in chemical nomenclature) (distinguish from bis+ (def. 2)) a indicating the presence in a molecule of two identical unsubstituted groups, e.g. diethylsulfide, 1,3-dihydroxyacetone. b indicating the presence in a molecule of two identical inorganic oxoacid residues in anhydride linkage, e.g. adenosine 5'-diphosphate. 2 or bis+ (def. I) denoting two, twofold, twice, doubled. • Homographs are not distinguished. 2.5 Hidden entries Hidden entries are terms that are not defined at their normal headword position. Instead, they are treated (implicitly or ex-

ix Guide to the Dictionary

plicitly) at some other headword. They are set in bold serif type. In the following example, 'bentonite flocculation test' is the hidden entry: bentonite a colloidal, native hydrated aluminium silicate clay consisting principal1y of montmorillonite, a complex aluminosilicate, Al z0 3 -4SiO z'H 20, which has marked adsorptive properties. It is used as an inhibitor of nucleases and also in the bentonite flocculation test, a passive agglutination test in which antigen-coated bentonite particles are used to detect specific antibody.

2.6 Other information 2.6.1 Plurals The plural form (or forms) of a headword is (are) given in parenthesis following the headword if its formation is nonstandard, e.g. for Latin headwords, or where there is more than one form of the plural. medulla (pl. medullas or medullae) the innermost part of an organ, tissue, or structure; marrow, pith. medullary ad). 2.6.2 Affixes and combining forms • In common with other dictionaries, this Dictionary lists and defines many word elements that are used to compose terms or to modify existing terms. These are either combining forms (which are derived from parent words) or affixes (infixes, prefixes, and suffixes, none of which have parents). • The usual lexicographical convention is to add a hyphen to suffixes and combining forms when listing them as headwords, although generally the hyphen is omitted in formation of composite terms. However, chemical and biochemical terminology also includes a considerable number of specialized affixes that retain the hyphen in the formation of composite terms (e.g. 'meso-' in 'meso-cystine'). In order to make an explicit distinction between these alternatives, this Dictionary departs from the common convention by adding a hyphen to an affix in a headword only when a linking hyphen is retained in a combination: meso- abbr.: ms-; prefix (in chemical nomenclature) designating a substance whose individual molecules contain .... By contrast, combining forms (e.g., 'meso' in 'mesoderm') together with affixes producing unhyphenated composite terms, are listed with an added plus sign, placed after and/or before the word-element as appropriate: meso+ or (sometimes before a vowel) mes+ comb. form denoting middle, or intermediate. +agogue or (US) +agog suffix denoting an agent that elicits or enhances the secretion of.. .. 2.6.3 Abbreviations and symbols • Where a term may be abbreviated or indicated with a symbol, this is noted after the headword. nuclear magnetic resonance abbr.: NMR or nmr; the phenomenon that occurs when atomic nuclei.... electric potential or potential symbol: Vor f; the work done in bringing unit electric charge.... • The distinction between an abbreviation and a symbol is a little blurred, since some abbreviations (e.g. Ig) also may be

used as symbols. In general, the term 'symbol' is used here for units and their decimal prefixes (e.g. m, mol; ~, M) physical quantities and constants (e.g. a, H; k, R) mathematical functions (e.g. exp, In) chemical elements (e.g. K, Mg) groups of letters that can be used in place of a chemical group or compound in an equation or formula (e.g. CoA, Me) recommended abbreviations for nucleotides, bases, or amino acids. • The symbols for SI base and derived units and their decimal prefixes are mandatory; all other symbols are recommendations of IUBMB or IUPAC. In conformity with these recommendations, symbols for physical quantities and fundamental physical constants are printed in a sloping (italic) typeface. • No distinction is made between acronyms, contractions, abbreviations, etc. All are classed as abbreviations. Abbreviations formed from the initial letters of two or more words are printed without periods (full-stops), in line with contemporary practice, but abbreviations that are shortened forms of single words have a terminal period. • In addition to recommended abbreviations, the Dictionary lists a selection of others commonly encountered in the scientific literature. 2.6.4 Derived terms Derived terms not meriting separate definition are listed at the end of the entry for the parent term, preceded by a bold em dash and followed by an abbreviation indicating the part of speech. bactericide or bacteriocide any agent (biological, chemical, or physical) that destroys bacteria. -bactericidal or bacteriocidal ad). 2.6.5 Etymology • Generally, the derivation of words is not explained in entries. The exceptions are for eponymous terms and other entries of particular etymological interest. • The etymology is given within square brackets at the end of the entry. lIngstrom or Angstrom symbol: A; a unit of len~th equal to 10 10 metres. '" [After Anders Jonas Angstrom (1814-74), Swedish physicist noted for his work on spectroscopy.] • Greek elements of etymologies are transliterated: chirality topological handedness; the property of nonidentity of an object with its mirror image.... [From Greek kheir, hand.] 2.6.6 Usage • The field within which the term is used may be specified in italics and in parenthesis before the definition. malonyl 1 (in hiochemistry) the univalent acyl group, HOOC-CHz-CO-, derived from malonic acid by loss of one hydroxyl group. 2 (in chemistry) the bivalent acyl

Guide to the Dictionary group, -CO-CH 2-CO-, derived from malonic acid by loss of both hydroxyl groups.

• Notes may also be given regarding the use of alternative terms and variant spellings: see section 2.3.2.

2.7 Cross-references 2.7.1 Format • Cross-references are set in bold sans serif type, e.g. thiouridine.

• Where a cross-reference refers to only one sense of a word with multiple definitions, this is indicated as in the following example: siderophage an alternative name for siderophore (def. 1).

2.7.2 Types of cross-reference • There are cross-references from a variant spelling, or a less commonly used term, etc., to the entry where the term is defined. For examples, see section 2.3.2.

• Some cross-references are to related entries giving more information. These may be either embedded in the text: octulose any ketose having a chain of eight carbon atoms in the molecule.

or listed at the end of the entry: vacuum evaporation a technique for .... See also shadow casting. • Cross-references may also be used to draw attention to contrasting terms: heterochromatin ... Compare euchromatin.

or to pairs of easily confused terms: prolidase another name for X-Pro dipeptidase. Distinguish from prolinase. prolinase the recommended name for Pro-X dipeptidase. Distinguish from prolidase.

3. Abbreviations abbr. ad). adv.

Brit. comb. form 3-D def. e.g. esp. etc. Fr. i.e. max. n. pI.

sing.

sp. or spp. US vb.

abbreviation adjective adverb British combining form (see section 2.6.2) three-dimensional definition [Latin, exempli gratia] for example especially etcetera French [Latin, id est] that is maximum noun plural singular species (singular and plural respectively) United States verb

Other abbreviations are defined in the text itself.

x

4. Other conventions 4.1 Spelling and hyphenation 4.1.1 Spelling • For chemical and biochemical terms, recommended international usage is followed; thus, for example, 'heme' is used rather than 'haem', 'estrogen' rather than 'oestrogen', 'sulfur' rather than 'sulphur', and 'oxytocin' rather than 'ocytocin'. All variants are listed as headwords, however, with cross-references to the corresponding main entries.

• For common terms, e.g. 'colour', British spelling is used. 4.1.2 Hyphenation • Hyphens are used attributively: 'T cell' but 'T-cell receptor' 'amino acid' but 'amino-acid residues'

• This also applies to enzyme names; thus for example, there is no hyphen following the 'glucose' in 'glucose 6-phosphate', but where this substrate forms part of an enzyme name, it is hyphenated, e.g. in 'glucose-6-phosphatase' or 'glucose-6-phosphate isomerase'.

4.2 Nomenclature In most cases, headwords conform with the recommendations of the various nomenclature bodies of IUB, IUBMB, and IUPAC (see Appendix B for information regarding their nomenclature publications). Other usages are, however, given (see Preface). The phrase 'not recommended' has been used to indicate that certain forms are not the recommendation of one of these nomenclature bodies. 4.2.1 Drug names The recommended international nonproprietary names are used (International nonproprietary names (INN) for pharmaceutical substances. World Health Organization, Geneva, 1992); hence,

for example, main entries are found under epinephrine and norepinephrine rather than under adrenaline and noradrenaline. 4.2.2 Proprietary names A few commonly used proprietary names are included; these may be listed at the end of an entry if considered to be of particular interest, especially to non-scientists: acetaminophen or paracetamol ... Proprietary names: Tylenol, Panadol. It inhibits ....

or may be the main headword: Sephadex. 4.2.3 Other substances The main entry is under the name used most widely in the scientific literature. Where this is not the recommended name, a cross-reference is given from the recommended name to the main entry. For example, the name 'follicle-stimulating hormone (FSH)' is widely employed instead of the recommended name 'follitropin', hence the former name has been used as the main headword. In such cases there is a cross-reference from the recommended name back to the entry where the substance is defined: follitropin the recommended name for follicle-stimulating hormone.

xi

Guide to the Dictionary

4.3 Representation of chemical structures 4.3.1 Typeset formulae In conformity with IUPAC nomenclature recommendations for typeset chemical formulae, parentheses (round brackets) indicate a side chain:

CH r CH(NH 2)-COOH, HQ-C(CH 2-COO-)2-COOand square brackets indicate a condensed chain: CHdCH21s-COOH 4.3.2 Carbohydrates • The cyclic forms of monosaccharides are depicted by Haworth representations as are some other compounds; for clarity, the carbon atoms of the heterocyclic ring, and their attached hydrogen atoms, are not shown. See the Haworth representation entry for more detail. • Where an abbreviated terminology is included for oligosaccharide chains, the extended or condensed forms described in the publication entitled Nomenclature of carbohydrates (recommendations 1996) (see Appendix B, item 22) are variously used. • Wherever possible, structure diagrams show absolute configura tions.

4.4 Periodic table of the elements The group numbers used in the text are those of the 18column format of the table given in the 1990 edition of the IUPAC 'Red Book' (see Appendix B, item 2). The correspondence between this and other versions of the table is described in the periodic table entry and shown below the table displayed on the endpapers. 4.5 Amino-acid sequences • For peptide sequences of up to IS amino-acid residues, the three-letter code is used; longer sequences are given in the one-letter code. • Motifs are given in the one-letter code. • The full sequences of many proteins can be found in protein sequence databases, and database codes are given to facilitate access to these. The database codes relate to a number of different databases. The style of the code gives an indication of the database from which the data origi-

nate, but if the user does not recognize the code, it is necessary to search for it in a composite database that integrates data from all the major databases. Further information is offered in Appendices D and E.

4.6 Genes • The accepted format of gene names (i.e., whether lower case or upper case or a mixture) varies between different organisms. Where an entry covers genes from various species, the convention for human genes is generally followed in the headword, i.e. all letters are given in upper case, e.g. 'JUN'. • However, when an entry refers only to a gene from a specified organism, the accepted convention for that organism is followed. 4.7 Names of organisms • Those organisms whose Latin names are used frequently are listed in Appendix H. • Where a binomial Latin name is repeated within an entry, the genus name is abbreviated after the first occurrence of the name; for example, the full form 'Escherichia coli' is used when first mentioned in any entry, but subsequent references to this organism in the same entry are abbreviated to 'E. coli'.

5. Appendices A number of appendices have been included after the main alphabetical text, as follows: • Appendix A - The Greek alphabet and Greek characters used as symbols (page 697). • Appendix B - Nomenclature publications (page 700). • Appendix C - Organizations that are helpful to biochemists and molecular biologists (page 705). • Appendix D - The Internet (page 709). • Appendix E - Exploring the language of bioinformatics (page 715). • Appendix F - Restriction enzymes and methylases (page 725).

• Appendix G - Sequence-rule priorities of some common ligands in molecular entities (page 739). • Appendix H - Species names (page 740).

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Aa a 1 abbr. for adsorbed. 2 symbol for atto+ (SI prefix denoting 10- 18). 3 axial. 4 year. a' symbol for pseudoaxial. a symbol for 1 absorption coefficient. 2 acceleration (in vector equations it is printed in bold italic (a)). 3 activity (def. 3). 4 van der Waals coefficient. 5 as subscript, denotes affinity. So symbol for Bohr radius. A symbol for 1 acid-catalysed (of a reaction mechanism). 2 a residue of the a-amino acid L-alanine (alternative to Ala). 3 a residue of the base adenine in a nucleic-acid sequence. 4 a residue of the ribonucleoside adenosine (alternative to Ado). 5 uronic acid. 6 ampere. A symbol for 1 absorbance. 2 activity (def. 2). 3 affinity. 4 Helmholtz function. 5 mass number/nucleon number. A, symbol for relative atomic mass. A. symbol for area. [AIo. s or [A).;, symbol (in enzyme kinetics) for the value of the concentration of a substrate, A, in mol dm-3, at which the velocity of the reaction, v, is half the maximum velocity, V; Le. when v = 0.5 V. [Also symbol for the molar concentration of an agonist that produces 50% of the maximal possible effect of that agonist. Other percentage values ([Aho, [A]40, etc.) can be specified. The action of the agonist may be stimulatory or inhibitory. Compare E~o. 2'-5'A symbol for any member of a series of oligonucleotides of the general formula PaA[2'p5' A]m where p and A are phosphoric and adenosine residues, respectively, and a and n are small integers (a ::: 1, 2, or 3 and n commonly = 2, 3, or 4). Potent inhibitors of protein biosynthesis in vivo and in vitro, they are believed to mediate the action of interferon on virusinduced cells. A23187 or calcimycin a toxic and weakly antibiotic substance isolated from cultures of Streptomyces chartreusensis. It is a lipophilic 523 Da monocarboxylic acid of complex structure, two molecules of which form stable lipid-soluble complexes at pH 7.4 with one atom of certain divalent metal cations, especially Mn 2+, Ca2+, and Mg2+; monovalent cations are bound only weakly. It also forms lipid-soluble complexes with certain amino acids. It is used experimentally as a calcium ionophore.

A symbol for angstrom (unit of length equal to 10- 10 m). aa 1 symbol for an unknown or unspecified aminoacyl group when acting as a substituent on a base or internal sugar in a (poly)nucleotide. 2 abbr. for amino acid. AA (formerly) symbol for an unknown or unspecified aminoacid residue. See Xaa. AAA a codon in mRNA for L-Iysine. AAC a codon in mRNA for L-asparagine. Aad symbol for a residue of the a-amino acid L-a-aminoadipic acid, L-2-aminohexanedioic acid.

J3Aad symbol for a resid ue of the ,B-amino acid L-ft-aminoadipic acid, L-3-aminohexanedioic acid. AAG a codon in mRNA for L-Iysine. A antigen the antigen defining the A blood group. See also blood-group substance, ABH antigens. AAU a codon in mRNA for L-asparagine. Ab abbr. for antibody. abamectin or avermectin B I a metabolite of Streptomyces avermitilis used as an acaricide, insecticide, and a veterinary anthelmintic. A-band an anisotropic band in a sarcomere. Abbe refractometer a refractometer in which the critical angle for total reflection at the interface of a film of liquid between two similar glass prisms is used in determining the refractive index of the liquid. [After Ernst Abbe (1840-1905), German physicist famous for his researches in optics.] ABC abbr. for 1 antigen-binding capacity. 2 ATP-binding cassette (see ABC transporter). ABC transporter membrane transport proteins having the ABC molecular domain, named after ATP-binding cassette, characteristic of all members of a large superfamily of membrane transport proteins that hydrolyse ATP and transfer a diverse array of small molecules across membranes. See also CITR, MDR protein, sugar transporter. abductin an insoluble, rubber-like protein from the internal triangular hinge ligament of scallops. Abe symbol for abequose. abequose symbol: Abe; 3,6-dideoxy-o-xylo-hexose; 3,6dideoxy-o-galactose; a deoxysugar that occurs, e.g., in a-specific chains of lipopolysaccharides in certain serotypes of Salmonella. For the L enanti orner see colitose. ABH antigens one of the systems of blood group antigens having determinants associated with oligosaccharide structures. It is the basis of the ABO system, which was the first human blood group antigen system to be detected, by Landsteiner in 190 I, and it remains the most important in blood transfusion. Individuals having neither A nor B antigen express the H antigen, the product of an independent gene belonging to the Hh system. Antigens of the ABH system are oligosaccharide chains, in the erythrocyte carried on band 3 (the anion transporter) and band 4.5 (the glucose transporter), or on ceramide. A highly branched N-glycan, consisting of a trimannosyl-di-Nacetyl-chitobiosyl core with Gal(ftI-4)G1cNAc(ftI-3) repeats, forms the basis of ABH antigens. The H determinant is the precursor; antigen A is formed by addition of N-acetyl-ogalactosamine by fucosylgalactose a-N-acetylgalactosaminyltransferase (EC 2.4.1.40); antigen B is formed by addition of o-galactose by fucosylglycoprotein 3-a-galactosyltransferase (EC 2.4.1.37). The terminal sugar residues of importance are: H determinant, Fuc(al-2)Gal,B-R; A determinant, GaINAc(al-3)(Fucal-2)Galft-R; B determinant, Gal(al-3) (Fucal-2)Galp-R. The enzyme responsible for adding the terminal fucosyl residue of the H determinant is galactoside 2-aL-fucosyltransferase (EC 2.4.1.69). See also A-transferase. B-transferase. abiogenesis or spontaneous generation the discredited doctrine that living organisms can arise from nonliving materials under current conditions. Compare biogenesis (def. 2). abiotic characterized by the absence of life. abl an oncogene from murine Abelson leukemia virus. The viral oncogene (v-abl) resulted from recombination of the Maloney murine leukemia virus with the protooncogene (c-abl). The protooncogene encodes a 145 kDa protein, which, together with the highly related arg gene, forms a unique family within the nonreceptor tyrosine protein kinases; database code KABL_HUMAN, 1130 amino acids (122.81 kDa). It was one

2

ABM

absorbance

of the first protooncogenes identified by the study of retroviruses. The transforming ability of v-abl results from increased tyrosine kinase activity of the gag-abl pl60 oncoprotein. In humans, inappropriate activation of c-abl occurs via a reciprocal translocation between chromosomes 9 and 22 in which c-abl (9q34) is joined at the breakpoint cluster region (bcr) of the phi gene on chromosome 22(qll). In the translocation, a 3' portion of c-abl is spliced in-frame to a 5' portion of the phi gene, resulting in an altered chromosome 22, which is referred to as the Philadelphia chromosome (Ph}). The protein product of the spliced genes in the Ph} chromosome is a molecule of 210 kDa, which has increased tyrosine kinase activity compared with the c-abl product and is similar in structure to the v-abl product in that the N-terminal portion of Abl is removed. The Phi chromosome occurs in more than 90% of individuals with chronic myelogenous leukemia and was the first description of a specific genetic translocation associated with a human malignancy. c-Abl can potentially regulate cell growth and may participate in growth regulation at multiple cellular locations, interacting with different cell components. It possesses SH2 and SH3 domains (see SH domains) and also domains involved in binding to F-actin and DNA. Thus it has been found in both cytoplasmic and nuclear locations and its DNA-binding activity appears to be cell cycle regulated by Cdc-2-mediated phosphorylation; it binds the retinoblastoma protein indicating involvement in transcriptional regulation. ABM abbr. for 2-aminobenzyloxymethyl, a group used for derivatizing cellulose or paper. It is converted by diazotization into DBM. abortive complex or dead-end complex or nonproductive complex any enzyme-substrate complex in which the substrate is bound to the enzyme in a manner that renders catalysis impossible so that products cannot be formed. abortive infection infection of a bacterium by phage lacking phage DNA, e.g. in generalized transduction. abortive transconjugate see transconjugate. abortive transduction a type of transduction in which the donor DNA is not integrated with the recipient chromosome but persists as a nonreplicating fragment that can function physiologically and can be transmitted to one daughter cell at each cell division. ABO system one of the systems of human blood groups, of great importance in blood transfusion because human plasma contains natural antibodies against A and B blood group antigens of the ABH system (see ABH antigens). The antigens on the red blood cells and the plasma antibodies corresponding to the various phenotypes are shown in the table. See also A-transferase, B-transferase, 0 antigen (def. 2). Phenotype (blood group) A B AB

o

Antigen on red cells

Antibody in plasma

A

anti-B anti-A neither anti-A + anti-B

B

A and B H

abrin a highly toxic ",65 kDa glycoprotein obtained from the seeds of jequirity or Indian liquorice (Abrus precatorius L.), a tropical Asian vine that also occurs in Florida. It consists of an acidic A chain, "'30 kDa, and a neutral B chain, "'35 kDa, held together by disulfide bonds. The A chain is a powerful inhibitor of protein synthesis while the B chain functions as a carrier to bind abrin to the membrane and perhaps to assist penetration of the A chain into the cell. One well-chewed seed can be fatal. The A and B chains are derived from a common precursor: database code ABRA_ABRPR, 528 amino acids (59.24 kDa). Compare abrine, ricin. See also ribosome-inactivating protein. abrine trivial name for Na-methyl-L-tryptophan, a-methyl-

amino-f:l-(3-indole)propionic acid; an imino acid obtained from seeds of jequirity (Abrus precatorius). Not to be confused with abrin. abscisic acid or (formerly) abscisin II or dormin abbr.: ABA; 5-( l-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-l-yl)-3methylpenta-2,4-dienoic acid; a chiral sesquiterpene. The naturally occurring form, the 22,4£,S isomer, also designated (S)-abscisic acid, is a phytohormone formed by the degradation of carotenoids. It controls abscission in flowers and fruit but probably not in leaves, and is also implicated in geotropism, stomatal closure, bud dormancy, dormancy of seeds requiring stratification (i.e. those that will only germinate after exposure to low temperatures), and possibly tuberization.

COOH

abscissa the horizontal or x coordinate in a plane rectangular (Cartesian) coordinate system. Compare ordinate. abscission the natural shedding of leaves, fruits, and other parts by a plant. absolute 1 pure, unmixed; e.g. absolute alcohol. 2 not relative; e.g. absolute configuration. 3 describing a measurement defined in fundamental units of mass, length, and time that does not depend on the characteristics of the measuring apparatus; e.g. absolute temperature. absolute alcohol the common name for pure ethanol, i.e. ethanol that has been freed of water. It may contain small amounts of benzene that have been added to aid in removing water. Substances may be added to absolute alcohol to render it unfit for human consumption and hence free of excise duty: industrial spirit contains 5% v/v methanol, while methylated spirit also contains pyridine, petroleum oil, and methyl violet dye, and surgical spirit also contains castor oil, diethyl phthalate, and methyl salicylate. absolute configuration the actual three-dimensional arrangement of the atoms in a chiral molecule. absolute reaction rate theory a theory that sets out to predict the absolute reaction rate of a chemical reaction from the quantum mechanical description of the potential energy changes during the interaction between chemical species. It is most widely drawn upon in applying thermodynamic reasoning to equilibria between reactants in the ground state and chemical species in the activated state or transition state. absolute temperature see thermodynamic temperature. absolute zero zero thermodynamic temperature, i.e. 0 K or -273.15 "C. absorb see absorption. absorbance symbol: A; a measure of the ability of a substance or a solution to absorb electromagnetic radiation incident upon it. It equals the logarithm of the ratio of the radiant power of the incident radiation, Po, to the radiant power of the transmitted radiation, P. For a solution, absorbance is expressed as the logarithm of the ratio of the radiant power of light transmitted through the reference sample to that of the light transmitted through the solution, the observations being made using identical cells. (Traditionally, radiant intensity was measured instead of radiant power, which is now the accepted form.) Two quantities are defined: (decadic) absorbance (symbol: A IO or A), and napierian absorbance (symbol: Ae or B). A lO = Ig (epo/W) = 19 I ' = -lg (I - a), and

3

acceptor

absorbancy

=

=

1

=

A. In (f/JrJf/J) In 1 -In (l - a), where T is the (internal) transmittance and a is the absorptance. These definitions suppose that all the light incident upon the sample is either transmitted or absorbed, reflection and scattering being negligible. The more general term attenuance should be used when scattering is considerable, as when the quantity Ig(f/Jolf/J) is measured to estimate the cell density of a culture. The older terms absorbancy, extinction, and optical density should no longer be used. Compare absorption coefficient. absorbancy or absorbency (formerly) an alternative term (no longer recommended) for absorbance. absorbate a substance that is absorbed into another substance. absorbed dose (in radiation physics) a measure of the energy deposition produced by ionizing radiation in any (specified) medium as a result of ion-pair formation. The CGS unit of absorbed dose is the rad; the SI derived unit is the gray (symbol: Gy); compare exposure (def. 3). See also dose equivalent, dose rate. absorbence a variant spelling of absorbance. absorbent 1 a substance that absorbs another substance. 2 having the capacity to absorb another substance. absorptance or absorption factor symbol: a; the ratio of absorbed to incident radiant or luminous flux. A dimensionless physical quantity given by a = f/Jab,lf/J O' where f/J o and f/J abs are the incident and absorbed radiant powers, respectively. absorptiometer 1 an apparatus, frequently a photoelectric device, for measuring light absorption by solids, liquids, or gases. 2 an apparatus for measuring the amount of gas absorbed by a liquid. absorption 1 the act or process whereby one substance, such as a gas or liquid, is taken up by or permeates another liquid or solid. Compare adsorption. 2 the retention by a material of energy removed from electromagnetic radiation passing through the material. 3 the removal of any form of radiation, or the reduction of its energy, on passing through matter. 4 the process whereby a neutron or other particle is captured by an atomic nucleus. 5 a (in cellular physiology) the uptake of fluids by living cells or tissues. b (in animal physiology) the totality of the processes involved in causing water, the products of digestion, and exogenous substances of low molecular mass such as drugs, salts, vitamins, etc. to pass from the lumen of the gastrointestinal tract into the blood and lymph. c (in plant physiology) the uptake of water and dissolved salts through the roots. 6 (in immunology) the process of removing a particular antibody (or antigen) from a mixture by adding the complementary antigen (or antibody) and discarding the antigen-antibody complex so formed. Compare immunosorption. absorption band or absorption line a region of darkness or absorption of radiation in the spectrum of heterochromatic radiation that has passed through an absorbing material. absorption coefficient four different coefficients are defined. The (linear) decadic absorption coefficient (symbol: a) is defined by a = A 1011; units m -1. The (linear) napierian absorption coefficient (symbol: a) is defined by a = A.II; units m- I . The molar (decadic) absorption coefficient (symbol: e) is defined by e = ale = A 10/d; units m2 mol-I. The molar napierian absorption coefficient (symbol: K) is defined by K ale A.II. A 10 and Ae are the decadic and napierian absorbances respectively (see absorbance), I =0 path length, and c = amount-of-substance concentration. absorption cross-section the probability that a photon passing through a molecule will be absorbed by that molecule multiplied by the average cross-sectional area of the molecule. The net absorption cross-section (symbol: a ne ,) is defined by a ne , KINA, where K is the molar napierian absorption coefficient and N A is the Avogadro constant. absorption factor an alternative name for absorptance. absorption index symbol: k; it is given by k = al4nP, where a

=

=

=

is the (linear) naplertan absorption coefficient and P the wavenumber in vacuum of the radiation. absorption line an alternative name for absorption band. absorption spectrometry the process of measuring an absorption spectrum with a spectrometer. Absorption spectrophotometry is a related process employing a spectrophotometer. See also absorbance, absorptiVity. absorption spectroscopy the spectroscopy of an absorption spectrum. absorption spectrum a spectrum produced when electromagnetic radiation is absorbed by a sample. The frequencies of the radiation absorbed are those able to excite the atoms or molecules of the sample from their ground states to excited states. The frequency, 1/, at which a particular absorption line occurs depends on the energy difference, tliE, between that of a particular ground state and that of the corresponding excited state. It is given by 1/ = tliElh, where h is the Planck constant. Compare emission spectrum. absorptivity a measure of the ability of a material to absorb electromagnetic radiation. It equals the absorptance of a sample of the material divided by the optical path-length. For very low attenuance, it approximates the absorption coefficient. Use of the term is not recommended. Abu symbol for a residue of the a-amino acid L-2-aminobutanoic acid L-a-aminobutyric acid. Azbu or Dab symbol for a residue of the a,y-diamino acid L-a,ydiaminobutyric acid, L-2,4-diaminobutanoic acid. abzyme abbr. for antibody enzyme (an antibody with enzyme activity; also known as catalytic monoclonal antibody). a.c. or AC or ac abbr. for alternating current. Ac symbol for 1 actinium. 2 the acetyl group, CH 3CO-. ACA a codon in mRNA for L-threonine. acanthosome an organelle of fibroblasts isolated from the dermis of hairless mice after chronic UV irradiation. It exists as a spinous membranous vesicle. acarbose a pseudotetrasaccharide, 0-4,6-dideoxy-4-([[ IS(I a,4a, 5/3, 6a) ]-4,5, 6-trihydroxy-3-(hydroxymethyl)-2-cyclohexen-l-yl] amino]-a-D-glucopyranosyl-( 1 ~4)-O-a-D-gluco­ pyranosyl-(1 ~4 )-glucose, that inhibits a-glucosidase, thereby reducing gastrointestinal absorption of glucose. It is a putative antidiabetic agent.

20H~3

tP

HO""" HO H...."

""" H

OH

'"''''''

H H OH

0 H

HHOH

HOCH2

H~H 0 OH H

H 0 H 9 H 0 OH 0 HOH

HOCH2

OH

H

HOH

ACC a codon in mRNA for L-threonine. a.c. calorimetry a technique in which the thermal response of a sample to an oscillating heat signal is measured in the form of a temperature wave propagating through the sample. The technique allows the measurement of the heat capacity of the sample on both cooling and heating and the monitoring of its isothermal time-dependence. It is useful in the study of phase transitions in solids and in gel to liquid-crystal systems. accelerator 1 (in chemistry) catalyst, especially one that increases the rate of a polymerization reaction. 2 (in physics) a device or machine used for imparting high kinetic energy to charged subatomic particles, e.g. electrons, protons, or alpha particles, by means of electric and/or magnetic fields. accelerator globulin an alternative name for factor V. See blood coagulation. accelerin an alternative name for factor Va. See blood coagulation. acceptor 1 (in chemistry) a chemical entity that in a chemical reaction receives an electron, atom, or group of atoms. Compare donor, donor atom. See also electron acceptor. 2 (in physiol-

4

accessory cell

acetoin

ogy) a receptor that binds a hormone without a biological response being demonstrable. 3 (in pharmacology) a receptor that binds a drug but has no identified endogenous ligand. accessory cell anyone of various types of cell that assist in the immune response. The term includes antigen-presenting cell, basophil, eosinophil, mast cell, and platelet. accessory chromosome an alternative name for 1 a B chromosome. 2 a sex chromosome. accessory DNA surplus DNA present in certain cells or during certain stages of cell development owing, for example, to gene amplification. accessory food factor or accessory growth factor a term originally used to describe any unknown substance - subsequently called vitamin - found in small amounts in some foods, such as milk, that was necessary for the normal growth of animals fed on diets of purified carbohydrates, fats, proteins, and salts. accessory pigment any of the pigments, such as the yellow, red, or purple carotenoids and the red or blue phycobiliproteins in photosynthetic cells. The carotenoids are always present, whereas the phycobiliproteins occur only in algae belonging to the Rhodophyceae, the Cyanophyceae, and the Cryptophyceae. Strictly speaking, chlorophyll b is also an accessory pigment. ACE abbr. for 1 amplification control element (a DNA sequence in vertebrates that functions as the origin for amplification). 2 angiotensin converting enzyme. ACeDB or acedb a partly object-oriented database of genetic and sequence information devised for the nematode Caenorhabditis elegans but applied to other eukaryotes including Arabidopsis thaliana. A cell or (formerly) alpha cell or t¥ cell one of the three main histological cell types found in the islets of Langerhans of the pancreas, also found in the gastric oxyntic mucosa. A cells produce, store, and secrete the hormone glucagon. A, cell (formerly) an alternative name for 0 cell. Aces or ACES abbr. for N-(2-acetamido)-2-aminoethane sulfonic acid; 2-[(2-amino-2-oxoethyl)amino]ethane sulfonic acid; a Good buffer substance, pKa (20 DC) = 6.9.

R'R2C(XR3)OH + R3XH == R'R2C(XR 3h + H 20 or R'R2C(XR3)OH + R 4XH == R1R 2C(XR3)XR4 + H 20. In carbohydrates such compounds are formed at the carbonyl group of the acyclic form of a saccharide or saccharide derivative. The terms 'ketal' (or 'thioketal') and 'hemiketal' (or 'thiohemiketal'), may be applied respectively to any acetal of general formula RIR 2C(XR3)XR4 or RIR 2C(OH)XR 3, i.e. to those derived from ketones. These terms, at one time abandoned, have recently been reintroduced as the respective names of subclasses of acetals and hemiacetals and as functional class names. acetaminophen or paracetamol 4-acetamidophenol; N-acetylp-aminophenol; N-(4-hydroxyphenyl)acetamide; a drug widely used as an analgesic and antipyretic. It inhibits formation of prostaglandins within, but not outside the brain. It is metabolized within the liver mostly to glucuronide and sulfate conjugates. A small amount is oxidized to a highly reactive intermediate, N-acetylbenzoquinoneimine, that is normally detoxified by conjugation with glutathione. If it is produced in excess of the capacity of the liver to detoxify it, hepatic necrosis can result. It can be administered with methionine, which increases glutathione in the liver. N-Acetylcysteine is administered in cases of poisoning to act as a glutathione substitute. Proprietary names include: Panadol, Tylenol. acetate 1 the traditional name for ethanoate; the anion, CH 3COO-, derived from acetic acid (ethanoic acid). 2 any salt or ester of acetic acid. acetate-CoA ligase EC 6.2.1.1; systematic name: acetate:CoA ligase (AMP-forming); other names: acetyl-CoA synthetase; acyl-activating enzyme; acetate thiokinase; acetyl-activating enzyme. An enzyme that catalyses a reaction between ATP, acetate, and CoA to form AMP, pyrophosphate, and acetylCoA. It is an important enzyme in organisms (e.g. Escherichia coli, many fungi, protozoans, algae) that utilize acetate as a carbon source. Example from E. coli: database code ACUA_ECOLI, 652 amino acids (72.01 kDa). Distinguish from acetate-CoA ligase (ADP-forming), EC 6.2.1.13. acetate thiokinase see acetate-eoA ligase. acetazolamide an inhibitor of carbonic anhydrase that is useful as a diuretic. It acts by preventing bicarbonate reabsorption in the proximal tubules of the kidney.

acesulfame 6-methyl-1 ,2,3-oxathiazin-4(3H)-one 2,2'-dioxide; a sweet-tasting material that, as the potassium salt, has been used in foods and cosmetics.

o H3C~O""'.!/ I

y=O NH

o acetal any member of a class of organic compounds having the general formula R 1HC(OR3)OR4 or R1R2C(OR3)OR4 - in a thioacetal the corresponding formulae are R' HC(SR 3)SR 4 or RIR2C(SR3)SR4 - where R3 and R 4 are alkyl groups (or R4 is H in a hemiacetal or hemithioacetal). An acetal molecule is formed by the acid-catalysed combination of the carbonyl group of an aldehyde or ketone molecule with either one or two alcohol (or mercaptan) molecules (which may be the same or different), or with a diol (or dithiol), by a reaction of the following general type, where X is 0 (or S in a mercaptan or dithiol): R'R2C==O + R3XH = R'R 2C(XR3)OH. The hemiacetal (or hemithioacetal) so formed may then undergo a further reaction:

(+)aceto+ comb. form denoting the acyl group derived from acetic acid. acetoacetate-CoA ligase EC 6.2.1.16; other name: acetoacetyl-CoA synthetase; an enzyme that catalyses the formation of acetoacetyl-CoA from ATP, acetoacetate, and CoA with release of AMP and pyrophosphate. In bacteria that carboxylate acetone to acetoacetate, it activates the latter for further metabolism. It is also present in animals, but utilization of blood acetoacetate after its entry into tissues involves 3-oxoacid CoA-transferase. acetoacetyl acetyltransferase see acetyl-CoA C-acetyltransferase. acetoacetyl-CoA synthetase see acetoacetate-CoA ligase. acetoacetyl-CoA thiolase see acetyl-CoA C-acetyltransferase. acetogenin any substance built up of two-carbon units that may formally be considered to derive from a polyacetyl chain intermediate; the carbon atoms derived from the carboxyl carbon atoms of acetic acid frequently remain oxidized. It is not a recommended term. See polyketide. acetoin 3-hydroxy-2-butanone; a compound formed by action

5

acetone body of acetolactate decarboxylase (EC 4.1.1.5) and, under some conditions, pyruvate decarboxylase (EC 4.1.1.1).

o

H3C~

Y J.~CH3 OH

acetone body see ketone body. acetone powder any preparation of ruptured cells obtained from a tissue or single-celled organisms that involves dehydration with acetone to form a powder. It is relatively stable, and is used in the preparation of some enzymes. acetyl the acyl group ethanoyl, CH,CO-, derived from acetic acid (= ethanoic acid). acetylation an acylation reaction in which an acetyl group, CH,CO-, is introduced into an organic compound. -acetylated adj. acetylation coenzyme the original name for coenzyme A. acetylcholine receptor see cholinoceptor. acetylcholinesterase abbr.: AChE; EC 3.1.1.7; systematic name: acetylcholine acetylhydrolase; other names: true cholinesterase; cholinesterase I; an esterase enzyme that catalyses the hydrolysis of acetylcholine to choline and acetate; it also acts on a variety of acetic esters and catalyses transacetylations. It is found in or attached to cellular or basement membranes of presynaptic cholinergic neurons and postsynaptic cholinoceptive cells. A soluble form occurs in cerebrospinal fluid and within cholinergic neurons. It is inhibited by a number of drugs, e.g. physostigmine, and by several organophosphates. Example from human: database code ACES_HUMAN, 614 amino acids (67.72 kDa). The 3-D structure is known for fragments obtained from the electric ray (fish). acetylcholine transporter protein an integral membrane protein of synaptic vesicles of cholinergic neurons. It transports newly synthesized acetylcholine molecules into the synaptic vesicles in exchange for protons, thereby replenishing vesicular stores of the neurotransmitter. Example from Caenorhabditis elegans: database code UNI7_CAEEL, 532 amino acids (58.58 kDa). acetyl-CoA abbr. for acetyl coenzyme A. acetyl-CoA e-acetyltransferase EC 2.3.1.9; other names: acetoacetyl acetyltransferase; acetoacetyl-CoA thiolase; an enzyme that catalyses the formation of two molecules of acetyl-CoA from CoA and acetoacetyl-CoA. During beta oxidation it catalyses the formation of acetyl-CoA from acetoacetyl-CoA, whereas it acts in the reverse direction to form acetoacetyl-CoA during ketogenesis. It is important in regulating the metabolic pathways for the production of acids, i.e. acetate, butyrate, or solvents, i.e. acetone, butanol, ethanol, during the growth of Clostridium acetobutylicum. Reduced activity of the enzyme favours production of acetate and ethanol, while increased activity favours production of butyric acid, butanol, and acetone. Example from human (mitchondrial, precursor): database code THIL_HUMAN, 427 amino acids (45. I 5 kDa). acetyl-CoA e-acyltransferase EC 2.3.1.16; systematic name: acyl-CoA:acetyl-CoA C-acyltransferase; other names: 3-ketoacyl-CoA thiolase; jJ-ketothiolase; an enzyme that catalyses the formation of acyl-Co A and acetyl-Co A from CoA and 3oxoacyl-CoA. This is the concluding reaction of each cycle of the fatty acid oxidation pathway (beta oxidation). Different enzymes exist in the mitochondrion and peroxisome, both being included in the thiolase family. Examples include rat peroxisomal enzyme A (one of two), homodimer: database code for precursor THII_RAT, 424 amino acids (43.77 kDa); also from yeast (precursor): database code THIK_YEAST, 417 amino acids (44.68 kDa); mitochondrial enzyme, homotetramer: database code THIM_RAT, 397 amino acids (41.82 kDa).

N-acetylcysteine acetyl-CoA carboxylase EC 6.4.1.2; systematic name: acetylCoA:carbon-dioxide ligase (ADP-forming); a multienzyme complex involved in the formation of malonyl-eoA, the first step in fatty-acid biosynthesis. It catalyses a reaction between ATP, acetyl-CoA, and HC0 3- to form ADP, orthophosphate, and malonyl-CoA. Biotin is a cofactor. In bacteria it is a heterohexamer of biotin-carboxyl-carrier-protein, biotin carboxylase, and a 2:2 complex of the two subunits of carboxyl transferase. Examples from Escherichia coli: biotin carboxylase (EC 6.3.4.14), which catalyses the reaction between ATP, biotin-carboxyl-carrier-protein, and CO 2 to form ADP, orthophosphate, and carboxybiotin-carboxyl-carrier-protein; database code ACCC_ECOLI, 449 amino acids (49.26 kDa); biotin-carboxyl-carrier-protein: database code BCCP_ ECOLI, 156 amino acids (16.67 kDa); carboxyl transferase usubunit, database code ACCA_ECOLI, 318 amino acids (35.07 kDa); carboxyl transferase p-subunit, database code ACCD_ECOLl, 304 amino acids (33.3 I kDa). Biotin-carboxyl-carrier-protein is carboxylated by biotin carboxylase and the carbonyl group is then transferred to acetyl-CoA by carboxyl transferase, thus forming malonyl-CoA. In mammals the activity is part of a trifunctional enzyme that has in a single protein the activities carboxyl carrier protein, biotin carboxylase (EC 6.3.4.14), and acetyl-CoA carboxylase (EC 6.4.1.2). Example from rat: database code COAC_RAT, 2345 amino acids (264.89 kDa). [acetyl-CoA carboxylase] kinase EC 2.7.1.128; an enzyme that catalyses the phosphorylation by ATP of[acetyl-CoA carboxylase] with release of ADP. This phosphorylation step is one of the regulatory mechanisms for acetyl-CoA carboxylase, causing that enzyme to dissociate from an active polymeric form to an inactive monomeric form. [acetyl-CoA carboxylase] phosphatase EC 3.1.3.44; an enzyme that catalyses the hydrolysis of phosphate from [acetylCoA carboxylase] phosphate. It reverses the phosphorylation catalysed by [acetyl-CoA carboxylase] kinase. acetyl coenzyme A abbr.: acetyl-CoA; a derivative of coenzyme A in which the sulfhydryl group is acetylated. Originally termed 'active acetate', it is an important metabolite, derived from pathways such as glycolysis, fatty-acid oxidation, and degradative metabolism of some amino acids. It is further metabolized by the tricarboxylic-acid cycle and represents a key intermediate in lipid and terpenoid biosynthesis and other anabolic reactions.

NH2

HsC CHs

~

HO, ""

o

6::"; ~N

0 0 0-P-0-P-0-CH2

N

I. I o1I11~ o·

)H

0

0

OH

O",lN~yCH' -0-1:,° H

0

N-acetylcysteine or N-acetyl-L-cysteine a thiol-protecting agent used intravenously as an antidote in acetaminophen poisoning. It acts by enhancing glutathione synthesis, thereby increasing the capacity for detoxification and excretion of acetaminophen as a mercapturic acid. Methionine can be similarly used. It also has mucolytic properties, and is used in aiding the isolation of mycobacteria from sputum.

6

acetylglutamic acid

N-acetylgalactosamine N-acetylgalactosamine symbol: D-GalpNAc; abbr.: NAGA;

the D isomer, 2-acetamido-2-deoxy-o-galactopyranose, is a common structural unit of oligosaccharides, such as the blood-group substances and O-linked glycoproteins, in which the sugar is in glycosidic linkage to a protein or serine resid ue, or, in the case of the blood-group substances, to a lipid hydroxyl group. The reactant in synthetic reactions is UDP-Nacetyl galactosamine, which is formed by epimerization of N-acetylglucosamine.

Hk;OCH2OH OH

HO NH

a==(

CH 3 poD-anomer

H~O~H ~ NH

a=
epinephrine, 560 amino acids (rat); alB, norepinephrine = epinephrine, 515 amino acids (rat); alC, norepinephrine = epinephrine (different antagonist sensitivity from alB), 466 amino acids (bovine); alD, 560 amino acids (rat). a2A Receptors all inhibit the formation of cyclic AMP; they also open K+ chan-

adsorptiochromism nels and inhibit Ca2+ channels; 450 amino acids (human). a2B Receptors inhibit Ca2+ channels; 450 amino acids (human). a2C Receptors have no effect on ion channels; 461 amino acids (human). Examples: alA receptor, database code AIAA_ HUMAN, 572 amino acids (60.46 kDa); a2A receptor (subtype clO), database code A2AA_HUMAN, 450 amino acids (48.96 kDa). p Adrenoceptors have actions that can be ascribed to the activation of adenylate cyclase. They may be divided phenomenologically into three classes: (I) ~I adrenoceptors, in which the relative order of agonist potency is isoprenaline> norepinephrine ~ epinephrine and the relative order of antagonist potency is practolol > propranolol. They are associated with cardiac stimulation and glycogenolysis, lipolysis in white adipose tissue, and calorigenesis in brown adipose tissue; (2) ~2 adrenoceptors, in which the relative order of agonist potency is isoprenaline> epinephrine> norepinephrine and the relative order of antagonist potency is propranolol> practolol; they are associated with skeletal muscle glycogenolysis, promotion of secretion of glucagon and insulin, vasodepression, and bronchodilation; and (3) ~3 adrenoceptors with agonist potency norepinephrine> epinephrine. Examples from human: ~), database code BIAR_HUMAN, 477 amino acids (51.16 kDa); ~2, database code B2AR_HUMAN, 413 amino acids (46.50 kDa); ~3' database code B3AR_HUMAN, 408 amino acids (43.47 kDa). See also p-adrenergic receptor kinase, p-arrestin. adrenoceptor kinase see p-adrenergic receptor kinase. adrenocortical of, pertaining to, or derived from the cortex of the adrenal gland, e.g. adrenocortical hormone. See adrenal androgen, corticosteroid. adrenocorticotropic hormone or adrenocorticotrophic hormone abbr.: ACTH; an alternative name for corticotropin. adrenocorticotropic hormone-releasing factor an alternative name for corticotropin releasing hormone. adrenocorticotropin or adrenocorticotrophin an alternative name for corticotropin. adrenodoxin or (sometimes) adrenoredoxin a ferredoxin isolated from adrenal-cortex mitochondria that acts as an electron carrier in hydroxylase systems acting on steroids. It transfers electrons from adrenodoxin reductase to cholesterol monooxygenase. Example from Bos taurus: database code ADXLBOVIN, 186 amino acids (19.76 kDa); residues I-58 are the mitochondrial transit sequence, 59-186 adrenodoxin. See also NADPH:adrenodoxin oxidoreductase precursor. Compare putidaredoxin. adrenodoxin reductase see NADPH:adrenodoxin oxidoreductase precursor. adrenomedullary of, pertaining to, or derived from the medulla of the adrenal gland. adrenomedullin a hypotensive peptide that may function as a hormone in circulation control. Example from human: database code ADML_HUMAN, 185 amino acids (20040 kDa). adrenoreceptor a variant spelling ofadrenoceptor. adrenoredoxin (sometimes) a variant spelling ofadrenodoxin. adrenosterone androst-4-ene-3, 11, 17-trione; a hormone with weak androgenic effect, originally called Reichstein's substance G. adrenotropic receptor an alternative name for adrenoceptor. adrex or adx abbr. for adrenalectomized. adriamycin former (generic) name for doxorubicin. adseverin another name for scinderin. adsorb to undergo or elicit adsorption. -adsorbable adj.; adsorbability n. adsorbate a substance that is adsorbed to the surface of another substance from either a gas or a liquid phase. adsorbent 1 capable of adsorption. 2 a solid that adsorbs another substance from either a gas phase or a liquid phase. adsorptiochromism the colour change that sometimes ac-

20

adsorption companies adsorption of organic compounds onto inorganic substances, e.g. onto alumina. adsorption 1 any process in which a gas, liquid, or solute adheres to the exposed surfaces of a material, especially a solid, with which it is in contact. In physical adsorption the adhesion is through van der Waals forces of interaction, whereas in chemisorption (or chemical absorption) the adhesion is through formation of weak chemical bonds. Compare absorption. 2 (in immunology) the nonspecific attachment of an antigen (or antibody) onto the surfaces of red cells or inert particles so that the antibody (or antigen) to it may be detected by agglutination of the cells or particles. Compare immunosorption. 3 (in microbiology) the process of attachment of a phage or other virus to a cell. adsorption chromatography any form of chromatography in which separation of the components of a mixture is based mainly on differences between the adsorption affinities of the components for the surface of an active solid. adsorption coefficient in any adsorption equilibrium (of a substance from a solution), the mass of adsorbed substance per unit mass of adsorbent divided by the concentration of the substance in solution. It has the dimensions of reciprocal concentration. Compare distribution coefficient, partition coefficient. adsorption isotherm any plot of the amount of solute adsorbed by an adsorbent (or of ligand bound by, e.g., a macromolecule, often expressed as the saturation fraction) versus the concentration of the free solute (or ligand), at constant temperature. Compare Langmuir adsorption isotherm. adx see adrex. AEBSF abbr. for aminoethylbenzenesulfonyl fluoride. +aemia see +emia. aequorin a Ca 2 +-dependent photoprotein responsible for luminescence by oxidation of the chromophore coelenterazine. It is obtainable from the hydrozoan jellyfish Aequorea forskaolea. In the absence of any other cofactors or oxygen it emits light on the addition of calcium ions, making it useful for the determination of free calcium ions. Example, aequorin I from Aequorea victoria: database code AEQ1_AEQVI, 196 amino acids (22.49 kDa). aerate 1 to supply with or expose to air. 2 to pass air through a liquid. -aeration n. aerobe any organism or class of organisms that can grow in the presence of dioxygen. Facultative aerobes are also capable of growing in the absence of dioxygen, whereas obligate (or strict) aerobes have an absolute requirement for dioxygen. Compare anaerobe. aerobic 1 describing conditions in which gaseous or dissolved dioxygen is present. 2 describing an organism or process that requires or is able to use dioxygen. 3 of or produced by an aerobe. Compare anaerobic. aerolysin a channel-forming protein secreted by the human pathogen Aeromonas hydrophila. The cytolytic toxin is a dimer but forms stable heptameric structures that insert into lipid bilayers to produce well-defined channels, leading to destruction of the membrane permeability barrier and osmotic lysis. Example (precursor) from A. hydrophila: database code AERA_ AERHY, 493 amino acids (54.28 kDa). aerosol a colloidal dispersion of solid particles or liquid droplets in air or another gas. Aet symbolfor the aminoethyl group, -CHz-CHz-NH 2 . aetiology see etiology. afamin a mammalian serum protein similar to albumin, a-fetoprotein, and vitamin D-binding protein. Example from human: database code HUMAFAMIN, 599 amino acids (68.99 kDa). afferent 1 conveying inwards to a part, organ, or centre, as of a blood vessel, nerve, or duct. 2 an afferent part, e.g. an afferent blood vessel or afferent nerve. Compare efferant. affine the quality of having affinity. affinity 1 chemical attraction; the tendency of a chemical substance to combine with, bind to, or dissolve in other chemical

affinity-purified substances. 2 any measure of such chemical attraction. 3 denoting biomolecular interaction that exhibits specificity. affinity adsorbent any biospecific adsorbent used in affinity chromatography. affinity chromatography a general chromatographic method that may, in principle, be used to isolate either of the components of a reversibly reacting chemical system provided that one component can be coupled to an insoluble matrix through a covalent linkage. The other component can then be bound to the immobilized component and the system eluted with a buffer that liberates the bound component. The technique has been applied to the separation of various substances, including enzymes, substrates, antigens, antibodies, nucleic acids, and even whole living cells. Pure antibodies can be prepared by this means: the antigen is covalently coupled to the dextran beads in the chromatography column, the antibody-containing solution is run into the column in neutral buffer, the specific antibody binds to the antigen, and the antibody is subsequently released with a buffer of high or low pH or with a denaturing reagent. The technique can also be used to isolate an tigen. See also affinity-elution chromatography, dye-ligand chromatography. -affinity-chromatographic ad). affinity constant or binding constant an alternative name for association constant (especially in relation to the binding of and/or to macromolecules, as in antigen-antibody, hormonereceptor, and enzyme-inhibitor reactions). affinity cytochemistry a technique for detecting the distribution of specific cell-surface receptors. An easily visible (or electron-dense) material conjugated with a reagent specific for a particular cell-surface receptor is allowed to react with the cells in question and is then detected by light or electron microscopy. affinity electrode a type of electrode useful for assaying specific proteins. It comprises a metal (e.g. titanium) wire whose surface has been oxidized and then covalently attached to a ligand capable of interacting biospecifically and reversibly with the protein in question. Binding of the complementary protein to the electrode results in a measurable change in electric potential relative to that given by a reference electrode. The latter is prepared in a similar way but lacks the specific ligand. affinity electrophoresis or affinoelectrophoresis a type of electrophoresis in which the support medium contains an agent, immobilized by entrapment or by covalent linkage, that interacts specifically and selectively with certain of the components of the mixture to be analysed, thereby altering the electrophoretic mobility of those components. affinity-elution chromatography a technique in which a compound that is nonspecifically bound to the matrix of a chromatographic column is specifically eluted by binding to a ligand in the eluting solvent. Biospecific-elution chromatography is a variant of this technique. affinity gel any gel that serves as an affinity matrix. affinity-isolated an alternative term for affinity-purified. affinity label an active-site-directed irreversible inhibitor of an enzyme, antibody, or other protein. It is a chemically reactive compound that resembles a substrate or other specific ligand and bonds covalently to the active site or specific site on the protein. The affinity labelled groups can then be identified by fingerprinting and thus reveal the composition at the active site. It is sometimes termed Trojan horse inhibitor. affinity matrix or affinity support any supporting material to which the biospecific reagent is attached in affinity chromatography. affinity precipitation the precipitation of an enzyme by a homo- or hetero-bifunctional derivative of its coenzyme or/and a substrate or inhibitor. An example is the precipitation of lactate dehydrogenase by N2'-adipodihydrazido-bis-(N6carbonylmethyl-NAD), a reactive derivative of its coenzyme, NAD. affinity-purified or affinity-isolated describing a specified sub-

21

affinity support

aglycon

stance, usually a biological macromolecule such as an antigen or antibody, that has been purified (or isolated) by a technique such as affinity chromatography or affinity electrophoresis, thus implying high purity. affinity support an alternative term for affinity matrix. affinoelectrophoresis an alternative term for affinity elec-

ter-paper disk containing the drug and located on an agar culture medium seeded with the microorganism in question. agarobiose 4-0-fJ-o-galactopyranosyl-3,6-anhydro-L-galactose; a disaccharide that forms the basic unit of agarose.

trophoresis. aflatoxin any of a group of related and highly toxic secondary metabolites (mycotoxins) produced by strains of the moulds As-

pergillus f/avus or A. parasiticus, together with further metabolites of these mycotoxins. Their main structural feature is a fused coumarin~bis(dihydrofuran) ring system. The most important are aflatoxins B], B2, G), and G 2 - so designated from the colour of their fluorescence (B, blue; G, green). The mycotoxins are produced naturally by the moulds growing on various seed crops, especially groundnuts (peanuts), and certain cereals (e.g. maize) during storage under moist conditions. They are acutely toxic and highly carcinogenic to many species of animals (probably including humans), and are responsible for turkey X disease. The main organ affected is the liver; aflatoxin B j is the most potent hepatocarcinogen known. The term is derived as a contraction of A. f/avus toxin.

aflatoxi n 6,

AFLP abbr. for amplification fragment length polymorphism. The use of the polymerase chain reaction to amplify DNA in the study of restriction fragment length polymorphism. A form 1 A form of DNA (abbr.: A-DNA or DNA-A); the molecular conformation adopted by fibres of the sodium salt of duplex DNA at a relative humidity of 75% or less. It consists of a right-handed double helix containing about II nucleotide residues per turn, with the planes of the base pairs inclined at about 70° to the axis of the helix. Unlike the B form of DNA it has a large hole (~0.8 nm diameter) at the axis and a very deep major groove. See also C form, Z form. 2 A form of RNA (abbr.: A-RNA); the molecular conformation of doublestranded regions of RNA that is favoured at low-salt concentrations and moderate temperatures; it resembles the A form of DNA. (see def. 1). AFP abbr. for a-fetoprotein. Ag 1 abbr. for antigen. 2 symbolfor silver. AGA 1 a codon in non-mitochondrial mRNA for L-arginine. 2 a codon in human mitochondrial mRNA for chain termination. 3 abbr. for N-acetylglutamic acid. agamic reproduction see asexual reproduction. agamogeny the development of a new individual from a single cell. Compare vegetative reproduction. agar or agar-agar a complex sulfated galactan extracted from certain seaweeds, especially Gelidium and related genera. The two main components are agarose and agaropectin. Agar forms an aqueous gel suitable for the solidification of microbiological culture media and for use as a support medium in zone electrophoresis or (immuno)diffusion techniques. It is not metabolized by most organisms. The gelling temperature varies from about 25 to 35°C for different types of preparation. The gel is then stable to about 90 °e. agar-diffusion method a method for determining the sensitivity of a microorganism to an antimicrobial drug. The zone of growth inhibition is measured around a ditch, hole, or a fil-

agarobiose

agaropectin a charged component of agar consisting of a mix-

ture of polysaccharides containing o-galactose, 3,6-anhydroL-galactose, and monoesterified sulfuric acid units. Samples from some algae may contain other components such as pyruvate, L-arabinose, and o-glucuronate units. agarose an essentially uncharged component of agar comprising a ~ 120 kDa alternating carbohydrate polymer. It consists of -3)o-Galp-(fJI-4)-3,6An-L-Galp(al- repeating units, containing small amounts of ionized sulfate and pyruvate groups. It is widely used as a matrix in zone and immunoelectrophoresis, immunodiffusion, and gel filtration and affinity chromatography. See also agarobiose. AGe a codon in mRNA for L-serine. agenized flour see methionine sulfoximine. AGG 1 a codon in non-mitochondrial mRNA for L-arginine. 2 a codon in human mitochondrial mRNA for chain termination. agglutinate 1 to adhere or cause to adhere. 2 to cause the clumping of cells, particles, etc., or to undergo such clumping. agglutination 1 the act or process of adhering. 2 the process in which suspended cells or other antigen coated particles clump together when antibody is added due to an antigen-antibody reaction. 3 the result of such a process. See also agglutinin. agglutinin an antibody that has the ability to agglutinate the corresponding antigen, e.g. when the antigen is present on the surface of a suspended cell or other particle. agglutinogen an antigen, usually particulate, that stimulates the production of agglutinin. aggrecan the major proteoglycan of cartilage. It has approximately one glycosaminoglycan chain for every 20 amino-acid residues, and a total mass of about 3 MDa. It assembles with glycosaminoglycans, especially hyaluronan, into aggregates several micrometres in diameter. Example (of protein precursor) from human juvenile cartilage chondrocyte: database code HUMAGPRO, 2316 amino acids (238.97 kDa). See also versican. aggregate

1 formed of separate units or particles collected into a whole or into larger units. 2 an assemblage or sum of many separate units or particles. 3 to form or be formed into a single body or larger body. aggregation 1 the process of forming an aggregate (def. 2). 2 a cluster or group of particles held together into larger units. aggregation number the number of monomers of an amp hipathic substance that form a micelle under any particular conditions. aggressin a diffusible nontoxic substance produced by a microorganism that promotes the invasive power of the microorganism in the host. aglucon or (formerly) aglucone an aglycon derived from a glucoside (i.e. where the sugar moiety was a glucose residue). aglycon or aglucon or (formerly) aglycone or aglucone the part

22

agmatine of any glycoside that remains after the sugar moiety has been chemically or enzymically removed. agmatine l-amino-4-guanidobutane; a putative endogenous ligand for imidazoline receptors synthesized from arginine by the enzyme arginine decarboxylase (EC 4.1.1.19). In some invertebrates e.g. the sponge Geodia gigas and some cephalopods, the guanidine group can undergo phosphorylation to phosphoagmatine, which acts as a phosphagen. agnotobiotic pertaining to the growth of organisms of a single species in the presence of one or more other species of which at least one is unknown. Compare synxenic. +agogue or (US) +agog suffix denoting an agent that elicits or enhances the secretion of the indicated substance. [from the Greek agogos, leading, drawing forth.]-+agogic adj. agonist any ligand, especially a drug or hormone, that binds to receptors and thereby alters the proportion of them that are in an active form, resulting in a biological response. A conventional agonist increases this proportion, whereas an inverse agonist reduces it. See also full agonist, partial agonist. Compare antagonist. -agonistic adj. Agranoff's turtle a zoomorphic mnemonic for avoiding the confusion that has tended to occur over the numbering of the carbon atoms of myo-inositol and its chiral derivatives, especially when their Haworth projections are converted into diagrams representing their normal chair conformations. The chair conformation of the parent compound is likened to a turtle, with its body corresponding to the C 6 ring, its coplanar limbs and tail representing the five equatorial hydroxyl groups, and its erect head the axial hydroxyl group. The turtle is viewed from above; then, for derivatives named as members of the 0 series, numbering of the turtle's appendages proceeds counterclockwise, commencing with its right front paw (i.e. its dextro 'hand'), which is designated 10; its head becomes 20, its left front paw is 30, and so on around its body. Conversely, numbering of the L series of derivatives commences with the left front paw (the laevo 'hand'), designated lL, and then proceeds clockwise, the head becoming 2L, and so on. [After its originator Bernard William Agranoff (1926- ), who devised it in 1978.] agrin a component of the synaptic basal lamina that causes aggregation of acetylcholine receptors and acetylcholinesterase on the surface of muscle fibres of the neuromuscular junction. It occurs in embryonic nervous tissue and muscle, especially during early development. At least five different forms arise by alternative splicing; they differ in their acetylcholine receptor clustering activity. An EGF-like domain is present. Example (precursor) from rat: database code AGRCRAT, 1959 amino acids (208.41 kDa). Agrobacterium a genus of Gram-negative aerobic rod-shaped soil bacteria. Most strains can initiate formation of galls in plants (see crown-gall disease). A feature of the infection of plants by Agrobacterium species is that the bacterium can subvert the host plant tissue to produce amino acids known as opines, which the bacterium can use as an energy, carbon, and nitrogen source. The type of opine produced is determined by the bacterial strain. Continued presence of the bacteria is not necessary for transformation of the cells of the host plant. Transformation by Agrobacterium tumefaciens has been shown to be due to large plasmids (140 - 235 kb). These are known as tumour-inducing or Ti plasmids, and they have been exploited in the production of transgenic plants. agrochemical a chemical that is used in agriculture or horticulture, especially as a biocide, fertilizer, etc. agroclavine 8,9-didehydro-6,8-dimethylergoline; a nonpeptide ergot alkaloid. agropine an opine; a rare amino-acid derivative that is produced by a certain type of crown-gall tumour. The genes responsible for its synthesis are part of the T-DNA from a Ti plasmid. See also crown-gall disease.

AIR carboxylase

H'~X~H ~H o

0

=

H

OH

§

OH

OH

agropine

AGU a codon in mRNA for L-serine. Ah abbr. for aromatic hydrocarbon; the name of a genetic locus in higher organisms that governs biological responses to some aromatic hydrocarbons. The proteins it encodes include cytochrome P450 lAl, a liver microsomal mono oxygenase that oxidizes a variety of unrelated compounds, including xenobiotics such as the environmental carcinogens, benzo[a]pyrene and 3-methylcholanthrene. This enzyme is induced by these compounds and, more potently, by polychlorinated biphenyls such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), acting through the Ah receptor. The 5'-flanking region of the gene for this enzyme contains several short sequence motifs known as xenobiotic response elements (XREs). ahnak a human gene that encodes a giant protein of ~700 kDa with a large internal domain (=4300 amino acids) of highly conserved repeated sequences, much of which are 128 aminoacid residues in length and contain a heptad repeat. The ahnak protein is found in human nuclei and is of unknown function. [From Hebrew Ahnak, giant.] Ah receptor abbr. for aryl hydrocarbon receptor; a protein encoded by the Ah gene that binds a number of aryl hydrocarbons and mediates their biochemical and toxic effects. It is activated when it binds a ligand, and then translocates from the cytoplasm to the nucleus, where it is believed to enhance gene transcription by binding to the xenobiotic-response element sequence. It contains a basic helix-tum-helix motif; the DNAbinding form is a heterodimer of this protein and ARNT. Example (precursor) from human: database code AHR_HUMAN, 808 amino acids (91.62 kDa). £Ahx or (formerly) £Acp symbol for a residue of the e-amino acid 6-aminohexanoic acid (formerly known as e-aminocaproic acid). aHyl symbol for a residue of the a-amino acid L-allohydroxylysine; threo-5-hydroxY-L s-lysine. AlB abbr. for 2-aminoisobutyric acid. AICAR abbr. for 5-amino-4-imidazolecarboxamide ribonucleotide (an intermediate in purine biosynthesis). AICAR transformylase see phosphoribosylaminoimidazolecarboxamide formyltransferase. AIDS abbr. for acquired immunodeficiency syndrome. aile (AIle) symbol for a residue of the a-amino acid L-alloisoleucine, (2S,3R)-2-amino-3-methylpentanoic acid. AIR abbr. for. for 5-aminoimidazole ribonucleotide, an intermediate in purine biosynthesis.

r H2N~N) N

o

II~

HG-)-O-CH2

0

OH

OH

OH

AIR carboxylase see phosphoribosylaminoimidazole carboxylase.

23

air-lift bioreactor

albumin

air-lift bioreaetor a bioreactor in which the reaction medium is kept mixed and gassed by the introduction of air or another gas at the base of a column-like reactor. aimaline ajmalan-17,20-diol; an alkaloid from the roots of Rauwolfia serpentina. It is useg clinical1y as an antihypertensive and antiarrhythmic, having the effect of normalizing heart rhythm. L-alanine

H

,OH

......~

AK (in clinical biochemistry) abbr. for adenylate kinase. AKAP abbr. for A-kinase anchor protein or cAMP-dependent protein kinase anchor protein; a protein that anchors the kinase to cytoskeletal and/or organelle-associated proteins, targeting the signal carried by cyclic AMP to specific intracellular effectors. The N-terminal region, which is highly basic, is required for interaction with calmodulin. Example (human): database code AK79_HUMAN, 427 amino acids (47.02 kDa). akaryotic describing a cel1 without a nucleus. akee a variant spelling of ackee. AKH abbr. for adipokinetic hormone. A-kinase an enzyme that phosphorylates target proteins in response to a rise in intracellular cyclic AMP. See cyclic AMPdependent protein kinase. Akt the mouse or human homologue of v-akt, the oncogene of the transforming retrovirus AKT8. v-akt encodes a serine/threonine protein kinase that contains an SH2 domain. Database code KAKT_MLVAT, SOl amino acids (57.87 kDa). al+ prefix denoting an acyclic monosaccharide or monosaccharide derivative. See also aldehydo-. +al suffix denoting an unbranched acyclic mono- or dialdehyde. AI symbolfor aluminium. Ala symbol for a residue of the a-amino acid L-alanine, 2aminopropanoic acid (alternative to A). /3Ala symbol for a residue of the p-amino acid p-alanine, 3aminopropanoic acid. ALA or dALA abbr. for t5-aminolevulinate. Ala AT or ALAT (in clinical biochemistry) (formerly) abbr. for alanine aminotransferase. ALT is preferred. ALA dehydratase see porphobilinogen synthase. alamethicin a linear ionophorous antibiotic polypeptide containing a high proportion of 2-methylalanine residues and blocked at both ends. See also peptaibophols. Ac-2-MeAla-L-Pro-2-MeAla-L-Ala-2-MeAla-L-AlaL-Gln-2-MeAla-L-Val-2-MeAla-GIY-L-Leu2-MeAla-L-PrO-LVal-2-MeAla-2-MeAla-L-GluL-Gln-L-phenylalaninol

alaninal the aldehyde obtained by reduction of the carboxyl group of alanine. alaninate 1 alanine anion, the anion CHrCH(NHz)-COO-. 2 any salt containing alanine anion. 3 any ester of alanine. alanine the trivial name for a-aminopropionic acid; 2-aminopropanoic acid; CH 3-CH(NH z)-COOH; a chiral a-amino acid. L-alanine (symbol: A or Ala), (S)-2-aminopropanoic acid, is a coded amino acid found in peptide linkage in proteins; codon: GCA, GCC, GCG, or GCU. In mammals it is a nonessential dietary amino acid and is glucogenic. Residues of D-alanine (symbol: D-Ala or DAla), (R)-2-aminopropanoic acid, are found in cel1-wal1 peptidoglycans of various bacterial species and in other materials, e.g. cyclosporin.

/3-alanine symbol: pAla; the trivial name for p-aminopropionic acid; 3-aminopropanoic acid; HzN-CHrCHz-COOH; an achiral p-amino acid. It occurs free in brain and in combination in pantothenate (and hence in coenzyme A) and in the isopeptides anserine and carnosine, but it is not a constituent of proteins. It has an inhibitory effect on the central nervous system. alanine cycle see glucose-alanine cycle. /3-8lanine-oxoglutarate aminotransferase see 4-aminobu· tyrate transaminase. alanine transaminase abbr. (in clinical biochemistry): ALT; EC 2.6.1.2; systematic name: L-alanine:2-oxoglutarate aminotransferase; other names: glutamic-pyruvic transaminase; glutamic-alanine transaminase. An enzyme that catalyses the reversible reaction: L-alanine + 2-oxoglutarate = pyruvate + L-glutamate. Widely distributed in all tissues and organisms, it is a pyridoxal-phosphate enzyme. Example, cytoplasmic isoform: database code ALAT_HUMAN, 495 amino acids (54.38 kDa). In clinical chemistry its assay alongside aspartate transaminase (AST) normal1y present in plasma in higher concentrations, may be useful as an indicator of liver damage, as levels of ALT are higher in liver than those of AST, in contrast to other tissues. In hepatitis, plasma levels of ALT may exceed those of AST. alaninium alanine cation, CH 3-CH(NH 3 +)-COOH. alanino the alkylamino group, CHrCH(COOH)-NH-, derived from alanine. alaninol the alcohol obtained by the successive reduction of the carboxyl group of alanine. alanyl the acyl group, CHrCH(NHz)-CO-, derived from alanine. alarmone any signal molecule that serves to reorient a cel1's economy in response to stress. Such molecules include ppGpp, which is produced, e.g., in microorganisms, in response to growth-rate limitation caused by amino-acid stress and acts to correct this in various ways, and diadenosine tetraphosphate (AppppA), which stimulates proliferation when DNA replication is halted at a replication fork. ALA synthetase see 5-aminolevulinate synthase. ALAT See Ala AT. albinism an inherited metabolic disorder in which there appears to be a complete or nearly complete failure to form melanin. It was first listed in 1908 by the British physician Archibald Garrod (\857-1936) in his lecture entitled 'Inborn Errors of Metabolism'. In some cases it is due to a deficiency of 'tyrosinase' (monophenol monooxygenase), but other types are known in which this enzyme is present, and for which the precise cause is unknown. albumin any of a group of globular proteins that are soluble in distilled water and solutions of half-saturated ammonium sulfate, but insoluble in ful1y saturated ammonium sulfate solutions. Serum albumin, the major protein of serum, has a good binding capacity for water, Ca2+, Na+, K+, fatty acids, hormones, bilirubin, and drugs. Its main function is the regulation of the colloidal osmotic pressure of blood; it has structural similarity to u-fetoprotein and vitamin D binding protein. Example (precursor) from human: database code ALBU_ HUMAN, 609 amino acids (69.29 kDa). See also endosperm albumin, lactalbumin, ovalbumin, serum albumin. [The name origi-

24

albuminoid nates from Latin albus, white, as it exists in nearly pure form in egg-white, from which it was easily obtained by the ancients.] albuminoid 1 of or relating to an albumin. 2 an alternative name for scleroprotein. albuminuria the presence of excessive amounts of protein in the urine. It is usually a sign of renal disease. albuterol see salbutamol. Alcalase the proprietary name for a proteolytic enzyme preparation obtained by fermentation of a strain of Bacillus subtilis. It is characterized by stability and activity at high temperatures and alkaline pH values, and is used in enzymic laundering and various industrial processes. alcapton 2,5-dihydroxyphenylacetic acid. See alcaptonuria, homogentisate. alcaptonuria or alkaptonuria a rare hereditary metabolic disease, usually due to an autosomal recessive gene, in which the enzyme homogentisic acid oxidase (homogentisate 1,2-dioxygenase, EC 1.13.11.5) is virtually absent. This leads to the inability to metabolize further the homogentisate produced by the normal metabolism of phenylalanine and tyrosine. Homogentisate therefore accumulates in the body and is excreted in the urine, which gradually turns dark as homogentisate is oxidized to a melanin-like product - a process speeded up at an alkaline pH. alcohol 1 any of a class of alkyl compounds containing a hydroxyl group. An alcohol is called primary, secondary, or tertiary according to whether the carbon atom bearing the hydroxyl group is itself attached to one, two, or three other carbon atoms. 2 specifically, ethyl alcohol, ethanol. See also absolute alcohol. -alcoholic adj., n. alcohol dehydrogenase any of the nicotinamide-nucleotidelinked dehydrogenase enzymes of groups EC 1.1.1.1 (NAD+) or EC 1.1.1.2 (NADP+) that catalyse the oxidation of alcohols to aldehydes. These are zinc proteins. Also EC 1.1.1. 71, alcohol dehydrogenase [NAD(P)+]; other name: retinal reductase; EC 1.1.99.8, alcohol dehydrogenase (acceptor), a quinoprotein. Examples: alcohol dehydrogenase I from Saccharomyces cerevisiae: database code ADHl_YEAST, 347 amino acids (36.66 kDa); alcohol dehydrogenase 6 (human): database code ADH6_HUMAN, 368 amino acids (39.03 kDa). alcoholic fermentation the conversion of glucose to ethanol by a group of reactions that are characteristic of yeast. alcohol oxidase abbr.: AOX or methanol oxidase abbr.: MOX; EC 1.1.3.13; a flavoprotein (FAD) enzyme that catalyses the oxidation by dioxygen of a primary alcohol to the corresponding aldehyde. It is important in methylotrophic yeasts, in which it is the first enzyme in the pathway for utilization of methanol, converting this to formaldehyde, thence to CO 2, alcoholysis the solvolysis of a covalent derivative of an acid by a reaction in which one of the products combines with the H atom of an alcohol's hydroxy group and the other product with the alcohol's alkoxy group. aldaric acid any dicarboxylic acid formed by oxidation of both terminal groups of an aldose to carboxyl groups. There are three tetraric acids (0-, L-, and meso-tartaric acids), four pentaric acids (0- and L-arabinaric acids, xylaric acid [meso], and ribaric acid [meso]), and ten hexaric acids (0- and L-glucarie acids, 0- and L-idaric acids, 0- and L-mannaric acids, 0and L-talaric acids, allaric acid [meso], and galactaric acid [meso]). aldehyde 1 an alternative name for the formyl group, -CHO. 2 any organic compound with the formula R-CH=O. Compare ketone. -aldehydic adj. aldehyde dehydrogenase any enzyme that catalyses the oxidation of an aldehyde group to a carboxylic acid. Many examples are known, acting specifically on a wide range of substrates. Those acting on aliphatic aldehydes are divided into four classes. Class 1, or AId C, are tetrameric cytosolic enzymes, and include aldehyde dehydrogenase (NAD+), EC 1.2.1.3; systematic name: aldehyde:NAD+ oxidoreductase; an

aldonic acid enzyme of wide specificity. Example from human: database code DHAC_HUMAN, 500 amino acids (54.73 kDa). This EC designation also includes Class 2 enzymes, or AId M, which are tetrameric mitochondrial enzymes. Class 3, or Aid D, are dimeric cytosolic enzymes, and include aldehyde dehydrogenase [NAD(P)+], EC 1.2.1.5; systematic name: aldehyde: NAD(P)+ oxidoreductase. Example from human: database code DHAP_HUMAN, 453 amino acids (50.35 kDa). aldehyde ferredoxin oxidoreductase an enzyme that catalyses the reversible oxidation of aldehydes to the corresponding carboxylic acid, using ferredoxin as an electron acceptor. Containing tungsten, molybdopterin molecules, and Fe4S4 clusters, the enzyme has remarkable thermostability. Its 3-D structure is known. aldehydo- abbr.: al-; prefix designating an uncyclized monosacccharide or monosaccharide derivative. It is used in (semi)systematic nomenclature to stress the acyclic nature of such compounds. Compare keto-. aldimine any imine that is an analogue of an aldehyde; the general structure is RCH=NR where R may be any organyl group or H. Compare ketimine. alditol any polyhydric alcohol derived from the acyclic form of a monosaccharide by reduction of its aldehyde or keto group to an alcoholic group. Older names for these compounds include glycitol and sugar alcohol. aldo+ prefiX indicating aldehydic; e.g. aldohexose. aldoketose any monosaccharide derivative containing both a (potential) aldehydic carbonyl group and a (potential) ketonic carbonyl group. aldol 1 any organic compound that is both an aldehyde and an alcohol, especially where the two functions are separated by two linked carbon atoms in accordance with the general structure: HO-C-C-CH=O. 2 the trivial name for acetaldol (3-hydroxybutanal) a compound formed by the self-condensation of two acetaldehyde molecules. aldolase 1 a generic name for nearly every enzyme of the subsubclass EC 4.1.2, the aldehyde-Iyases, enzymes catalysing aldol condensations and their reversal. 2 abbr. (in clinical biochemistry): ALS; common name for the enzyme fructose-bisphosphate aldolase; EC 4.1.2.13; systematic name: D-fructose1,6-bisphosphate D-glyceraldehyde-3-phosphate-Iyase; other name: fructose-l,6-bisphosphate triosephosphate-Iyase. An enzyme that catalyses the reversible fission of D-fructose 1,6bisphosphate to glycerone phosphate and D-glyceraldehyde 3phosphate. It acts also on (3S,4R)-ketose I-phosphates. In mammals three isoenzymes are known: aldolase A in muscle; aldolase B in liver, kidney, and small intestine; and aldolase C in brain. All three isoenzymes catalyse the reversible splitting of both D-fructose 1,6-bisphosphate and D-fructose I-phosphate, but with different relative limiting rates; liver aldolase B shows approximately the same limiting rate with both substrates, while aldolase A and aldolase C show, respectively, a 50-fold and a 10-fold lower maximal activity with fructose 1phosphate than with fructose 1,6-bisphosphate. Each is of ~160 kDa and is composed of four subunits, which are immunologically distinct in the three isoenzymes. Examples, aldolase A from Mus musculus: database code ALFA_MOUSE, 363 amino acids (39.22 kDa); aldolase from Pisum sativum: database code ALFLPEA, 357 amino acids (38.44 kDa). Three different but related aldolase genes (probably formed from a single ancestral gene) have been identified; in humans the aldolase-A gene is in chromosome 16, the aldolase-B gene is present as a single copy in chromosome 9, and the aldolaseC gene is in chromosome 17. See also hereditary fructose intolerance. aldol condensation the base-catalysed addition reaction of two aldehydes or an aldehyde and a ketone to form an aldol (def. 1). aldonic acid a monocarboxylic acid having a chain of three or more carbon atoms and formally derived from an aldose by oxidation of the aldehydic group.

25

alkali

aldopentose aldopentose any of the eight possible five-carbon-atom aldoses. aldopyranose any aldose in the pyranose form. aldose a monosaccharide in which the (potential) carbonyl group is terminal (i.e. aldehydic). The term is frequently modified to indicate the number of carbon atoms in the chain, as in aldotriose, aldotetrose, etc. aldosterone IlfJ,21-dihydroxy-3,20-dioxopregn-4-en-18-al; the most powerful naturally occurring mineralocorticoid hormone, originally named electrocortin by its discoverers Sylvia Simpson and James Tait in 1954. The name was changed to aldosterone after its structure had been determined by Reichstein in 1953. It exists in solution as an equilibrium mixture of the aldehyde and the hemiacetal formed with the hydroxyl at position II. Produced by the cells of the zona glomerulosa of the adrenal cortex, its main action is to increase reabsorption of sodium ions by the distal renal tubules and thus to regulate water and electrolyte metabolism. The biosynthesis of aldosterone is stimulated by angiotensin II (see angiotensin, reninangiotensin system), corticotropin, and increased potassium-ion concentrations. II-Deoxycorticosterone is converted into aldosterone by aldosterone synthase. Aldosterone exerts its effects through binding to cytosolic receptors. The resulting complex is transferred to the nucleus, where it acts to stimulate production of mRNA for sodium transport proteins. The action is thus on a timescale of many minutes.

aldehyde form

hemiacetal form

aldosterone synthase EC 1.14.15.4; recommended name: steroid IlfJ-monooxygenase; other names: cytochrome P450 IIB2; steroid 18-hydroxylase; P450C18. A heme-thiolate enzyme that converts II-deoxycorticosterone to aldosterone, by successive hydroxylations at the IlfJ and 18 positions. Reduced adrenodoxin is a reactant, being converted to oxidized adrenodoxin. Example, human (precursor): database code CPN2_HUMAN, 503 amino acids (57.58 kDa). aldotetrose any of the four possible four-carbon-atom aldoses. aldotriose either 0- or L-glyceraldehyde; see aldose. aldrin 1,2,3,4,10, IO-hexachloro-I ,4,4a,5,8,8a-hexahydro-1 ,4:5,8dimethanonaphthalene; an organochlorine compound formerly used as an insecticide, but now banned in certain countries on account of its toxicity.

CI

aldrin

aleuron or aleurone 1 granules of insoluble protein found in plant cells, especially in the seeds of cereals, where they appear to act as storage material. 2 the single layer of cells on the outside of the endosperm of cereal seeds containing such granules. Translocated gibberellins stimulate the cells to synthesize a-amylase, which is secreted into the endosperm to hydrolyse the stored starch. aleuroplast any colourless plastid or leukoplast storing protein. Aleuroplasts are found in plant cells, particularly seeds. alexin or alexine former term for complement; hence alexinated means treated with complement. ALG abbr. for anti-lymphocyte globulin. alga (pl. algae) any of a group of simple eukaryotic photosynthetic protists. They may be unicellular or multicellular, and are generally aquatic. The prokaryotes formerly called bluegreen algae are now known as cyanobacteria.-algal adj. algicide any chemical agent that selectively kills algae. algin the sodium salt of alginic acid alginate lyase EC 4.2.2.3; recommended name: poly(fJ-o-mannuronate) lyase; systematic name: poly(fJ-o-I,4-mannuronide) lyase. An enzyme that catalyses a reaction resulting in eliminative cleavage of polysaccharides containing fJ-o-mannuronate residues to give oligo saccharides with 4-deoxy-a-L-erythrohex-4-enopyranuronosyl groups at their ends. Example from Pseudomonas aeruginosa: database code PSEALGL, 367 amino acids (40.78 kDa). alginic acid a hydrophilic polysaccharide ("'240 kDa) occurring in brown algae (brown seaweeds), especially the Californian giant kelp (Macrocystis pyrifera) and horsetail kelp (Laminaria digitata). Sodium alginate is used commercially as an emulsifier and thickener in foodstuffs, pharmaceuticals, etc. It has an interrupted structure of stretches of al-4-linked a-L-gulopyranosyluronic acid residues, stretches of fJl-4linked fJ-o-mannopyranosyluronic acid residues, and stretches where both uronic acids occur in alternating sequence. Similar glycans are secreted by some bacteria. algorithm any systematic mathematical procedure that allows a problem to be solved in a finite number of steps. Compare heuristic, stochastic. alicyclic describing an organic compound derived from a saturated cyclic hydrocarbon. Compare aliphatic, aromatic. aliphatic describing organic compounds in which the carbon atoms form open (noncyclic) chains. Compare alicyclic, aromatic. aliquant one of a number of unequal parts of a whole. aliquot one of number of equal parts of a whole; often used loosely, and erroneously, for a sample. alizarin 1,2-dihydroxyanthraquinone; the aglycon of ruberythric acid. alkalemia or (esp. Brit) alkalaemia a condition in which there is increased alkalinity (i.e. lowered hydrogen-ion concentration and hence raised pH) of the blood. Compare acidemia, alkalosis. alkali any of a class of bases that neutralize acids and are themselves neutralized by acids, and form caustic andlor corrosive aqueous solutions. The term is applied in particular to hy-

26

alkali metal droxides of the alkali metals, though the term is often extended to other substances with similar though weaker properties. alkali metal any element of group 1 of the IUPAC periodic table; the group comprises lithium (Li), sodium (Na), potassium (K), rubidium (Rb), cesium (Cs), and francium (Fr). alkaline 1 having the properties of an alkali; basic. 2 describing an aqueous solution having a pH > 7. alkaline earth any metallic element belonging to group 2 of the IUPAC periodic table; the group comprises beryllium (Be), magnesium (Mg), calcium (Ca), strontium (Sr), barium (Ba), and radium (Ra). alkaline phosphatase EC 3.1.3.1; systematic name: orthophosphoric monoester phospho hydrolase (alkaline optimum); other names: alkaline phosphomonoesterase; phosphomonoesterase; glycerophosphatase. An enzyme that catalyses the hydrolysis of orthophosphoric monoester to an alcohol and orthophosphate. The cofactors are zinc and magnesium. In human plasma the level is raised in the last trimester of pregnancy. Plasma levels may also be greatly elevated in cases of Paget's disease of bone, osteomalacia, and cirrhosis or biliary obstruction; levels may become moderately elevated in other types of bone disease. The assay of tissue-specific isoenzymes increases the value of these estimations; e.g. the placental isoenzyme is elevated in plasma in testicular seminoma. The normal range in human plasma is 30-90 IU L -1. Example from intestine (bovine): database code PPBCBOVIN, 44 amino acids (4.77 kDa); example from Escherichia coli (precursor): database code PPB_ECOLI, 471 amino acids (49.38 kDa). alkaline tide the slight increase in plasma and urine pH that occurs after meals. It is believed to be due to withdrawal of hydrogen ions from the blood during the formation of gastric HCI. alkali reserve or alkaline reserve a term formerly used to denote the bicarbonate-C0 2 extractable from blood plasma. alkaloid any member of a broad group of nitrogen-containing basic organic compounds present in various dicotyledonous plants and some fungi. Although only about 5% of the world's plant species have so far been examined, they have yielded over 2000 different alkaloids. Heterocyclic alkaloids derived from amino acids are termed true alkaloids. Alkaloids with and without heterocyclic rings and not derived from amino acids are termed pseudoalkaloids; in these the carbon skeleton is usually isoprenoid derived. Alkaloids often have marked and specific pharmacological activity. alkalosis a clinical condition in which total base excess or total acid deficit has the potential to cause decreased hydrogen-ion concentration (i.e. raised pH) in the blood, in the absence of compensating biochemical and physiological changes. alkane any saturated aliphatic hydrocarbon compound. alkanet the plant, Alkanna tinctoria, and its root, which contains the pigment alkannin. alkannin (S)-5, 8,-dihydroxy-2-( l-hydroxy-4-methyl-3-pentenyl)-1,4-naphthalenedione; a red pigment derived from the root of the alkanet plant, and used as a dye in cosmetics and food. The (+)(R) enantiomer is also a natural product, shikonin, and the racemate is known as shikalkin.

alkaptonuria a variant spelling of alcaptonuria. alkatriene any unsaturated aliphatic hydrocarbon containing two (conjugated or unconjugated) double bonds. alkatrienyl any group derived from an alkatriene by removal of a hydrogen atom.

allele alkenyl any group derived from an alkene by removal of a hydrogen atom. 1-alkenyl-2-acylglycerol cholinephosphotransferase EC 2.7.8.22; an enzyme that catalyses the formation of the plasmalogen, plasmenylcholine (i.e. l-alkenyl-2-acylglycerophosphocholine), from CDPcholine and l-alkenyl-2-acylglycerol with release of CMP. 1-alkenylglycerophosphocholine ().acyltransferase EC 2.3.1.104; an enzyme that catalyses the formation of the plasmalogen, plasmenycholine (i.e. l-alkenyl-2-acylglycerophosphocholine) from acyl-CoA and I-alkenylglycerophosphocholine with release of CoA. alkenylglycerophosphocholine hydrolase EC 3.3.2.2; other name: Iysoplasmalogenase; a phospholipase involved in the turnover of plasmalogens. It catalyses the hydrolysis of 1(l-alkenyl)-sn-glycero-3-phosphocholine to an aldehyde and sn-glycero-3-phosphocholine. 1-alkenylglycerophosphoethanolamine D-acyltransferase EC 2.3.1.121; an enzyme that catalyses the formation of the l-alkeny1-2-acyI-glycerophosphoethanolamine, plasmalogen, from acyl-CoA and I-alkenylglycerophosphoethanolamine with release of CoA. alkenylglycerophosphoethanolamine hydrolase EC 3.3.2.5; a phospholipase enzyme involved in the turnover of plasmalogens. It catalyses the hydrolysis of 1-(1-alkenyl)-sn-glycero3-phosphoethanolamine to an aldehyde and sn-glycero-3phosphoethanolamine. alkyl any group derived from an alkane by the removal of one hydrogen atom. Alklyl groups are often designated by the symbol R. alkylating agent any of a group of compounds that react with another compound so as to introduce an alkyl group into the second compound. alkylation the process of replacing a hydrogen atom in a compound by an alkyl group. 1-alkylglycerophosphocholine D-acetyltransferase EC 2.3.1.67; an enzyme that catalyses the formation of l-alkyl-2acetyl-sn-glycero-3-phosphocholine (see platelet-activating factor) from acetyl-CoA and l-alkyl-sn-glycero-3-phosphocholine with release of CoA. See also 1-alkylglycerophosphocholine 0acyltransferase. 1-alkylglycerophosphocholine D-acyltransferase EC 2.3.1.63; an enzyme that catalyses the formation of the ether lipid, l-alkyl-2-acyl-sn-glycero-3-phosphocholine, from acylCoA and l-alkyl-sn-glycero-3-phosphocholine with release of CoA. OS-alkylguanine alkyltransferase see O&-methylguanine. alkyne any unsaturated aliphatic hydrocarbon compound containing one or more triple bonds. alkynyl any group derived from an alkyne by the removal of one hydrogen atom. All symbol for allose. all+ see allo+. allantoic acid or diureidoacetate the end product of purine metabolism in mammals and some fish, formed from allantoin by a hydrolytic reaction. Most fish metabolize allantoic acid further to urea and glyoxalate. It is widely distributed in plants as an important source of stored nitrogen.

allantoin (2,5-dioxo-4-imidazolidinyl)urea; 5-ureidohydantoin; an intermediate or end product of purine catabolism, formed from uric acid by urate oxidase. In certain animal groups it is converted to allantoic acid. allele or allelomorph any of the forms of the same gene that occur at the same locus on a homologous chromosome but dif-

allele-specific oligonucleotide fer in base sequence. Two or more alleles are said to be allelic or allelomorphic to each other, and if more than two alleles exist in a population, the locus is said to show multiple allelism.

allantoin

allele-specific oligonucleotide abbr.: ASO; an oligonucleotide that is constructed with a DNA sequence homologous to a specific allele. Two ASOs can be made so that they differ in sequence at only one nucleotide base, thereby distinguishing a mutant allele with a point mutation from its corresponding wild-type allele. allelic exclusion the process by which a cell uses either the gene from its maternal chromosome or the one from the paternal chromosome, but not both. It seems to occur only in genes that encode antibodies and T-cell receptors. Individual B-Iymphocytes display allelic exclusion of their heavy and light IgG genes. allelomorph another term for allele. allelopathic agent any plant excretory product that may be autotoxic or affect neighbouring plants, such as salicylate in Quercus falcata. allelozyme any of two or more variants of a particular enzyme (with similar catalytic properties) whose amino-acid sequences are encoded in allelic structural genes (see allele); a class of isoenzyme. Compare multilocus enzyme. allergen any antigen that stimulates an allergic reaction, inducing a type I hypersensitive reaction. See allergy, hypersensitivity. allergic of, relating to, or involving allergy. allergy or allergic reaction 1 a state of altered (usually increased) reactivity of the body to foreign material. 2 hypersensitivity. allicin 2-propene-l-sulfinothioic acid S-2-propenyl ester; an antibacterial compound derived from garlic (Allium sativum) and having an odour of garlic.

27

allometry compound that has more than one pair of enantiomers. Compare iso+ (def. 3), nor+ (def. 1). 8110+ prefix denoting the configuration of a set of four (usually) contiguous >CHOH groups, as in D- or L-allose. See monosaccharide. alloantigen an antigen that is part of an animal's self-recognition system, e.g. major histocompatability complex molecules. When injected into another animal, they trigger an immune response aimed at eliminating them. Compare alloreactivity. allocystathionine see cystathionine. allogeneic or allogenic describing cells, tissues, organisms, etc. that are of different genetic constitution. Compare heterogenic, homologous. allograft any tissue graft between allogeneic individuals; i.e. from a donor of one genotype to a host of another genotype. allohydroxylysine see hydroxylysine. alloisoleucine trivial name for a-amino-p-methylvaleric acid; (2R* ,3S*)-2-amino-3-methylpentanoic acid, CH 3-CHr CH (CH 3)-CH(NH 2 )-COOH; an a-amino acid with two chiral centres. Because molecules of alloisoleucine possess a second chiral centre, at C-3, in addition to the chiral centre at C-2 common to molecules of all a-amino acids other than glycine, the enantiomers L-alloisoleucine (symbol: aIle), (2S,3R)-2amino-3-methylpentanoic acid, and D-alloisoleucine (symbol: D-aIle), (2R,3S)-2-amino-3-methylpentanoic acid, are diastereoisomeric with those of isoleucine, (2R*, 3R*)-2-amino-3-methylpentanoic acid. L-Alloisoleucine does not occur in peptide linkage in proteins. Residues of D-alloisoleucine are found in the peptidolipid of the actinomycete, Nocardia esteroides, and various members of the actinomycin group of antibiotics contain (usually) two residues per molecule.

L-alloisoJeucine

o-alloisoleucine

alliin 3-(2-propenylsulfinyl)-L-alanine; S-allyl-L-cysteine sulfoxide; a component of garlic (Allium sativum) and other plants that develops an odour of garlic following the action of alliinase (alliin lyase; EC 4.4.1.4).

allolactose trivial name for p-D-galactopyranosyl-(l ~6)-D­ glucopyranose; an isomer of lactose and the natural intracellular inducer of the lac operon in Escherichia coli.

~ 2

HO H

0

o--CH2

OH H

H

H

H

allitol a meso-hexitol; derived formally by reduction of the aldehyde group of either D- or L-allose. allo+ or (before a vowel) all+ comb.form 1 denoting other, dissimilar, different. Compare hetero+ (def. I), homo+ (def. I), iso+ (def. I), xeno+ (def. I). 2 referring to a dissimilar genome. Compare homo+ (def. 2), hetero+ (def. 2), iso+ (def. 2), xeno+ (def. 2). 3 referring to an isomeric form of an enantiomer of a

OH

H~O OHH OH

HO H

OH

allomerism a state of similarity in the crystalline structures of substances of different chemical composition. -allomerous adj. allometric 1 differing in relative growth rates. 2 of or relating to allometry. allometry 1 the study of the growth of parts of an organism

28

allomone relative to the growth of the whole organism. 2 change in the proportion of any part of an organism occurring during growth. allomone any chemical substance produced or acquired by an organism that, when it contacts an individual of another species in the natural context, evokes in the receiver a behavioural or developmental reaction adaptively favourable to the transmitter. Compare kairomone, pheromone. allomorphism variability in the crystalline structure of certain substances having the same chemical composition. allophycocyanin a phycobiliprotein present in small amounts in red algae and cyanobacteria. allopurinol 4-hydroxypyrazolo[3,4-djpyrimidine; a constitutional isomer of hypoxanthine and a competitive inhibitor of xanthine oxidase (EC 1.2.3.2). It is a synthetic drug used in the treatment of gout and other conditions characterized by raised blood urate content. Patients with gout excrete less urate and more xanthine and hypoxanthine than normal. OH

(:eN N

N

H

alloreactivity the T-cell response to non-self MHC molecules. all-or-none describing a chemical reaction, or a pharmacological or physiological response, that either occurs to the fullest extent or not at all, depending on the conditions. allose symbol: All; alia-hexose; an aldohexose that differs from glucose only in the configuration of the hydroxyl on C-3. allosteric describing protein molecules that are assumed to possess two or more stereospecifically different, nonoverlapping receptor sites. One of these, the active site, binds the substrate; the other, the allosteric site, is complementary to the structure of another, or the same, metabolite, the allosteric effector, which binds specifically and reversibly. The formation of the enzyme-allosteric effector complex does not activate or deactivate a reaction involving the effector itself; it is assumed only to bring about a discrete reversible alteration of the molecular structure of the protein, called allosteric transition. This modifies the properties of the active site, changing one or several of the kinetic parameters that characterize the biological activity of the protein. See also Monod-Wyman-Changeux model. allosteric activation any activation of an enzyme by a positive allosteric effector. allosteric constant symbol: L; the equilibrium constant for the transition between two forms of an allosteric protein in the absence ofligand: L = TaiRa, where To and R o are the concentrations of the less affine T-form and the more affine R-form of the protein, respectively. See Monod-Wyman-Changeux model. allosteric effect an effect that arises when the reaction of ligands with one site of any polyvalent molecule affects the reaction of ligand(s) at one or more o1:her sites as a result of conformational changes. The reactions mayor may not both be reversible; when they are, and represent equilibria, they are reciprocal effects or linked functions. allosteric effector a specific ligand that binds to the allosteric site of a protein with different affinities in the two states of the protein (R and T) in the Monod-Wyman-Changeux model of allosteric transition. An effector may be described as positive if it has an activating effect, or as negative if it is inhibitory. See allosteric. Compare autosteric effector. allosteric enzyme designating any enzyme that: (I) contains a site topologically distinct from the active site; (2) shows sigmoid kinetics; (3) occurs at a branch point in a metabolic pathway; and (4) obeys the concerted model for allosteric proteins. Since all these properties may sometimes, but not always, go together, the term is somewhat imprecise.

allotype allosteric inhibition any inhibition of an enzyme by a negative allosteric effector. allosteric protein a protein that exhibits allosterism. See also allosteric. allosteric site see allosteric. allosteric transition see allosteric, Monod-Wyman-Changeux model. allosterism or allostery a property of an enzyme or other macromolecule by which its principal biological reactivity is modified by the binding of an effector to a site other than the binding site of the principal reactant, thereby bringing about a conformational change in the macromolecule such as to alter its principal reactivity. See allosteric. allothreonine trivial name for a-amino-fJ-hydroxybutyric acid; (2R*,3R*)-2-amino-3-hydroxybutanoic acid; CH 3-CH(OH)CH(NH 2)-COOH; an a-amino acid with two chiral centres. Because molecules of allothreonine possess a second chiral centre, at C-3, in addition to the chiral centre at C-2 common to all a-amino acids other than glycine, the enantiomers L-allothreonine (symbol: aThr), (2S,3S)-2-amino-3-hydroxybutanoic acid, and D-allothreonine (symbol: D-aThr), (2R,3R)-2-amino-3-hydroxybutanoic acid, are diastereoisomeric with those of threonine, (2R*,3R*)-2-amino-3-hydroxybutanoic acid. [Note: The enantiomers of allothreonine may also be named semisystematically as derivatives of erythrose: Ls-allothreonine in amino-acid nomenclature is synonymous with 2-amino-2,4-dideoxy-L g -erythronic acid in carbohydrate nomenclature, and Ds-allothreonine with 2-amino-2,4dideoxy-Dg-erythronic acid (the subscript letters d or g being added to the configurational prefixes where there might be uncertainty regarding the reference centre of chirality; see OIL convention).] L-Allothreonine does not occur in peptide linkage in proteins; however, one residue per molecule is present in the peptide antibiotic telomycin. Residues of D-allothreonine have been found in the glycolipid and peptidolipid of actinomycetes, and in mycobacteria.

'> angiotensin III. In peripheral tissues, AT 1 receptors, but not AT 2 receptors, interact with G-proteins, inhibit adenylate cyclase, and activate phospholipases C and A 2. AT 2 receptors may stimulate a phosphotyrosine phosphatase leading to inhibition of guanylate cyclase. Sulfhydryl reducing agents inhibit the binding of angiotensin II to AT 1 receptors but enhance its binding to AT. Both types are G-protein-coupled seven-transmembrane domain proteins. Examples: AT! receptor, database code AG2R_BOVIN, 359 amino acids (41.09 kDa); AT 2 receptor, database code AG22_MOUSE, 363 amino acids (41.37 kDa). angle I the inclination between two lines or planes: plane angle. It is dimensionless and given in radians (symbol: rad), degrees (symbol: 0; 10 = 1[/180 rad); minutes (symbol: ') l' = nil 0800 rad; or seconds (symbol: "); 1"= n/64800 rad. 2 the (three-dimensional) vertex of a cone: solid angle. It is dimensionless but may be expressed in steradians (symbol: sr). angle head or angle rotor any rotor for a centrifuge in which the tubes containing the liquid are at a fixed angle to the axis of rotation. Compare swinging bucket rotor. Angstrom or Angstrom symbol: A; a unit of length equal to 10- 10 metres. It is used in atomic measurements and for wavelengths of electromagnetic radiation, and is temporarily approved for use with SI units. [After Anders Jonas Argstrom (1814-74), Swedish physicist noted for his work on spectroscopy.] angular velocity symbol: w; the rate of rotation of an object expressed as its rate of motion through an angle about an axis. It is expressed in rad S-I. anhydrase see carbonic anhydrase. anhydride a derivative of a substance that yields the substance when combined chemically with water. anhydro+ symbol: An; prefix (in a chemical name) denoting the loss of the elements of water from within one molecule or residue. The positions from which removal has occurred may be indicated by a pair of locants, e.g. 2,5-anhydro-D-gluconic acid. anhydrosialidase EC 3.2.1.138; other names: anhydroneuraminidase; sialidase L; an enzyme that catalyses the hydrolysis of a-sialosyl linkages in N-acetylneuraminic acid glycosides, releasing 2,7-anhydro-a-N-acetylneuraminic acid. anhydrosugar any intramolecular ether formed by the elimination of water from two (indicated) alcoholic hydroxyl groups of a single molecule of a monosaccharide, whether aldose or ketose; i.e. any an hydro monosaccharide whose formation does not involve the reducing group. anhydrous devoid of water, especially (of a substance or material) lacking water of crystallization or adsorbed water, or (of an environment) very dry. See also dehydration. animal pole see vegetal pole. animal protein factor a name formerly used for a growth factor for livestock, found to be present in meat and fish but not

40

anion in feeds of plant origin. It was later shown to be identical with anti-pernicious anemia factor, i.e. vitamin B!2' anion an ion with a net negative charge; during electrolysis of a solution anions migrate towards the anode. Compare cation.anionic adj. anion exchanger or anion-exchange resin any ion-exchange resin that carries positively charged groups, e.g. quaternary ammonium groups, and binds anions. anion gap (in clinical chemistry), the difference, in meq L -1, between the concentrations of serum sodium plus potassium and of the serum chloride plus bicarbonate; i.e. anion gap = [Na+ + K+] - [CI- + HCOf]. Normal values are 12 ± 2 meq L 1. Variations in the anion gap provide a useful insight into the acid-base status of a subject. anionic detergent a detergent in which the polar part of the molecule carries a negative charge. Compare nonionic detergent. anisotropic describing a medium in which physical properties, such as the velocity of electromagnetic radiation transmission, electrical or heat conductivities, or compressibility, have different values when measured along axes in different directions. -anisotropically adv.; anisotropy or anisotropism n. anisotropic motion rotation about a single axis, especially of a molecule or a spin label. ankyrin or band 2.1 (protein) or nexin or syndein a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins. It is bound tightly to the cytoplasmic surface of the human erythrocyte membrane, to which it attaches the cytoskeletal protein spectrin. Example from human: database code ANKI_HUMAN, 1880 amino acids (206.14 kDa). [After the Greek ankyra, anchor]. annealing 1 the renaturation of heat-denatured nucleic acids or proteins by slow cooling. 2 the formation of hybrid doublestranded nucleic-acid molecules by the slow cooling of a mixture of denatured, single-stranded nucleic acids. It is used to detect complementary regions of different nucleic-acid molecules. 3 the slow regulated cooling, especially of metals or glasses, to relieve the stresses caused by heating or other treatments. -annealer n. annexin any of a ubiquitous family of Ca 2+-dependent phospholipid-binding proteins. They have been isolated from organisms as diverse as mammals, Drosophila melanogaster, and Hydra vulgaris. Characteristically they have a low intrinsic affinity for Ca2+ (Kd 25-1000 11M), although annexin VI has Kd "'111M, but in the presence of phospholipid the affinity for Ca2+ increases up to 100-fold. The Ca2+_ and phospholipidbinding properties that typify the family derive from a region of common primary structure (identity with any other member of the family is 40-60%) in a conserved 34 kDa C-terminal region (the 'core'); each different type of annexin has a unique N-terminal domain known as the 'tail'. The C-terminal region in all cases except one consists of four repeats of a ",70 aminoacid sequence, in which there is a high homology region known as the endonexin fold, with a characteristic motif GXGTDE; the exception is annexin VI, which has eight repeats. The true physiological roles of the annexins remain unknown, but their main characteristics, exhibited variously by different annexins and reflected in the alternative names they acquired in the course of discovery, include: the ability to aggregate membranes and vesicles (all annexins); inhibition of phospholipase A z (especially I, but also IT to VI); formation of ion channels (especially I and V to VII); anticoagulant properties (especially I, and VIII); and acting as substrates for tyrosine kinases (I and II) and protein kinase C (I, II, IV, and XIT). Alternative names and database codes are given under the individual entries. annexin I other names: lipocortin I; p35 (EGF receptor substrate); calpactin II; chromobindin 9; GIF; lipomodulin; macrocortin; renocortin. Example from rat: database code ANXI_RAT, 345 amino acids (38.65 kDa).

anodic to annexin II other names: calpactin I heavy chain; lipocortin II; p36 (pp6OS rc substrate); chromobindin 8; protein I; placental anticoagulant protein (PAP)-IV. Example from human: database code ANX2_HUMAN, 338 amino acids (38.43 kDa). annexin III other names: Iipocortin III; placental anticoagulant protein (PAP)-III; 35-a-ca1cimedin; calphobindin III; inositol 1,2-cyclic phosphate hydrolase. Example from rat: database code ANX3_RAT, 324 amino acids (36.28 kDa). annexin IV other names: endonexin I; protein II; 32.5K calelectrin; Iipocortin IV; chromobindin 4; placental anticoagulant protein (PAP)-II; placental protein PP4-X; 35-p-ca1cimedin; placental anticoagulant protein II. Example from human: database code ANX4_HUMAN, 318 amino acids (35.68 kDa). annexin V other names: placental anticoagulant protein (PAP)I; inhibitor of blood coagulation (IBC); Iipocortin V; 35K calelectrin; endonexin II; placental protein PP4; vascular anticoagulant (VAC)-a; 35-y-ca1cimedin; calphobindin I; anchorin CIT. Example from human: database code ANX5_ HUMAN, 319 amino acids (35.76 kDa). annexin VI other names: p68; p70; 73K; 67K calelectrin; lipocortin VI; protein III; chromobindin 20; 67K calcimedin; calphobindin II; synhibin. Ex.ample from human: database code ANX6_HUMAN, 672 amino acids (75.66 kDa). annexin VII another name for synexin. annexin VIII other name: vascular anticoagulant (VAC)-~. Example from human: database code ANX8_HUMAN, 327 amino acids (36.84 kDa). annexin IX other name: Drosophila melanogaster annexin. Database code (fragment) from D. melanogaster: ANX9_ DROME. annexin X other name: intestine-specific annexin. Example from human: database code ANXCHUMAN, 315 amino acids (35.29 kDa). A similar protein occurs in Drosophila melanogaster. annexin XI other names: (sometimes, e.g. in rabbit) calcyclinassociated annexin (CAP); CAP-50. There are two variants (derived by alternative splicing). Example, variant I, bovine: database code ANXA_BOVIN, 503 amino acids (53.96 kDa). annexin XII a member of the annexin family obtained from Hydra attenuata (Hydra vulgaris). It is of unknown function. Example from H. vulgaris: database code ANXC_HYDAT, 316 amino acids (35.07 kDa). annihilation radiation electromagnetic radiation of wavelength 2.4 pm (energy 0.51 MeV) that is emitted as a pair of photons when a positron absorbed into matter reaches the end of its range and combines with an electron in mutual destruction. anode 1 the electrode of an electrolysis cell or electrophoresis apparatus towards which anions of the electrolyte migrate under the influence of an electric field applied between the electrodes. 2 the positive electrode, pole, or terminal of such a cell or apparatus, or of a discharge tube, solid-state rectifier, or thermionic valve; the electrode by which electrons flow out of the device. 3 the negative pole or terminal of an electric (primary or secondary) cell or battery (of cells). Compare cathode. -anodal or anodic adj; anodally or anodically adv. anodic stripping voltammetry abbr.: ASV; an electrochemical procedure for estimating the concentration of metal ions in a solution. Exhaustive or partial (depending on the concentrations involved) deposition of the metal occurs on the cathode of an electrolytic cell at a constant applied electric potential (controlled potential deposition can be used for selectivity when mixtures are involved). The metal deposit is then anodically stripped by using a rapid sweep of voltage of opposite polarity and a peak-type current-voltage curve is obtained. The amount of metal deposited may be calculated coulometrically from the area under the peak, or by other means, and hence the concentration of metal ions in the initial solution may be determined. anodic to during electrophoresis, migrating further towards

41

anolyte the anode or less far towards the cathode than (the specified substance) . anolyte the electrolyte in immediate contact with the anode in isoelectric focusing. anomalous dispersion 1 an X-ray crystallographic dispersion that occurs when the frequency of the X-rays used falls near an absorption frequency of an atom in the crystal. Anomalous dispersion techniques are frequently used in the determination of absolute configuration. 2 an optical rotatory dispersion that cannot be expressed by a simple one-term Drude equation. anomer either of the two stereoisomers of the cyclic form of an aldose or a ketose, or an aldose or ketose derivative, dependent on the position of the free hydroxyl group belonging to the internal hemiacetal grouping. The anomer having the same configuration, in the Fischer projection, at the anomeric and the reference asymmetric carbon atom is designated a; the other anomer is designated p. In correct usage in regard to carbohydrates, the anomeric and configurational descriptors must always be linked together; e.g. a-D-glucopyranose, not a-glucose. anomeric 1 of or pertaining to an anomer. 2 or glycosidic of or pertaining to the free hydroxyl group belonging to the internal hemiacetal grouping in the cyclic form of a monosaccharide or monosaccharide derivative. anomeric effect the tendency for an electronegative substituent at C-I of a pyranose to assume the axial orientation, in contrast to the equatorial orientation predicted on steric grounds. anorexia absence of desire for food. anosmia loss of the sense of smell. anoxia the absence or a deficiency of dioxygen. Compare hypoxia. -anoxic adj. ANP abbr. for atrial natriuretic peptide. See natriuretic peptide. ANPR abbr. for atrial natriuretic peptide receptor. ANS abbr. for l-anilino-8-naphthalene sulfonate; a common fluor used in extrinsic fluorescence studies of proteins. ansamycin any antibiotic belonging to the rifamycin or the streptovaricin classes. anserine N-p-alanyl-Nn-methyl-L-histidine; an isopeptide occurring in skeletal muscle and brain of some animals and humans (up to 20 mmol kg-I). Compare carnosine.

Anson unit an old measure of the activIty of a proteinase. It was based upon the extent to which a sample containing a particular proteinase can digest denatured hemoglobin, under standard conditions appropriate to the enzyme in question, with liberation of nonprecipitable material giving the same colour value as one millimole of tyrosine on reaction with a diluted Folin-Ciocalteau reagent. [After Mortimer Lewis Anson (1901-68), US protein chemist, who described it in 1958.] ant+ a variant of anti+. Antabuse proprietary name for disulfiram. antagonism 1 opposition; counteraction. 2 the mutual opposition of an agonist and an antagonist. 3 the interference with, or inhibition of, the growth of an organism by one of another kind, as by competing for nutrients or producing an antibiotic substance. antagonist 1 anything that antagonizes. 2 any agent, especially a drug or hormone, that reduces the action of another

anthralin agent, the agonist. Many act at the same receptor as the agonist. Such antagonists may be either surmountable or insurmountable, depending on prevailing conditions. Antagonism may also result from combination with the substance being antagonized (chemical antagonism), or the production of an opposite effect through a different receptor (functional antagonism or physiological antagonism), or as a consequence of competition for the binding site of an intermediate that links receptor activation to the effect observed (indirect antagonism). The term 'functional antagonism' is also used to describe a less well-defined category in which the antagonist interferes with other events that follow receptor activation. 3 a muscle that works in opposition to another (the agonist). See also competitive antagonism, noncompetitive antagonism. Compare agonist, inverse agonist, synergist. -antagonistic adj.; antagonistically adv. antagonize or antagonise to act in opposition to; to counteract. -antagonized or antagonised ad). antanamide a highly lipophilic homodetic cyclic decapeptide, cyclo(-Pro-Phe-Phe-Val-Pro-Pro-Ala-Phe-Phe-Pro-). It occurs in the death-cap fungus, Amanita phalloides, together with the amatoxins and phallotoxins. When administered to experimental animals (at I mg per kg of body weight), either before or at most a few minutes after a lethal dose of phallotoxin, it acts as an antidote to the toxin, apparently by competing for binding sites. In vitro it readily forms complexes with sodium and calcium ions, and can act as a sodium ionophore. ANT-C abbr. for antennapedia complex; one of two major families of homeotic genes of Drosophila (the other being aX-C), mutation which affects head and thoracic segments. ante+ prefix denoting before in time or position. antegrade a variant of anterograde. anteiso+ prefix denoting a branched-chain fatty acid having a methyl group at the n-3 position; e.g. 16-methyloctadecanoic acid, also named anteisononadecanoic acid. antenna complex any of the light-harvesting pigment-protein complexes of photosynthetic organisms that funnel absorbed incident radiation to the photochemical reaction centres. antennapedia complex see ANT-C. anterograde or antegrade 1 moving forwards; extending towards the front. 2 moving along the axon of a nerve cell in a direction away from the cell body (as in anterograde transport of vesicles). Compare retrograde. antheridiol a steroid hormone produced by water moulds (e.g. Achyla spp.) to regulate their sexual reproduction. anthocyanidin any member of a group of water-insoluble red, blue, or violet polyhydroxylated 2-phenylbenzopyrylium compounds that occur as glycosides - anthocyanins - in plants. They comprise one class of the widespread group of flavonoids. anthocyanin any member of a group of intensely coloured soluble glycosides of anthocyanidins that occur in plants. They are responsible for most of the scarlet, purple, mauve, and blue colouring in higher plants, especially of flowers. antho-K amide L-3-phenyllactyl-Phe-Lys-Ala-NH 2; a neuropeptide from the sea anemone Anthopleura eleganrissima. anthracene a tricyclic aromatic compound, C I4 H IO ; it is a component of a number of scintillation cocktails.

anthralin 1,8-dihydroxyanthrone; a substance that inhibits leukotriene biosynthesis. It is used as an antipsoriatic drug.

42

anthranilate

LU ~ anthralin anthranilate 2-aminobenzoate (anion, salt, or ester); an intermediate in the biosynthesis of tryptophan. anthranilate synthase EC 4.1.3.27; systematic name: chorismate pyruvate-lyase (amino-accepting). An enzyme that catalyses the first step in tryptophan biosynthesis, in which chorismate and L-glutamine react to form anthranilate, pyruvate, and L-glutamate. It is a tetramer of two components, I and II: in the absence of II, I catalyses the formation of anthranilate using NH 3 rather than glutamine; II provides glutamine amidotransferase activity. Example from yeast: I database code TRPE_YEAST, 528 amino acids (59.70 kDa); II database code TRPG_YEAST, 484 amino acids (53.46 kDa). anthrone 9(IOH)-anthracenone; a compound used in the colorimetric determination of carbohydrates, especially hexoses, with which it gives a green colour.

anti+ or (sometimes before a vowel or h) ant+ prefix 1 acting against, counteracting, or inhibiting. 2 opposite to (in direction). 3 converse or reverse of; complementary to. anti+ prefix (obsolete) denoting a cis isomer. antiamoebin or antiamebin see peptaibophol. antiarose the D isomer, 6-deoxY-D-gulose; occurs in glycosidic linkage in some cardiac glycosides.

~oo OH OH poD-pyranose form

antibiotic 1 any of numerous substances of relatively low M r produced by living microorganisms (and also certain plants) that are able selectively and at low concentrations to destroy or inhibit the growth of other organisms, especially microorganisms. Also included are the many semi- or wholly synthetic organic compounds with similar antimicrobial properties. Many are useful chemotherapeutic agents. 2 of or relating to an antibiotic. antibody any glycoprotein of the immunoglobulin family that is capable of combining noncovalently, reversibly, and in a specific manner with a corresponding antigen. Antibodies frequently, but not always, counteract the biological activity of antigens. They are produced in higher animals by cells of the lymphoid cell series, especially plasma cells, in direct response to the introduction of immunogens or autocoupling haptens. Antibodies were originally identified as a class of serum pro-

antigen teins, and most are present in the y-globulin fraction of the serum. In the ultracentrifuge most antibodies have a sedimentation coefficient of 7S, except for the pentameric IgM at 195. See also cell-bound antibody. antibody-mediated hypersensitivity or type II hypersensitivity an immune response caused by the presence of antibody to cell-surface antigens and components of the extracellular matrix. These antibodies can sensitize the cells for antibodydependent cytotoxic attack by K cells or complement-mediated lysis. Type II hypersensitivity is seen in the destruction of red cells in transfusion reactions and in hemolytic disease of the newborn. anticholinesterase any agent, other than an antibody, that inhibits cholinesterase (def. 2). An example is physostigmine, used in the diagnosis and treatment of myasthenia gravis. anticircular chromatography a technique of thin-layer chromatography in which the substances to be separated are applied just inside the perimeter of a circular thin-layer plate and are made to travel radially inwards by subsequent application of the developing solvent at the edge of the plate. It is very fast and is particularly useful for the resolution of substances whose R r values approach unity. Compare circular chromatography. anticlinal see conformation (def. 2). anticoagulant 1 retarding or preventing coagulation. 2 any substance that retards or prevents coagulation, especially of blood or milk. anticoagulate to treat (esp. blood) so as to prevent coagulation. anticodon a triplet of nucleotides in any particular transfer RNA that is complementary to and therefore pairs with a given codon in messenger RNA. The pairing is antiparallel, 5' ~3' in the messenger, 3' ~5' in the anticodon. Thus the anticodon of 5'-ACG-3' is 3'-UGC-5'. However, to maintain the convention of writing sequences in the 5'~3' direction, the anticodon is thus written, but with a reverse arrow above: ~. anticodon arm the part in the clover-leaf model of transfer RNA containing a loop bearing the anticodon. anticooperativity negative cooperativity between binding sites on the same (macro)molecule by which binding of a ligand to one site makes the binding of a second ligand more difficult. antidiuretic 1 describing any drug or other agent that decreases the excretion of urine. 2 an antidiuretic substance. antidiuretic hormone abbr.: ADH; an alternative name (esp. in clinical chemistry) for vasopressin. It is so named from the hormone's most important biological action, viz. reduction of the rate of urine output by stimulation of the rate of water reabsorption by the kidney(s). antidote a substance or other agent that limits or reverses the effects of a poison. antifolate any of a class of drugs that interfere with the formation of tetrahydrofolate, and are used in the treatment of acute leukemia and choriocarcinoma. One of the best known is methotrexate. antifreeze glycoprotein any of a group of glycoproteins found in the serum of certain cold-water fish, particularly notothanids and chaenichthyids, which inhabit polar seas; e.g. Trematomus borchgrevinki and Dissostichus mawsoni. These glycoproteins depress the freezing point of aqueous solutions about 200-500 times as effectively as sodium chloride on a molar basis. They differ only in mass (10.5 kDa, 17 kDa, and 21.5 kDa) and are composed of repeating units of a diglycosyl tripeptide, Ala-Ala-Thr-O-disaccharide, in which the disaccharide consists of a p-galactosyl residue bound to an internal a-N-acetylgalactosaminyl residue. antigen 1 (or complete antigen) any agent that, when introduced into an immunocompetent animal, stimulates the production of a specific antibody or antibodies that can combine with the antigen. It may be a pure substance, a mixture of substances, or particulate material (including cells or cell fragments). In this sense the term includes agglutinogen and

antigen-antibody complex

43

allergen and is synonymous with immunogen (def. 1). 2 (or incomplete antigen) any substance that can combine with a specific antibody but is not an immunogen (def. 2), i.e. it is not by itself able to stimulate antibody production though it may do so if combined with a carrier (def. 8). In this sense the term includes hapten. -antigenic adj. antigen-antibody complex or immune complex any specific macromolecular complex of antigen and antibody. It may be soluble, especially in antigen excess, or insoluble (as a precipitate) when antigen and antibody are present in optimal proportions. Components of complement may bind to antigenantibody complexes. See also immune complex-mediated hypersensitivity. antigen-binding capacity abbr.: ABC; the total amount of antibody in a preparation, e.g. serum, based on a determination of the amount of antigen bound by unit amount of the preparation. antigen excess the condition when a mixture of antigen and antibody contains sufficient antigen to combine with all the combining sites of the specific antibody molecules, leaving some free uncombined antigenic determinants and resulting in the formation of soluble antigen-antibody complexes. This is the explanation for the type of 'precipitin' curve when increasing amounts of antigen are incubated with a fixed amount of antibody and the amount of precipitate is measured. antigenic determinant any specific chemical structure within, and generally small in relation to, an antigen molecule that is recognizable by a combining site of an antibody, or T-cell or B-cell receptor, and at which combination takes place. It determines the specificity of the antibody-antigen reaction. Several different antigenic determinants may be carried by a single molecule of antigen. See also epitope. antigenic drift any of the minor changes in the antigenicity of influenza virus that result from spontaneous mutation, with corresponding minor changes in the amino-acid sequence of the viral hemagglutinin. Compare antigenic shift. antigenicity the capacity of an agent to stimulate the formation of specific antibodies to itself. antigenic shift any of the major changes in the antigenicity of influenza virus that result from spontaneous mutation, with corresponding major changes in the amino-acid sequence of the viral hemagglutinin. Compare antigenic drift. Cantigen-independent) mitogenic factor a Iymphokine that acts as a mitogen for lymphocytes. antigen-presenting cell abbr.: APC; a cell, especially a macrophage or dendritic cell, that recognizes an antigen to be targeted for neutralization. It takes up the antigen and processes it, incorporating antigen fragments into its own membrane and presenting them in association with class n major histocompatibility complex molecules to T lymphocytes, which are then stimulated to mount a response. antigibberellin any of the organic compounds that cause plants to grow with thick stems or with an appearance differing from that obtained with gibberellin. The effect can usually be reversed by gibberellin. antiglobulin consumption test a serological method for demonstrating antibody (globulin) attachment to cells. It is based on showing that antiglobulin is removed from solution on addition of the cells in question. antiglobulin test or Coombs test a test for the presence of incomplete antibody against red blood cells. It entails the addition of heteroantibody to immunoglobulin (i.e. antiglobulin) to cause the agglutination of red blood cells previously coated with nonagglutinating incomplete antibody. Compare doubleantibody method. [After Robin Royston Amos Coombs (b. 1921), British immunologist and hematologist who (with others) described it in 1945.] antihemophilic factor or antihemophilic factor A or antihemophilic globulin an alternative name for factor VIII; see blood clotting lactors.

antioxidant antihemophilic factor B an alternative name for factor IX; see blood coagulation. antihemophilic factor C an alternative name for factor XI; see blood coagulation. antihemophilic globulin an alternative name for antihemophilic factor. antihistamine any drug or other agent that antagonizes an action of histamine on the body. Antihistamines are used in the treatment of immediate-type hypersensitivity. antihormone any substance that acts to attenuate hormoneinduced responses, regardless of the mechanism involved. anti-idiotype an antibody that reacts with epitopes on the V region of the T-cell receptor. anti-inducer any compound that inhibits operon induction by competing for inducer binding to free repressor and stabilizing the repressor-operator complex. antilipolytic 1 describing any agent that inhibits lipolysis. 2 an antilipolytic agent. antilipotropic 1 describing any agent that is active metabolically in deflecting methyl groups from the synthesis of choline. 2 an antilipotropic agent. antilogarithm abbr.: antilog; symbol: (decadic) Ig-I; (napierian) In-I; the number that is represented by a logarithm. antilymphocyte globulin the globulin fraction of an antilymphocyte serum. antilymphocyte serum abbr.: ALS; any serum containing antibodies to lymphocytes. It is used as a selective immunosuppressive agent. anti-messenger DNA abbr.: amDNA; an alternative name for complementary DNA. antimetabolite any substance that inhibits the utilization of a metabolite, e.g. by acting antagonistically through competition in a transport system or at a key enzyme site. antimicrobial 1 describing a drug, antibiotic agent, physical process, radiation, etc. that is inimical to microbes. 2 any substance having antimicrobial properties. antimicrobial spectrum a list of the types of microbes against which an antimicrobial agent is effective. antimitotic 1 describing any agent that decreases the rate of mitosis. 2 an antimitotic agent. antimonial 1 of, relating to, or containing antimony. 2 a drug containing antimony. antimorph 1 a mutant gene producing an effect opposite to the wild-type gene at the same locus. Compare allele. 2 obsolete term for an enantiomorph. antimutagen any agent (often a purine nucleoside) that can decrease the rate of induced or spontaneous mutation. anti mutator gene any mutant gene that decreases the mutation rate. antimycin any member of a group of antibiotics produced by Streptomyces spp. They associate strongly with mitochondria and block the passage of electrons from cytochrome b to cytochrome CI; as little as 7 pmol antimycin Al per gram of mitochondrial protein is effective. They are used experimentally to distinguish between events in the earlier and later parts of the electron-transport chain. antineoplastic 1 describing any drug or other treatment that prevents or limits the growth of a neoplasm. 2 an antineoplastic agent. antinuclear factor or antinuclear antibody any antibody that reacts with a component of the cell nucleus. antioxidant or antoxidant any substance, often an organic compound, that opposes oxidation or inhibits reactions brought about by dioxygen or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, such as a-tocopherol (see vitamin E), thereby breaking the chain reaction that normally leads to extensive biological damage. The mechanism by which the free-radical scavenger is discharged of its free radical is not clear, but it is likely that ascorbate, glutathione, and,

antiparallel ultimately, NAD+ and the respiratory chain are involved. Compounds such as di-tert-butyl-p-cresol act as antioxidants and are often added to protect labile compounds during storage or incubation. See also quinhydrone. antiparallel 1 (in biochemistry) (describing of a pair of paralleI linear structures, such as two polynucleotide or polypeptide chains, having directional polarity or asymmetry in opposite directions. 2 (in quantum physics) (of the spins of a pair of electrons occupying the same atomic or molecular orbital) described by different spin quantum numbers. Compare parallel (def. 2). -antiparallelism n. antiperiplanar see conformation. antipernicious anemia factor former name for vitamin B12 . antiport or countertransport the process of coupled solute translocation in which two solutes equilibrate across an osmotic barrier, the translocation of one solute being coupled to the translocation of the other in the opposite direction. Compare symport. antiporter any substance or structural feature, but usually a protein, that promotes the exchange diffusion of two specific substances across a membrane by anti port. The convention for denoting such a protein (e.g. a tetracycline-resistance protein) is tetracycline/H+ antiporter. antirachitic 1 describing any agent that opposes or prevents the development of rickets. 2 any agent with antirachitic properties. antirachitic factor or antirachitic vitamin former term for any substance with vitamin D activity. antirepressor any gene product that acts to decrease repression by a repressor of gene expression. anti restriction the process whereby a host bacterium is prevented from inactivating foreign duplex DNA; i.e. the prevention of restriction. It is commonly achieved by host-controlled modification of the DNA, but in certain cases a specific bacteriophage-coded antirestriction protein is produced that directly inhibits the host's restriction endonuclease. antirestriction protein see antirestriction. anti-RNA single-stranded RNA complementary to mRNA. See antisense RNA. antiscorbutic 1 describing an agent that opposes or prevents the development of scurvy. 2 any agent with antiscorbutic properties. antiscorbutic factor or antiscorbutic vitamin former term for any substance with vitamin C activity. antisense DNA see noncoding strand. antisense oligonucleotide an oligoribonucleotide, or an analogue of one, having properties similar to those of antisense RNA. antisense RNA or messenger-RNA-interfering complementary RNA (abbr.: micRNA) an artificial single-stranded RNA molecule complementary in sequence to all or part of a molecule of messenger RNA or of some other specific RNA transcript of a gene. It can therefore hybridize with the specific RNA and so interfere with the latter's actions or reactions. Compare complementary RNA. antisense strand see noncoding strand. antisepsis the elimination of pathogenic and other microorganisms using chemical or physical methods; the promotion of asepsis. antiseptic 1 of, relating to, or bringing about antisepsis. 2 any chemical agent used in antisepsis, especially one that can be safely applied to the skin. antiserum (pl. antisera or (esp. US) antiserums) serum that contains a high level of antibodies, usually antibodies against specific antigens. antisigma factor a protein that interferes with the recognition of initiation sites by the sigma factor of DNA-dependent RNA polymerase. antistasin the generic name for a family of potent inhibitors of factor Xa. Antistasins are isolated from leeches, and the name

44

antivitamin was first given to a 119-amino-acid protein present in salivary gland of the Mexican leech Haementeria officinalis; the protein has 20 cysteine residues, all in disulfide bridges (probably characteristic of the family). It appears to present a bait-like structure to factor Xa, which cleaves it at Arg 34 . The 3-D structure has been partially solved, indicating a reactive site in domain I, sequence CRKTC. Antistasins have been considered as possible chemotherapeutic anticoagulants but have strong metastatic activity. Example, ghilanten from the Amazonian leech H. ghillianii: database code ANTA_HAEGH, 119 amino acids (13.30 kDa). antistreptolysin-O abbr.: ASO; antibody formed against streptolysin-O. See streptolysin. antisuppressor any mutation that diminishes the effects of a suppressor of gene expression. antitemplate strand see coding strand. antiterminator (or antitermination factor) a protein that prevents the termination of RNA synthesis. It is found as a regulatory device in, e.g., phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed. Antiterminators are associated with switches from early to middle expression following induction (gene N product, database code REGN_LAMBD, 107 amino acids (12.24 kDa») and from early to late expression (gene Q product, database code REGQ_LAMBD, 207 amino acids (22.45 kDa». The N system is referred to under nus. Antitermination is an important mechanism in the reproduction of some bacteriophages, allowing RNA polymerase to read through the terminator to the immediate early genes of the phage and thus initiate production of the mature phage with consequent cell lysis. antithrombin'" or heparin cofactor or factor Xa inhibitor a 62 kDa protein inhibitor of serine proteinases, normally present in plasma, that reacts with factor IIa (thrombin), and also factors IXa, Xa, XIa, and XIIa to form inert 1: 1 stoichiometric complexes. The formation of complexes is slow in the absence of heparin but very fast in its presence. Example from Bos taurus: ANT3_BOVIN, 433 amino acids (49.13 kDa). antitoxin any antibody to a toxin of a (micro)organism that neutralizes the toxin both in vitro and in viva. Q'1-antitrypsin ar Q'l"proteinase inhibitor a major ai-globulin. normally present in human plasma, that inhibits many serine proteinases, including trypsin but especially elastase, and is the archetypal serpin. Its concentration rises dramatically in response to infection or tissue injury (compare acute-phase protein). A 51 kDa glycoprotein, its prime physiological role is to inhibit elastase released by neutrophil leukocytes. In hu· mans, its synthesis is controlled by an autosomal allelic system and over 20 different phenotypes have been classified, one of which is associated with emphysema of early onset; in particular, the so-called Z mutant (Glu ~ Lys at position 342) is associated with a decreased level of a-antitrypsin in the blood. Smoking tends to cause oxidation of Met 358 , by increasing hydrogen peroxide formation by lung neutrophils, and this leads to a less active aI-antitrypsin and hence reduced inhibition of elastase. Excessive activity of elastase may damage lung tissue, resulting in emphysema. Thus smoking is associated with emphysema of early onset. Individuals who are homozygous for the Z mutant and who also smoke suffer decreased levels of a less active anti-elastase and have a high probability of developing emphysema. The protein has two chains; examples (human): chain A, database code NRL_7APIA, 339 amino acids (38.09 kDa); 3·D structure known; chain B, database code NRL_7APIB, 36 amino acids (4.13 kDa); 3-D structure known. antitussive 1 relieving or suppressing coughing. 2 an agent with antitussive properties. antivitamin any agent that antagonizes a specific vitamin. Sometimes it is a structural analogue of the vitamin and a competitive inhibitor of the vitamin's action.

45

antixerophthalmic factor

apolar interaction

antixerophthalmic factor former term for any substance with vitamin A activity. antoxidant a variant spelling oj'antioxidant. antrin a decapeptide, isolated from rat gastric antrum. It has

OH

the sequence Ala-Pro-Ser-Asp-Pro-Arg-Leu-Arg-Gln-Phe and is identical to residues 25-34 of preprosomatostatin (see somatostatin). anucleate or anucJeated lacking a nucleus. anucleolate lacking a nucleolus. AOX ahhr. for alcohol oxidasa. AP see AP endonuclease, AP protein. 6-APA ahhr. for 6-aminopenicillanic acid. apamin a neurotoxin comprising about 2% of the dry mass of

the venom of the honey bee (Apis mellifera). It is a highly basic octadecapeptide amide, structure CNCKAPETALCAKKCEEH-NH z, containing two disulfide bridges (between Cys residues I and 11, and 3 and 15), and is the smallest neurotoxic peptide known. Compare melittin. APe abbr. for I activated protein C. 2 antigen-presenting cell. APe the human gene for adenomato us polyposis coli protein. The gene is a tumour suppressor, and mutations are associated with familial adenomatous polyposis, Gardner's syndrome, etc. and contribute to colorectal cancer. The protein product is of unknown function and has serine phosphorylation, glycosylation, and myristoylation sites. It is concentrated in the basolateral region of crypt epithelial cells. Product database code: APC_HUMAN, 2843 amino acids (311.32 kDa). Ape symbol for a residue of the a-amino acid L-a-aminovaleric acid, L-2-aminopentanoic acid. AP endonuclease abhr. for apyrimidinic or apurinic nuclease; any of various DNA repair enzymes that make breaks at sites generated by DNA glycosylase. There are three types: (1) deoxvribonuclease V; (2) exodeoxynuclease III (endonuclease activity) see deoxvribonuclease Ill; and (3) DNA-(apurinic or apyrimidinic site) lyase, EC 4.2.99.18; other names: AP lyase; AP endonuclease class I; endodeoxyribonuclease (apurinic or apyrimidinic); deoxyribonuclease (apurinic or apyrimidinic); Escherichia coli endonuclease Ill; phage-T4 UV endonuclease; Micrococcus luteus UV endonuclease. They catalyse a reaction in which the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a p-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate. Example: endonuclease III from E. coli; this binds a Fe4S4 cluster, which is not important for the catalytic activity but which is probably involved in the proper positioning of the enzyme along the DNA: database code END3_ ECOLl, 21 I amino acids (23.53 kDa). A peptide the octadecapeptide cleaved from the 0. chains of a fibrinogen molecule when it is converted into fibrin by the proteolytic action of thrombin. Compare B peptide. aperture (in physics) 1 an opening in an optical or other similar instrument that controls the amount of radiation entering or leaving it. 2 the diameter of the refracting surface of a lens or reflecting surface of a mirror. See also f-number. aphidicolin a potent antiviral and antimitotic agent, first isolated as an antibiotic from the fungus Cephalosporium aphidicola. It inhibits eukaryotic DNA polymerase. Api symbolfor o-apiose. apical surface the surface of an epithelial cell that faces the lumen. apigenin 4',5,7-trihydroxyflavone; the aglycon of apiin. It inhibits cyclooxygenase and estrogen synthase. See o-apiose.

apigenin

apiin apigenin-7-apiosylglucoside, apioside; the name is de-

rived from Apium (celery) from which apiin is isolated. See also apigenin, apiose. apiose symbol: Api; the 0 isomer, 3-C-(hydroxymethyl)-o-glycero-aldotetrose is a branched carbon chain sugar that occurs widely in plants either in glycosides or polysaccharides. It is a component of apiin.

D-apiose

aplasia incomplete or deficient development of an organ or

tissue. aplastic 1 not showing normal growth or change in structure. 2 relating to or showing aplasia. Apm symbol for a residue of the a-amino acid a-aminopimelic

acid, 2-aminoheptanedioic acid. the di(a-amino acid) a.e-diaminopimelic acid, 2,6-diaminoheptanedioic acid. APMSF p-amidinophenylmethylsulfonylfluoride; a specific irreversible inhibitor of trypsin-like serine endopeptidases, with greater inhibitory activity than phenylmethylsulfonylfluoride. apo+ prefix denoting detached, separate. It is used especially of enzymes and other proteins. For example, apocarboxylase is the protein part of the holoenzyme carboxylase, i.e. it lacks the covalently bound biotin residue(s). Apoferritin is a 450 kDa protein with 24 identical subunits, that combines with ferric hydroxide-phosphate to form ferritin. See also apoenzvme. Apo(a) or lipoprotein(a) a serine endopeptidase (EC 3.4.21.-) related to plasminogen, having 37 repeats of plasminogen kringle domains and capable of cleaving fibrinogen. It is covalently linked (by disulfide bond) to apolipoprotein B-IOO. Its plasma concentration is related to the incidence of atherosclerosis. Example from human: database code APOA_HUMAN, 4577 amino acids (500.77 kDa). apocrine 1 describing a type of secretion that entails loss of part of the cytoplasm of the secretory cell. 2 describing a gland made up of such cells. Compare eccrine, holocrine, merocrine. apoenzyme the protein part of an enzyme that forms a catalytically active enzyme (holoenzyme) when combined with an activator, a coenzyme, or a prosthetic group. It determines the specificity of the catalytic system. apoferritin see ferritin. apolar 1 lacking poles, especially of nerve cells. 2 nonpolar. apolar interaction any of the entropy-driven interactions between nonpolar parts of molecules when in polar solvents. It is important in maintaining the structure of protein molecules in polar solvents, in antigen-antibody interactions, in virusprotein and enzyme-subunit aggregation and disaggregation, and in determining enzyme specificity. Azpm or Dpm symbol for

46

apple domains

apolipophorin apolipophorin a protein component of lipophorin. This protein increases the lipid-carrying capacity of lipophorin by covering the expanding hydrophobic surface resulting from diacylglycerol uptake. Example (precursor) apolipophorin IIlB from Locusta migratoria: database code APL3_LOCMI, 179 amino acids (19.09 kDa). apolipoprotein the protein component of any lipoprotein, but especially of plasma lipoproteins. The latter are designated by the abbreviation 'Apo', e.g. ApoA (for apolipoprotein A), ApoB, etc., and are subdivided into subtypes, e.g. ApoA-I for apolipoprotein A, subtype 1. See following entries for individual types of apolipoprotein. apolipoprotein A-I abbr.: ApoA-I; the major protein of plasma high-density lipoprotein (HDL), also found in chylomicrons. It is synthesized in the liver and small intestine, and participates in the reverse transport of cholesterol from tissues to the liver by promoting cholesterol efflux from tissues; it acts as a cofactor for lecithin-cholesterol acyltransferase. Deficiency of ApoA-I is associated with Tangier disease. Example (precursor) from human: database code APAl_HUMAN, 267 amino acids (30.74 kDa). apolipoprotein A-II abbr.: ApoA-II; an apolipoprotein associated with high-density lipoprotein, which it stabilizes. It is a homodimer (disulfide linked). Example from human: database code APA2_HUMAN, 100 amino acids (11.62 kDa). apolipoprotein A-IV abbr.: ApoA-IV; an apolipoprotein that is a major component of high-density lipoprotein and chylomicrons. It is involved in the catabolism of chylomicrons and very-low-depsity lipoprotein, being required for efficient activation of lipoprotein lipase by apolipoprotein CoIl. It is a potent activator of lecithin-cholesterol acyltransferase. Example from human: database code APA4_HUMAN, 396 amino acids (45.32 kDa). apolipoprotein B abbr.: ApoB; a major protein constituent of chylomicrons, very-low-density lipoprotein, and lowdensity lipoprotein. It exists in two forms, B-IOO (amino acids 28-4563 of the sequence) and B-48 (amino acids 28-2179); the latter is of intestinal origin and derived from editing of mRNA to form an internal stop codon. Excessive plasma levels occur in familial hypercholesterolemia. Example from human: database code APB_HUMAN, 4563 amino acids (514.97 kDa). apolipoprotein C-I abbr.: ApoC-I; a component of chylomicrons and very-low-density lipoprotein (VLDL), synthesized mainly in liver. It modulates the interaction of apolipoprotein E with ~-migrating VLDL and inhibits binding of ~- VLDL to low-density lipoprotein receptor-related protein. Example from human: database code APCLHUMAN, 83 amino acids (9.32 kDa). apolipoprotein C-II abbr.: ApoC-II; a component of very-Iowdensity lipoprotein (VLDL) and an activator of several triacylglycerol lipases. It has a reversible association with plasma chylomicrons, VLDL, and high-density lipoprotein. Deficiency results in hypertriglyceridemia, xanthomas, and increased risk of pancreatitis and early atherosclerosis (hyperlipoproteinemia, type IB). Example from human: database code APC2_HUMAN, 101 amino acids (11.27 kDa). apolipoprotein C-III abbr.: ApoC-III; an apolipoprotein that constitutes 50% of the protein fraction of very-low-density lipoprotein. It binds to sugar and sialic-acid residues and inhibits lipoprotein and hepatic lipases. Example from human: database code APC3_HUMAN, 99 amino acids (10.84 kDa). apolipoprotein D abbr.: ApoD; an apolipoprotein that occurs in a macromolecular complex with lecithin-cholesterol acyltransferase and in high-density lipoprotein. It is a lipocalin of known 3-D structure, probably involved in the transport and binding of bilin. The homodimer shows wide tissue distribution. Example from human: database code APD_HUMAN, 189 amino acids (21.25 kDa). apolipoprotein E abbr.: ApoE; an apolipoprotein that constitutes 10-20% of very-low-density lipoprotein. It mediates

binding, internalization, and catabolism of lipoprotein particles and is a ligand for the low-density lipoprotein (ApoB/E) receptor and for the ApoE receptor (chylomicron remnant) of hepatic tissues. It is present in brain and may have a role in cholesterol transport. O-Glycoside and sialic-acid residues occur, but it is de-sialylated in plasma. It has nine allelic variants and two of these are associated with hyperlipoproteinemia type III. The 3-D structure is known; it contains a heparin-binding motif. Example from human: database code APE_HUMAN, 317 amino acids (36.11 kDa). apolipoprotein H abbr.: ApoH; other names: ~2-glycoprotein II precursor; APC inhibitor (see activated protein C). An apolipoprotein that binds to anions such as heparin and phospholipids. It may prevent activation of the intrinsic blood coagulation cascade by binding to phospholipids on the surface of damaged cells. See also amyloid A protein. apolipoprotein receptor see LDL receptor, VLDL receptor. apomorphine 6ap-aporphine-lO, II-dial; 5,6,6a,7-tetrahydro6-methyl-4H-dibenzo[de,g]quinoline-IO, II-dial; a synthetic opiate. The (R)-enantiomer is a potent dopamine receptor agonist, noted for its powerful emetic effects.

HO

apoplast the nonliving part of plant tissue, external to the plasmalemma and composed of the cell walls, the intercellular spaces, and the lumen of dead structures such as xylem cells. apoprotein the protein part of a conjugated protein. apoptosis cell death may occur by accident, by cell necrosis, or by an intracellular controlled process characterized by a condensation and subsequent fragmentation of the cell nucleus during which the plasma membrane remains intact. The term apoptosis may be used broadly to encompass all forms of such normal or pathological cell death or may be confined to those processes involving morphological changes such as occur in normal animal development. A cascade of caspases, (cysteine endopeptidases that cleave at specific aspartic residues hence the name) is involved. In this cascade, caspases cleave procaspases to form additional caspases. Some of the caspases thus formed cleave other proteins, including deoxyribonucleases. [From apo+ + Greek ptosis, falling.] aporepressor the protein component of a complex that can act to inhibit gene expression. See also repressor. apparent describing a physical quantity, especially an association constant, dissociation constant, equilibrium constant, etc., that has been determined under particular experimental conditions and hence is not the true (i.e. thermodynamic) constant. See equilibrium constant. apparent exchangeable mass a term used in tracer kinetics in whole animals for a mass obtained by dividing the quantity of administered radioactivity that is retained by the specific activity of the tracer in the (blood) plasma. It equals the total exchangeable mass when the specific activities are equal throughout the system. Compare compartment. apparent molecular weight former name for apparent relative

molecular mass. apparent relative molecular mass relative molecular mass that has been determined by a method that does not make allowance for any nonideality of the system. apple domains sequences of 90 or 91 amino-acid residues that contain three highly conserved disulfide bonds linking the first and sixth, second and fifth, and third and fourth cysteine

47

arabinose

applicator residues present in each repeat. They can be drawn in the shape of an apple. Four are present in human kallikrein and in human coagulation factor XI. See also Appendix E. applicator any device or instrument, such as a comb, rod, spatula, or tube, for applying samples in a reproducible manner to a small defined area, e.g. in chromatography, or for applying something to a particular part of the body. approach to (sedimentation) equilibrium method or Archibald method a method for determining the relative molecular masses of (macro)molecules by sedimentation in an ultracentrifuge, by measuring the depletion of the macromolecules from the meniscus and their accumulation at the cell bottom. Its advantage is that only very short periods of sedimentation are required. [After William James Archibald (1912- )) AP protein abbr. for activator protein, one of two transcription factors; API, a product of c-jun (see JUN), interacts with Fos (product of c-fos) to form a dimer. It harbours two functional domains, one responsible for DNA binding and one for binding to Fos, and includes a leucine zipper. Example from human: database code TAPLHUMAN, 331 amino acids (35.63 kDa). AP2 interacts with inducible viral and cellular enhancer elements to stimulate transcription of selected genes. It contains the consensus binding sequence CCCAGGC and a helix-span-helix motif. Example from human: database code TAP2_HUMAN, 437 amino acids (48.01 kDa). A 2 pr or Dpr symbol for a residue of the a,p-diamino acid L-a,pdiaminopropionic acid; L-2,3-diaminopropanoic acid. aprotic describing a substance, especially a solvent, that is unable to act as a proton acceptor or donor. aprotinin a proteinase inhibitor derived from animal tissues. It is a basic polypeptide of known sequence of 58 amino-acid residues (~6.5 kDa) that exists as a dimeric aggregate. It is stable in acid or neutral media and at high temperature, and it inhibits kallikrein, trypsin, chymotrypsin, plasmin, and, to a lesser extent, papain. See also Trasylol. APRT abbr. for adenine phosphoribosyltransferase. APS abbr. for adenosine 5'-phosphosulfate. APT abbr. for alum-precipitated toxoid. aptitude (in microbiology) the specific physiological state of a lysogenic bacterium that enables it, upon induction, to react so as to produce infectious bacteriophage particles. apud or APUD abbr. for amine precursor uptake and decarboxylation; designating any of a series of cells that produce peptides and/or amines active as hormones or neurotransmitters, share a spectrum of cytochemical qualities, and appear in many cases to have a common embryological origin. They are thought to include the A, B, and D cells of the endocrine pancreas, the C cells of the thyroid, and the various hormone-producing cells of the pituitary and the gut. apudoma any tumour of an apud cell, e.g. a gastrinoma, glucagonoma, insulinoma, or VIPoma. apurinic acid a DNA derivative in which all the purine bases have been removed by selective hydrolysis, leaving the pyrimidine-deoxyribose bonds and the phosphodiester bonds of the backbone intact. It results from the gentle acid hydrolysis of DNA at pH 3.0. apurinic endonuclease see AP endonuclease. apyrase EC 3.6.1.5; other names: ATP-diphosphatase; adenosine diphosphatase (abbr.: ADPase); a Ca 2+-requiring enzyme that catalyses the hydrolysis of ATP to AMP and 2 orthophosphate. It also hydrolyses other nucleotides, especially ADP to AMP and orthophosphate. It was originally identified in plants, especially potatoes, but enzymes of this type have also been found in animals, e.g. as a surface enzyme on lymphoid cells identical to CD39, and as a secreted enzyme of the yellow-fever mosquito, Aedes aegypti. It is used in platelet incubations to destroy ADP. Example from A. aegypti: database code APY_AEDAE, 562 amino acids (62.73 kDa). apyrimidinic acid a DNA derivative from which the pyrimidine bases have been removed chemically, leaving the

purine-deoxyribose bonds and the phosphodiester bonds of the backbone intact. apyrimidinic endonuclease see AP endonuclease. aq (in chemistry) abbr. for aqueous. aqua+ comb. form 1 denoting acting on or reacting with water. 2 denoting presence of water as a neutral ligand in a coordination entity, e.g. aquacobalamin. The number of water molecules per entity is indicated by an approximate multiplying prefix, e.g. hexaquachromium trichloride. aquacide a substance that when added to a mixture removes water molecules, usually by forming a compound with the elements of water. -aquacidal ad}. aquaporin any of a class of CHIPS that are specific for the transfer of water. Example, specific for erythrocytes and kidney proximal tubule, from human: database code AQP1_ HUMAN, 269 amino acids (28.49 kDa). aqueous 1 of, having the characteristics of, or relating to water. 2 dissolved in or mixed with water. 3 or aqueous humour the fluid occupying the space between the crystalline lens and the cornea of the eye. aquo+ comb. form 1 containing one or more water molecules in a coordination complex. 2 (in chemical nomenclature) derived from water. aquo-ion a complex ion containing one or more water molecules held by coordination. Ar symbol for 1 argon. 2 aryl. Ara symbol for arabinose. ara a plant gene related to fas. araBAD an operon characterized in Escherichia coli and encoding L-ribulokinase, L-arabinose isomerase, and L-ribulose 5phosphate 4-epimerase, three of the enzymes that metabolize arabinose. See also arae. Arabidopsis fha/iana a small Cruciferous plant (common wall cress) widely used in plant genetic research because of its small genome and very short generation time. arabin+ a variant (before a vowel) of arabino+. arabinan a branched homopolymer of L-arabinose found in plant pectins. arabinaric acid see aldaric acid. arabino+ or (before a vowel) arabin+ comb. form indicating arabinose. arabino- prefix (in chemical nomenclature) indicating a chemical compound containing a particular configuration of a set of three (usually) contiguous >CHOH groups, as in the acyclic form of D- or L-arabinose. See monosaccharide. arabinofuranosylcytosine cytosine arabinoside; see cytarabine. arabinogalactan any member of a subgroup of plant hemicelluloses that contain arabinose and galactose and are particularly abundant in larch. arabinonucleoside the l-p-D-arabino-N-furanoside of a purine or pyrimidine base. It is a structural analogue of a riboside. arabinose arabino-pentose; a monosaccharide. L-Arabinose occurs free, e.g. in the heartwood of many conifers, and in the combined state, in both furanose and pyranose forms, as a constituent of various plant hemicelluJoses, bacterial polysaccharides, etc. D-Arabinose occurs to some extent in plant glycosides and is a constituent of the arabinonucleosides. H

Itt ~

0 OH

HO

OH H

OH

H

{I-D-arabinose

48

o-arabinose isomerase

argentaffin cell

D-arabinose isomerase EC 5.3.1.3; systematic name: D-arabi-

arachidoyl or (formerly) arachidyl or arachyl symbol: Ach; the

nose ketol-isomerase. An enzyme that catalyses the reaction: D-arabinose = o-ribulose. See also L-arabinose isomerase. L-arabinose isomerase EC 5.3.1.4; systematic name: L-arabinose ketol-isomerase. An enzyme that catalyses the reaction: L-arabinose = L-ribulose. It initiates the metabolism of L-arabinose. Example from Escherichia coli: database code ARAA_ECOLI, 500 amino acids (55.98 kDa). See also araBAD, D-arabinose isomerase. arabinose-5-phosphate isomerase EC 5.3.1.13; systematic name: o-arabinose-5-phosphate keto I-isomerase. An enzyme that catalyses the reaction: o-arabinose 5-phosphate = o-ribulose 5-phosphate. arabinoside any glycoside derived from arabinose. arabinoxylan any of various neutral polysaccharides that occur in association with acidic polysaccharides in cereal gums. They consist of a chain of (l~4)-linked P-D-xylan units with single a-L-arabinofuranosyl groups in (l~3) linkage. arabitol or arabinitol arahino-pentitol; the pentitol formally derived by reduction of the aldehyde group of arabinose or lyxose. The D enantiomer is present in lichens and mushrooms. arae the gene for the AraC protein, which acts as a regulator of expression of the araBAD operon and of araC itself. AraC acts as both a repressor (when intracellular arabinose levels are low), binding to araD operator sites, and an activator (in the presence of arabinose), when bound to the aral site, but only in the presence of cyclic AMP-CRP complex. It is a typical helix-turn-helix DNA-binding regulatory protein. Database code ARAC_ECOLl, 292 amino acids (33.35 kDa). ara-C abbr. for arabinosylfuranosylcytosine. arachain an unclassified proteinase obtained from the peanut, Arachis hypogaea. arachidic acid the trivial name for eicosanoic acid; CH r [CH 2]lS-COOH; a constituent of arachis oil (from the peanut, Arachis hypogaea) and other oils. See also arachidoyl. arachidonate 5-lipoxygenase EC 1.13.11.34; other names: 5lipoxygenase; leukotriene-A4 synthase; a lipoxygenase (def. 2) enzyme that catalyses the reaction of arachidonate with dioxygen to form (6E,8Z, liZ, l4Z)-(5S)-5-hydroperoxyeicosa6,8,1I,14-tetraenoate. Iron is a cofactor. Example from human: database code LOX5_HUMAN, 673 amino acids (77.76 kDa). arachidonate 12-lipoxygenase EC 1.13.11.31; other name: 12-lipoxygenase; a Iipoxygenase (def. 2) enzyme that catalyses the reaction of arachidonate with dioxygen to form (5Z,8Z, I OE, 14Z)-( l2S)-12-hydroperoxyeicosa-5,8, 10, 14tetraenoate. Iron is a cofactor. Example from human: database code LOX2_HUMAN, 662 amino acids (75.45 kDa). arachidonate 15-lipoxygenase EC 1.13.11.33; other names: arachidonate w-6 lipoxygenase; 6-lipoxygenase; a Iipoxygenase (def. 2) enzyme that catalyses the reaction of arachidonate with dioxygen to form (5Z,8Z, 11 Z, 13E)-(l5S)-15hydroperoxyeicosa-5,8, 11, 13-tetraenoate. Iron is a cofactor. Example from human: database code LOXL HUMAN, 661 amino acids (74.59 kDa). arachidonic acid see eicosatetraenoic acid. arachidonoyl symbol: ,14Ach; the trivial name for (all-Z)eicosa-5,8,11,14-tetraenoyl; CH r [CH 2h-[CH r CH=CH]4[CH 2h-CO- (all-Z isomer); the acyl group derived from arachidonic (i.e.(all-Z)-eicosa-5,8, II, l4-tetraenoic) acid, a polyunsaturated, unbranched, acyclic, aliphatic acid. It occurs naturally in membrane phospholipids, and is a biochemical precursor of prostaglandins and leukotrienes. It is also present in mosses, algae, and ferns, but not in higher plants. Distinguish from arachidonyl and arachidoyl. arachidonyl the trivial name for the alkyl group, CH 3-[CH 2h[CH r CH=CH]4-[CH 2 h-CH r , derived from the alkenol analogue of arachidonic acid. Distinguish from arachidonoyl.

trivial name for eicosanoyl; CH r [CH 2hs-CO-; the acyl group derived from arachidic (or eicosanoic or (formerly) arachic) acid, a saturated, unbranched, acyclic, aliphatic acid. It occurs naturally as triarachin in certain seeds, oils, and butter fat. Arachidyl is now the name for the alkyl group, CH r [CH 2]lS-CH r . Distinguish from arachidonyl. arachidyl the trivial name for the alkyl group, CH 3-[CH 2hsCHr, the alkanol analogue of arachidic acid. See also arachidoyl. arachin the major protein of the groundnut, Arachis hypogaea,

comprising a 345 kDa globulin with 12 subunits. Not all groundnuts contain the same arachin; there exist at least two forms, designated A and B, having similar amino-acid compositions and general properties but differing in their subunit composition. Examples of subunits: database code ARA1_ ARAHY, 176 amino acids (20.86 kDa); ARA5_ARAHY, 201 amino acids (22.22 kDa). See also conarachin. Arber, Werner (1929- ), Swiss microbiologist; Nobel Laureate in Physiology or Medicine (1978) jointly with D. Nathans and H. O. Smith 'for the discovery of restriction enzymes and their application to problems of molecular genetics'. arbovirus abbr. for arthropod-borne virus (a term formerly used for togavirus). arc a continuous curved line, as part of a circle or ellipse; e.g. the line of antigen-antibody precipitate obtained in immunodiffusion or immunoelectrophoresis. Archaea one of three primary kingdoms of cells, together with Eukarya and Bacteria (formerly Eubacteria), defined when cells

are classified on the basis of rRNA sequence homologies. Archaea include all methanogens, extreme halophiles and most extreme thermophiles. Representative genera are: Halobacterium, Methanobacterium, Sulfolobus, Thermoplasma, and Purodictium (growth optimum = 105°C); about 40 others are known. -archaeal adj. Archaebacteria former name for Archaea. Archibald method see approach to (sedimentation) equilibrium method. Archimedes' principle the principle that when a body is

partly or wholly immersed in a fluid there is an apparent loss of weight equal to the weight of the fluid displaced. [After Archimedes of Syracuse (?287-212 Be), Greek philosopher and applied mathematician.] architectural gene a gene that determines the site of an enzyme within a cell. A-region the presumptive initial oxidation site of a carcinogenic polycyclic aromatic hydrocarbon, on the terminal ring of the bay region, in the metabolic pathway leading to carcinogenesis (corresponding to what has sometimes been called the M-region). Compare B-region, K-region, L-region. arenavirus any of a group of RNA viruses consisting of enveloped pleomorphic particles of 80-120 nm with helical nucleocapsids. The group includes Lassa virus and other viruses that spread to humans from rodents. arene any monocyclic or polycyclic aromatic hydrocarbon. arene oxide any epoxide formed by the addition of an atom of oxygen across any double bond of an arene. ARF abbr. for ADP-ribosylation factor; a small monomeric cytosolic GTPase that, when bound to GTP, binds to the membranes of cells. It was originally discovered as a factor required for cholera toxin to ribosyl ate G" hence its name. Its structure is known and is highly conserved. It is a member of the HAS superfamily. Functions of ARF include regulation of membrane traffic in both endocytic and exocytic pathways, maintenance of organelle integrity, assembly of coat proteins (see coatomer), and activation of phospholipase D. See phospholipase. Arg symbol for a residue of the a-amino acid L-arginine (alter-

native to R). argentaffin cell a type of cell of the apud class, characterized

by taking up silver stains with high affinity, without the addi-

49

argentation chromatography

aro1

tion of reducing agent. [Named from Latin argentum, silver, and affinity./ argentation chromatography any method of chromatography in which an adsorbent impregnated with silver nitrate is used to separate lipid classes according to the degree and geometry of their saturation. The technique may be used with either thin-layer chromatography or column chromatography, or in conjunction with gas-liquid chromatography. arginase abbr. (in clinical biochemistry): ARS; recommended name for EC 3.5.3.1; other names: arginine amidinase; systematic name: L-arginine amidinohydrolase. An enzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea; it also acts on a-N-substituted L-arginines and canavanine. It is a key enzyme in the ornithine-urea cycle, occurring in high concentrations in the liver of ureotelic vertebrates and being absent or nearly so from the liver of uricotelic species. It has a very wide species distribution. In humans it is defective in the inherited disorder argininemia. Examples: from Bacillus subtilis, database code ARGCBACSU, 296 amino acids (32.15 kDa); from Rattus norvegicus, database code ARGCRAT, 323 amino acids (34.97 kDa). argininate 1 arginine anion; H 2N-C(=NH)-NH-[CH 2hCH(NH 2)-COO-. 2 any salt containing the arginine anion. 3 any ester of arginine. arginine trivial name for N 5-amidino-ornithine; a-amino-bguanidinovaleric acid; 2-amino-5-guanidinopentanoic acid; H2N-C(=NH)-NH-[CH2h-CH(NH2)-COOH; a chiral aamino acid. L-Arginine (symbol: R or Arg), (S)-2-amino-5guanidinopentanoic acid, is a coded amino acid found in peptide linkage in proteins; codon: AGA (not in mitochondria of fruit fly or mammals) or AGG (not in mitochondria of mammals); CGA, CGC, CGG, or CGU. It is an essential dietary amino acid in rats and probably in young humans, and is glucogenic in mammals. D-Arginine (symbol: D-Arg or DArg), (R)-2-amino-5-guanidinopentanoic acid, is not known to occur naturally.

HO~~yNH2 o

NH L-arginine

arginine (base) the ionic form of an arginine residue when the guanidino group is unprotonated. arginine carboxypeptidase see Iysine(arginine) carboxypeptidase. arginine kinase EC 2.7.3.3; an enzyme that catalyses a reaction between ATP and L-arginine to form ADP and Nw-phospho-L-arginine. The latter compound may play a role in invertebrate muscle analogous to that of creatine phosphate in vertebrate muscle. Example from Homarus gammarus (European lobster): database code KARG_HOMGA, 355 amino acids (39.81 kDa). arginine phosphate former name (not recommended) for phosphoarginine. arginine-urea cycle see ornithine-urea cycle. [8-arginine]vasopressin or (less correctly) argmme vasopressin abbr.: AVP or [Arg~]vasopressin; the molecular form of vasopressin in which the variable eighth position in its aminoacid sequence is occupied by an arginine residue. This is the form present in humans and most other mammals. arginine vasotocin or [Arg 3)oxytocin a pituitary peptide found in nonmammalian vertebrates with activity resembling both oxytocin and vasopressin. argininium 1 argininium(1 +); the monocation of arginine. In theory, the term denotes any ion or mixture of ions formed from arginine and having a net charge of plus one, although in practice the predominant species is generally H 2N-C(=NH 2+)-

NH-[CH 2h-CH(NH 3+)-COO-. 2 the systematic name for argininium(2+); the dication of arginine. arginino 1 N2-arginino; the alkylamino group, H 2N-C(=NH)NH-[CH 2h-CH(COOH)-NH-, derived from arginine by loss of a hydrogen atom from its a-amino group. 2 NW-arginino; the alkylguanidino group, HOOC-CH(NH 2HCH 2h-NHC(=NH)-NH-, derived from arginine by loss of a hydrogen atom from its w-amino group. argininosuccinase EC 4.3.2.1; systematic name: N-(L-argininosuccinate) arginine lyase; recommended name: argininosuccinate lyase. An enzyme of the ornithine-urea cycle that catalyses the hydrolysis of N-(L-arginino )succinate to fumarate and L-arginine. Example (human) homotetramer (deficiency in argininosuccinicaciduria; very strong similarity to bird and reptile I)-crystallin): database code ARLY_HUMAN, 464 amino acids (51.78 kDa). argininosuccinate 2-( NW-arginino)succinate; L-argininosuccinate is an intermediate in the ornithine-urea cycle, where it is synthesized by the enzymic condensation of L-citrulline with L-aspartate. See arginosuccinate synthase. K,

NH2

H

HO~NYH o

NH

HOOC~O

argininosuccinate synthase EC 6.3.4.5; systematic name: L-citrulline:L-aspartate ligase (AMP-forming); other names: argininosuccinate synthetase; citrulline-aspartate ligase. An enzyme of the ornithine-urea cycle that catalyses a reaction between ATP, L-citrulline, and L-aspartate to form L-argininosuccinate with release of AMP and pyrophosphate. A deficiency occurs in citrullinemia. Example (human) homotetramer: database code ASSY_HUMAN, 412 amino acids (46.37 kDa). arginyl the acyl group, H 2N-C(=NH)-NH-[CH 2/ r CH(NH 2)-CO-, derived from arginine. argon detector a sensitive detector used in gas chromatography that depends on the unique ionization properties of argon whereby its long-lived metastable excited atoms can transfer their energy of excitation by collision to other gas molecules of lower excitation potential. Thus argon can be used as the chromatographic carrier gas, the detector being an ionization chamber containing a source of ionizing radiation. Detectable changes of the level of ionization occur when the argon issuing from the column has another gas mixed with it. The detector was invented by James E. Lovelock. Its great advantage is that it does not depend on the chemical nature of the substances being separated. [Arga]va80pressin abbr. for [8-arginine/vasopressin. arithmetic mean see mean. arm a base-paired segment of the clover-leaf model of transfer RNA. There are several such arms: amino-acid arm, anticodon arm, dihydrouridine arm, extra arm, and Tlfle arm. ARNT abbr. for aryl-hydrocarbon receptor nuclear translocator; other name: dioxin receptor; a protein that mediates translocation of the Ah receptor from the cytoplasm to the nucleus after ligand has been bound. Example from human: ARNT_HUMAN, 789 amino acids (86.64 kDa). A-RNA abbr. for A form of RNA. Br01 a fungal gene for aromatic amino-acid biosynthesis. It encodes a multifunctional protein for, e.g., 3-dehydroquinate synthase, 3-dehydroquinase, shikimate 5-dehydrogenase, shikimate kinase, EPSP synthase. Example from Emericella (Aspergillus) nidulans: database code AROI_EMENI, 1603 amino acids (174.89 kDa).

50

aroA-H, aroL

arylsulfatase

aroA-H, aroL Escherichia coli genes for chorismate synthesis. arogenate or pretyrosine 3-( I'-carboxylato-4'-hydroxy-2',5'cyclohexadienyl)alanine; an intermediate in phenylalanine and tyrosine biosynthesis in Euglena gracilis and some other microorganisms, and in plants. It is formed by transamination of prephenate and is subsequently decarboxylated and converted to tyrosine, or converted to phenylalanine by dehydration and decarboxylation.

~

eOOH

HOOe

I

I

NH2

OH

aromatic describing any organic compound characterized by one or more planar rings, each of which contains (usually) three conjugated double bonds and (4n + 2) delocalized pielectrons, where n is a small integer. They undergo substitution reactions more readily than addition reactions. The simplest member of the class is benzene. The term was originally used to distinguish fragrant compounds from aliphatic compounds. -aromaticity n. aromatic amino acid any amino acid containing an aromatic ring. In proteins these are phenylalanine, tryptophan, and tyrosine. aromatic-L-amino acid decarboxylase EC 4.1.1.28; systematic name: aromatic-L-amino-acid carboxy-lyase; other names: dopa decarboxylase; tryptophan decarboxylase; hydroxytryptophan decarboxylase. An enzyme that catalyses the decarboxylation of L-tryptophan to tryptamine; pyridoxal 5'phosphate is a coenzyme. The popular name derives from the fact that the enzyme also acts on 5-hydroxY-L-tryptophan to yield 5-hydroxytryptamine and on dihydroxy-L-phenylalanine (dopa) to yield dopamine. Example from human: database code DCD_HUMAN, 480 amino acids (53.83 kDa); it is a homodimer, and structurally similar to certain other eukaryotic decarboxylases. ARPa abbr. for assimilatory regulatory protein a, i.e. ferredoxin-thioredoxin reductase. ARP b abbr. for assimilatory regulatory protein b, i.e. thioredoxin. arrestin or S antigen any protein of a family that includes the Ca 2+ -binding protein of rod-cell outer segments. It binds to photoactivated-phosphorylated rhodopsin, thereby apparently preventing the transducin-mediated activation of phosphodiesterase. It has been implicated in autoimmune uveitis. Example from human: database code ARRS_HUMAN, 405 amino acids (45.00 kDa). ~-Arrestins are similar in their Cterminal parts to a-transducin and other purine-nucleotidebinding proteins. ~-Arrestins regulate ~-adrenergic receptor function; they seem to bind phosphorylated ~-adrenergic receptors, thereby significantly impairing their capacity to activate G s proteins. Example (I3-arrestin 2) from human: database code ARRC_HUMAN, 409 amino acids (45.99 kDa). Arrhenius, Svante August (1859-1927), Swedish chemist and physicist; Nobel Laureate in Chemistry (1903) 'in recognition of the extraordinary services he has rendered to the advancement of chemistry by his electrolytic theory of dissociation'. IArrhenius) activation energy symbol: E a or EA; see Arrhenius equation. Arrhenius equation an equation representing the effect of temperature on the velocity of a chemical reaction. It may be expressed in the forms: dlnk/dT=Ea/RT2 (I) or

d Ink/d(l/T) = -EalR

(2)

k = Ae- Ea / RT

(3)

or where k is the rate constant for the reaction, E a is its IArrhenius) activation energy, R is the gas constant, T is the thermodynamic temperature, and A is a constant termed the frequency factor or the pre-exponential factor. Version 2 may be integrated to: (4). Ink = InA - Ea/RT Version 4 of the equation requires a plot of Ink against liT, known as an Arrhenius plot, to be a straight line of slope -EalR, a relationship that has been shown to obtain for a considerable number of chemical reactions. See also temperature coefficient of reaction. Arrhenius plot see Arrhenius equation. ARS abbr. for 1 autonomously replicating sequence; any DNA sequence that can confer upon a plasmid the property of becoming a replicon in a particular host. The term is largely confined to fungal genetics. 2 (in clinical biochemistry) abbr. for arginase. Arsenazo III 2,2'-(1 ,8-dihydroxy-3,6-disulfonaphthalene-2, 7bisazo)bisbenzenearsonic acid; an indicator substance used in the determination of low (micromolar) concentrations of free calcium ions. The free acid is purple; the calcium adduct is blue-violet. arsenic symbol: As; a semi-metal element of group 15 of the IUPAC periodic table; atomic number 33; relative atomic mass 79.41. It exists in three forms: yellow, grey, and black. The yellow form, comparable to white phosphorus, is less stable than the other forms and is converted into the grey (metallic) form by heat. The black form is more stable than the yellow form but is metastable with respect to the grey form. Arsenic is required in trace amounts by some organisms, but generally it acts as an antimetabolite. arsenical 1 of or containing arsenic. 2 a drug or other agent (e.g. an insecticide, rodenticide, or nerve gas) containing arsenic as an active principle. artemesinin see sesquiterpene lactone. arteriosclerosis a pathological condition in which there is a thickening and loss of elasticity of the walls of the arteries, which may become calcified. This interferes with the blood supply to various organs and tissues, resulting in impaired function. It normally, though not invariably, results from atherosclerosis. Arthus reaction a complement-dependent hypersensitivity reaction caused when antigen reacts with precipitating antibody in the skin or other tissues, forming microprecipitates in and around the small blood vessels and, secondarily, damaging cells. In the passive Arthus reaction antibody is injected intravenously and the antigen applied locally; in the reversed passive Arthus reaction the opposite applies. An active Arthus reaction may occur when antigen is injected locally subsequent to previous injection of the same antigen. The inflammation that results is by type III mechanisms (see hypersensitivity (def. 2)). [Described by (Nicholas) Maurice Arthus (1862-1945), French physiologist and bacteriologist, in 1903.) articulin any of a family of cytoskeletal proteins of the epiplasm of flagellate and ciliate organisms. They form filaments and larger sheets or tubes. They contain repeated valine- and proline-rich motifs with the consensus VPVP__V V. aryl any univalent organic radical derived from an arene by loss of one hydrogen atom. arylene any bivalent organic group derived from an arene by loss of two hydrogen atoms. arylsulfatase any of a group of enzymes that catalyse the hydrolysis of a phenol sulfate to a phenol and sulfate. Example from Escherichia coli: database code ASLA_ECOLI, 551 amino acids (60.65 kDa). Arylsulfatases A, B, and Care com-

51

As

ASO

mon names for cerebroside-sulfatlll, N-acetylgalactosamine4-sulfatase, and steryl'sulfatase respectively. As symbol for arsenic. ASA dehydrogenase see aspartate-semialdehyde dehydrogenase. ASAT (in clinical biochemistry) abbr. for aspartate aminotransferase. See aspartate transaminase. AS-C abbr. for Achaete-Scute complex. See also AS-C protein. ascarylose 3,6-dideoxy-L-mannose; 3,6-dideoxy-L-arabinohexose; a component of glycolipids found in eggs of the nematode, Ascaris, and in the bacterium, Yersinia pseudotuberculosis, type V. For the D enantiomer see tyvelose. ascending boundary the solute boundary that moves upwards in one arm of the cell during electrophoresis in a Tiselius apparatus. ascending chromatography any of the techniques of chromatography in which the mobile phase moves upwards over the

solid phase. ascites the accumulation of serous fluid in the peritoneal

cavity. The presence of ascites may be due to the growth of a tumour elsewhere in the body, the ascitic fluid then containing a suspension of single tumour cells. Administration of a hybridoma results in the formation of monoclonal antibodies which can be recovered from the ascitic fluid. -ascitic adj. Ascoli test a precipitin test used in the serological diagnosis of anthrax. The antigens are extracted with boiling saline and detected by a ring test with immune serum. ascorbic acid a carbohydrate-like compound, containing six carbon atoms per molecule, the L enantiomer of which is found in fruit and vegetables. It has vitamin C activity in humans (most other primates can synthesize ascorbic acid) and guinea pigs. Humans are among the few higher animals that are unable to synthesize L-ascorbic acid, owing to a deficiency of l-gulonolactone oxidase, the enzyme catalysing the terminal step in L-ascorbic acid synthesis. The molecule contains an ene-diol group, one hydroxyl group of which is acidic (pKa 4.04) and ionizes to give an anion ascorbate; the other ene-diol hydroxyl acts as a reducing group (EO' = +0.058 V, pH 7), and is oxidized on conversion to dehydroascorbate. Ascorbate is required together with ferric ion as a cofactor in the oxidation of prolyl residues in collagen to hydroxyprolyl residues and in other reactions.

ascorbic acid

ascorbate ion

?H2 0H

H-~o o

0

dehyd roascorbic acid

ascospore a (usually sexually derived) haploid spore formed within an ascus. AS-C protein abbr. for Achaete-Scute complex protein; any of

a family of proteins encoded by the Achaete-Scute complex, a gene cluster first discovered in Drosophila but with analogues in mammals and other organisms. They are involved in the determination of the neuronal precursors in the peripheral and central nervous systems. The T3, T4, and T5 proteins label strongly in the presumptive stomatogastric nervous system, while T8 is more prominent in the presumptive procephalic lobe. They resemble other members of the MYC family of helixturn-helix transcription factors. Example, AS-C protein T4 (Drosophila melanogaster): database code AST4_DROME, 345 amino acids (38.08 kDa). ascus (pl. asci) a sac-like fruiting body formed in ascomycete fungi, e.g. yeasts and Neurospora; it contains (typically eight) ascospores when mature. +ase suffix denoting an enzyme; it is generally attached to a root indicating the substrate and/or the nature of the reaction catalysed. [From diastase.) a.emantic molecule any molecule that is not produced by an organism and therefore does not express any of the information that the organism contains. Absorbed molecules, although not derived from information contained within the organism, may nevertheless offer information about the organism relating to its absorption mechanisms. See semantide. See also episemantic molecule. asepsis 1 the state of being aseptic. 2 the methods of making or keeping something aseptic. Compare antisepsis. aseptic sterile; free from pathogenic microorganisms. Compare antiseptic (def. 2). aseptic technique any technique incorporating measures that prevent the contamination of cultures, sterile media, etc. and/or the inappropriate infection of persons, animals or plants, by extraneous microorganisms. asexual reproduction or agamic reproduction the development of a new individual from either a single cell or a group of cells without any sexual process. The term includes agamogeny and vegetative reproduction. Ash protein another name for Grb2. asialo+ comb. form denoting the absence from a compound of sialic-acid residues, e.g. after their deliberate enzymic removal from a naturally occurring sialo- (def. 2) compound. A side the side of the nicotinamide ring of NAD(P)H from which projects the pro-R hydrogen atom (known as H A ) at the 4 position. Compare B side. See also pro-R,pro-S convention. A site abbr. for aminoacyl-tRNA site (of a ribosome). Asn symbol for a residue of the a-amino acid L-asparagine (alternative to N). AsnC the asparagine biosynthetic operon regulatory protein, the product of asnC. In Escherichia coli it is the activator of asnA expression, the autogenous regulator of asnC expression, and the repressor of gidA (a gene of E. coli associated with glucose-inhibiting division) at the post-transcriptionalleve\. It is a helix-turn-helix (HTH) protein and the prototype for AsnC HTH family of regulatory proteins; database code ASNC_ ECOLI, 152 amino acids (16.87 kDa). ASO abbr. for antistreptolysin-O; see streptolysin.

52

Asp

aspartic acid

Asp symbol for a residue of the a-amino acid L-aspartic acid

(alternative to D). asparaginase EC 3.5.1.1; other names; L-asparaginase; systematic name; L-asparagine amidohydrolase; an enzyme that catalyses the hydrolysis of L-asparagine to L-aspartate and NH 3 . It is an effective antileukemic drug when injected into the bloodstream, its action being to deprive fast-growing tumour cells of the exogenous asparagine they require for rapid growth. Its clinical usefulness is limited because it causes damage to tissues with low asparagine synthetase activity. Several isoenzymes are found in several bacteria. Example, L-asparaginase I from Escherichia coli, a homotetramer: database code ASGl_ECOLI, 338 amino acids (37.08 kDa). asparaginate 1 asparagine anion; the anion, H 2 N-COCH 2-CH(NH z)-COO-, derived from asparagine. 2 any salt containing the asparagine anion. 3 any ester of asparagine. asparagine trivial name for the p-amide of aspartic acid: aspartic 4-amide; a-aminosuccinamic acid; 2-amino-3-carbamoylpropanoic acid, H 2N-CO-CH z-CH(NH z)-COOH; a chiral a-amino acid. L-Asparagine (symbol: A or Asn; (formerly) also Asp(NH z)), (S)-2-amino-3-carbamoylpropanoic acid, is a coded amino acid found in peptide linkage in proteins; codon: AAC or AAU. It is a nonessential dietary amino acid in mammals and is glucogenic. One residue per molecule of D-asparagine (symbol: D-Asn or oAsn), (R)-2-amino-3-carbamoylpropanoic acid, may occur in the antibiotic bacitracin A as an alternative to one of o-aspartic acid. Compare isoasparagine.

L-asparagine

asparagine synthase (glutamine-hydrolysing) EC 6.3.5.4; other name: asparagine synthetase (glutamine-hydrolysing).

An enzyme that catalyses a reaction between ATP, L-aspartate, and L-glutamine to form AMP, pyrophosphate, L-asparagine, and L-glutamate. Example from asparagus: database code ASNLASPOF, 589 amino acids (65.97 kDa); it contains a glutamine amidotransferase motif. Compare aspartateammonia ligase. asparagino 1 N1-asparagino; the alkylamino group, HzN-CO-CHz-CH(COOH)-NH-, derived from asparagine by loss of a hydrogen atom from its a-amino group. 2 N 4 _ asparagino; the acylamino group, HzN-CH(COOH)-CHz-

CO-NH-, derived from asparagine by loss of a hydrogen atom from its amide group. asparaginyl the acyl group, HzN-CO-CHz-CH(NH2)-CO-, derived from asparagine. Compareisoasparaginyl. aspartame N-L-a-aspartyl-L-phenylalanine methyl ester; a low-calorie artificial sweetener, about 160 times sweeter than sucrose in aqueous solution. Its sweetness is lost in cooking due to hydrolysis of the methyl ester. It is to be avoided in patients with phenylketonuria. aspartase EC 4.3.1.1; recommended name: aspartate ammonialyase; other name: fumaric aminase. An enzyme that catalyses the hydrolysis of L-aspartate to fumarate and NH 3 . Example from Escherichia coli, homotetramer: database code ASPA_ECOLI, 478 amino acids (52.30 kDa). aspartate 1 aspartate(l-) or hydrogen aspartate; the monoanion derived from aspartic acid. In theory, the term denotes any ion or mixture of ions formed from aspartic acid and having a net charge of -I, although the species -OOC-CH zCH(NH 3+)-COO- generally predominates in practice. 2 the systematic name for aspartate(2-); the dianion derived from aspartic acid. 3 any salt containing an anion of aspartic acid. 4 any ester of aspartic acid.

aspartate aminotransferase see aspartate transaminase. aspartate-ammonia ligase EC 6.3.1.1; other name: as-

paragine synthetase; an enzyme that catalyses the reaction of ATP with L-aspartate and NH 3 to form AMP, pyrophosphate, and L-asparagine. Example from Escherichia coli: database code ASNA_ECOLI, 330 amino acids (36.61 kDa). Compare asparagine synthase (glutamine-hydrolysing). aspartate carbamoyltransferase see aspartate transcarbamylase. aspartate kinase EC 2.7.2.4; other name: aspartokinase; an

enzyme that catalyses the formation of 4-phospho-L-aspartate from ATP and L-aspartate with release of ADP. The reaction is the first step in the biosynthesis of lysine, methionine, and threonine in plants and bacteria. In Escherichia coli, the pathway for the synthesis of each amino acid is independently controlled by regulation of isoenzymes specific for each pathway. Example from yeast: database code AK_YEAST, 527 amino acids (58.04 kDa). See homoserine dehydrogenase for another example. aspartate-semialdehyde dehydrogenase EC 1.2.1.11; systematic name: L-aspartate-4-semialdehyde:NADP+ oxidoreductase (phosphorylating); other name: ASA dehydrogenase; an enzyme that, although reversible, normally catalyses the formation of L-aspartate-4-semialdehyde, orthophosphate, and NADP+ from L-4-aspartylphosphate and NADPH. Its product is a component of a pathway involved in the biosynthesis of lysine and methionine, and can be converted either into dihydropicolinate (a precursor of lysine) or into homoserine (a precursor of methionine). Example from Escherichia coli: DHAS_ECOLI, 367 amino acids (39.97 kDa). aspartate transaminase abbr. (in clinical biochemistry): AST; BC 2.6.1.1; systematic name: L-aspartate:2-oxoglutarate aminotransferase; other names: transaminase A; glutamicoxaloacetic transaminase; glutamic-aspartic transaminase. An enzyme that catalyses a reaction between L-aspartate and 2oxoglutarate to form oxaloacetate and L-glutamate. It is a pyridoxal-phosphate enzyme, very widely distributed, performing a pivotal role in amino-acid metabolism. In mammals this includes the transfer of amino groups to aspartate, which then transfers them into the urea cycle through argininosuccinate synthase. Very high plasma concentrations of AST (more than 100 times normal) are found in cases of severe tissue damage including acute hepatitis, crush injuries, and tissue hypoxemia. In jaundice and myocardial infarction the levels reach 10 to 20 times normal; in myocardial infarction AST starts to rise about 12 h after the infarct, reaching a peak at 24 to 36 h, then declining over 2 to 3 days. The normal level in human plasma is in the range 10-50 IU L -I (method-dependent; assumed presence of vitamin B6 in the assay). Examples: (I) mitochondrial enzyme, homodimer: database code (precursor) AATM_HUMAN, 430 amino acids (47.42 kDa); (2) cytoplasmic isoform, homodimer: database code AATC_ HUMAN, 412 amino acids (46.08 kDa). aspartate transcarbamylase abbr.: ATCase; EC 2.1.3.2; recommended name: aspartate carbamoyltransferase; other names: carbamylaspartotranskinase. An enzyme that catalyses a reaction between carbamoyl phosphate and L-aspartate to form Ncarbamoyl-L-aspartate with release of orthophosphate. In many eukaryotes it is an activity of the CAD protein. In Escherichia coli, operon pyr BI codes for catalytic and regulatory chains; database code ECOPYRBI, catalytic chain 311 amino acids (34.37 kDa). There are six motifs and the 3-D structure of the enzyme in several states is known, e.g. database code NRL_IATlA. The protein has a very high a-helical content. Carbamoyl aspartate is an important component of the pathway for de novo synthesis of pyrimidines. aspartic denoting a residue of aspartic acid, whether or not the p-carboxyl group is protonated. aspartic acid trivial name for a-aminosuccinic acid; 2aminobutanedioic acid, HOOC-CHz-CH(NHz)-COOH; a chiral a-amino acid. L-Aspartic acid (symbol: D or Asp), (S)-

53

aspartic amide 2-aminobutanedioic acid, is a coded amino acid found in peptide linkage in proteins; codon: GAC or GAU. In mammals it is a nonessential dietary amino acid and is glucogenic. Residues of o-aspartic acid (symbol: o-Asp or oAsp), (R)-2aminobutanedioic acid, are found in the cell-wall material of bacteria of various species, and one residue per molecule may occur in the antibiotic bacitracin A as an alternative to one of o-asparagine. It is also formed by racemization of L-aspartic acid residues in long-lived proteins such as crystallins, dentine, and myelin.

HO~

NH 2 0

H"X -Jl

n ""-/

'OH

o

L-aspartic acid

aspartic amide 1 aspartic I-amide; an alternative name for isoasparagine. 2 aspartic 4-amide; an alternative name for asparagine. aspartic andopeptidase or (formerly) acid proteinase or aspartyl protease or carboxyl protease any enzyme of the subsubclass EC 3.4.23, comprising endopeptidases having a pH optimum below 5 by virtue of an aspartic residue being involved in the catalytic process. The group includes cathepsin D, chymosin, the pepsins, and renin. asparto the alkylamino group, HOOC-CH 2CH(COOH)-NH-, derived from aspartic acid. aspartoacylase see aminoacylase. aspartokinase see aspartate kinase; see also aspartokinasel homoserine dehydrogenase. • spartokinase/homoserine dehydrogenase a multifunction enzyme, characterized in Escherichia coli, that catalyses two steps in the pathway from aspartate to diaminopimelate and lysine, to methionine, and to threonine and isoleucine. It is allosterically regulated by threonine. Example from E. coli: database code AKIH_ECOLI, 820 amino acids (89.02 kDa); homotetramer; the first 149 amino acids form the aspartokinase domain, while the last 350 residues form the homoserine dehydrogenase domain. aspartoyl the diacyl group, -CO-CH 2-CH(NH 2)-CO-, derived from aspartic acid. a-aspartyl aspart-I-yl; the a-monoacyl group, HOOC-CH r CH(NH 2)-CO-, derived from aspartic acid. J3-aspartyl or (formerly) isoaspartyl aspart-4-yl; the p-monoacyl group, HOOC-CH(NH 2)-CH 2-CO-, derived from aspartic acid. J3-aspartyl-N-acetylglucosaminidase EC 3.2.2.1 I; systematic name: I-p-aspartyl-N-acetyl-o-glucosaminylamine L-asparaginohydrolase. An enzyme that catalyses the hydrolysis of I -p-aspartyl-N-acetyl-o-glucosaminylamine to N-acetyl-o-glucosamine and L-asparagine. Example from Flavobacterium meningosepticum: database code A42259, 339 amino acids (37.16 kDa). See also aspartylglucosaminuria. aspartylglucosaminuria a metabolic disorder with autosomal recessive inheritance; it results in progressive mental retardation due to lysosomal accumulation of aspartylgl ucosamine (2-acetamido-l-p-L-aspartamido-I,2-dideoxyp-o-glucose), which is excreted in abnormally high amounts in the urine. This compound is commonly found in several glycoproteins in normal individuals. The first sign of the condition is usually a delay in speech development (1-4 years). The enzymic effect is a deficiency of lysosomal aspartylglucosaminidase (N4-(p-N-acetylglucosaminyl)-L-asparaginase, EC 3.5.1.26). aspartylglucosylamine deaspartylase see N'-(J3-N-acetylglucosaminyl}-t-asparaginase. J3-aspartyl phosphate or 4-phospho-L-aspartate or aspartyl-J3-

association constant phosphate an intermediate in the biosynthesis of lysine, threonine, and methionine in bacteria and plants. It is formed by aspartate kinase. It is converted to p-aspartyl semi-aldehyde, which is converted by the action of homoserine dehydrogenase to homoserine, a precursor of threonine or methionine. Alternatively addition of pyruvate to p-aspartyl phosphate leads to formation of dihydropicolinate, a precursor of lysine. A p-aspartyl phosphate residue is formed by phosphorylation of an aspartyl residue of Na+,K+-ATPase during the transport process. aspartyl protease an older name for aspartic proteinase. J3-aspartyl semi-aldehyde OHC-CH r CH(NH 2)-COOH; see J3-aspartyl phosphate. aspartyl shift or a -7 J3-aspartyl shift an intramolecular rearrangement reaction involving aspartic-acid residues that can occur during chemical synthesis or degradation of peptides. The p-carboxyl group of an aspartic residue displaces the acarboxyl of the same residue from its amide ( = peptide) linkage to the amino group of the adjacent amino-acid residue, thus forming an acid-sensitive p-amide (= isopeptide) linkage. Conditions must favour ionization of the p-carboxyl group. The reaction may be used to advantage in the partial hydrolysis of polypeptides and proteins by very dilute acid, but may occur to disadvantage during base-catalysed hydrolytic removal of protecting groups in the course of peptide synthesis. Aspergillus a genus of filamentous fungi containing species of industrial and genetic importance. A. niger and A. oryzae are used in the production of citric acid, industrial enzymes, and fermented foods. The sexual species A. nidulans has been an important research tool in both biochemical and mitochondrial genetics. A. flavus is a source of aflatoxins. asperlicin a naturally occurring antagonist of the peptide cholecystokinin, produced by various strains of Aspergillus alliaceus . aspirin or acetylsalicylic acid 2-(acetyloxy)benzoic acid; an irreversible inhibitor of prostaglandin-endoperoxide synthase, through covalent acetylation of the a-amino group on the terminal serine active site. It is used as a drug for its antithrombotic activity and nonsteroidal anti-inflammatory and associated actions (antipyrexia, analgesia). See also salicylic acid. Asp(NH 2 ) (formerly) symbol for L-asparagine. Asp-NH2 symbol for L-isoasparagine, an a-amino acid. Asp(OMe) symbol for p-methyl aspartate; 04-methyl hydrogen aspartate. Asp-OMe symbol for a-methyl aspartate; Ol-methyl hydrogen aspartate. assay n. 1 the determination of the activity, potency, strength, etc. of a substance, either on an absolute basis or in comparison with that of a standard preparation. 2 the determination of the relative amount(s) of one or more components of a mixture, or of the degree of purity of a substance. 3 to carry out such a determination. See also bioassay, immunoassay, microbiological assay, radioassay. assimilation the absorption of simple foodstuffs (or of the products of their digestion) and their use in the biosynthesis of complex constituents of the organism; sometimes restricted to photosynthesis. -assimilatory adj. assimilatory nitrate reduction see nitrate reduction. assimilatory regulatory protein a abbr.: ARPa; obsolete name for ferredoxin-thioredoxin reductase, obtained from chloroplasts. assimilatory regulatory protein b abbr.: ARP b ; obsolete name for thioredoxin, obtained from chloroplasts. association a reversible union between two chemical entities, whether alike or different, to form a more complex substance. Compare dissociation (def. I). association constant symbol: K ass or K a ; the equilibrium constant for the reversible formation of a complex chemical compound from two or more simpler entities; the reciprocal of the dissociation constant, K diss ' Sometimes an apparent association

assortment constant, K' ass, constrained with respect to stated values of certain variables (e.g. pH), is determined (see equilibrium constant). For an association of the type: A + B AB the (concentration) association constant is given by; Kass = [AB]/([A) x [B]) = l/Kdiss See also affinity constant, off-rate, on-rate, stability constant. assortment or reassortment during meiosis, the distribution to opposing cell poles of the two members of each pair of chromosomes at anaphase I and of the two members of each pair of chromatids at anaphase II. AST (in clinical biochemistry) abbr. for aspartate transaminase. astacin EC 3.4.24.21; other name: Astacus proteinase; crayfish small-molecule proteinase; an enzyme that catalyses the hydrolysis of peptide bonds in substrates containing five or more amino acids, preferentially with Ala in the PI' and Pro in the P2' positions (see peptidase P-sites). Zinc is a cofactor. Example, including 3-D structure, from the European fresh water crayfish: database code NRL_IAST, 200 amino acids (22.58 kDa). astatin any of a subfamily of zinc metalloendopeptidases of unallocated number within sub-subclass EC 3.4.24, i'lcluding tolloid (Drosophila) and bone morphogenetic protein 1 (human), involved in differentiation. astatine symbol: At; a halogen element of group 17 of the IUPAC periodic table; atomic number 85. It occurs as shortlived isotopes of mass numbers 215, 216, and 218 resulting from ~-decay of other radioactive elements. Astatine-211, an a-emitter of half-life 7.5 h, results from a-bombardment of bismuth; it has potential in radiotherapy. astaxanthin 3,3'-dihydroxy-p,p-carotene-4,4'-dione; a carotenoid pigment found mainly in animals (e.g. crustaceans, echinoderms) but also occurring in plants. It can occur free (as a red pigment), as an ester (e.g. the dipalmitate), or as a blue, brown, or green chromoprotein. Aston, Francis William (1877-1945), British experimental physicist; Nobel Laureate in Chemistry (1922) 'for his discovery, by means of his mass spectrograph, of isotopes in a large number of non-radioactive elements, and for his enunciation of the whole-number rule'. astral microtubule see prometaphase. Astrup technique a micro technique for the rapid determination of the acid-base status of a sample of blood. The pH of the blood as taken is measured and the remainder of the sample split into two and each part equilibrated with a different COz/0 2 mixture of known p(C0 2) and their pH values measured. These last two pH values and the corresponding p(C0 2 ) values are plotted on a Siggaard-Andersen nomogram and the points joined by a straight line. The p(C0 2) of the original sample may be obtained from the point on this line corresponding to the pH of the blood as taken. Furthermore, the standard bicarbonate value of the blood may be obtained from the point where the straight line intersects with a scale on the p(C0 2 ) axis at 5.33 kPa (40 mmHg). ASV abbr. for anodic stripping voltammetry. Asx symbol for a residue of either of the a-amino acids L-aspartic acid or L-asparagine when the state of amidation is uncertain (alternative to B). asymmetric synthesis any synthesis of a compound that produces only one of two possible enantiomers of the product. This is usually the case for enzymic but not for nonenzymic reactions. asymmetry absence of symmetry. A particular example of its meaning in biochemistry relates to the different phospholipid composition of the inner and outer leaflets of a lipid bilayer, said to confer asymmetry of composition. -asymmetric ad). asymmetry potential the usually small potential across a membrane electrode, such as a glass electrode, when both sides are immersed in identical solutions. It is probably due to slight imperfections in the membrane.

54

atomic orbital asy",apsis absence of synapsis (def. I); i.e. the failure of homologous chromosomes to pair during meiosis. At symbol for astatine. atactic characterized by or showing irregularity in the spatial arrangement of the parts of a molecule. atactic polymer any regular polymer in which the molecules display essential randomness with regard to the configurations at all main-chain sites of steric isomerism. +ate suffix 1 designating any anion (including mixtures of anion and free acid), salt, or ester of any oxoacid (def. I) other than an +ous acid. 2 denoting the product of a process, e.g. distillate, hydrolysate. ATF abbr. for activating (or activator) transcription factor; any of various transcription factors for eukaryotic RNA polymerase II promoters that bind to CRE. Example, ATF-A and ATF-A-8 (human); these form a dimer; they have different sequences (amino acids 114-134 missing in 8), and possess a leucine zipper; database code ATFA_HUMAN, 483 amino acids (54.70 kDa). (A + T}/(G + C) ratio the ratio of the sum of the adenine plus thymine bases to the sum of the guanine plus cytosine bases in a DNA molecule or preparation. The ratio is to some extent a characteristic of an individual type of DNA molecule. Compare Chargaff's rules. athero-ELAMs endothelial leukocyte-adhesion molecules, i.e. selectins, expressed in atherosclerotic plaques. atheroma a condition or process affecting blood vessels in which plaques form beneath the intima (i.e. inner lining). These start as infiltration by lipid-containing cells but later become invaded by fibrous tissue or become calcified. It is associated with hypercholesterolemia and defects in the apolipoprotein B receptor -atheromatous ad). atherosclerosis a degenerative condition affecting arteries in which there is hyperplasia of the outer coat and fatty degeneration of the middle coat of the arteries due to atheroma. aThr symbol for a residue of the a-amino acid L-allothreonine, (2S,3S)-2-amino-3-hydroxybutanoic acid. atmosphere 1 the envelope of gas surrounding the Earth. 2 any local gaseous environment. 3 symbol: atm; a non-SI unit of pressure equal to 101.325 kPa; the pressure that will support a column of mercury 760 mm high at 273.15 K, sea-level, and latitude 45°. atom a unit of matter consisting of a single nucleus surrounded by one or more orbital electrons. The number of electrons is normally sufficient to make the atom electrically neutral; adding or removing electrons converts the atom into a negative or positive ion, but this is regarded as a state of the same atom since the atom is characterized by its nucleus. atomic absorption spectrophotometry a quantitative version of atomic absorption spectroscopy in which the absorption of electromagnetic radiation by the ground-state atoms in the flame is measured photoelectrically and the concentration of the element in question calculated by reference to the absorption observed with solutions of the elements of known concentration. atomic absorption spectroscopy an analytical technique, based on the observation of the absorption of light energy by atoms, in which an atomic vapour of an element is formed by aspiration of a solution of the element into a flame, or otherwise, so that the large majority of the element's atoms remain in the non-emitting ground state. These ground-state atoms absorb electromagnetic radiation of their own specific resonance frequency, to an extent that is proportional to the density of the elemental atoms in the flame. atomic mass constant symbol: m u ; a fundamental constant equal to the mass of a carbon-12 atom divided by 12; it is equal to the unified atomic mass unit. atomic mass unit abbr. (formerly); amu; see unified atomic mass unit. atomic number an older alternative name for proton number. atomic orbital the volume containing all the points within a

55

atropine

atomic radius free atom at which the Schrodinger wave-function of an electron is of appreciable magnitude. atomic radius the distance between the centre of the nucleus and the outermost electron shell of an atom. Compare van der Waals radius. atomic weight abbr.: at. wt.; former name for relative atomic mass. atomic weight unit abbr.: awu; one-twelfth of the mean mass of the neutral atoms of naturally occurring carbon. atomizer or atomiser an instrument for breaking up a solution into a spray of fine droplets. atom percent the proportion of any nuclide in a mixture expressed as a numerical percentage of all the atoms of that element present irrespective of their nuclidic masses. atom percent excess a measure of the abundance of a stable nuclide in a sample expressed in terms of the excess, in atom percent, over that naturally present. It is used to express the extent of enrichment or dilution of substances labelled with stable isotopes. atopy or atopic allergy the tendency of some individuals to develop immediate hypersensitivity reactions to allergens. It is probably hereditary. ATP abbr. for adenosine 5'-triphosphate. ATPase abbr. for adenosine triphosphatase. ATP-diphosphatase see apyrase. ATPla,JJ-CH2 l abbr. for a,p-methyleneadenosine 5'-triphosphate; i.e. adenosine 5'-[a,p-methylene]triphosphate. ATPr.e,y-CH 2 l abbr. for p,y-methyleneadenosine 5'-triphosphate; i.e. adenosine 5'-[p,y-methylene]triphosphate. ATP[tJ,y-NHl abbr. for p,y-imidoadenosine 5'-triphosphate; i.e. adenosine 5'-[p,y-imido]triphosphate. ATP(S) abbr. for adenosine 5'-y-thiotriphosphate. ATP synthetase see H+-transporting AlP synthase.

Hoot

H

atractyloside

atractyloside an extremely toxic glycoside, obtained from the rhizomes of the Mediterranean thistle Atractylis gummifera,

that produces hypoglycemia and convulsions in animals. It inhibits oxidative phosphorylation, in particular the translocation of mitochondrial adenine nucleotides. Carrier-bound adenine nucleotides are apparently replaced by atractyloside owing to the latter's higher affinity for a common translocation site. Compare bongkrekic acid. A-transferase EC 2.4.1.40; recommended name: fucosylgalactose a-N-acetylgalactosaminyltransferase; other names: fucosylglycoprotein a-N-acetylgalactosaminyitransferase, [histoblood group] A-transferase; an enzyme that can catalyse a reaction between UDP-N-acetyl-o-galactosamine and glycoprotein a-L-fucosyl-(1,2)-o-galactose to form UDP and glycoprotein N -acetyl-a-o-galactosaminyl-( 1,3)-[L-fucosyl(1,2)]-D-galactose. It thus catalyses the addition of N-acetylgalactosamine to the H antigen of the ABH antigen system, forming the A antigen. This and the B-transferase protein are products of alleles of the ABO gene, differing in only four residues. atrial of or pertaining to an atrium.

atrial natriuretic peptide see natriuretic peptide. atrial natriuretic peptide receptor see natriuretic peptide receptor. atrioaetivase a specific serine protease, present in bovine cardiac atria, that catalyses processing of the precursor of natriuretic peptide by selective cleavage at Arg 89 . atriopeptins biologically active peptides isolated from mam-

malian cardiac atria. Atriopeptin I (I) has 21 amino acids, with the structure SSCFGGRIDRIGAQSGLGCNS (3-19 disulfide link); atriopeptin II (II) is the same with additional Phe-Arg residues at the C terminus; atriopeptin III is the same as II but with an additional Tyr residue at the C terminus. I relaxes intestinal smooth muscle but not vascular smooth muscle, while II relaxes both. Compare natriuretic peptide. atrium (pl. atria) or (formerly) auricle 1 either of the two chambers of the heart that lie above the ventricles. They receive blood from the afferent veins and pump it into the ventricles. 2 any of various anatomical chambers that receive the openings of other cavities. atrolysin B EC 3.4.24.41; other names: Crotalus atrox metalloendopeptidase B; hemorrhagic toxin B (abbr.: HT-B); a snake-venom enzyme that catalyses the cleavage of His 5-!Leu 6, His LO -I-Leu 11 , Ala 14 _I_Leu I5 , Tyr I6 _I_Leu I7 , and Gly23-!Phe z4 of the insulin B-chain. The reaction is identical to the cleavage of insulin B-chain by atrolysin C. The enzyme also cleaves Ser-I-Xaa bonds in glucagon. It is a zinc-requiring enzyme. atrolysin C EC 3.4.24.42; other names: Crotalus atrox metalloendopeptidase C; hemorrhagic toxin C and D; a snakevenom enzyme that catalyses the cleavage of His 5-I-Leu6, HisIO-I-Leu I1 , Ala I4 -I-Leu I5 , Tyr 16 _I_Leu 17 , and GlyZ3_I_Phe z4 of the insulin B-chain. With small-molecule substrates it prefers hydrophobic residues at the P2' position and small residues such as Ala or Gly at the PI position (see peptidase P-sites). It is a zinc-requiring enzyme. Example from C. atrox (the Western diamondback rattlesnake): database code HRTD_ CROAT, 203 amino acids (23.22 kDa). atrolysin E EC 3.4.24.44; other names: Crotalus atrox metalloendopeptidase E; hemorrhagic toxin E; a snake-venom enzyme that catalyses the cleavage of Asn 3 -I-Gln4, Ser9-I-His 10 , and Ala I4-I-Leu I5 bonds in the insulin B-chain and Tyr4-I-Gln 5 and Ala 8-I-Ser 9 in the A chain. It cleaves type IV collagen at Alaz58_I_Glnz59 in aI-collagen and at Gl y I91_I_Leu l92 in az-collagen. It is a zinc-requiring enzyme. Example from C. atrox (the Western diamondback rattlesnake): database code HRTE_CROAT, 478 amino acids (53.58 kDa). atrolysin F EC 3.4.24.45; other names: Crotalus atrox metalloendopeptidase F; hemorrhagic toxin F; a snake-venom enzyme that catalyses the cleavage of VaJ2-I-Asn3, Gln 4-!His 5, Leu 6-I-Cys7, HislO-I-Leu ll , Ala I4 _I_Leu I5 , and Tyr l6 Leu 17 bonds in the insulin B-chain. It is a zinc-requiring enzyme. atrophy diminution in the size of a tissue or organ after full normal development has been attained. It is often a result of nutritional deficiency andlor decreased functional activity. atropine (±)-hyoscyamine; tropyl DL-tropate; laH,5aHtropan-3-ol (±)-tropate a tropane alkaloid obtained from deadly nightshade, Atropa belladonna; and other Solanaceae. The racemic mixture is a tertiary ammonium compound that acts as a muscarinic receptor antagonist. It is used as an anticholinergic, mydriatic, etc. See also hyoscine.

+

56

attachment proteins

automutagen

atropine attachment proteins general term for proteins that are involved in binding other proteins to cell structures, e.g. vinculin, or a-actinin (see actinin), which bind actin to the plasma membrane. attachment site see active site (def. 2). A-T tailing homopolymer tailing of two types of duplex DNA molecule or fragment by the successive addition of adenine deoxynuc1eotide residues (A) to the 3' ends of molecules of one type and the complementary addition of thymine deoxynucleotide residues (T) to the 3' ends of molecules of the second type. attenuance symbol: D; the logarithm to the base 10 of the ratio of the radiant powers of the incident radiation, Po, and the transmitted radiation, P; thus: D = Ig(PoIP) = Igr- I , where T is the transmittance. Attenuance reduces to absorbance if the incident beam is only either transmitted or absorbed, but not reflected or scattered. attenuated virus a virus that has become less pathogenic following passage in culture outside its natural host, or by the use of physical or chemical means. attenuator a sequence in DNA that is located between the operator and the gene for the first protein in an operon. It can cause transcription termination. The operon for the synthesis of tryptophan in bacteria is an example of an operon that contains an attenuator. atto+ symbol: a; prefix used with SI units denoting IO~18 times. attractant or chemoattractant a substance that a motile cell or organism tends to move towards; i.e. one that elicits positive chemotaxis. For a responsive bacterium, attractants can be either nutritive or nonmetabolizable. An example is cytotaxin. Au symbol for gold. AUA 1 a codon in mRNA, excluding that of mammalian mitochondria, for L-isoleucine. 2 a codon in mammalian mitochondrial mRNA for L-methionine (and for N-formyl-L-methionine, chain initiation, in some species). AUC a codon in mRNA for L-isoleucine. AUG a codon in mammalian mitochondrial mRNA, and in nonmitochondrial mRNA the only codon for L-methionine and usually for N-formyl-L-methionine, chain initiation. Auger effect a process by which an orbital electron in an atom passes from an excited to a lower energy level. The X-ray so produced collides with, and ejects, another orbital electron, known as an Auger electron, with energy in the X-ray range. [After Pierre Victor Auger (1899-1993), French physicist.] auracyanin a small blue copper-containing bacterial outer membrane glycoprotein (one Cu2+ ion per protein) that donates electrons to cytochrome C554' Example from Chloroflexus aurantiacus: database code AUBI_CHLAU, 154 amino acids (15.53 kDa). aureomycin 7-chlortetracycline. See tetracycline. auriculin either of two fragments of atrial natriuretic peptide; auriculin A is the 4-27 and B the 4-28 fragment. Auriculin a proprietary name for atrial natriuretic peptide. aurosome an artificially induced organelle occurring in animal

cells cultured in the presence of gold. It is an electron-dense lysosomal body containing gold particles. Australia antigen an alternative name for hepatitis B antigen. See hepatitis. aut+ a variant form ofauto+. autacoid any druglike principle that is produced in or can be extracted from the organs of internal secretion. Autacoids include both excitatory substances (hormones) and inhibitory substances (chalones). auto+ or (before a vowel) aut+ comb. form 1 self; one's own. 2 occurring within oneself or itself. 3 acting by itself; automatic; spontaneous. autoagglutination the tendency of a suspension of bacteria or other cells to agglutinate spontaneously in a simple medium not containing an agglutinin or other similar reagent. autoallergyan alternative term for autoimmunity. autoanalyser or (esp. US) autoanalyzer any instrument for effecting analyses automatically. autoantibody an antibody produced in an animal that reacts with a constituent of the animal's own tissues, which thus acts as a 'self' antigen or autoantigen. autoantigen an antigen that is a normal constituent of an individual and has the capacity to produce an immune response in the same individual in certain circumstances. autocatalysis the catalysis of a chemical or biochemical reaction by one of the reaction products. -autocatalytic adj. autochthonous derived from that part of the body where found; native. Compare autologous. autoclave an instrument, used for sterilizing culture media, instruments, etc., that consists of an airtight chamber which can be filled with, or surrounded by, steam at high pressure. autocoupling hapten a reactive compound of low molecular mass that, when injected into an animal, reacts with tissue antigens to form hapten-antigen compounds. These then lead to the formation of antibodies to the hapten. autocrine describing an agent that acts on the cell in which it is produced. autofluorogram an alternative name for fluorogram (when produced by f1uorography (def. 2)). autofluorography an alternative term for fluorography (def. 2). autogenesis or autogeny an alternative term for abiogenesis. autogenetic ad). autogenous 1 self-produced. 2 originating within, especially within one's own body. autogenous regulation the mechanism by which a protein directly controls the expression of its own structural gene. autograft any graft or transplant of the subject's own tissue(s). autoimmunity or autoallergy a state of immunological reactivity against constituents of the subject's own tissues. autoimmunization or autoimmunisation the process of inducing autoimmunity. autologous derived from the same organism. Compare autochthonous. autolysate or (esp. US) autolyzate a product of autolysis, e.g. a suspension of broken cells. autolysin EC 3.5.1.28; other name: N-acetylmuramoyl-L-alanine amidase; an enzyme that catalyses the hydrolysis of the link between N-acetylmuramoyl residues and L-amino-acid residues in certain bacterial cell-wall glycopeptides. The enzyme is required for cell separation, cell-wall turnover, etc. Example from Staphylococcus aureus: database code ALYS_STAAU, 481 amino acids (53.76 kDa). See also lysostaphin. autolysis the process of self-digestion that occurs in plant and animal tissues after death of the organism or following separation of tissue from the rest of the organism. It is due to the action of the tissue's own enzymes. -autolytic ad). autolysosome an autophagic vacuole. automutagen any mutagen formed in an organism as a normal or abnormal metabolic product that is mutagenic in the same organism.

57

autonomic nervous system autonomic nervous system abbr.: ANS; those parts of the peripheral nervous system and central nervous system that govern homeostasis in vertebrates and are generally independent of voluntary control. autonomous existing or able to exist independently; used, e.g., of a tumour cell that is free of host control or of an episome or plasmid that replicates independently of the chromosome. autophagic vacuole an enlarged lysosome containing subcellular structures such as mitochondria; a secondary lysosome. autophagosome a phagosome containing endogenous cellular debris. Compare heterophagosome. autophagy a process, apparently ubiquitous among eukaryotes, by which cells digest parts of their own cytoplasm. Compare heterophagy. -autophagic ad). autophosphorylation the phosphorylation by a protein of one of its own residues. It is important in signal transduction by growth hormone receptors (see, e.g., epidermal growth factor receptor), but occurs in the case of other proteins, e.g. caldesmon. autoprothrombin I an alternative name for factor VII; see blood coagulation. autoprothrombin II an alternative name for factor IX; see blood coagulation. autoprothrombin IIA an alternative name for protein C. autopsy or necropsy the examination of a dead body, commonly to determine the cause of death or the presence of disease processes; a post-mortem (examination). Compare biopsy. autoradiogram an autoradiograph, especially of a chromatogram or electrophoretogram. autoradiograph or autoradiogram the image produced by autoradiography. autoradiography a method by which radioactive material can be localized in, e.g., a tissue, cell, a cell part, or molecule, or in a chromatogram or electrophoretogram. The sample containing a radioactive substance is put in direct contact with a thick layer of specially prepared photographic emulsion. The radiation emitted in the decay of the radionuclide(s) activates individual silver halide grains in the emulsion rendering them susceptible to conversion to metallic silver grains by a photographic developer. After fixation the silver grains may be located either visually or by microscopy. autosomal of, relating to, or being an autosome. autosomal disease disease that results from an abnormality affecting the autosomes. autosome any chromosome except the sex chromosomes. Hence the genes carried by the autosomes show autosomal linkage (or autosomal inheritance) according to the assortment of their respective autosomes to gamete cells during meiosis. Humans have 22 pairs of autosomes in addition to a pair of sex chromosomes. autosteric eHector any effector that binds to, and exerts its effect at, part of or immediately adjacent to the active site of an allosteric protein. It is distinguished from an allosteric effector operating at a distant site. autotroph or Iithotroph any organism that requires only simple inorganic substances to fulfil its nutritional requirements and for which gaseous or dissolved carbon dioxide is the sole source of carbon for the synthesis of cellular constituents. The term often includes any microorganism for which trace amounts of certain substances, e.g. vitamins, must also be supplied. Autotrophs may be subdivided into chemoautotrophs (or chemolithotrophs) and photoautotrophs (or photolithotrophs) according, respectively, to whether they are chemotrophs or phototrophs. Compare heterotroph. -autotrophic adj.; autotrophy n. AUU a codon in mRNA for L-isoleucine. auxiliary amino acid any amino-acid residue in the active site

Avogadro constant (def. I) of an enzyme that is more than one bond distance removed from the substrate molecule in the enzyme-substrate complex. Compare contact amino acid. auxin any of a group of plant hormones, produced by regions of actively dividing and enlarging cells, that regulate aspects of plant growth. They include indole-3-acetic acid and indole3-acetonitrile. auxochrome any saturated atomic grouping (e.g. -OH, -CH 3 , -NH 2 , -CI, -SH) that, when attached directly to a chromophore, shifts the selective absorption of light in the direction of longer wavelengths and enhances the intensity of absorption. auxostat in industrial fermentation, a chemostat in which the dilution rate can be varied, normally in response to some parameter such as growth rate or pH, so that growth rate is more readily maximized. auxotroph any strain of microorganism (alga, bacterium, or fungus) that differs from the wild-type by requiring a supply of one or more growth factors. Compare prototroph. -auxotrophic ad). auxotrophy the condition of being an auxotroph. average an alternative term for (arithmetic) mean. average life see mean life. average molar mass or (formerly) average molecular weight any of a series of numeric characteristics of a macromolecular system that are useful for assessing the extent of its polydispersity. The three most important are the number-average molar mass, M n , the mass-average molar mass, M m , and the Zaverage molar mass, Mo. These three characteristics are given by the expressions: M n = "injM/'i..n; (kg mol-I) M m = "in;M/I"in;M; (kg mol-I)

=

M z "in;M/I"in;M/ (kg mol-I) where n; is the amount of substance of species i and M; is the molar mass of species i. Measurement of a colligative property, e.g. osmotic pressure, or end-group analysis, gives M n ; light scattering, dielectric dispersion, or fluorescence depolarization measurements give M m ; and data obtained by equilibrium ultracentrifugation will yield either M m or M z depending on how they are treated. For polydisperse or heterogeneous systems, M z > M m > M n , whereas for monodisperse systems these three characteristics are equal (i.e. equal to the relative molecular mass, M ro of the single species). average molecular weight former name for average molar mass. average radius of gyration an alternative term for mean radius of gyration. average relative molecular mass former name for average molar mass. avermeetin B, an alternative name for abamectin. avidin a 66 kDa glycoprotein comprising four essentially identical subunits, each of which consists of a single polypeptide chain of 128 amino-acid residues. Isolated from the white of the eggs of birds and amphibia, it binds extremely strongly to biotin and produces biotin deficiency when fed to experimental animals. Example from Gallus gallus (precursor): database code AVID_CHICK, 152 amino acids (16.77 kDa); residues 1-24 form the signal. avidity 1 the tendency of an antibody to form more-or-Iess stable complexes with a (macromolecular) antigen; a measure of this tendency. 2 an alternative term for affinity. avirulent lacking virulence. avitaminosis a condition resulting from deficiency of one or more vitamins. The deficient vitamin may be specified, as in avitaminosis A, B, etc. Avogadro constant or (formerly) Avogadro's number symbol:

avogram L or N A ; the number of molecular entities in one mole of any chemical species. It is a fundamental physical constant, of value 6.0221367(36) x IO z3 mol-I. Compare Loschmidtconstant. Avogadro number or Avogadro's number the numerical value of the Avogadro constant. Avogadro's hypothesis or Avogadro's law the principle that equal volumes of all ideal gases, at the same temperature and pressure, contain equal numbers of molecules. [After Lorenzo Romano Amadeo Carlo Avogadro, Count of Quaregna and Cerreto (1776-1836), Italian physicist and chemist who formulated it in 1811.) avogram see dalton. AVP abbr. for arginine vasopressin. axenic pertaining to the growth of organisms of a single species in the absence of living organisms or living cells of any other species (also, strictly, in the absence of living cells of the organism itself except those in the intact living organism and its gametes). -axenity n.; axenically adj. axenize or axenise to render axenic. axenite an organism grown axenically. axial 1 of, relating to, or being an axis (def. I or 2); located on or close to such an axis. 2 (in stereochemistry) Symbol: a. See conformation. axial ratio the ratio of the length of the major axis to that of the minor axis of a prolate ellipsoid of rotation, a model often used for a protein or other macromolecule in solution. axis 1 a straight line about which a body or three-dimensional figure, e.g. a crystal, is considered to rotate. 2 one of the reference lines of a co-ordinate system. 3 the second vertebra of the neck in higher vertebrates. axis of rotation see rotation axis. axis of symmetry see symmetry, axis of. axokinin a heat-stable phosphoprotein, M r 56 000, present in flagella and cilia of vertebrate and invertebrate species. Its cyclic AMP-dependent phosphorylation is required for initiation and maintenance of flagellar motility. axon the long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals which are the site of storage and release of neurotransmitter. Compare dendrite. axonal transport the directed transport of organelles and molecules along the axon of a neuron. It can be anterograde (i.e. outwards from the cell body) or retrograde (i.e. towards the cell body). axoneme the bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements. axoplasm the cytoplasm of the axon of a neuron, especially after it has been extruded from the axon. aza+ prefix 1 (in systematic chemical nomenclature) denoting the replacement of a designated carbon atom (together with one associated hydrogen atom) by a nitrogen atom. 2 (in trivial chemical names) denoting presence of one or more nitrogen atoms. azaserine trivial name for serine diazoacetate; O-diazoacetyl-Lserine, Nz=CH-CO-O-CHz-CH(NHz)-COOH; an antibiotic substance produced by Streptomyces spp. It is an inhibitor of amidotransferase enzymes and interferes with purine synthesis; it also retards the growth of transplantable animal neoplasms and is a specific inhibitor of L-glutamate ferredoxin oxidoreductase (transaminating), EC 1.4.7.1, in ammonium assimilation in plants. azathioprine 6(1-methyl-4-nitro-5-imidazolyl) mercaptopurine: 6-[(1-methyl-4-nitroimidazol-5-yl)thio)purine; a derivative of mercaptopurine, into which it is converted in vivo. It is useful as an immunosuppressive and antimitotic agent. One proprietary name: Imuran. azelaic acid 1,7-heptanedicarboxylic acid, nonanedioic acid; a substance that acts as a substitute for biotin in the growth of a number of microorganisms and is proposed as an intermediate in biotin biosynthesis from oleic acid.

58

azurophil(e) granule azeotrope a mixture of two or more liquids that distils without change in composition and has a constant boiling temperature. azide 1 any organic compound containing the monovalent azido group, -N=N+=N-. 2 the ion N 3-, derived from hydrazoic acid, HN 3 . This ion blocks the electron transport chain by reacting with the ferric form of cytochrome aa3 and thus acts as an inhibitor of respiration. 3 any salt or ester of hydrazoic acid. azidothymidine see AZT. azo the bivalent group -N=N-. It participates in noncyclic covalent linkage in organic molecules forming azo compounds or diazo compounds. azocoll an insoluble bright-red collagen-rich proteinaceous material prepared by dyeing powdered cowhide or kangarootail tendon with a dye prepared from tetrazolized benzidine, disodium 2-naphthol-3,6-disulfonate and sodium acetate. It is digested by most types of proteinase, the consequent solubilization of dye forming the basis of a simple nonspecific technique for the assay of proteolytic activity. azo compound any organic compound with the general formula R-N=N-R'. Such compounds thus contain the bivalent azo group in covalent linkage, each nitrogen atom being linked to a carbon atom and replacing one hydrogen atom of each of the parent molecules RH and R'H. The latter may be the same or different, aliphatic or aromatic; e.g. azomethane, CH 3-N=N-CH 3 ; naphthalene-2-azobenzene, C IO H 7-N=NC 6 H s. Compare diazo compound. azoferredoxin or protein II a very oxygen-sensitive iron-sulfur protein that is a component of the nitrogenase enzyme system. It is a dimer of identical ~30 kDa peptide chains. Each dimer contains two iron atoms, four S2- groups, and 12 titratable thiol groups. In nitrogenase it is believed to be the electron carrier responsible for the reduction of molybdenum in molybdoferredoxin. azomethine strictly, any imine having the more limited general structure RR'C=NR where Rand R' are any organyl groups, but often extended to include any compound where R' is H, the term then being considered to be synonymous with Schiff base. azoprotein any of the modified proteins formed by coupling an aromatic diazo compound to one or more of the tyrosine residues of a protein, e.g. azoalbumin, azocasein. azotemia former term for the accumulation of abnormally large concentrations of nitrogenous compounds, especially urea, in the blood. Azotobacter a genus of Gram-negative strictly aerobic soil bacteria, all members of which can effect nitrogen fixation. azotoflavin a somewhat larger than normal flavodoxin that is believed to act as a one-electron carrier between ferredoxin and azoferredoxin during nitrogen fixation in some bacteria, e.g. Azotobacter. AZT abbr. for azidothymidine; 3'-azido-3'-deoxythymidine; other names: zidovudine; Retrovir; an analogue of thymidine, the phosphorylated form of which is an inhibitor of reverse transcriptase in retroviruses; it also terminates DNA synthesis. AZT undergoes phosphorylation in human T-cells to a nucleoside 5'-triphosphate, which competes with thymidine triphosphate and serves as a chain terminating inhibitor of HIV reverse transcriptase. It is used clinically to treat patients with HIV infection and AIDS. azurin any member of a group of brilliant blue copper-containing proteins of low M, found in some bacteria and thought to transfer electrons to cytochrome oxidase. Example from Pseudomonas j7.uorescens biotype B: database code AZUR_ PSEFB, 128 amino acids (13.78 kDa). azurophil\e) or azurophilic staining readily with blue aniline dyes. azurophil(e) granule or primary granule a blue-staining lysosome of neutrophil leukocytes.

Bb b symbolfor 1 molality. 2 one of two van der Waals coefficients. 3 breadth. B symbol for 1 boron. 2 a residue of either of the a-amino acids L-aspartic acid or L-asparagine when the state of amidation is uncertain (alternative to Asx). 3 a residue of an incompletely specified base in a nucleic acid sequence that may be cytosine or guanine or either thymine (in DNA) or uracil (in RNA). 4 the ribonucleoside (5-)bromouridine (alternative to BrUrd). 5 the B blood group. See ABO system. B symbol for 1 Napierian absorbance (see absorbance). 2 magnetic flux density (bold italic). -8 conformational descriptor designating the boat conformation of a six-membered ring form of a monosaccharide or monosaccharide derivative. Locants of ring atoms that lie on the side of the structure's reference plane from which the numbering appears clockwise are indicated by superscripts preceding the letter, and those that lie on the other side of the reference plane by subscripts following the letter; e.g. methyl 2,6-anhydro-a-D-altropyranoside- 2,5 B. See also conformation (under cyclic compounds). symbol for the amount of drug required to saturate a specific population of receptors in a membrane sample and hence an index of the density of receptor binding sites in the sample. It is usually derived from Scatchard analysis (see Scatchard plot) or from nonlinear regression analysis of data from a saturation binding assay, Ba symbol for barium. Baa helices abbr. for basic amphiphilic II helices; II helices that contain an array of basic amino-acid residues (His, Lys, or Arg) on one side and hydropathic residues on the other. They are found, e,g., in the calmodulin-binding regions of many proteins. Babes-Ernst body or Babes-Ernst granule a volutin granule seen in Corynebacterium diphtheriae, [After Victor Babes (18541926), Romanian bacteriologist, and Paul Ernst (1859-1937), German pathologist.] BAC abbr. for bacterial artificial chromosome, based on the F factor (F plasmid) of Escherichia coli, Compare VAC. Bacillaceae a family of eubacteria that includes the genera Bacillus and Clostridium. bacillary or bacillar 1 of, relating to, caused by, or containing bacilli. 2 an alternative term for bacilliform (def. I), bacilliform 1 rod-shaped. 2 resembling a bacillus. bacillus (pl. bacilli) any straight rod-shaped bacterial cell. Bacillus a genus of large rod-shaped Gram-positive eubacteria belonging to the family Bacillaceae, Its members are aerobic or facultatively anaerobic, spore-bearing organisms, B. subtilis has become widely established as a vehicle for genetic engineering and many cloning vectors are available, B. thuringiensis synthesizes a toxin that is active against insects; different strains of the bacterium produce different forms of the toxin specific for different insect species. bacitracin a cyclic antibiotic polypeptide complex produced by Bacillus subtilis and B, licheniformis. Commercial bacitracin is a mixture of at least nine bacitracins, mostly bacitracin A. Bacitracin A contains, in addition to several L amino acids, a number of D amino acids. Bacitracin inhibits bacterial cell wall synthesis by blocking the dephosphorylation of undecaprenyl diphosphate (undecaprenyl pyrophosphate) to the monophosphate form; it similarly inhibits the dephosphorylation of dolichyl diphosphate thereby blocking the formation of the core oligosaccharides of glycoproteins. backbone 1 (in biochemistry) the sequence of bonded atoms of a polymer to which the side groups and/or the side chains are attached. 2 (in zoology) the vertebral column or spine, backcross 1 any cross of a first-generation hybrid, F], with

s....x

one parent or an individual genetically identical to one of the two parents, 2 the offspring of such a mating. back-flush an alternative term for back-wash. background any intrusive sound or electronic signal registered by a detector but not coming from the source being measured, e.g. the radioactivity registered by a counter in the absence of a radioactive sample. back mutation an alternative term for reverse mutation. back scattering an alternative term for backward scattering. back titration an indirect titration procedure in which a measured excess of the reagent is added and the amount remaining after reaction with the analyte is titrated back to an end-point, the proportion consumed in the reaction being obtained by difference. backward scattering or back scattering any scattering of radiation in a direction towards the source of the incident radiation. back-wash or back-flush to pass a fluid through a chromatographic column in the direction opposite to that of the eluent flow. It is useful, e,g" to relieve bed-compression and to remove entrained gas. baclofen y-amino-p-(p-chlorophenyl)butyric acid; 3-(aminomethyl)-3-(4-chlorophenyl)propanoic acid; a 4-chlorophenyl derivative of y-aminobutyric acid (GABA) that acts as a selective agonist for the GABAs receptor and inhibits the release of other neurotransmitters in the central nervous system. It is used for its antispastic (muscle-relaxing) effects.

bactenecin any of several highly cationic polypeptides, originally isolated from bovine neutrophil granules but also found in sheep, that exert, in vitro, a potent antimicrobial activity, possibly due to inhibition of respiratory chain function. Example, bactenecin 5 (precursor) from Bos taurus: database code BCT5_BOVIN, 176 amino acids (20.03 kDa); residues 131-173 are bactenecin 5, bacteremia or (esp, Brit.) bacteraemia the presence of live bacteria in the blood. bacteria plural of bacterium. Bacteria one of three superkingdoms (domains) of cellular organisms, the others being Archaea and Eukarya. Bacteria are unicellular and anucleate Le. prokaryotes, They embrace a great diversity of forms, major divisions including the Cyanobacteria, Proteobacteria (which includes Gram-negative bacteria), and Gram-positive bacteria. bacterial conjugation the process whereby genetic material is transferred from one bacterial cell (the donor) to another (the recipient). Material is usually transferred via a tubelike pilus, which extends from the donor cell to the recipient cell. The terms 'donor' and 'recipient' are preferred to 'male' and 'female' since the latter refer only to the presence or absence of Fplasmid, bacterial histone see H-NS, bacterial photosynthetic reaction centre see photosynthetic reaction centre, bacterial porin see porin. bacterial recombinant see transconjugant. bacterial virus see bacteriophage. bactericide or bacteriocide any agent (biological, chemical, or

60 bacterioferritin

bactericidin physical) that destroys bacteria. -bactericidal or bacteriocidal adj. bactericidin or bacteriocidin or bacteriolysin any antibody that, with complement, kills bacteria against which it is active. bacteriochlorophyll any of the chlorophylls of photosynthetic bacteria. They differ structurally from the chlorophylls of higher plants. Bacteriochlorophylls a to g are known. Bacteriochlorophylls a and b are the best known, being the photosynthetic pigments of purple bacteria. Their purple colour results from the fact that they are reduced in both rings Band D, and thus may be regarded as tetrahydropyrroles. Tetrapyrrole carbon atoms and carbon rings are numbered according to the Fischer and IUPAC systems as indicated below. The structure of bacteriochlorophyll a is shown. Bacteriochlorophyll b has =CH-CH 3 in place of the ethyl group on ring B of bacteriochlorophyll a. In some bacteriochlorophylls a the phytyl group may be replaced by a geranylgeranyl group. Bacteriochlorophylls c, d, and e are antenna pigments of Chlorobiaceae, located in chlorobium vesicles (a core structure is shown). These are dihydropyrrole structures, being reduced in ring D only. The esterifying alcohol is farnesol. In these bacteriochlorophylls, the side chain R[ (see core structure) on ring B varies, being ethyl, n-propyl, or isobutyl (in bacteriochlorophyll d neopentyl is also possible). On ring C the side chain R 2 is ethyl (in bacteriochlorophyll d methyl is also possible). R 3 is methyl in bacteriochlorophylls c and e, and H in bacteriochlorophyll d.

Farnesyl 0 tetrapyrrole carbon numbering Fischer system

Farnesyl 0 tetrapyrrole carbon numbering IUPAC system

Farnesyl 0 bacteriochlorophyll

R

~co-{

C,

d, e core structure

0

0

R= ' 0 bacteriochlorophyll a

bacteriocide a variant spelling o/bactericide. bacteriocidin a variant spelling a/bactericidin. bacteriocin any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. Examples: colicin El from Escherichia coli: database code CEALECOLI, 522 amino acids (57.21 kDa); this is a channel-forming transmembrane protein that results in membrane depolarization; colicin E3 from E. coli: database code CEALECOLI, 541 amino acids (57.90 kDa); this is an rRNA ribonuclease; plantaricin A from Lactobacillus plantarum: database code (of precursor) PLNA_LACPL; plantaricin A is a channel-forming peptide dimer of a and ~ chains; the aminoacid sequence of the ~ chain is: AYSLQMGATAIKQVKKLFKKWGW; the a chain lacks the N-terminal A. -bacteriocinogenic adj. bacteriocinogenic factor any plasmid that carries genetic information for the production of a bacteriocin. Generally only a small proportion of cells containing the factor actually produce bacteriocin. See also Col plasmid. bacterioferritin a bacterial bl-type cytochrome of 18 kDa subunit containing 13-20% wlw of iron. It has similar properties to mammalian ferritin. It may be concerned with iron orland electron storage in the bacterium. Similar proteins may be present in other species of bacteria. Example from Azotobacter

61

Baltimore

bacteriology vinelandii: database code BFR_ECOLI, 158 amino acids (18.49 kDa). These proteins are oligomers of 24 identical subunits. bacteriology the branch of science that deals with the study of bacteria. bacteriolysin an alternative term for bactericidin. bacteriolysis the lysis of bacteria. -bacteriolytic adj. bacteriophaeophytin a variant spelling of bacteriopheophytin. bacteriophage or pbage or bacterial virus any virus that can infect and multiply in a bacterium. Phages parasitize almost every group of prokaryotes. Commonly they consist of a core of nucleic acid enclosed within a protein coat, the capsid; additional components, e.g. lipid, occur in some phages. Depending on the type of phage, the nucleic acid may be either DNA (single-stranded or double-stranded) or RNA (singlestranded), and may be either linear or circular. Phages may be filamentous, polyhedral, or polyhedral and tailed; the tubular tails, to which one or more tubular tail fibres are attached in certain circumstances, are involved in attachment of the phages to the bacterial surface and for the injection of the DNA into the host cells. The smallest phages, e.g. ~X174, are z25 nm in diameter, whereas tailed polyhedral phages, such as the T-even phages, are 200-250 nm long, while filamentous phages measure roughly 800 nm x 5 nm. In general, a given bacteriophage can infect only one particular species, or strain, or group of closely related strains, though a given strain may be susceptible to infection by a number of different phages. Bacteriophages can bring about transduction (def. I) between bacterial cells. Compare cyanophage. See also (bacterio)phage conversion, lysogeny, phage induction, phage typing, prophage, temperate phage, virulent phage. (bacteriolphage conversion or prophage-mediated conversion or lysogenic conversion the introduction of new properties to a host bacterium by the genome of an infecting lysogenic prophage. Such properties may include resistance to lysis by related phages, changes in antigenic constitution, or the appearance of toxigenicity. bacteriophage vector see cloning vector. bacteriopheophytin or (esp. Brit.) bacteriophaeophytin a bacteriochlorophyll in which MgH is replaced by 2 H+. bacteriorhodopsin a retinal-containing protein, resembling animal rhodopsin, formed by Halobacterium halobium and other halophilic Archaea and inserted into patches of purple membrane in the cell surface. The purple membranes serve as light-operated hydrogen-ion pumps to translocate hydrons from the inside to the outside of the cells. Example from H. halobium (precursor): database code BACR_HALHA, 262 amino acids (28.22 kDa); residues 1-13 form the propeptide and the C-terminal Asp is also missing from the mature protein, which is a seven-helix transmembrane protein of known 3-D structure and a model for opsin and related G-protein-linked receptors in eukaryotic cells. bacteriostatic or bacteristatic describing a drug, antibiotic, or other agent that inhibits the growth and multiplication of bacteria. Compare bactericide. -bacteriostasis n. bacterium (pl. bacteria) any of a vast and ubiquitous group of prokaryotic microorganisms that exist as single cells or in clusters or aggregates of single cells. Most authorities now place them in the exclusively prokaryotic kingdom Monera, along with the cyanobacteria (blue-green algae). The majority of bacteria possess a rigid cell wall; those lacking this feature are termed Archaea. Bacteria, Archaea, and Eukarya constitute the three primary Kingdoms (domains). -bacterial adj. Bacteroides a genus of Gram-negative anaerobic rod like bacteria. Mostly nonmotile, they are commonly present in the alimentary and urogenital tracts of mammals and may behave as opportunistic pathogens. bactoprenol an alternative name for undecaprenol. Bactrim see sulfamethoxazole. baculovirus any of a group of DNA viruses that are known to multiply only in invertebrates and are now classified in the

family Baculoviridae. Their genome consists of doublestranded circular DNA of 58-100 MDa. Because of their host range they have potential as pest-control agents. Baculovirus vectors are valuable as a means of expressing certain animal proteins (see expression system). BAF abbr. for B-cell activating factor (see interleukin 1). baicalein 5,6,7-trihydroxyflavone; a pigment (greenish-brown in dilute alkali) found in the root of Scute/laria baicalensis. It is a selective 12-lipoxygenase inhibitor. Baicalein inhibits leukotriene biosynthesis and cellular Ca H uptake and mobilization.

HO HO

bait a hybrid protein contammg the GAL4 DNA-binding domain, used in the yeast two-hybrid system. See also bait region. bait region a restricted region in the sequence of !Xz-macroglobulin (u2M) that is cleaved by proteinases in the process leading to the conformational changes instrumental in the proteinase inhibitory function of uzM. The bait region occurs in all umacroglobulins but shows great variation in length and amino-acid sequence between different u-macroglobulin and animal species. In human u2M, it covers approximately residues 666-706. Outside of the bait region, u2M from different species shows very high sequence homology. See also trap hypothesis. bakers' yeast any of various strains of the yeast Saccharomyces cerevisiae that are used in baking. baking soda see soda. BAL abbr. for British anti-lewisite (see dimercaprol). balance 1 (in physiology) the relation between the intake of a particular nutrient and its excretion (or the excretion of its metabolites). 2 any instrument for determining the equality in mass of two objects (or sets of objects). In cases where one (set) is of known mass the mass of the second (set) is thus obtained; e.g. an analytical balance. 3 any instrument designed to measure the weight of an object, e.g. spring balance, torsion balance. balanced growth a type of growth such that over a time interval (within the exponential phase) every extensive property of the growing system increases by the same factor. Balanced growth for an individual cell requires that each cell after division is an exact replica of the one of the previous cycle. balanced salt solution any solution designed to provide a normal environment, in terms of ionic composition, pH, and osmotic pressure, for cells in tissue culture. balance study any study to determine balance (def. I). balata see rubber. BALB/c a strain of inbred white mice that readily develop experimental myelomatosis. Balbiani ring a large puff of giant chromosomes present during a greater portion of larval development in members of the Diptera. The structural modification of specific loci is characteristically large and ring-shaped. [After Eduard Gerard Balbiani (1823-99), French entomologist who reported it in 1881.] Baltimore. David (1938- ), US microbiologist and molecular biologist distinguished for his studies of viral nucleic-acid biosynthesis, particularly his discovery (at the same time as H. M. Temin) of reverse transcription by the enzyme RNAdirected DNA polymerase in the virions of tumour-producing retroviruses, and for the classification of animal viruses named after him; Nobel Laureate in Physiology or Medicine

Baltimore classification (1975) jointly with R. Dulbecco and H. M. Temin 'for their discoveries concerning the interaction between tumour viruses and the genetic material of the cell'. Baltimore classification a method of classification of animal viruses based on the nature of the genome and the mechanism for synthesis of mRNA, which is always regarded as the plus strand (def. 2). There are six classes: Class I Viruses having a double-stranded (ds) DNA genome that make mRNA by asymmetric transcription. In many, different mRNA species come from different DNA strands. Class II Viruses having a single-stranded (ss) DNA genome of the same polarity as the mRNA. Some have strands of both polarity in different particles. Class III Viruses having a dsRNA genome that make mRNA by asymmetric transcription. Most have multiple pieces of dsRNA, each of which apparently contains the information for the synthesis of a single protein. Class IV Viruses having an ssRNA genome that make mRNA of base sequence identical to the genomic RNA. Class V Viruses having an ssRNA genome that make mRNA with a base sequence complementary to the genomic RNA. Class VI Retroviruses having an ssRNA genome and a DNA intermediate in their growth. band 1 an absorption band in an electromagnetic spectrum. 2 a zone of (macro)molecules such as that obtained in densitygradient centrifugation, zone electrophoresis, isoelectric focusing, chromatography, or other similar method. 3 any of the zones readily distinguishable by microscopy in a sarcomere of a muscle. 4 the specific association of a large number of chromomeres at the same level in somatically paired polytenic giant chromosomes of members of the Diptera. See also cytochrome absorption bands. band centrifugation see isopycnic centrifugation. band compression inadequate separation of the bands on a gel electrophoretogram, especially in DNA sequencing gels. It results in poor resolution and difficulties in interpretation. band electrophoresis an alternative name for lone electrophoresis. banding the formation of distinct bands or zones in densitygradient centrifugation, column chromatography, or other separation techniques. banding density the density of the suspending medium at which a particular type of particle, e.g. a cell organelle, forms a band during centrifugation in a specified density gradient. band intensity (in NMR spectrometry) the area under the band between the signal trace and the baseline. See nuclear magnetic resonance. band-pass filter 1 an electric circuit or other device that transmits only frequencies within a selected band. 2 an interference filter. band protein erythrocyte proteins are referred to as bands, numbered according to the position they occupy on electrophoresis gels. Some of the more important bands are: 1 and 2, a and p spectrin; 3, an anion channel protein; 4.1, always referred to as such, is involved in spectrin junctions; 5, actin. band width (in N MR spectrometry) the distance between the sides of the band at half the band height of a reasonably smooth and symmetrical band. See nuclear magnetic resonance. Bangasome or Bangosome (colloquially) an alternative name for liposome. [After its inventor, Alec Douglas Bangham (1921-), British biophysicist and medical scientist.] Banting, (Sir) Frederick Grant (1891-1941), Canadian surgeon, physiologist, and endocrinologist distinguished for his discovery (with C. H. Best) of a means of extracting the hormone insulin from pancreatic tissue and for demonstrating its antidiabetic efficacy; Nobel Laureate in Physiology or Medicine (1923) jointly with J. J. R. Macleod 'for the discovery of insulin'. See also Best. Macleod. Bantu siderosis see iron overload. BAPTA I,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetate; a Ca2+ chelator exhibiting a 105-fold greater affinity (110 nM)

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barometric pressure than for Mg2+. Its UV absorption maximum is at 254 nm which, after Ca 2+ is bound, shifts to 279 nm, a property that can be exploited in its use as an indicator of intracellular Ca 2 + concentration. Its esterified form can enter cells where it is hydrolysed to BAPTA.

bar a unit of pressure temporarily approved for use with SI units. 1 bar = 105 Pa = 10 5 N m- 2 • barbed end see plus end. barbital or barbitone 5,5-diethylbarbituric acid; 5-diethylmalonylurea; 5,5-diethyl-2,4,6(lH,3H,5H)-pyrimidinetrione; a long-acting depressant of the central nervous system, widely used as a buffer substance; pKa = 7.98 (25 QC), 8.06 (20 QC). One proprietary name: Verona!. barbiturate 1 the tautomeric anion derived from barbituric acid (malonylurea; 2,4,6(lH,3H,5H)-pyrimidinetrione). 2 any mixture of free barbituric acid and its anion. 3 any salt of barbituric acid. 4 any of various pharmacologically active derivatives of barbituric acid, including barbitone, pentobarbitone, phenobarbitone, and thiopentone. Barbiturates are potent CNS depressants that potentiate the actions of GAB A by binding to the GABAA receptor. Pentobarbitone and thiopentone are used to induce anesthesia. Barcroft apparatus or Barcroft respirometer a differential respirometer for studying gas exchange of cells, tissue slices, or tissue homogenates, now rarely used. It is a closed system comprising two flasks of equal volume connected by a Ushaped manometer (the Barcroft manometer). In operation, both flasks contain the same volumes of liquid and gas; one, the reaction flask, contains the cells or tissue; the other, the compensation flask, is free from cells or tissue and serves to compensate for changes in temperature and barometric pressure during the course of an experiment. The respirometers are arranged so that they may be shaken with the flasks in a constant-temperature bath. The reading of the apparatus is the difference between the levels of the manometer fluid in the two sides of the manometer. [After Joseph Barcroft (1872-1947), British physiologist, who described it in 1908.] Barfoed's reagent a solution containing cupric acetate in dilute acetic acid that is reduced when heated with monosaccharides but not with disaccharides or oligosaccharides. [After Christen Thomsen Barfoed (1815-99), Swedish physician.] barn symbol: b; a non-SI unit of area equal to 10-28 m2• It is used as a unit of atomic nuclear cross section. barnase or ribonuclease BA; a small extracellular endoribonuclease from Bacillus amyloliquefaciens. Its action involves formation of a 2':3'-cyclic phosphate (see ribonuclease). It has been studied as a model for protein folding. The sequence and 3-D structure are known: database code RNBR_BACAM, 157 amino acids (17.47 kDa). baroceptor a variant spelling of baroreceptor. barometer an instrument for measuring the pressure of the atmosphere. barometric pressure the pressure exerted by the atmosphere at a given place and time. It is often expressed in terms of the supported height of a column of mercury, usually measured in millimetres. The SI unit is the pascal. Other non-SI units frequently used in addition to the millimetre of mercury are the atmosphere, the bar, and the torr.

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baroreceptor baroreceptor or baroceptor any physiological receptor that is sensitive to changes in pressure, especially the sensory nerve endings in the carotid sinus that set off nerve impulses in response to alterations in blood pressure at that point. Barr body see sex chromatin. barrier an extracellular protein, probably a proteinase, excreted by yeast cells of mating type a. Its role may be to act as an antagonist of the a-type mating pheromone and establish optimal pheromone concentration for conjugation. Example (precursor) from Saccharomyces cerevisiae: database code BARLYEAST, 587 amino acids (63.66 kDa). Barton, (Sir) Derek Harold Richard (1918-98), British organic chemist; Nobel Laureate in Chemistry (1969), the prize being shared with O. Hassel 'for their contributions to the development of the concept of conformation and its application in chemistry' . barwin a barley seed protein (possibly a lectin) involved in defence mechanisms. It is closely related to the C-terminal domain of proteins encoded by wound-induced plant genes. It gives its name to a family of such proteins. Example, database code BARW_HORVU, 125 amino acids (13.77 kDa); 3-D structure known. basal 1 at, of, or being a base (def. 4). 2 at, of, or being the minimum level for maintaining the normal or essential functioning of an organism. basal body 1 (in prokaryotes) a structure that apparently attaches the flagellum (def. 1) to the cell envelope. The proximal end of the flagellum, the hook, appears curved and thickened and leads into the basal body, which consists of parallel ringshaped structures, arranged around a rod-shaped core. The rings of the basal body make contact with the layers of the cell envelope. 2 (in eukaryotes) a structure at the base of a cilium consisting of spherical granules or short rods arranged in rows below the cell surface. Electron microscopically they are cylindrical bodies, 300-500 nm long and 120-150 nm in diameter, open at one or both ends. They consist of nine sets of triplet microtubules, each triplet containing one complete microtubule fused to two incomplete microtubules. basal granule an alternative term for basal body (esp. in ciliated epithelium). basal lamina a thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix, forming a region between the cells and adjacent connective tissue. The basal lamina has important functions in the organ ization of tissues including an influence on cell polarity, cell differentiation, and cell migration. The basal lamina is subdivided into the lamina lucida (an electron-lucent region) immediately adjacent to the cell layer, and the lamina densa (an electron-dense region) external to it. Frequently there is a further outermost layer, the lamina reticularis, containing collagen fibrils. The three laminae are often collectively referred to as the basement membrane. basal medium any culture medium that will support the growth of nutritionally undemanding chemoorganotrophs. basal metabolic rate abbr.: BMR; the rate of energy metabolism of an animal at rest but not asleep. It is measured with the animal in a 'comfortable' ambient temperature, and in the postabsorptive state, at least 12 hours after taking food. It may be determined from the oxygen consumption and carbon dioxide (and urinary nitrogen) excretion, or from the heat prod uction of the animal. base 1 (in chemistry) a a Brensted-Lowry base. b a Lewis base. See also acid (def. 2). 2 (in molecular biology) any purine or pyrimidine that occurs as a component residue in polynucleotides or nucleic acids. Purines and pyrimidines are nitrogen bases, hence the terminology. 3 a unit of length of a polynucleotide or nucleic acid, equal to one nucleotide residue. Large molecules are usually measured in kilobases (10 3 bases; symbol: kb) or megabases (10 6 bases; symbol: Mb). See also nitrogenous base. 4 (in mathematics) a the number of units in a system of counting that is equivalent to one unit in

basic dissociation constant the next higher counting place. b the number that when raised to a specified power, its exponent, has a logarithm equal to the specified power. 5 the bottom or supporting part of anything; the point of attachment of an organ or part to an organism. base analogue or (esp. US) base analog any unnatural purine or pyrimidine base that can be incorporated in vivo into DNA but that, because of its different properties, causes altered base-pairing during incorporation or in subsequent DNA replication. Thus 5-bromouracil, an analogue of thymine, pairs with guanine thereby causing transitions of A-T ~ G-C. Similarly, 2-aminopurine, an analogue of adenine, pairs with cytosine thereby causing transitions of A-T ~ G-C. Some base analogues have been used as anticancer and antivirus agents. base calling the automated reading of DNA-sequencing gels using a scanner and appropriate software. base composition the relative amounts of the various purines and pyrimidines occurring in a specimen of polynucleotide or nucleic acid. It is often expressed as moles percent. baseline an imaginary line or a standard or reference value, etc. by means of which measurements may be compared, especially the zero line in the tracing of a chromatogram, spectrum, ultracentrifuge pattern, etc. basement membrane a thin layer of dense material found in various animal tissues interposed between the cells and adjacent connective tissue. It consists of the basal lamina, comprising fine fibrillar material in a glycoprotein matrix, plus an associated layer of reticulin fibres. Occurring in, e.g., capillary linings, kidney tubules, lung alveoli, and renal glomeruli, basement membrane has a supportive function in some tissues and may also act as a passive selective filter for substances diffusing in or out of the cells; e.g. in renal glomeruli it retains protein molecules. It gives a strong periodic acid-Schiff reaction. base pair symbol: bp; any of the possible pairings between two bases in opposing strands of double-stranded DNA or RNA molecules. Adenine forms a base pair with thymine (in DNA) or uracil (in RNA) and guanine with cytosine, hence the number of adenine residues equals the number of thymine (and/or uracil) residues while the number of guanine residues equals that of the cytosine residues. See also Chargaffs rules. -basepair vb.; base-pairing n. base-pair ratio see Chargaffs rules. base sequence the sequential order of nucleotide residues in a polynucleotide or nucleic acid molecule. base stacking the arrangement of base pairs in parallel planes, at an angle to the helix axis, in the interior of a helical double-stranded polynucleotide or nucleic acid molecule. base triplet any sequence of three bases in a nucleic acid that codes for an amino acid, or some other signal, in protein synthesis. Compare anticodon; codon. basic 1 of, relating to, containing, or characteristic of a base (def. I). Compare acidic (def. I). 2 having an alkaline reaction; of or relating to an aqueous solution having a pH value>7.0. Compare acidic (def. 2). basic amino acid any amino acid possessing a net positive charge at neutral pH. basic azo-dye binding protein abbr.: B-ABP; a 45 kDa (Sephadex) protein, isolated from the soluble cell supernatant fraction from livers of rats given 4-dimethylaminoazobenzene. It was later named ligandin. basic dissociation constant or basicity constant symbol: K b ; the thermodynamic dissociation constant for the dissociation of a base (def. 1, 2). For a dilute solution of a weak base, B, dissociating in water according to the equilibrium: BOH ...... B+ + OH-, K b =aB+ X aow / aBOH where a is the activity of the species designated by the subscripts. The activity of the water has been omitted from the equation since it may be taken as unity in dilute aqueous solution. K b is a measure of the strength of a base, Le. of its ability to accept hydrons from water (compare acid dissociation con-

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basic dye stant; see also pK). The concept is no longer used since the conjugate acid, B+, may be considered as an acid and an acid dissociation constant, K a , for it defined. Also, in aqueous solutions K a x Kb [H+][OH-] Kw' where Kw is the ion product of water, whence Kb may be calculated from Ka or vice versa. basic dye or basic stain any cationic dye that binds to, and hence stains, anionic macromolecules or other materials. basic salt any salt containing hydroxyl or oxide groups in partial replacement of, or in addition to, ions or groups derived from an acid, e.g. basic lead acetate, (CH 3COOhPb'Pb(OHh basic stain an alternative term for basic dye. basic zipper see bZIP. basolateral surface the surface of an epithelial cell that adjoins underlying tissue. Compare apical surface. basonuclin a zinc finger nuclear protein of epidermis, likely to be a transcription factor specific for squamous epithelium and its keratinocytes prior to terminal differentiation. It is present mainly in the nuclei of the basal cell layer. Example from human: database code BASO_HUMAN, 993 amino acids (110.85 kDa). basophil or basophil(ic) leukocyte a polymorphonuclear phagocytic leucocyte of the myeloid series that is distinguished by the presence of coarse cytoplasmic granules that stain with basic dyes. The granules are believed to contain histamine, heparin, and other vasoactive amines. Basophils are closely related to mast cells and constitute 400 Da). bile acid any member of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine (see bile salt). The C 24 acids are hydroxy or keto derivatives of cholanic or allocholanic acids; some C 27 bile acids are known in eutherian mammals. In mammals, the C 24 acids are found conjugated with glycine (see glycocholate) as well as with taurine (see taurocholate); in the rest of the animal kingdom only taurine conjugates have been found. bile alcohol any of a group of polyhydroxy derivatives of cholestane, present as their sulfuric acid esters in the bile of amphibians and some fishes. bilene the semisystematic name for either of two tetrapyrroles in which the carbon bridges contain one more double bond than bilane; i.e. one of the three bridges in the molecule is a methine group. bile pigment any bilirubinoid pigment present in bile; i.e. any linear tetrapyrrole derived from a porphyrin (which is a cyclic tetrapyrrole). For physiological reasons certain dipyrroles are also sometimes regarded as bile pigments. bile salt the sodium salt of the conjugate of any bile acid with either glycine or taurine. Bile salts are potent surfactants; in the gut they emulsify ingested lipid, promote its hydrolysis by the activation of Iipases, and facilitate its absorption, thereafter being excreted in the feces. See also glycocholate, taurocholate. biliary of or relating to bile. bilin I the systematic name for the linear tetrapyrrole in which the carbon bridges contain three more double bonds than bilane; Le. all three bridges are methine groups. This name is preferred to bilatriene. 2 any coloured bile pigment formed by the oxidation of a colourless bile pigment, or bilinogen (def. 2). Thus the bilinogens urobilinogen and stercobilinogen form urobilin and stercobilin, respectively, on oxidation. bilinogen I trivial name for bilane. 2 any colourless bile pigment that may be oxidized to a coloured bile pigment (see bilin (def. 2)). biliprotein an alternative name for phycobiliprotein. bilirubin or (formerly) bilirubin IXa the recommended trivial name for the linear tetrapyrrole 8,12-bis(2-carboxyethyl)2,7,13, 17-tetramethyl-3,18-divinylbiladiene-ac-l, 19(21 H,24H)dione. It is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin. In the liver, bilirubin is rendered watersoluble by conjugation of the carboxyethyl side-chains to form bilirubin bisglucuronide, most of which is excreted in the bile. Bilirubin accumulates in the blood and tissues in jaundice.

bilirubin oxidase EC 1.3.3.5; an enzyme that catalyses the oxidation by dioxygen of bilirubin to biliverdin and H 20. Example from the fungus Myrothecium verrucaria: database code B48521, 572 amino acids (63.88 kDa). biliverdin or (formerly) biliverdin IXa the recommended trivial name for the linear tetrapyrrole 8,12-bis(2-carboxyethyl)2,7,13, 17-tetramethyl-3,18-divinylbilin-l, 19(21H,24H)-dione. It is formed in the reticuloendothelial system by the first step in heme degradation, catalysed by heme oxygenase (decyc1izing), EC 1.14.99.3, a reaction in which the a-methene group of heme is oxidized to carbon monoxide. Biliverdin is then reo duced by biliverdin reductase, EC 1.3.1.24, to bilirubin.

COOH

biliverdin reductase EC 1.3.1.24; an enzyme that catalyses the reaction of bilirubin with NAD(P)+ to form biliverdin and NAD(P)H. Example from human: database code PN0159, 204 amino acids (21.83 kDa). bimodal (in statistics) distribution with two modes. bimolecular having a molecularity of two; relating to, consisting of, or involving two molecular entities. bimolecular layer a layer that is two molecules thick. bimolecular reaction any chemical reaction in which there is a transition state composed of the atoms of two separate molecular entities, which may be the same or different. binal double; twofold. binary I consisting of or forming two things or parts; dual. 2 describing a number system having the numeral 2 as its base (def. 4b). See also bit. binary compound a compound consisting of only two chemical elements; e.g. ammonia. sodium chloride. water. binary digit see bit. binary fission the reproduction of a living cell by division into two equal, or near-equal, parts. binary operator any arithmetic or logical operator (e.g. +, AND, OR) that operates on two quantities. binary representation a notation by which alphanumeric symbols are represented by two digits, 0 and I, in a known sequence. The displacement of one digit position to the left denotes multiplication by a power of 2. binder protein I see cortisol metabolite binding protein (Iargel. bindin a protein of 285 amino acids, M r 35 000, extracted from the insoluble granular material of sea-urchin sperm, responsible for the attachment of the sperm to the vitelline layer of the egg. Bindins may mediate the species-specific recognition of eggs by sperm. See also spermadhesin, zona pellucida spermbinding protein. binding the act or process by which one molecule attaches to another by noncovalent forces; ligation see Iigete (def. 3). See ligand. See also binding site. binding assay an alternative term for saturation analysis. binding capacity a measure of the quantity of ligand or the number of ligand molecules that can be bound by a given amount of a particular binding agent or system. binding constant an alternative term for affinity constant.

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binding curve binding curve any graphical representation of the extent of binding between two compounds at varying relative concentrations of the reactants. binding energy the free energy change accompanying the binding of ni ligand molecules to a macromolecule to produce a particular configuration of the liganded macromolecule. binding fraction an alternative term for saturation fraction. binding potential symbol: II; a concept introduced to clarify the definition of linked functions, linkage groups, and linked sites in ligand binding. It is defined by: Vi ::: oIIloJii where Vi is the ratio of component i to that of a reference component and Jii is the chemical potential of i. binding protein abbr.: BiP; a luminal protein of the endoplasmic reticulum that is a member of the hsp70 family of heat-shock proteins and is a typical molecular chaperone. It recognizes incorrectly folded proteins as well as protein subunits that have not yet assembled into their oligomeric complexes and facilitates their oligomerization of folding. BiP activity requires the participation of ATP, which is hydrolysed to ADP and inorganic phosphate. Example (precursor) from human: database code GR 78_HUMAN, 653 amino acids (72.03 kDa); this is also known as 78 kDa glucose regulated protein. binding set the spatially organized collection of all the groups or residues of one protomer that are involved in its binding to one other protomer. binding site a specific region in a macromolecule or other molecular entity, or in a membrane, that takes part directly in the combination with a ligand. Binding sites may be independent or interacting, depending on whether or not the binding of one ligand to one site affects the binding of other ligands to other sites on the same macromolecule, or membrane. See also cooperative ligand binding. binomial 1 a mathematical expression made up of two terms, e.g. 2x + 5y. 2 a two-part taxonomic name (see binomial nomenclature). binomial coefficient the coefficient of any term arising from the expansion of the algebraic binomial (a + b)n. binomial distribution a statistical function in which the probabilities that an event will or will not occur are given by the successive coefficients of a binomial expansion of the form (a + b)", where a and b are the probabilities that an event will and will not occur, respectively. binomial nomenclature a system of naming organisms, devised by the Swedish botanist Carolus Linnaeus (1707-78), that employs two Latin names, the first being the genus and the second the species to which the organism belongs. bio+ comb. form denoting life or living organisms, or systems derived from them. bioaetivation the activation of a drug or other substance in an organism or by means of a biological or biochemical system. bioaetive an alternative term for biologically active. bioanalytical of or pertaining to biochemical analysis. bioassay or biological assay any quantitative estimation of biologically active substances by measurement of the magnitude of their actions on living organisms or parts of organisms. It is performed under standard conditions and by reference to preparations of defined potency or activity. bioautograph the record obtained in bioautography. bioautography a method for detecting, in a complex mixture, small amounts of substances that are able to act as essential growth factors for a test organism(s). The components of the mixture are first separated by chromatography. The resulting chromatogram is then placed in contact with a culture of the test organism in a solid medium lacking a specific component. Hence, the organism will only grow where the component is present in the chromatogram, thereby establishing its presence in the original mixture. bioavailability 1 the relative amount of the dose of a drug or other substance reaching the systemic circulation. 2 the rate and extent to which the therapeutic moiety of a drug is absorbed and becomes available to the site of drug action.

biodegradable bioblast any very small mass of protoplasm having formative powers, formerly considered to be the ultimate elementary living particles; it is now thought the particles seen may have been mitochondria. biocatalyst any agent, present in or obtained from living material, that can increase the rate at which a chemical reaction occurs without itself undergoing permanent change; a biological or biochemical catalyst. Biocatalysts are commonly enzymes. See also ribozyme. -biocatalysis n. biochemical 1 of or pertaining to biochemistry. 2 any chemical substance occurring in or isolated from an organism. biochemical engineering or bioengineering the scientific discipline underlying the industrial processing of biological materials, e.g. fermentation-based pharmaceuticals, foods, and effluents. biochemical evolution the evolution of the biochemical processes and components of living organisms, such as the structure and function of biologically important molecules, metabolic pathways, subcellular structures, and cells. biochemical genetics the branch of genetics concerned with the chemical nature of hereditary determinants and how they function at the molecular level. biochemical imprinting the adaptive increase in enzyme activities that can occur along specified metabolic pathways when there is a large and sustained traffic through them. biochemical lesion any biochemical change, such as the absence or inactivation of an enzyme, that diminishes the fitness of an organism or leads to a pathological condition. biochemical marker any specific character that may be detected by a biochemical test, e.g. the presence or absence of a particular enzyme. biochemical oxygen demand or biological oxygen demand abbr.: BOD; a measure of pollution of water in lakes, rivers, etc. due to the presence of organic matter. Oxidation of the latter by microorganisms removes dissolved oxygen, hence reducing the ability of the water to sustain aquatic life. BOD is the amount of oxygen (mg) taken up by a I-litre sample of water in 5 days (BODs) at 20°C in the dark; it may be necessary to add additional, uncontaminated, water to augment the amount of oxygen available. Sometimes incubation is for a longer time, e.g. 20 days, in which case it is indicated by BOD zo . Compare chemical oxygen demand. biochemistry or biological chemistry the branch of science dealing with the chemical compounds, reactions, and other processes that occur in living organisms. Lehninger expressed the challenge to the biochemist as follows: 'Living things are composed of lifeless molecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behaviour of inanimate matter. Yet living organisms possess extraordinary attributes not shown by collections of inanimate molecules.' In this regard Horowitz has proposed a set of criteria for living systems: 'Life possesses the properties of replication, catalysis and mutability.' Biochemists are, therefore, concerned with the manner in which living organisms exhibit these properties. -biochemist n. biochip an integrated circuit in which electrical and logical functions are performed by protein molecules appropriately manip ula ted. biocide any chemical substance that kills living cells or organisms. -biocidal adj. biocompatible compatible with life; having no injurious effect on living organisms. -biocompatibility n. bioconversion a technique in which the enzymic apparatus of an organism is used to convert or process a chemical substance, not normally present in the organism, into another, (often commercially) useful one. biocytin e-N-biotinyl-L-Iysine; a naturally occurring complex of biotin, found especially in autolysates of rapidly growing yeast. It is liberated from biotin holoenzymes by proteolysis. biodegradable capable of being broken down by the action of living organisms. -biodegradability n.

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biodegradation biodegradation 1 the processes by which exogenous, usually waste materials are broken down by living organisms. Sometimes this breakdown involves two or more kinds of organisms acting in cooperation. Such degradative abilities are employed to convert waste materials into more acceptable and manageable forms or to produce useful end products. 2 an alternative term for catabolism. Compare biosynthesis. biodeterioration any undesirable change in the properties of a material brought about by the activities of organisms. bioelectricity electric current or electric potential produced in living organisms. -bioelectric ad). bioelectrochemistry the application of electrochemical models and techniques to biological problems. bioelectronics the application of biomolecular principles to microelectronics, as in biosensors and biochips. bioelement any element that is an essential component of living organisms. Bioelements include: as major elements, C, H, 0, N, P, and S, found chiefly in combination in organic compounds, and the elements, Na, K, Mg, Ca, and CI, found mainly as monatomic ions. Many other 'trace elements' occur in relatively minute amounts. bioenergetics the study of energy transformations in living systems. bioengineering 1 engineering relating to the operation on an industrial scale of biochemical processes, especially fermentation. This is usually now termed biochemical engineering. 2 the application of the physical sciences and engineering to the study of the functioning of the human body and to the treatment and correction of medical conditions. biofuel cell any fuel cell (a cell in which electricity is produced directly by oxidation of fuel) in which one or both electrode reactions are promoted or catalysed by a biological process. Bio-Gel proprietary name for a group of materials used in gel filtration, consisting of either cross-linked agarose (Bio-Gel A) or porous polyacrylamide (Bio-Gel P). biogenesis 1 the synthesis of a substance in a living organism; biosynthesis. 2 the principle that a living organism can originate only from a parent or parents that are similar to itself. Compare abiogenesis. -biogenetic, biogenetical, biogenous adj. biogenic produced by living organisms. biogenic amine any of various amines, especially those with neurological activity, isolated from plants or animals. bioinformatics see Appendix E. biohazard any organism or material derived from a biological source that is hazardous to health or life. bioinorganic chemistry a branch of inorganic chemistry concerned with the interactions between inorganic substances (especially metallic ions or their complexes) and biological or biochemical systems, and with the properties of related model systems. Compare inorganic biochemistry. biolistics descriptive of the administration of DNA in gold particles, using a device known as a 'gun' to deliver the particles to the cell interior. One use has been in the development of vaccines by the administration of suitable genes to foreign cells. biolith a rock or other deposit (e.g. peat, humus) formed from organic material. biological adj. 1 of or pertaining to biology. 2 of or pertaining to life or living organisms. 3 a biological product that is used prophylactically or therapeutically. -biologically adv. biological activity any activity of a substance that is demonstrable in living organisms. Biologically active substances are often of biological origin themselves. biological clock any biological mechanism that allows the expression of a certain biological structure (e.g. a gene) or a biological function (e.g. sleep) at periodic intervals. The term is also used colloquially to describe ageing, e.g. in respect to a woman's ability to bear a child. biologically active or bioactive active in a living organism. biological value abbr.: B.V.; a measure of the value of a protein in a foodstuff for the maintenance of growth and normal

biopterin functioning of any given animal or species. It is based on the amino-acid composition of the protein, its digestibility, and the availability of its digestion products. biology 1 the scientific study of living organisms, including their structure, functioning, development, distribution, interrelationships, and evolution. 2 the animal and plant life of a particular region considered as a unit. 3 the structure, functioning, etc. of a particular organism or group of organisms. -biologist n. bioluminescence the production of light by certain enzymecatalysed reactions in living organisms. -bioluminescent adj. biolysis any decomposition of organic material by biological means. -biolytic ad). biomass 1 the total mass of living organisms, of a specified kind, forming a population inhabiting a given region. 2 the material produced by the growth of microorganisms, plants, or animals, especially as a product of or raw material for an industrial process, such as farming or fermentation. biomedical science or biomedicine any branch of science that is relevant to medicine. biomembrane any membrane surrounding a cell or a subcellular organelle, or derived from these structures. biometry the statistical study of biology. -biometric adj.; biometrically adv. biomimetic chemistry a branch of organic chemistry that aims to imitate natural reactions and enzymatic processes as a means to improve the power of organic chemistry. biomolecular engineering a term sometimes used to cover those branches of biotechnology dealing with enzyme engineering and genetic engineering. biomolecule any molecule, especially a macromolecule, that occurs in or is formed by living organisms. -biomolecular adj. bioorganic chemistry a branch of organic chemistry concerned with the study of organic molecules from living systems. biophotolysis any type of photolysis reaction occurring in a biological system; e.g. the lysis of a water molecule in the reactions of photosystem II during photosynthesis. biophysical chemistry the application of the techniques or methods of physical chemistry to biological systems. It is principally concerned with the conformations, shape, structure, conformational changes, dynamics, and interactions of macromolecules and complexes or arrays of macromolecules. Compare biophysics. physical chemistry. biophysics the application of physical techniques and physical methods of analysis to biological problems. Traditionally, the discipline has focused on two main areas: first, the transmission of nerve signals and the maintenance of electrical potentials across membranes; and second, large-molecule crystallography and enzyme structure and mechanisms. For the latter X-ray crystallography has been supplemented by a number of physical techniques, including nuclear magnetic resonance spectrometry, mass spectrometry, fluorescence-depolarization measurements, and circular-dichroism studies. -biophysical adj.; biophysicist n. biopolymer any polymer, such as a protein, nucleic acid, or polysaccharide, occurring in, or formed by, living systems. biopotency the extent to which a material (e.g. drug or hormone) influences a biological process. bioproduct any (usually) useful product produced by living organisms or by systems derived from living organisms. biopsy examination of (usually) a sample of tissue, cells, or fluid from a living human or animal for diagnostic purposes. The term is also now commonly used for the process of removing such a sample. Compare necropsy. biopterin 2-amino-4-hydroxy-6-( I,2-dihydroxypropyl)-pteridine; 1-(2-amino-4-hydroxy-6-pteridinyl)-1,2-propanediol; a growth factor for certain protozoans, e.g. Crithidiafasciculata and Trypanosoma platydactyli. It is widely distributed in tissues and functions in a reduced form, tetrahydrobiopterin, as a hydroxylation coenzyme, e.g. in the conversion of phenyl ala-

72

bioreaetor nine to tyrosine. It has been isolated from queen-bee jelly and is considered a growth factor for some insects.

bioreactor any reactor containing immobilized enzymes or

cells that is used to effect specific chemical reactions in the production of some economically desirable product. bioregulator omnibus term sometimes used for any substance occurring within a cell or organism that has a specific and reversible controlling action on a particular biochemical event within that cell or organism; it may be, e.g., a hormone, an enzyme, an intermediate metabolite, an inorganic ion, or a cyclic nucleotide. bioremediation the use of biological systems to remedy environmental damage. bios the former name for various growth factors required by yeast. Originally believed to be a single factor, it was later fractionated into bios I (shown to be inositol), bios lIA (II-alanine), and bios lIB (biotin). bioscience(s) collectively all the individual branches of science that are concerned with biology. biose disaccharide; stem name used in the established trivial names for particular disaccharides whether or not they contain a single type of sugar residue and linkage, as in cellobiose and gentiobiose. +biose suffix used in nomenclature of glycolipids to indicate a compound containing an oligosaccharide moiety composed of two sugar residues (which may be the same or different), as in galabiose. biosemiotics the study of signs, of communication, and of information in living organisms. biosensor a device that uses specific biochemical reactions mediated by isolated enzymes, immunosystems, tissues, organelles, or whole cells to detect chemical compounds, usually by electrical, thermal, or optical signals. biospecific describing: 1 a reagent, e.g. an antibody or hormone, that can recognize and interact only with cells (e.g. within a mixed population of cells) displaying a particular surface characteristic, e.g. a corresponding antigen or receptor. 2 any reagent that, in a similar way, recognizes and interacts with a particular biospecifically occurring substance. 3 any reagent that interacts specifically with a particular biomolecule (e.g. an enzyme). 4 the reaction between two biospecific reagents. biospecific-elution chromatography an alternative name for affinity-elution chromatography (when the ligand in the eluting solvent is a biospecific macromolecule). biosphere the parts of the Earth's crust and atmosphere that contain living organisms. biosynthesis the production of substances by processes occurring in living systems; anabolism; biogenesis. Compare biodegradation. biosynthetic 1 of or relating to biosynthesis. 2 any substance

produced by biosynthesis. biosynthetic pathway any metabolic pathway effecting biosynthesis; an anabolic pathway. biotechnology 'the integration of natural sciences and engi-

neering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services' (European Federation of Biotechnology General Assembly, 1989); a field of technological activity in which biochemical, genetic, microbiological, and engineering techniques are combined for the pursuit of technical and applied aspects of research into biological materials and, in particular, into biological processing. It includes traditional technologies such

bisalbuminemia as fermentation processes, antibiotic production, and sewage treatment, as well as newer ones such as biomolecular engineering, and single-cell protein production. -biotechnological adj. biotin cis-tetrahydro-2-oxothieno[3,4-djimidazoline-4-valeric acid; hexa hydro-2-oxo-1 H -thieno[3 ,4-djimidazole-4-pentanoic acid; vitamin H; formerly known as bios lIB and coenzyme RC0 2 ; a substance the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymic p-carboxylation reactions. In biotin-containing enzymes the biotin is covalently bound at the active site through an amide link to the e-amino group of a lysine residue. It was first found as a growth factor for yeasts. Compare biocytin. See also streptavidin.

biotin carboxylase see acetyl-eoA carboxylase. biotinyl the acyl group derived from biotin. biotinylation the act or process of attaching a biotinyI residue

by use of an appropriate reactive derivative, e.g. biotin 4-nitrophenyl ester. It is useful for labelling cell-surface functional groups or biologically active molecules. The presence of the label is subsequently detected, or the labelled material is separated, by means of the specific and high-affinity avidin-biotin reaction, using avidin or streptavidin conjugated with, e.g., a fluorochrome, an enzyme, an antibody, or an immobilizing agent. -biotinylate vb.; biotinylated adj. biotransformation the conversion or conjugation of a foreign compound introduced into an organism or a culture of cells, especially (in biotechnology) with formation of a substance of commercial value. Compare detoxication. SiP abbr. for binding protein. biphenylylphenyloxadiazole abbr.: PBD; 2-phenyl-S-(4biphenylyl)-l ,3,4-oxadiazole; a high-efficiency primary scintillator. The tert-butyl derivative, 2-(4-tert-butylphenyl)-S(4-biphenylyl)-1 ,3,4-oxadiazole (abbr.: butyl-PBD) has greater solubility and only a slightly lower photon yield. See also scintillation cocktail.

biphosphate an obsolete name for the anion H ZP0 4- or

POz(OHh-, now correctly termed dihydrogenphosphate. biradical or diradical any molecular entity in an electronic

state (described by a formula or by a combination of contributing structures) that contains two unpaired electrons in atomic orbitals on different atoms (compare carbene). Both singlet and triplet species are embraced. birefringence an alternative term for double refraction. birefringent adj. bis+ comb. form 1 denoting two, twice, doubled; see also bi+ (def. I), di+ (def. 1).2 (in chemical nomenclature) a indicating the presence in a molecule of two identical organic groups each substituted in the same way, e.g. bis(2-chloroethyl)sulfide. b indicating the presence in a molecule of two separate inorganic oxoacid residues, e.g. fructose I ,6-bisphosphate (formerly known as fructose 1,6-diphosphate). Compare di+ (def. I). bisalbuminemia or (esp. Brit.) bisalbuminaemia a symptom-

73

2,5-bis(3,4,5-trimethoxyphenyl)-1,3-dioxolane

bisbenzimide less human condition in which the presence of a variant serum albumin leads to a double albumin band on electrophoresis of serum proteins. bisbenzimide 4-{[5-(4-methyl-I-piperazinyl)-2-benzimidazolyl]-2-benzimidazolyl} phenol (Hoechst 33258) or its ethyl ether (Hoechst 33342); a substance that is useful as a DNAbinding fluorochrome for staining chromosomes within cell nuclei. It is believed to be specific for A-T base pairs.

bis(methylthio)gliotoxin

bisl2-chloroethyl)sulfide or (formerly) mustard gas (CICH 2CH 2 hS; a bifunctional alkylating agent that causes lethal cross-linking of DNA chains. Bishop, John Michael (1936- ), US microbiologist; Nobel Laureate in Physiology or Medicine (1989) jointly with H. E. Varmus 'for their discovery of the cellular origin of retroviral oncogenes' . bisindolylmaleimide GF I09203X; a protein kinase inhibitor, structurally similar to staurosporine, that is highly selective for protein kinase C (PKC), though not between isotypes cr, ~I, ~II, or y. It acts as a competitive inhibitor at the ATP-binding site on PKC. It exhibits a K j of 14 nM for the purified enzyme, but its potency on whole cells is much lower (Kj 1-2 flM), possibly owing to high cellular ATP levels. H

N

N H

N H

bismethylstyrylbenzene abbr.: bis-MSB; 1,4-bis(2-methylstyryl)-benzene; a secondary scintillator with good resistance to quenching and low reactivity with compounds in samples. See also scintillation cocktail.

2,3-bislphospho)-D-glycerate a recommended name for (R)-[2,3-dihydroxypropanoate 2,3-bis(dihydrogenphosphate)] (formerly termed 2,3-diphosphoglycerate); abbr.: BPG; it decreases the dioxygen affinity of hemoglobin, its concentration in the erythrocyte being regulated by bisphosphoglycerate mutase (synthesis) and bisphosphoglycerate phosphatase (degradation). It does not pass through the erythrocyte membrane. See also bispbosphoglrcerate pocket. bisphosphoglycerate mutase abbr.: BPGM; EC 5.4.2.4; systematic name: 3-phospho-D-glycerate 1,2-phosphomutase; other names: 2,3-bisphosphoglycerate mutase; 2,3-bisphosphoglycerate synthase; diphosphoglycerate mutase; glycerate phosphomutase; bisphosphoglycerate synthase. An enzyme that catalyses the reaction: 3-phospho-D-glyceroyl phosphate = 2,3-bisphospho- D-glycerate. The enzyme plays a major role in regulating the dioxygen affinity of hemoglobin by controlling 2,3-bisphosphoglycerate concentration in the erythrocyte, but with a reduced activity. Example from human: database code PGME_HUMAN, 258 amino acids (29.84 kDa). bisphosphoglycerate phosphatase EC 3.1.3.13; systematic name: 2,3-bisphospho-n-glycerate 2-phosphohydrolase; an enzyme that catalyses the hydrolysis of 2,3-bisphosphoglycerate to 3-phosphoglycerate and orthophosphate; it thereby assists regulation of the concentration of 2,3-bisphosphoglycerate. bisphosphoglycerate pocket abbr.: BPG pocket; the cavity (pocket) between the two ~ chains of deoxyhemoglobin in which a single molecule of 2,3-bisphospho-D-glycerate (BPG) binds; the binding of this molecule reduces the affinity of hemoglobin for dioxygen. Residues VaIl (terminal-NH 3+), His 2 , Lys 82, and His l43 of each ~ chain participate in this binding. It plays an important part in establishing the difference in oxygen affinity that is found between maternal and fetal hemoglobin; in fetal hemoglobin, the y chain has a serine in the position occupied by His l43 of the ~ chain of the adult hemoglobin, which weakens the affinity of fetal hemoglobin for BPG and thus results in a higher affinity for dioxygen than adult hemoglobin. bis[2-succinimidooxycarbonyloxyethyl]sulfone a non cytotoxic, homo bifunctional, lysine-specific cross-linking agent that reacts at 0 °C; the cross-links can be reversed at pH 11.6 at 37°C.

CH3

bis(methylthio)gliotoxin a naturally occurring analogue of gliotoxin. It inhibits platelet activating factor (PAF)-induced platelet aggregation (IC so = 84 flM) (but not platelet aggregation induced by arachidonic acid or ADP) and in vivo PAFinduced bronchoconstriction; it lacks the antiviral and immunomodulating effect of gliotoxin. (Illustrated top right.) bis-MSB abbr. for bismethylstyrylbenzene. bisphosphate any compound containing two independent phosphoric residues in ester linkages, at positions indicated by locants. Compare diphosphate (def. 3,4). bisphospho+ prefix to a chemical name indicating the presence of two independent phosphoric resid ues in ester linkages, at positions indicated by locants. Compare diphospho+.

2,5-bisI3,4,5-trimethoxyphenyl)-1,3-dioxolane a substance, the trans-isomer of which inhibits platelet activating factor-induced platelet aggregation. The cis-isomer is inactive.

74

Bistris

Bloch

HSCO¢~O I I 0

HsCO

~

OCHs

?'"

OCHs

~

OCHs

HsCO

2,5-bis(3,4,5-trimethoxyphenyl)-1,3-dioxolane Bistris or bis-tris abbr. for bis(2-hydroxyethyl)imino-tris(hydroxymethyl)methane; 2-[bis(2-hydroxyethyl)amino]-2(hydroxymethyl)-propane-I,3-diol. A buffer substance useful for the calibration of glass electrodes and for the preparation of biochemical and biological buffer solutions; pKa (25°C) = 6.5. It is inexpensive, stable, and readily crystallizable.

OH

~~H (

OH

OH bis-tris propane abbr. for 1,3-bis[tris(hydroxymethyl)methylamino)propane; a water-soluble buffer substance used for the preparation of biochemical and biological buffer solutions; pKa (20°C) = 6.8.

bit a single binary digit having the value of either 0 or I; the smallest unit of information in a binary system. A group of (usually) eight bits comprises a byte, which can represent numbers between 0 and 11111111 in binary (equal to 0 and 255 in decimal). [abbr. for binary digit.] bithorax complex see BX-C. Bittner factor or Bittner particle former name for murine mammary tumour virus. [After John Joseph Bittner (1904-61), US biologist.) biuret reaction the formation of a characteristic purple colour when biuret (carbamoylurea) or compounds containing two or more adjacent peptide bonds (e.g. proteins) react with copper sulfate in alkaline solution. It forms the basis of the biuret test, a colorimetric method for the qualitative or quantitative determination of proteins. Bjerrum formation function a function used in studies of the binding of n ligand atoms, ions, or molecules to an acceptor atom, ion, or molecule. It is: r= (KI[L] + 2K IK z[L]z +...nK,Kz... Kn[L]n)/(1 + KI[L] +2KJK z[Lz] +...nK,Kz··.Kn[L]n), where r is the average number of ligand molecules bound per molecule of acceptor; K" Kz, ...K" are the stepwise formation (stability) constants of the n complexes; and [L) is the free ligand concentration. This function expresses an unambiguous connection between the quantity f/ and [L]. It is a generalized form of the Adair equation. [After Jannik Bjerrum (1909- ), Danish chemist who described it in 1941.]

Bjerrum plot a plot of r, the average number of ligand molecules bound per molecule of acceptor, versus -log[L], where [L] is the free ligand concentration. It is used for evaluating the association constants in a Bjerrum formation function. Bk symbol for berkelium. BK abbr. for bradykinin. BK 1-8 abbr. for des-Arg 9 -bradykinin (see bradykinin). bla symbol for p-Iactamase gene. Black, (Sir) James Whyte (1924- ), British pharmacologist distinguished for his discoveries of blockade of ~-adrenoceptors and of Hz-receptors by novel drugs; Nobel Laureate in Physiology or Medicine (1988) jointly with G. B. Elion and G. H. Hitchings 'for their discoveries of important principles for drug treatment'. black lipid membrane abbr.: BLM; other names: black lipid film; bimolecular lipid membrane; bilayer lipid membrane; lipid bilayer. An experimental membrane formed by introducing a small amount of suitable lipid solution on to an opening in the wall of a hydrophobic support immersed in an aqueous solution. The thickness of the black membrane does not differ greatly from the length of two of the lipid molecules used and is often about 4.5 nm. blank (determination) any analytical mixture from which analyte is deliberately omitted and which undergoes the same procedures as the complete mixture. It is used to ascertain the contribution of extraneous factors, e.g. reagent impurities or photometric absorption by the reagents, to the analytical result. blast+ a variant form of blasto+. +blast suffix denoting a formative cell, e.g. erythroblast, fibroblast, osteoblast. blast cell or blastocyte any undifferentiated embryonic cell. Such cells characteristically have a cytoplasm rich in RNA, and are actively synthesizing DNA. blast crisis the appearance of heterogeneity in the cell surface characteristics of white blood cells when chronic myeloid leukemia evolves into acute leukemia. This process is virtually inevitable and often rapid. blasto+ or (before a vowel) blast+ prefix denoting 1 an embryo in its early stages; e.g. blastocyst, blastula. 2 a germ cell; e.g. blastocyte. blastokinin see uteroglobin. blast transformation see transformation (def. 3). bleb 1 a spherical vesicle, about 10 J.lm in diameter, formed when a chloroplast swells on suspension in very hypotonic medium. It is bounded by a single membrane, on the surface of which a part of the thylakoid system remains concentrated in a few patches. 2 animal membranes are said to form blebs under special conditions that cause small vesicles to pinch off. blender or (sometimes, US) blendor a device for disrupting tissue or any aggregate. It consists of blades rotating at the bottom of a glass or stainless-steel vessel (originally named a Waring blendor, from a trade name); in an alternative design, known as a top-drive blender, the blades rotate on a spindle from the top of the vessel. The method is undiscriminating and may damage organelle membranes through excessive force or generation of heat. For more precise work, a Potter-Elvehjem homogenizer or a Dounce homogenizer preserves organelle structure. bleomycin any of a group of related glycopeptide antibiotics isolated from Streptomyces verticillus. Bleomycin acts to stop the cell cycle in the G z phase (see cell-division cycle). It is used to induce synchrony in cell cultures and as an antineoplastic agent, especially in lymphomas. blepharoplast an alternative term for basal body of a flagellate. Blk a gene encoding a protein tyrosine kinase of the Src family, specifically expressed in the B-celllineage. BLM abbr. for black lipid membrane. Bloch 1 Felix Bloch (1905-83), Swiss-born US physicist notable for his extensive studies in solid-state physics, for his measurement (with L. W. Alvarez) of the magnetic moment of the neutron, and for his discovery (independently of E. M. Purcell) of

75

block the phenomenon of nuclear magnetic resonance of certain atomic nuclei; Nobel Laureate in Physics (1952) jointly with E. M. Purcell 'for their development of new methods for nuclear magnetic precision measurements and discoveries in connection therewith'. 2 Konrad Emil Bloch (1912- ), German-born US biochemist distinguished for his extensive studies by isotope techniques of the biosynthesis of cholesterol, creatine, and protoporphyrin; Nobel Laureate in Physiology or Medicine (1964) jointly with F. Lynen 'for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism'. block 1 (in chemistry) a portion of a polymer molecule comprising many constitutional base units; such a portion has a constitutional or configurational feature not present in the adjacent multiple-unit portions. 2 (in physiology) an interference in the normal metabolic or physiological functioning of an organ or tissue; e.g. metabolic block, heart block. 3 to impede, retard, or prevent an action or activity, e.g. of an agonist, antigen, chemical reagent, enzyme, or receptor. blockade 1 (in pharmacology) the saturation of a specific type of receptor with an antagonist to its normal agonist. 2 (in immunology) the overloading or saturation of the reticuloendothelial system with inert particles, such as carbon particles. 3 to impose any such blockade. blocker something that blocks an action or activity; an antagonist or inhibitor. blocking agent 1 a chemical reagent that introduces a blocking group. 2 a specific pharmacological antagonist. blocking antibody 1 an incomplete antibody that does not agglutinate its antigen but attaches to it and so prevents its agglutination by normal, complete antibody. 2 antibody formed during specific desensitization in atopy. blocking group I or protecting group a chemical group, often easily removable, that is substituted into a reactive part of a molecule to prevent its participation in subsequent chemical or enzymic reactions occurring at another part of the molecule. 2 a chemical group, not easily removable, that is substituted into the active site of an enzyme to prevent its action. block polymer a polymer whose molecules contain two or more species of block (def. 1) attached linearly. blood a fluid tissue in animals that acts primarily as a transport medium. It is contained in vessels or spaces lined with endothelial cells. Metabolites, nutrients, and excretory substances are carried in solution or suspension from one part of the body to another. Respiratory pigments are often present to assist in the transport of dioxygen. It may also contain suspended cells. blood-brain barrier the semipermeable membranous barrier that regulates the passage of dissolved materials from the blood into the cerebrospinal fluid that bathes the brain and spinal cord. blood coagulation or blood clotting a mechanism that prevents blood loss at the site of an injury. It involves the formation of a semisolid mass of material, the blood clot, which plugs the wound. The clot consists of aggregated platelets and a mesh of fibrin molecules. The fibrin components include 13 or 14 plasma proteins, at least one tissue protein, phospholipid membrane surfaces, Ca2+ ions, and platelets. The current concept of the mechanism has changed from one involving a linear sequence of activations of proenzymes to one involving protein-protein and protein-lipid-Ca2+ interactions between proteinase, protein substrates, and protein cofactors to give discrete complexes and reaction steps. The following factors are involved in coagulation: Factor I (or fibrinogen) concn. =2-4 g L- 1 human plasma; a soluble fibrous protein of 330 kDa, it has an axial ratio of =5 and is made up of six disulfide-linked polypeptide chains; two Aa chains (66 kDa); two BfJ chains (52 kDa); and two y chains (47 kDa). After proteolysis by thrombin it polymerizes to form an insoluble fibrin clot.

blood coagulation Factor II (or prothrombin) concn. 200 mg L -I human plasma, 72.5 kDa; a vitamin K-dependent single-polypeptide-chain glycoprotein containing ten y-carboxyglutamate residues. It is converted to thrombin (or fibrinogenase), EC 3.4.21.5, by the proteinase factor Xa. Factor III (or thromboplastin or tissue factor) a factor that, when added to blood plasma, markedly shortens the time required for clot formation. Example from human (precursor): database code TF_HUMAN, 295 amino acids (33.07 kDa). Factor IV (or calcium ion) calcium ions form bridges between vitamin K-dependent proteins and acid phospholipids of cell membranes. They also stabilize factor V and fibrinogen, and are involved in activation of factor XIII. Factor V (or accelerator globulin or proaccelerin) a glycoprotein of =330 kDa. After activation to factor Va (accelerin) it acts with the proteinase factor Xa in activating prothrombin. Example from human (precursor): database code FA5_ HUMAN, 2224 amino acids (251.70 kDa). Factor VI an obsolete term (originally named accelerin). Factor VII (or proconvertin) concn. 2 mg L-I human plasma; 50 kDa; a vitamin K-dependent single-polypeptide-chain glycoprotein containing y-carboxyglutamate residues. It is the precursor of factor VIla, convertin, a Ca 2+-dependent proteinase, EC 3.4.21.21, that activates factor X and is the first component of the extrinsic pathway of coagulation. Example from rabbit (precursor): database code FA7_RABIT, 443 amino acids (48.85 kDa). Factor VIII (or antihemophilic factor); an accessory protein that participates with proteinase factor IXa in the activation of factor X in the intrinsic pathway of coagulation. Example from mouse (precursor): database code FA8_MOUSE, 2319 amino acids (266.15 kDa). Factor IX (or Christmas factor) concn. 3-4 mg L-I human plasma; 57 kDa (human), 55.4 kDa (bovine); a vitamin Kdependent single-polypeptide-chain glycoprotein containing 17% carbohydrate (human; 25% in bovine) and y-carboxyglutamate residues. After proteolytic activation it consists of two chains: factor IXa, a serine proteinase, EC 3.4.21.22, of 27 kDa that activates factor X in the intrinsic pathway of coagulation; and a light chain of 16 kDa that contains the y-carboxyglutamate residues. Example from dog (precursor): database code FA9_CANFA, 452 amino acids (50.83 kDa). Factor X (or Stuart-Prower factor; other names: Stuart factor; thrombokinase; prothrombase; prothrombinase) concn. 6-8 mg L- 1 human plasma; a vitamin K-dependent two-polypeptide-chain glycoprotein, containing 15% carbohydrate (human; 10% in bovine). The 40 kDa chain is a serine proteinase while the 15 kDa chain contains 12 y-carboxyglutamate residues. Example (precursor) from human: database code FAlO_HUMAN, 488 amino-acid residues (54.67 kDa). It is the circulating precursor to the proteinase factor Xa, EC 3.4.21.6, that converts prothrombin into thrombin by selective cleavage of Arg-I-Thr then Arg-j-Ile bonds. Factor XI (or plasma thromboplastin antecedent) 160 kDa (human), 124 kDa (bovine); a protein of two disulfide-linked chains of apparently equal molecular mass. Example from human: database code FAll_HUMAN, 625 amino acids (70.03 kDa). It is the circulating precursor of the serine proteinase factor XIa, EC 3.4.21.27, to which it is converted by proteolysis: selective cleavage of Arg-I-Ala and Arg-I-Val bonds in factor IX to form factor IXa triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX. Factor Xla converts factor IX into factor IXa. Factor XII (or Hageman factor) 80 kDa (human), 74 kDa (bovine); a single-polypeptide-chain glycoprotein. It is the circulating precursor of the proteinase factor XIIa, which activates factor XI. Example from human (precursor): database code FAI2_HUMAN, 615 amino acids (67.82 kDa).

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blood group Factor ~lII (or plasma transglutaminase) 320 kDa (plasma, tetramenc), 160 kDa (platelets, dimeric). An enzyme precursor whose subunits are proteolytically cleaved by thrombin to form the transglutaminase, factor XlIla, EC 2.3.2.13, which covalently cross-links fibrin monomers into the fibrin polymer. Prekallikrein a plasma protein, 88 kDa (bovine), that is the precursor of the proteinase kallikrein. This consists of a heavy chain (52 kDa) and a light chain (33-38 kDa) and cleaves factor XII to form factor XIIa. High-molecular-weight kininogen a single-polypeptide-chain glycoprotein of~150 kDa (human), 76 kDa (bovine). It is the source of bradykinin, which is released from it by kallikrein, and acts as an accessory protein in the activation of factor XI by factor XIIa. Example from Bos taurus (precursor): database code KNHl_BOVIN, 621 amino acids (68.89 kDa). Plasminogen 86 kDa (human); a single-polypeptide-chain protein that, on proteolysis, is converted into the protease plasmin, which degrades the fibrin clot. There are two pathways of coagulation: in the intrinsic pathway, which occurs during the clotting of platelet-poor plasma, activation of factor X to factor Xa is effected by the combination of factor IXa + factor VIlla + Ca2+ + phospholipid; in the extrinsic pathway the earlier stages of the cascade are bypassed and the activation of factor X to factor Xa is effected by the combination of factor VIla + thromboplastin; this second pathway occurs when tissue extracts are present in optimal amounts and is much more rapid than the intrinsic pathway. blood group any of various systems of classifying erythrocytes according to their surface isoantigens. In humans 14 different genetically independent blood-group systems are known. They arise from naturally occurring antibodies and from the bloodgroup substances, antigenic substances present on the surface of the erythrocytes of only certain members of a species. These anti~ens are also found in a wide variety of other tissues, includmg endothelial and epithelial cells, and in certain body fluids. The specificities of the blood-group antigens arise in some cases from oligosaccharide chains linked to protein or lipid (ceramide); antigens that fall into this category are those associated with the ABH system, Lewis system, Ii system, and PllP-related system. In other cases, antigenicity arises directly from the polypeptide chain composition of a surface protein; antigens that fall into this category are associated with the MN system, Ss system, Gerbich system, Rhesus system, Kell system, Duffy system, and Cromer-related system. The bloodgroup substances were discovered because of the presence in human blood of naturally occurring antibodies (Le. not resulting from infection or other external cause) that react with these antigens on red blood cells causing them to agglutinate. Only the presence of a blood-group antigen during fetal life ensures that no antibody against it will be produced. Hence if blood from an individual (the donor) who lacks a particular antigen is transfused into an individual (the recipient) who possesses the same antigen, a transfusion reaction will result in the recipient owing to the presence in the donor's blood of antibody against the antigen in question. The blood-group substances have therefore been of interest largely in relation to blood transfusion, and in most cases the true physiological function of these substances is unknown. blood-group substance any of numerous antigenic substances present on the surface of erythrocytes of certain members of a species but absent from those of other members of the same species. These same antigens are also found in a wide variety of tissues and in certain body fluids, e.g. saliva, milk, gastric juice, seminal fluid, urine, and ovarian-cyst fluid. The specificities of the A, B, and H antigens of the ABO system are determined by structures present at the nonreducing ends of oligosaccharides of both glycoproteins and glycolipids. The Lew.is an.tigens, Lea and Leb, are associated with glycosphmgohptds adsorbed from plasma lipoproteins on to adult

blue shift cells and are not synthesized in the developing erythrocyte. Antigenic determinants of the MN system are associated with glycoproteins rich in sialic acid. blood plasma 1 the fluid portion of blood in which the red blood cells and other cellular components (the 'formed elements') are suspended. Clotting may be prevented by the addition of disodium hydrogen citrate which removes ionized Ca2+ by the formation of an un-ionized complex. Fluoride or oxalate may also be used to precipitate the Ca as an insoluble salt. Heparin is often used. When whole blood containing such an anticoagulant is centrifuged, the formed elements sediment in a volume equal to about 45% of the total volume of blood. The supernatant is known as the plasma. In vertebrates it is clear and almost colourless and clots as easily as whole blood. See also anticoagulant. Compare serum. blood sugar old term for the glucose concentration in the blood; when estimated by older methods it included small amounts of other reducing substances. See also glycemia. blotting or blot transfer a technique useful for identifying similar macromolecules, e.g. sets of DNA or RNA fragments, or mixtures of intact proteins, that are separable by gel electrophoresis. The separated components are then transferred from the gel to a sheet of an appropriate medium while preserving their two-dimensional relationships. This can be achieved either by capillary flow between an underlying wick loaded with buffer solution and an overlay of dry blotting paper, or by applying an electric potential to move separated components on to the medium, to which they bind firmly. Once on the transfer medium the substances may be detected with specific radioactive or fluorescent probes, e.g. complementary polynucleotides or antibodies. The original version of the technique, used for DNA fragments and often referred to as Southern blotting, has been extensively developed and adapted for other applications, e.g. dot hybridization (or dot blotting), colony hybridization, electrophoretic transfer, Northern blotting, and Western blotting. blue agarose any insoluble beaded form of agarose gel that is artificially cross-linked between the individual polysaccharide chains and conjugated with the dye Reactive Blue 2. Carboxymethyl (CM) or diethylaminoethyl (DEAE) groups may also have been introduced. It is useful in triazine-dye affinity chromatography. blue dextran a soluble dextran, of average M r 10 6, conjugated with the dye Reactive Blue 2. It is useful in gel filtration for checking column packing and determining the void volume. blue-green algae an alternative name for cyanobacteria. blue oxidase any of a small number of copper-containing oxidase enzymes in which the product of enzyme action in the reduction of dioxygen is water. Blue oxidases are the most complicated of copper proteins; the blue colour is due to a strong absorption band around 600 nm. Among the blue oxidases are laccase (EC 1.10.3.2), L-ascorbate oxidase (EC 1.10.3.3), and the weak oxidase ceruloplasmin. blue shift any shift of the peaks of absorption or emission of a spectrum of electromagnetic radiation to shorter wavelengths, including from the visible to the ultraviolet region.

Blue Tetrazolium

77

Blue Tetrazolium Blue Tetrazolium or Tetrazolium Blue 3,3'-dianisole bis[4,4'(3,5-diphenyl)tetrazolium chloride]; a dye that yields a darkblue diformazan pigment on reduction; it has a redox potential of approximately -0.08 V. It is useful as a stain for bacteria and moulds, in histochemical studies to demonstrate oxidoreductase activity, and in the colorimetric assay of some dehydrogenases. blunt end (of DNA) an alternative term for flush end (of DNA). B lymphocyte or B cell or (archaic) bursacyte any 'bursadependent' lymphocyte concerned in the synthesis of circulating antibody. B lymphocytes arise from primitive lymphoid cells of the bone marrow and develop into the plasma cell series. Their maturation is determined by processing within the bursa of Fabricius in birds, or equivalent hematopoietic tissue in other vertebrates. B lymphocytes may be differentiated from T lymphocytes by their surface markers which contain immunoglobulins. In humans the majority of B lymphocytes are derived from bone marrow stem cells, but a minor population, distinguished by the CD5 marker, appears to form a selfrenewing set. Cells in this set respond to a number of common microbial antigens and sometimes generate autoantibodies. 8mi-1 a murine gene encoding a protein that is probably a transcriptional regulator. It is named from B-cell-specific Moloney murine leukemia virus integration site. The protein contains putative zinc finger and heliX-loop-helix domains, as well as C-terminal PEST sequences. See PEST hypothesis. BMP abbr. for bone morphogenetic protein. BMR abbr. for basal metabolic rate. BNP abbr. for brain natriuretic peptide (see natriuretic peptide). boat conformation any conformation of a nonplanar sixmembered saturated ring compound when ring atoms in relative positions I, 2, 4, and 5 lie in one plane, and those in relative positions 3 and 6 lie on the same side of that plane. Boat conformations of a monosaccharide or monosaccharide derivative may be designated by the conformational descriptor -E. See also cyclic compounds at conformation. Boc or ,-BOC symbol for the tert-butoxycarbonyl group, (CH 3hC-O-CO-, a protecting group used in polypeptide chemistry. It can be introduced using reagents such as di-tert-butyl dicarbonate (Boc anhydride). BOD abbr. for biochemical oxygen demand. body water the water content of the body of an organism. The total body water (abbr. TBW) of a man of average build (70 kg) has a volume of approximately 42 L and represents'" 60% of the body weight. It may be divided functionally into two parts: intracellular fluid and extracellular fluid. Bohr 1 Christian Bohr (1855-191 I), father of N. H. D. Bohr (see def. 2), Danish physiologist noted for his researches on the binding of dioxygen to hemoglobin (see Bohr coefficient, Bohr effect). 2 Niels Henrik David Bohr (1885-1962), son of C. Bohr (see def. I), Danish physicist distinguished for his theories of atomic and nuclear structure and their applications; Nobel Laureate in Physics (1922) 'for his services in the investigation of the structure of atoms and of the radiation emanating from them'. Bohr coefficient (for hemoglobin) the ratio of the change in the logarithm of the partial pressure of oxygen when there is half-saturation of the hemoglobin to the change in pH; i.e. dlogP50/dpH. See also Bohr effect. [After C. Bohr; see Bohr (def.2).] Bohr effect the variation of oxygen affinity of hemoglobin with pH (the oxygen affinity increases with increasing pH). It is one of the effects arising from oxygen-linked acid groups in hemoglobin and similar oxygen-carrying proteins, and also encompasses similar effects involving other acid-linked functions, e.g. oxidation loss of protons causing increased dioxygen binding. The effect was discovered by C. Bohr et al. following observations that changes in the partial pressure of CO 2 influence the oxygen equilibrium of the blood. Bohr magneton symbol: PB; the intrinsic magnetic moment of an electron given by PB = eh/41tm e , where e is the elementary charge, h is the Planck constant, and me is the rest mass of an

bombyxin electron. It is a fundamental physical constant, of value 9.2740154(31) x 10-24 J T-l. Compare nuclear magneton. [After N. H. D. Bohr; see Bohr (def. 2).] boivinose the o-enantiomer, 2,6-dideoxy-o-xylo-hexose, is a component of some cardiac glycosides. Bollum's enzyme DNA nucleotidylexotransferase, EC 2.7.7.31. See terminal transferase. [After Frederick James Bollum (1927- ), who described it in 1971.] Bolton and Hunter reagent or Bolton-Hunter reagent 3-(4hydroxyphenyl) propionic acid N-hydroxysuccinamide ester, iodinated with 1251. This may be the di-iodo derivative, or the commercially available mono-iodo N-succinimidyl 3-(4hydroxy-5-[lz5I]iodophenyl)propionate; a reagent for conjugation labelling of polypeptides or proteins with iodine-125. It is specific for free amino groups, which under mild conditions become acylated to form (4-hydroxy-5-[l z5 I]iodophenyl)propionylamino groups. [After Anthony E. Bolton and William M. Hunter who described its use in 1972.] Boltzmann constant symbol: k; the ratio of the gas constant, R, to the Avogadro constant, N A . It is given by k R/N A = 1.380658 (12) x lO- z3 J K-I [After Ludwig Boltzmann (1844-1906), Austrian physicist.] Boltzmann distribution law a law describing the population distribution of a system of particles in different energy states but at thermal equilibrium, given by: n;lno = e-(Ej-EO)lkT, where nj is the number of particles in energy state i, no is the number in the lowest energy state, E j and Eo are the energies of states of i and 0 respectively, T is the thermodynamic temperature, and k is the Boltzmann constant. bolus 1 a soft, rounded mass, especially of chewed food. 2 a large pill, as used in veterinary or clinical medicine. bomb calorimeter an apparatus with which the heat of combustion of a substance may be determined. The substance is placed in a metal bomb with dioxygen under pressure, and then ignited electrically. The heat evolved is measured by the rise in temperature of the water in a surrounding jacket. bombesin a tetradecapeptide amide isolated from frog skin. It has an N-terminal 5-oxoprolyl residue and shows striking sequence homology with other peptides isolated from amphibian skin, all of which have a C-terminal methioninamide residue. The sequence is (toad): XQRLGNQWAVGHLM-NH z, database code (for precursor) BOMB_BOMOR, 119 amino acids (13.86 kDa). In mammals it is a potent releaser of, inter alia, gastrin and cholecystokinin, and bombesin-like immunoreactivity has been detected in mammalian gut and brain. It is mitogenic in a number of cell types and stimulates smooth muscle contraction. The peptide is said to occur in gastrointestinal nerves of mammals, while in frogs and birds it occurs in endocrine cells. bombesin receptor any of several membrane proteins that bind bombesin and mediate its intracellular effects. Binding studies have indicated two receptor subtypes: on gastrin releasing peptide (GRP)-preferring receptors (e.g. rat pancreas), GRP is more potent than neuromedin B; on other receptors (e.g. rat esophagus) neuromedin B is more potent than GRP. All receptors are of the seven-transmembrane-helix, G-protein-coupled type. The effector pathway involves the phosphoinositide/Ca 2 + second messenger system (see phosphatidylinositol cycle). Example from human: database code BRS3_ HUMAN, 399 amino acids (44.41 kDa). bombolitin any of five structurally related peptides from the venom of the bumblebee, Megabombus pennsylvanicus, that are rich in hydrophobic amino-acid residues. They all lyse erythrocytes and liposomes, release histamine from mast cells, and stimulate phospholipase A z; their properties are similar to those of melittin. Example, bombolitin I: database code BOLl_ MEGPE, sequence IKTITTMLAKLGKVLAHV (1.836 kDa). bombyxin any of a family of brain secretory peptides of the silkmoth that activate pro thoracic glands to produce

=

78

bond ecdysone. They contain an A and B chain joined by disulfide bonds, and are homologous to vertebrate insulins. Example, bombyxin A-9 (precursor): database code BXA9_BOMMO, 92 amino acids (10.29 kDa); residues 20-47 are the B chain, 73-92 the A chain. bond 1 or covalent bond a region of high electron density between atoms that arises, at least partly, from sharing of electrons and gives rise to an attractive force and a characteristic internuclear distance between the atoms. See coordination, dipolar bond, hydrogen bond. 2 the representation of a covalent bond in an extended chemical formula. 3 to join or link together (esp. chemical entities); to ligate (def. I). bond angle the angle formed between two bonds at a given polyvalent atom. bond-dissociation energy see dissociation energy. bond energy 1 the average value of the gas-phase bond dissociation energies (usually at 298 K) of a given type of bond in the same chemical species: mean bond energy. 2 loosely, the free energy change occurring on hydrolysis of a hydrolysable chemical bond. bonding the act or process of forming a covalent bond (def. I); the state of being so linked. See also domain of bonding. bond length the distance between the centres of the nuclei of two bonded atoms. bone the hard, dense connective tissue that constitutes the skeleton of many animals. It consists of an organic matrix impregnated with bone mineral salts. The matrix is made up of 90-95% type I collagen, a small amount of proteoglycan, and a 49-residue protein containing three y-carboxyglutamate residues, the formation of which is vitamin K-dependent. This protein binds strongly to the hydroxyapatite crystals of the bone mineral. The inorganic part of the bone consists largely of basic calcium phosphate, which is organized into small crystals of hydroxyapatite, 0.8-1.5 nm thick, 2-4 nm wide, and 20-40 nm long, of approximate composition CalO(P04)6(OHh. Other anions present are carbonate, fluoride, hydroxide, and citrate. Most of the body's M g2+, about 25% of its Na+, and a smaller proportion of its K+ is found in bone. bone GLA-protein (BGPl see osteocalcin. bone marrow the soft tissue contained within the internal cavities of bones. Red marrow (or myeloid tissue), found in developing bone, ribs, vertebrae, and in parts of the long bones, is actively hemopoietic and contains all the cells of the circulating blood and their precursors together with megakaryocytes, reticulum cells, macrophages, and plasma cells. In adult animals the marrow of many bones, particularly limb bones, becomes filled with fatty tissue known as yellow marrow. In adult mammals, B lymphocytes develop and differentiate in the bone marrow. bone-marrow-derived cell any cell derived from bone marrow tissue, including erythrocytes, lymphocytes, granulocytes, etc. The term is often used misleadingly to refer to the B lymphocytes. bone morphogenetic protein any of several zinc metalloendopeptidases enzyme belonging to the sub-subclass EC 3.4.24 and having an EGF motifrepeat; they are members of the astacin subfamily.BMP enzymes are disulfide-linked homodimers of the transforming growth factor-~ family and are related to tolloid. They are involved in induction of bone and cartilage formation. Example BMP-I precursor from human: database code BMPLHUMAN, 730 amino acids (82.81 kDa). bone sialoprotein 1 see osteopontin. bongkrekic acid 3-carboxymethyl-17-methoxy-6,18,21trimethyldocosa-2,4,8, 12, 14, 18,20-heptaenedioic acid; a toxic antibiotic formed by Pseudomonas cocovenenans grown on partially defatted coconut. It is named after 'bongkrek', a product of mouldy Indonesian coconut that becomes highly toxic when the Pseudomonas outgrows the mould. It is an inhibitor of oxidative phosphorylation, an effect ascribable to its inhibitory action on mitochondrial adenine nucleotide

botulinus toxin translocation, apparently by fixing the adenine nucleotides to the translocation sites thus rendering dissociation of the nucleotides from the translocator rate-limiting in the overall transport process. Compare atractyloside.

COOH

booster dose a second or subsequent dose of antigen, especially in the form of a vaccine, given after the priming dose with the object of stimulating rapid production of large amounts of antibody. Born. Max (1882-1970), German-born British physicist; Nobel Laureate in Physics (1954) 'for his fundamental research in quantum mechanics, especially for his statistical interpretation of the wavefunction' [prize shared with W. W. G. F. Bothe). Born equation an equation for the free energy change, ~G, when a sphere of charge e and radius r is brought into a uniform medium of unvarying dielectric constant D: -~G = (1 - IID)(e 2f2r).

borohydride any member of a group of compounds with the structure MBH4 , where M is an alkali metal. These compounds will reduce aldehydes, ketones, and Schiff bases in nonaqueous solvents, and also acids, esters, acid chlorides, and nitriles. 3H-labelled borohydrides are useful for the facile reductive tritiation of the aforementioned compounds. boronyl the group -B(OHh; it is used attached to a matrix to complex with cis-diols (as in some saccharides). borosilicate (glass) a silicate glass containing at least 5% boric oxide. Such a material has a high melting point and a low coefficient of thermal expansion, and hence is useful for the manufacture of heat-resistant glassware. boss symbol for bride-of-sevenless gene (see Sevenless protein). Bothe. Walther Wilhelm Georg Franz (1891-1957), German experimental physicist noted for his development (with H. Geiger) of the coincidence method of particle counting and for his discovery of the particle later identified as the neutron; Nobel Laureate in Physics (1954) 'for the coincidence method and his discoveries made therewith' [prize shared with M. Born). bottom yeast the popular name for any of various strains of brewers' yeast that effect fermentation at a comparatively low temperature and tend to sediment to the bottom of the fermentation vessel. It is used for the manufacture of light beers, e.g. lager. Bottom yeast is generally distinguishable from top yeast by its ability to produce extracellular p-galactosidase, EC 3.2.1.23. botulinus toxin a mixture of exotoxins formed by Clostridium botulinum, the causal agent of botulism, that is a potent inhibitor of acetylcholine release from cholinergic neurons, possibly by inactivation of actin involved in transmitter exocytosis. There are several types, depending on the strain of the producing organism; all comprise a disulfide-linked heterodimer of heavy (H) and light (L) chains. The L chain has the pharmacological activity and the B chain has domains that mediate channel formation (N terminus) and toxin binding (C terminus). Example, type A precursor: database code

79 Bouguer-Beer law BXA_CLOBO, 1295 amino acids (149.15 kDa): amino acids 1-447 form the L chain and 448-1295 form the H chain. Bouguer-Beer law another name for Beer's law (def. 1). Bouguer's law a physical law stating the relation between the amount of light transmitted by an absorbing medium and its thickness, based upon the finding that successive equal thicknesses of sheets of glass absorbed equal fractions of the light incident upon them. It may be expressed in the form I trs Ioe~kd, where 10 is the intensity of the incident light, I trs is the intensity of the transmitted light, d is the thickness of the absorbing medium, and k is a constant. The law was later restated by Lambert ~ see Lambert's lew (of absorption) ~ and extended to solutions by Beer ~ see Beer's law (def. I). [After Pierre B. Bouguer (1698-1758), French astronomer and mathematician who discovered it in 1728.] boundary any zone of transition, either between solvent and solution or between two solutions; i.e. a zone in which the composition of a solution changes. boundary spreading the broadening of a boundary during ultracentrifugation of macromolecules due to the effects of diffusion. bound-to-free ratio abbr.: B/F ratio; the ratio of the amount of a ligand bound by a specific macromolecule or receptor to the amount of ligand free in solution, in a specified system. Plotting [B]/[F] versus [F] yields a Scatchard plot. bouvardin a cyclic hexapeptide isolated from the plant Bouvarda ternifolia, used as a drug against dysentery. It has antitumour properties and inhibits eukaryotic protein synthesis. bovine of, belonging to, or characteristic of the ox tribe Bovini, which includes cattle, especially of the genus Bos. bovine albumin or bovine serum albumin see serum albumin. bovine pancreatic inhibitor or bovine pancreatic trypsin inhibitor or basic protease inhibitor a protein from cattle pancreas that inhibits trypsin, kallikrein, chymotrypsin, and plasmin. A popular molecule for studies on protein folding, etc., it contains three disulfide bonds. Database code: NRL_5PTI and others (e.g. NRL_lTGSZ with bound proteinase). The sequence is: RPDFCLEPPYTGPCKARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA. (10.903 kDa). The 3-D structure is also known. bovine spongiform encephalopathy abbr.: BSE; a transmissible dementia in cattle, sometimes also known as 'mad cow disease', characterized by a spongy degeneration of neuronal cells in the brain and also enlargement of the astrocytes therein. It appears to be caused by a prion, and original outbreaks were thought to be the result of feeding cattle on offal derived from sheep infected with scrapie. Bowman-Birk inhibitor see soybean trypsin inhibitor. Bowman's capsule or glomerular capsule the dilated, cupshaped vesicle at the proximal end of a nephron that encloses a knot of blood capillaries constituting the glomerulus. It is the site of primary filtration of blood into the nephron. [After William Paget Bowman (1816-92), British histologist and ophthalmic surgeon.] Boyden chamber an apparatus, consisting of two small chambers separated by a micropore filter, used in the study of chemotaxis. Boyle's law see gas laws. [After Robert Boyle (1627-91), Irish chemist and physicist.] bp symbol for base pair(s). b.p. abbr. for boiling point. BP abbr. for 1 blood pressure. 2 British Pharmacopoeia. BPC abbr. for British Pharmaceutical Codex. B peptide or fibrinopeptide B the 20-residue peptide cleaved from the ~ chains of a fibrinogen molecule when it is converted into fibrin by the proteolytic action of thrombin. BPG abbr. for 2,3-bis(phospho)-D-glycerate. BPOC abbr. for biphenylisopropyloxycarbonyl-; an acid-labelling

Bragg group for amino acids, introduced using, e.g., 2-(4-biphenylyl)prop-2-yl 4'-methoxycarbonylphenylcarbonate (reagent structure shown).

=

Bq symbolfor becquerel. Br symbol for 1 bromine. 2 the butyryl group. brachyurin EC 3.4.21.32; other name: collagenolytic proteinase; a serine proteinase that catalyses the hydrolysis of proteins with broad specificity for peptide bonds. It degrades native collagen at about 75% of the length of the molecule from the N terminus; it also shows low activity on smallmolecule substrates of both trypsin and chymotrypsin. Example from Uca pugilator (fiddler crab): database code COGS_UCAPU, 226 amino acids (23.47 kDa). bradykinin or kinin-9 abbr.: BK; a vasoactive nonapeptide, HArg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg-OH, formed by the action of plasma kallikrein, which hydrolyses the sequence out of the plasma globulin kininogen. Glandular kallikrein cleaves kininogen one residue earlier to give the decapeptide Lysbradykinin (kallidin, abbr.: Lys-BK). Met-Lys-bradykinin is also formed, perhaps by the action of leukocyte kallikrein. Pharmacologically important analogues include des-Arg 9 or BK,~& and lIe-Ser-bradykinin (or T-kinin), [Hyp3]bradykinin, and [Hyp4]bradykinin. Bradykinin is formed in a variety of inflammatory conditions and in experimental anaphylactic shock. It is a powerful blood-vessel dilator, increasing vascular permeability and causing a fall in blood pressure; it is also a constrictor of smooth muscle. See also Iysine(arginine) carboxypeptidase. bradykinin receptor any membrane protein that binds bradykinin (BK) and mediates its intracellular effects. Two types of receptor are recognized: B, (previously BK,), on which order of potency is des-Arg 9-bradykinin (abbr.: BKl~&) = kallidin (Lys-BK) > BK; and B2 (previously BK 2), with order of potency kallidin> BK » BK,_&. Hence, BK 1_& is a powerful discriminator. B, receptors are considerably less common than B2 receptors, which are present in most tissues. The rat Bz receptor is a seven-transmembrane-domain protein which has been shown on activation to stimulate phosphoinositide turnover. Examples: B" database code BRBl_ HUMAN, 353 amino acids (40.44 kDa); B z, database code BRB2_HUMAN, 364 amino acids (41.44 kDa). Bragg 1 (Sir) William Henry Bragg (1862-1942), father of W. L. Bragg (see def. 2), British experimental physicist remembered for his invention of the X-ray spectrometer named after him and particularly for his use of it in collaboration with his son in solving many problems of concerning the arrangement of atoms in crystals; Nobel Laureate in Physics (1915) jointly with W. L. Bragg 'for their services in the analysis of crystal structure by means of X-rays'. 2 (Sir) William Lawrence Bragg (1890-1971), son of W. H. Bragg (see def. 1) British experimental physicist, born in Australia, remembered for his formulation of Bragg's law of X-ray diffraction and for the X-ray crystallographic studies in collaboration with his father that were thus made possible, for his subsequent concern with the application of X-ray crystallography to biological macromolecules, and for playing an important part in establishing molecular biology as an independent discipline; Nobel Laureate in Physics (1915) jointly with W. H. Bragg (see def. 1).

80

Bragg's law Bragg's law a law stating that when a crystal is pictured as a

set of reflecting planes uniformly spaced at a distance d and a beam of X-rays of wavelength A strikes the crystal at an angle 8, reinforcement of the reflected waves occurs when sin 8 '" nA/2d, where n is an integer known as the order of reflection. [After W. L. Bragg; see Bragg (see deL 2).] brain-derived neurotrophic factor abbr.: BDNF; a protein that promotes the survival of neuronal populations located either in the central nervous system or directly connected to it. Example (precursor) from chicken: database code BDNF_ CHICK, 246 amino acids (27.68 kDa). brain natriuretic peptide see natriuretic peptide. branch 1 a subdivision of the stem or the root of a plant; any smaller structure growing or arising from a larger one. 2 a side chain attached to the main chain of a molecular entity. 3 to form a branch; to bifurcate; to divide into offshoots. branched adj.; branching n. branched-chain describing any molecular entity with one or more branches (def. 2). branched-chain a-keto-acid dehydrogenase abbr.: BCKDH; EC 1.2.4.4; recommended name: 3-methyl-2-oxobutanoate dehydrogenase (Iipoamide); other name: 2-oxoisovalerate dehydrogenase. An enzyme that catalyses the conversion of a-oxo acids to acyl-CoA and CO 2 , Thiamine diphosphate is a coenzyme. The enzyme consists of a multienzyme complex of branched chain a-keto-acid dehydrogenase (El), lipoamide acyltransferase (E2), and Iipoamide dehydrogenase (E3). Human enzyme details: El is a dimer of a and p subunits; precursor database code ODBA_HUMAN, 444 amino acids (50.16 kDa) and ODBB_HUMAN, 392 amino acids (43.07 kDa); E2 database code (precursor) ODB2_ HUMAN, 482 amino acids (53.43 kDa). branched-chain a-kato-acid dehydrogenase kinase see [3-methyl-Z-oxobutanoate dehydrogenase (Iipoamidell kinase. branched-chain oxo-acid dehydrogenase phosphatase see [3-methyl·Z-oxobutanoate dehydrogenase (Iipoamidell-phosphatase. branched polymer any polymer in which there are side chains

attached to a main chain. brancher-deficiency amylopectinosis an alternative name for type IV glycogen disease. branching (in nuclear physics) the simultaneous existence of

more than one disintegration pathway for a particular radionuclide. branching enzyme EC 2.4.1.18; recommended name: 1,4-aglucan branching enzyme; systematic name: 1,4-a-D-glucan: 1, 4-a- D-glucan 6-a-v-( 1,4-a- D-glucano)- transferase; 0 ther names: amylo-( 1,4-1 ,6)-transglycosylase; corn starch branching enzyme II; amylo-transglycosylase; glucanotransferase; starch branching enzyme II; any 1,4-a-glucan branching enzyme that catalyses the transfer of a segment of 1,4-a-glucan chain to a primary C-6 hydroxyl group in a similar glucan chain. Branching enzymes fall into two types: the plant Q. enzymes and the mammalian enzymes, which are able to produce glycogen, a more highly branched molecule than the amylopectin produced in plants by Q-enzymes. The name should always be qualified, e.g. glycogen branching enzyme, amylopectin branching enzyme. Example from Zea mays: database code MZEGLUCTRN, 799 amino acids (90.42 kDa). branch migration a proposed model to explain the occurrence of apparently branched DNA structures, as seen by electron microscopy, and their conversion into linear duplex DNA. The branched structures may form by association over parts of their lengths of three or more polynucleotide strands. The migration of the branch point is presumed to occur by displacement of a strand from its fellow in one branch by a strand in another. Such a process may occur in transcription or in recombination. BRCA BRCAI and BRCA2 either of two genes implicated in susceptibility to breast cancer. Up to 80% of women who in-

bridge herit mutated forms of either gene develop breast cancer, and BRCAI mutations imply a high risk of ovarian cancer. brdU or BrdU abbr. for bromodeoxyuridine (the symbol BrdUrd is recommended). BrdUrd symbol for bromodeoxyuridine. Compare BrUrd. breakage and reunion model the classical and generally accepted model of chromosomal crossing-over; it involves breakage of the chromatids and reunion of the alternative fragments. breakpoint cluster region term originally suggested for a limited region of 5-6 kb in the base sequence of chromosome 22, in which breakpoints involved in formation of the Philadelphia chromosome were found to cluster. Molecular cloning of specific areas of DNA (e.g. band 22qll) gave a probe specific for the breakpoint translocation domain. Subsequent work led to this region being identified as the BCR gene. breathing a colloquial term for transient dynamic changes in the structure of macromolecules involving expansion and contraction of the 3-D structure. brefeldin A a fungal metabolite, isolated from Penicillium brefeldianum, that inhibits a wide variety of membrane transformations of importance in intracellular transport. It effects a rapid increase in the volume of Golgi cisternae and loss of recognizable Golgi apparatus in treated cells. There is a rapid reversible dissociation of a Golgi-associated peripheral protein identical with a coat protein subunit of non-clathrincoated vesicles (P-COP). See coatomer.

B region the site of final epoxidation of carcinogenic polycyclic aromatic hydrocarbons. It is located on the terminal ring of the bay region on a bond adjacent to the bay region. Compare A region, Kregion, Lregion. brei a finely and uniformly ground tissue suspension containing

all the enzymes of the original material but with the normal spatial relationships between them disrupted. Compare homo· genate. bremsstrahlung the X-rays produced when an electrically

charged particle, usually a P particle or an accelerated electron, is decelerated by the electric field of an atomic nucleus. The yield is directly dependent upon the magnitude of the atomic number of the target element. [German: braking radiation.] brevetoxin any of the highly toxic lipid-soluble polyether compounds isolated from Ptychodicus brevis (Gymnodinium breve), the red-tide organism. They cause the death of fish and are responsible for shellfish poisoning in humans. They are activators of voltage-dependent Na+ channels. brevin an alternative term for gelsolin. brevinin a secreted amphibian peptide with antibacterial and hemolytic activities. Example, brevinin-l from Rana brevipoda porsa: database code BR LRANBP, sequence FLPVLAGIAAKVVPALFCKITKKC. brewers' yeast the common name for strains of the yeast Saccharomyces cerevisiae that are used in brewing. In addition to their ability to produce, and remain viable under, appreciable levels of ethanol, such strains are able to ferment maltose, maltotriose, and other sugars in the wort, and to withstand its relatively high osmotic pressure. See also bottom yeast. bridge (in chemistry) a valence bond, atom, or unbranched chain of atoms connecting two different parts of a molecule.

81

Bromothymol Blue

bridgehead bridgehead (in chemistry) either of the two atoms, e.g. tertiary carbon atomks, that are connected by a bridge. bridge-receptor any molecular entity with two or more specific binding sites able to interact with and join a corresponding number of complementary ligands, which mayor may not be the same. Briggs-Haldane theory an alternative to the Michaelis-Menten theory of the kinetics of enzyme reactions for cases where breakdown of the enzyme-substrate complex to products is not slow ill comparison with its dissociation to enzyme and substrate. Compare Michaelis kinetics. [After George Edward Briggs (1893-1985), British plant physiologist, and John Burdon Sanderson Haldane (1892-1964), British enzymologist, geneticist, philosopher, and popularizer of science, who put forward their theory in 1925.] Brij proprietary name for any of a series of polyethylene ethers of higher fatty alcohols. They are surfactants useful for the solubilization of membrane fractions. Brij 35 is polyoxyethylene (23) lauryl ether, aggregation number 40, CMC 92 ).1M. British antilewisite abbr.: BAL; another name for dimercaprol. British thermal unit abbr.: Btu; a non-SI unit given by the energy required to raise the temperature of I pound of water through 1°F. Since this depends on the temperature of the water, the temperature range should be specified. The Btu(mean), defined as the 1/180 part of the energy required to raise the temperature of I pound of water from 32 of to 212 OF, is equal to 1055.06 J. Srk abbr. for Bek-related kinase; an alternative name for Cek2. See Cek. SRN a family of neurally expressed genes encoding brainspecific transcription factors. They contain a POU domain. Brn3.1 and Brn-3.2 modulate the terminal differentiation of auditory and visual system development respectively. Example, Brn-I from Mus musculus: database code BRNI_MOUSE, 495 amino acids (50.01 kDa). broad host range relating to the ability of a plasmid to be subjugated as a vector in a broad range of hosts, especially Gramnegative bacteria. Such plasmids are also termed promiscuous. broad-spectrum antibiotic any antibiotic that is active against a wide range of bacterial species. Brockmann body a discrete organ, occurring in fish, that contains tissue corresponding to that found in the islets of Langerhans of mammals. One or more Brockmann bodies occur in various teleost species. They are free of pancreatic acinar tissue, which makes them particularly suitable for biochemical studies and a good source of fish insulin. The principal islet weighs in the region of I-50 mg; smaller secondary islets may also occur. Brodie's fluid a manometer fluid containing 23 g NaC!, 5 g sodium tauroglycerate, 100 mg Evan's Blue, and a few drops of an ethanolic thymol solution, in 1000 mL of water; D = 1.033. The standard pressure (760 mmHg) in mm of manometer fluid is 10 000. brom+ a variant form ofbromo+. bromelain or bromelin either of two similar cysteine proteinases: stem bromelain, EC 3.4.22.32, isolated from the stem of the pineapple, Ananas comosus; and fruit bromelain, EC 3.4.22.33, from the same plant. They are broad-specificity proteinases, similar to other cysteine proteinases but with so far unique geometry and reactivity at the active site. The two types of enzyme are distinguished by the substrate Z-Arg-Arg-NHMec, which is hydrolysed by stem bromelain but not by fruit bromelain. Stem enzyme: database code BROM_ANACO, 212 amino acids (22.81 kDa). bromination the introduction of one or more bromine atoms (bromo residues) into an organic molecule, whether by addition or substitution. -brominate vb. bromine symbol: Br; a halogen element of group 17 of the IUPAC periodic table; atomic number 35; relative atomic mass 79.909. Natural bromine consists of the two isotopes 79Br and slBr at almost equal relative abundances.

bromine-82 the radioactive nuclide ~3Br; half-life 35.3 h; it emits beta radiation (0.444 MeV) and gamma radiation of various energies. bromo+ or (sometimes before a vowel) brom+ prefix denoting a bromine atom in organic linkage. bromocriptine or bromoergocriptine 2-bromoergocryptine; an ergotoxin ergot alkaloid derivative that acts as a dopamine (D z) receptor agonist. It inhibits the secretion of prolactin and somatotropin by the pituitary gland, and has potential applications in the treatment of Parkinson's disease.

Br

bromodeoxyuridine symbol: BrdUrd; 5-bromo-2'-deoxyuridine; 5-bromouracil 2'-deoxyriboside; a synthetic analogue of thymidine. It acts as an inhibitor of cell differentiation, and also has antiviral properties. See bromouracil. Bromophenol Blue a dye used as a pH indicator, changing from yellow to blue over the pH range 3.0-4.6

Br

Br

Bromophenol Red a dye used as a pH indicator, changing from yellow to red over the pH range 5.2-6.8

Br OH

Bromothymol Blue a dye used as a pH indicator, changing from yellow to blue over the pH range 6.0-7.6

Br OH

82

bromouracil

B-transferase

bromouracil

medium. [After Robert Brown (1773-1858), British botanist who first observed it in 1827.] browning reaction any of a group of complex reactions, both enzymic and nonenzymic, that occur in some foods during processsing and/or storage and cause a brownish discoloration. Members of this group include the oxidation of phenolic compounds (which is believed to be enzymic) together with caramelization, ascorbate decomposition, and the Maillard reaction (all of which are believed to be nonenzymic). brucine 2,3-dimethoxystrychnidin-lO-one; a highly toxic bittertasting alkaloid obtained from Strychnos seeds. It is used as a resolving agent for some racemates. Compare strychnine.

symbol: BrUra; 5-bromouracil; 5-bromo2,4(1H,3H)-pyrimidine-dione; a synthetic analogue of thymine with mutagenic activity. It is incorporated into DNA as bromodeoxyuridine, which replaces thymidine and induces transitions of G-C base-pairing to A-T pairing. It can be used as a density marker for DNA. The free compound is an inhibitor of dihydrouracil dehydrogenase.

Br~

l ~O .... NH

H

bromouridine symbol: B or BrUrd; 5-bromouridine; 5-bromo-

uracil riboside; a synthetic analogue of ribothymidine. Br.nsted catalysis law an expression of the relation between the rate constant, k, of a catalysed reaction, and the pK of the catalyst: logk = c + bpK, where band c are constants and the

value of b provides a measure of the balance between nucleophilic and general base character of the catalysis. [After Johannes Nicolaus Bmnsted (1879-1947), Danish physical chemist.] Br.nsted-Lowry acid any chemical species capable of donating a hydron to a base. Examples are H 20, H 30+, CH 3COOH, H2P04~, NH 4+. [After J. N. Bmnsted (see BrBnsted catalysis law) and Thomas Martin Lowry (1874-1936), British chemist.] Br.nsted-Lowry base any chemical species capable of accepting a hydron from an acid. Examples are OH~, H 20, CH3COO~, HP042~, NH 3. Brookhaven database see PDB. broth (in bacteriology) any liquid culture medium, especially nutrient broth. Brown. Michael Stuart (1941- ), US physician and molecular geneticist notable for his discovery (in collaboration with J. L. Goldstein) of cellular receptors for low-density lipoproteins and their role in the removal of cholesterol from the bloodstream; Nobel Laureate in Physiology or Medicine (1985) jointly with J. L. Goldstein 'for their discoveries concerning the regulation of cholesterol metabolism'. brown adipose tissue a highly specialized tissue with a high content of lipid and cytochromes found in some animals, particularly hibernating animals and the newborn of some species. It is highly vascular and consists of small polygonal cells, each containing many separate lipid droplets and many mitochondria. Its function is thermogenesis during the arousal period after hibernation or, in the young, to provide heat before shivering has developed. It is active also in normal but not in obese humans. The colour is due to the high cytochrome content. Heat is generated by lipid oxidation through electron transport not coupled to oxidative phosphorylation. The uncoupling is mediated by brown fat uncoupling protein. Compare white adipose tissue. brown fat uncoupling protein abbr.: UCP; other names: mitochondrial UCP; thermogenin; a dimeric integral mitochondrial inner membrane protein that forms an H+-channel, is unique to brown adipose tissue mitochondria, and is important for thermogenesis of this tissue. By causing the membrane to leak protons, it abolishes the proton gradient that drives oxidative phosphorylation, so that electron transport results solely in heat production. Example from mouse: database code UCP_MOUSE, 306 amino acids (33.08 kDa). Brownian movement the peculiar random movements shown by microscopic particles in a disperse phase, i.e. when suspended in a liquid or gas. It is caused by the continuous irregular bombardment by the molecules of the surrounding

BrUra symbol for bromouracil. BrUrd symbol for bromouridine (alternative to B). Compare BrdUrd. brush border the dense covering of microvilli on the apical sur-

face of epithelial cells in the intestine and kidney. The microvilli aid absorption by increasing the surface area of the cell. bryostatin any of a number of highly potent activators of protein kinase C found in bryozoans, especially Bugula neritina. They were isolated as the active anti-leukemic agent of bryozoan extracts. They block phorbol ester-induced differentiation of human promyelocytic leukemia cells and other actions of phorbol esters.

bryostati n 1

BSA abbr. for bovine serum albumin. See serum albumin. BSE abbr. for bovine spongiform encephalopathy. B side the side of the nicotinamide ring of NADH or NADPH at which projects the pro-S hydrogen atom (known as H B) at the 4 position. Compare A side. BTEE abbr. for N-benzoyl-L-tyrosine ethyl ester (a substrate for

the assay of chymotrypsin). B-transferase EC 2.4.1.37; recommended name: fucosylglyco-

83

Btu protein 3-a-galactosyltransferase; other name: [histo-blood group] B transferase; an enzyme that catalyses the reaction: UDPgalactose + glycoprotein a-L-fucosyl-(l,2)-D-galactose = UDP + glycoprotein a-D-galactosyl-(I ,3)-[a-L-fucosyl-(l ,2)]L-galactose, thus adding galactose to the H antigen of the ABH antigen system, leading to formation of the B antigen. The protein is a product of one allele of the ABO gene. It has virtual identity of sequence with that catalysing A-transferase activity, differing only at residues 176 (A has Arg, B has Gly), 235 (A Gly, B Ser), 266 (A Leu, B Met), and 268 (A Gly, B Ala). Database code BGAT_HUMAN, 354 amino acids (40.89 kDa). Btu abbr. for British thermal unit. Bu symbolfor the butyl group. BU (sometimes) abbr. for bromouracil (BrUra is recommended). bubble column a column-shaped bioreactor in which the reaction medium is kept mixed and aerated by the introduction of air at the bottom. Buchner, Eduard (1860-1917), German chemist and biochemist renowned for his seminal discovery that alcoholic fermentation could be initiated with a cell-free press juice from brewers' yeast, the active principle of which he considered to be a protein denoted zymase; Nobel Laureate in Chemistry (1907) 'for his biochemical researches and his discovery of cell-free fermentation' . Buchner funnel a cylindrical funnel for filtration, usually of porcelain or plastic, that includes a perforated plate on which a filter paper is placed. It is generally used with a vacuum. See also Hartley fiher funnel. bud 1 a small lateral or terminal protuberance on the stem of a plant that contains undeveloped foliage or floral leaves. 2 a budlike protuberance on the surface of a yeast cell or other simple organism. 3 to form a bud. 4 to reproduce asexually, as in yeasts, by the process of budding. Buddha suite of computer programs for structure refinement and energy minimization. budding 1 the production of a bud or buds. 2 a form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell. BUdR or BUDR (sometimes) abbr. for bromodeoxyuridine (the symbol BrdUrd is preferred). bufadienolide any of various naturally occurring doubly unsaturated lactones of certain steroids with important pharmacological effects on heart muscle (see cardiac glycoside). They are so named because they were originally found in the venomous secretion of the skin glands of some toads (Bufo), and are hence also known as toad poisons. They also occur in certain plants, e.g. Digitalis. See also bufogenin B. buffer 1 any substance or mixture of substances that, when dissolved (usually in water), will maintain its solution at approximately constant pH despite small additions of acid or base. The commonest examples are moderately strong solutions containing both a weak acid and its conjugate base (or a weak base and its conjugate acid). A substance is useful as a buffer over a range of about one pH unit either side of its pK, but is most effective at or near the pK. Buffer substances used for biochemical or biological purposes include: acetate, bicarbonate, bis-tris propane, borate, citrate, dimethylmalonate, glycinamide, glycylglycine, imidazole, phosphate, succinate, and Tris together with any Good buffer substances. By extension, the term may be applied to agents controlling the activities of various other specified entities, e.g. redox buffer, carbon-dioxide buffer, metal-ion buffer. Also used attributively: e.g. buffer action; buffer salt; buffer solution. 2 a solution of a buffer (def. 1).3 a short-term storage facility (e.g. as part of the memory of a computer), especially one whose patterns or rates

buoyant density of input and output can differ. 4 to treat with or to incorporate a buffer (def. I); to act as a buffer. See also buffering capacity, buffer value. -buffered ad}.; buffering n. buffering capacity or buffering power 1 the number of gramequivalents of either hydrogen ions or hydroxide ions required to change the pH of I litre of I M buffer solution by one unit. Buffering capacity = (11m) (dn/dpH), where m is the number of moles of buffer, and dpH is the pH change produced by addition of dn equivalents of hydrogen ions or hydroxide ions. 2 an alternative term for buffer value. buffer solution see buffer (def. 2). buffer value or Van Slyke buffer value or buffering capacity symbol: fJ; the amount of acid or base, in gram-equivalents, needed to change the pH of I litre of a buffer solution by one unit at any pH; i.e. P = db/dpH, where b is the molar concentration of base in the solution. [After Donald Dexter Van Slyke (1883-1971), US biochemist, who described it in 1922.] buffy coat the layer of white cells that forms between the layer of red cells and the plasma when unclotted blood is centrifuged or allowed to stand. bufogenin B 3P, 14, 16p-trihydroxy-5p-bufa-20,22-dienolide; a bufadienolide found in the Chinese drug Ch'an Su, prepared from Chinese toads (Bufo asiaticus).

bulge loop a structure in a polynucleotide duplex in which one strand contains a nonterminal extra sequence that is not able to base-pair with the second strand, thereby forming a bulge on one side of the duplex. BUN abbr. for blood urea nitrogen, an index of the blood-urea concentration. bundle sheath a parenchymal sheath surrounding a vascular bundle in plants. bungarotoxin any of various neurotoxins derived from the venom of the elapid snake, Bungarus multicinctus. The chief components are: (I) a bungarotoxin, a single polypeptide chain of 74 amino-acid residues; it is an irreversible antagonist of nicotinic cholinergic receptors and causes paralysis; (2) ~ bungarotoxin, a multicomponent protein composed of two polypeptide chains: a long chain (120 amino-acid residues) and a short chain (60 residues); it prevents the release of acetylcholine from cholinergic neurons. Bunsen coefficient symbol: a; the absorption coefficient of a gas in a solution. It is defined as the volume of gas in Iitres, reduced to 273.15 K and I atm (101 325 Pal pressure, that dissolves in I litre of liquid when the partial pressure of the gas in the gas phase is I atm. [After Robert Wilhelm Bunsen (1811-99), German chemist.] bunyavirus any of a group of RNA animal viruses consisting of enveloped particles, 90-100 nm in diameter with helical nucleocapsids, and containing segmented RNA (minus strand) of 3-4 MDa. The group has been recognized as different from togaviruses and includes arthropod-borne viruses that can cause encephalitis. buoyant density the density of a solute molecule as determined by density-gradient ultracentrifugation. It is the density of the solution, p, at the point in the gradient where: p = lIy, where y is the partial specific volume of the solute in question.

84

buoyant force buoyant force symbol: F B ; the force acting on an object suspended in a liquid due to the liquid displaced by the object. It is given by: F B = VPPMg, where V p is the volume of the object, PM is the density of the displaced liquid M, and g is the acceleration due to gravity. burette or (US) buret a graduated (often glass) tube with a pinch-clamp, stopcock, or valve at one end used for measuring or dispensing known volumes of fluids, especially liquids. A graduated syringe used for the same purpose may also be termed a burette. Burkitt's lymphoma a malignant tumour of the lymphatic system, most commonly affecting children in tropical Africa within 15° north and south of the Equator. Epstein-Barr virus can be demonstrated in a proportion of cultured tumour cells though it is unlikely that the virus is the sole cause of the malignancy. [After Denis Parsons Burkitt (\911-93), British surgeon.] Burnet, (Sir) Frank Macfarlane (1899-1985), Australian physician, virologist, and immunologist notable in particular for formulation of the clonal selection theory of acquired immunity; Nobel Laureate in Physiology or Medicine (\960) jointly with P. B. Medawar 'for discovery of acquired immunological tolerance' . Burnet's theory of immunity see clonal selection theory. bursacyte an alternative name (archaic) for B lymphocyte. bursa of Fabricius or cloacal bursa a saclike Iymphoepithelial structure opening into the dorsal part of the cloaca in young birds. It usually degenerates as the birds reach maturity. It is associated with humoral immunity and the lymphocytes processed by it are termed B lymphocytes. In mammals it is likely that hemopoietic tissue itself fulfils the equivalent role, providing the appropriate microenvironment for the maturation of B lymphocytes from precursor stem cells. bursectomy removal of the bursa of Fabricius, either by surgery in ovo or shortly after hatching, or by destruction in ovo by application of, e.g., testosterone. Bursectomy inhibits the formation of B lymphocytes and hence circulating antibody. bursin the tripeptide Lys-His-Gly-NH 2 ; a selective B-cell differentiating hormone from the bursa of Fabricius of chickens. burst 1 the initial pre-steady-state liberation of the first product, B, in an enzymic reaction of the type: E + AB = EAB ---} EA + Band EA ---} E + A, where E is the enzyme and A is the second product. 2 the sudden release of phage particles accompanying lysis of a phage-infected bacterial cell. See also burst size. respiratory burst. burst size the mean number of bacteriophage particles set free per infected bacterium upon lysis of phage-infected cells. butanediol fermentation a type of fermentation effected by some members of the Enterobacteriaceae, e.g. Enterobacter, Erwinia, Klebsiella, and Serratia, in which glucose is fermented with the production of 2,3-butanediol and other substances.

BZLF1 butanoyl another name for butyryl. Butenandt, Adolf Friedrich Johann (\ 903-95), German organic chemist and biochemist renowned for his pioneering studies of steroid hormones and pheromones, especially for his isolation and determination of the structures of the first sex hormones (androsterone, estrone, and progesterone) and the first insect hormone (ecdysone), and for the isolation of the first pheromone (bombykol); Nobel Laureate in Chemistry (\939) 'for his work on sex hormones' [prize shared with L. Ruzicka]. butyl symbol: Bu; the alkyl group, CH r [CH 2h-CH 2-, derived from butane. butyl-PBD see biphenylylphenyloxadiazole. butyrate 1 trivial and preferred name for butanoate; the anion CH 3-[CH 2h-COO-, derived from butyric acid (butanoic acid), a saturated, unbranched, aliphatic acid. 2 any mixture of free butyric acid and its anion. 3 any salt or ester of butyric acid. butyric acid fermentation a type of fermentation effected by some saccharolytic species of Clostridium, e.g. C. butyricum, in which glucose is fermented, with the production of acetic acid, butyric acid, carbon dioxide, and dihydrogen. butyrophenone any of a group of antipsychotic drugs, e.g. haloperidol, that are more selective than the phenothiazine group. Butyrophenones interact rather more specifically with dopamine D 2 receptors and reduce the firing of dopaminergic neurons. butyrophilin a type I membrane protein of mammary gland, probably involved in stimulating the secretion of droplets of fat in milk. Example (bovine, precursor): database code BUTY_BOVIN, 526 amino acids (59.20 kDa). butyryl symbol: Br; trivial and preferred name for butanoyl; the acyl group, CH 3-[CH 2h-CO-, derived from butyric acid (butanoic acid). BX-C abbr. for the bithorax complex, one of two (see ANT-C) major families of homeotic genes in Drosophila, mutations in which affect thoracic and abdominal segments. byte a single unit of information handled by a computer; the binary unit required for storage of a character, usually comprising eight bits. Bz symbol for the benzoyl group. bZIP abbr. for basic zipper; a fingerprint of a family of proteins, named after their two main features: a basic region (b) and a leucine zipper domain (ZIP). The basic region harbours a DNA-contact surface, and the leucine zipper domain is essential for homodimer formation or formation of heterodimers with other leucine zipper proteins. The family includes the AP, ATF, and CREB protein transcription factors. Bzl symbol for the benzyl group. BZLF1 one of a group of transcription factors related to the jun andfos gene products. It is involved in the switch from latency to virus-particle production following infection by Epstein-Barr virus. Database code BZLF_EBV, 245 amino acids (26.83 kDa).

Cc c I symbol for a centi+ (SI prefix denoting 10-2). b cyclic (def. 3) or cyclo+ (denoting cyclic compounds, as in cAMP for cyclic AMP or Hx c for cyclohexyl. c (obsolete) curie (use Ci). 2 abbr. for a complementary (as in eDNA). b cis (not recommended). c (obsolete) cubic (i.e. to the third power). c- (in genetics) prefix denoting cellular, as in c-myc, the cellular as opposed to viral (v-) version of a (proto)oncogene; see, e.g., MYC. C symbol for I amount-of-substance concentration; that for a particular substance may be denoted by adding a subscript, e.g. CB for amount concentration of a substance B. 2 speed (alternative to v, u, or w). 3 (bold italic) velocity (alternative to v, u, or w). c- abbr. for cis-. Co symbol for speed of light in vacuo. The subscript may be omitted when there is no risk of ambiguity. C I symbol for a carbon; see carbon-11, carbon-12, carbon-13, carbon-14. b designating a specific carbon atom, e.g. Col, C-2. c a residue of the a-amino acid L-cysteine (or L-half-cysteine) (alternative to Cys). d a residue of the base cytosine in a nucleic acid sequence. e a residue of the ribonucleoside cytidine (alternative to Cyd). r coulomb. g or (formerly) C' complement (the main components of complement are designated Cl-C9). 2 a high-level computer language based on function evaluation and much used in the development of computer software for molecular biology. ·C symbol for degree Celsius (formerly degree centigrade). See Celsius temperature. C H symbol for the constant region of an immunoglobulin heavy chain. The particular constant domain in question may be indicated as CHI, C H2, C H3. C L symbol for the constant region of an immunoglobulin light chain. C symbolfor I capacitance. 2 heat capacity (Cp at constant pressure, C vat constant volume, Cm molar heat capacity). 3 number concentration (CB for a substance B). C- (in chemical nomenclature) a locant indicating substitution on carbon; a particular carbon atom may be specified by a right superscript. -C a conformational descriptor designating the chair conformation of a six-membered ring form of a monosaccharide or monosaccharide derivative. Locants of ring atoms that lie on the side of the structure's reference plane from which the numbering appears clockwise are indicated by left superscripts and those that lie on the other side of the reference plane by right subscripts; e.g. _ICC, .cc,. See also conformation (def. 2). _1C4 or (formerly) -Ie conformational descriptor for an aldopyranose in the chair conformation, with C2, C3, C5, and 05 in the structure's reference plane, and with Cl above and C4 below the plane; e.g. a-D-glucopyranose-1C4 .

°H

ftr OH

5

4

_

3

HO

,

H

2

OH

'C.

•4C, or (formerly) -ct a conformational descriptor for an aldopyranose in the chair conformation, with C2, C3, C5, and 05 in the structure's reference plane, and with Cl below and C4 above the plane; e.g. a-D-glucopyranose-4 C 1.

Ca symbol for calcium. CAA a codon in mRNA for L-glutamine. CAAT box or CAT box a conserved sequence in DNA found within the promoter region of the protein-encoding genes of many eukaryotes. It has the consensus sequence GGCCAATCT and is believed to determine the efficiency of transcription from the promoter. Cab·O-Sil proprietary name for fumed silica supplied by Cabot Carbon Ltd. CaBP3 see calreticulin. CAC a codon in mRNA for L-histidine. cachectic factor a 24 kDa proteoglycan isolated from the murine adenocarcinoma MAC16 that has been implicated in the production of cachexia. The peptide has the N-terminal sequence YDPEAASAPGSGDPSHEA and has N- and O-glycans. Intravenous injection of the proteoglycan produces rapid weight loss. cachectin see cachexia, tumour necrosis factor-a. cachexia a condition caused by chronic disease, such as cancer, and characterized by wasting, emaciation, feebleness, and inanition. It led to the name 'cachectin' for the protein now known as tumour necrosis factor but a 24 kDa proteoglycan has more probably been implicated in this. See cachectic factor. cacodylate I dimethyl arsinate, the anion (CH 3h-AsOOderived from cacodylic acid. It is useful as a buffer substance (pK. = 6.2). 2 any salt of cacodylic acid. cadaverine 1,5-pentanediamine; a substance formed by microorganisms in decaying meat and fish by the decarboxylation of lysine. It also occurs as an intermediate in the biosynthesis, via lysine, of some quinolizidine alkaloids (e.g. lupinine) in plants. cadherin any member of a family of calcium-dependent cell adhesion proteins that preferentially interact in a homophilic manner in cell-cell interactions. Cadherins may thus contribute to the sorting of heterogeneous cell types; they are type I membrane proteins. The names of different classes indicate the tissues in which they were first found: E-cadherin is present on many types of epithelial cells; N-cadherin is present on nerve, muscle, and lens cells; and P-cadherin is present on placental and epidermal cells. Typically, cadherins have five similar extracellular domains, the outermost three of which have Ca 2+binding sites, and an intracellular C-terminal domain that interacts with the actin cytoskeleton. Examples (all human) Ecadherin precursor: database code CADE_HUMAN, 882 amino acids (97.35 kDa); N-cadherin precursor: database code CADN_HUMAN, 906 amino acids (99.75 kDa); P-cadherin precursor: database code CADP_HUMAN, 829 amino acids (91.32 kDa); three motifs. cadmium mycophosphatin a cadmium-binding phosphoglycoprotein, M, 12 000; it lacks sulfur-containing amino acids, but is rich in aspartic and glutamic acids and phosphoserine . CAD protein a multifunctional protein found in many eukaryotes and containing domains for three enzymes of pyrimidine biosynthesis: carbamoyl phosphate synthase (glutamine-hydrolysing); aspartate transcarbamylase; and dihydroorotase. Ex-

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caerulein

calcitonin

ample from Drosophila melanogaster: database code PYRI_DROME, 2236 amino acids (248.95 kDa). CaeRorhabditis elegaRs a nematode (roundworm), with a genome of about 97 million base pairs. Its cellular anatomy has been fully described, and the nucleotide sequence of the genome determined, revealing over 19 000 genes, 40% of the predicted protein products having significant matches in other organisms. caerulein the Brit. spelling ofcerulein. caeruloplasmin the Brit. spelling of ceruloplasmin. caesium alternative spelling (esp. Brit.) for cesium. caffeine 1,3,7-trimethylxanthine, 3,7-dihydro-I,3,7-trimethylIH-purine-2,6-dione; a substance found in certain plants, notably in tea and coffee and the beverages derived from them. It is an adenosine (AI and A z) receptor antagonist and phosphodiesterase inhibitor, and a stimulant of the central nervous system, affecting the cardiovascular system and causing diuresis. Its actions are similar to those of theophylline but less potent.

o

CH 3

H'C'~:r~> O:::?'-N

N

I CH3

caffetannic acid an alternative name for chlorogenic acid. CAG a codon in mRNA for L-glutamine. cage carrier see ionophore. cage compound 1 an alternative name for clathrate (def. 1).2 any compound possessing a nonplanar bicyclic or polycyclic molecular structure that encloses a cavity. caged ATP a type of protected ATP analogue, e.g. adenosine5'-triphospho-I-(2-nitrophenyl)ethanol (or the methanol-containing equivalent), that releases ATP in good yield when photolysed by a short pulse of light of 360 nm wavelength. Similarly, guanosine-5'-triphospho-I-(2-nitrophenyl)ethanol is used as caged GTP. These compounds can be introduced into cells prior to photolysis. Caged ATP has been used, e.g., to study muscle contraction on the millisecond timescale. caged GTP see caged AlP. Cahn-Ingold-Prelog rule or Cahn-Ingold-Prelog system an alternative name for sequence rule. cal symbol for calorie. calbindin other names: cholecalcin; calbindin D9K; CABP; vitamin D-dependent calcium-binding protein; an EF-hand Ca2+binding protein from intestine. It is present in a variety of cells, including absorptive cells of the duodenum (in which its synthesis is vitamin D 3-dependent), in hippocampal cells, and in kidney. Example from Rattus norvegicus: database code CABCRAT, 78 amino acids (8.90 kDa). Example from human: database code CABI_HUMAN, 78 amino acids (8.88 kDa). calcemic factor or (esp. Brit.) calcaemic factor the prohormone of parathyrin. calcidiol the recommended trivial name for calcifediol, 25hydroxycholecalciferol. It is formed in liver from cholecalciferol, and is the major store of the vitamin in the body, being present largely in plasma. It is the precursor of the hormonal form of the vitamin, calcitriol. See also vitamin D.

calciductin a name proposed for a 23 kDa sarcolemmal protein that, when phosphorylated by a cAMP-dependent protein kinase, causes an approximately two-fold stimulation of the slow Ca 2 + inward current. calcifediol 25-hydroxyvitamin D 3 ; another name for calcidiol. See also vitamin D. calciferol an alternative (older) name for ergocalciferol, also known as vitamin D 2 • See also vitamin D. calcification the deposition of calcium salts in the tissues. It is part of the normal process of bone formation in which hydroxyapatite crystals are deposited, in the neighbourhood of osteoblast cells, in a pre-existing collagen-containing matrix. calcified describing a tissue that has been solidified by deposition of calcium; having undergone calcification. calcimedin see annexin. calcimycin see A23187. calcineurin or protein phosphatase 2B (abbr.: PP-2B) or CaMBPso a major heat-labile calmodulin-binding protein isolated from bovine brain but later found in all cells from yeast to mammals. It has protein serine/threonine phosphatase activity, and is classified as a protein phosphatase 2B (EC 3.1.3.16). It plays an important role in terminating synaptic transmission, and in T-cell activation. It is only weakly inhibited by okadaic acid, but potently inhibited by certain pyrethrin compounds. It consists of two subunits, A and B, the A subunit having the catalytic activity and the B subunit conferring calcium sensitivity. Examples, from human, A subunit: database code P2BI_HUMAN, 514 amino acids (58.01 kDa); B subunit: database code CALB_HUMAN, 169 amino acids (19.17 kDa). The B subunit has a myristoylation site at the N terminus. calciol an alternative trivial name for cholecalciferol. calciosome a discrete cytoplasmic organelle in non-muscle cells, and a candidate for the inositol 1,4,5-trisphosphate-sensitive Ca 2 + store. It has a high content of a calsequestrin-like protein. calciotropic describing any hormone or other agonist acting on calcium metabolism. calciphorin a calcium ionophore polypeptide, M, 3000, isolated from the inner membrane of calf mitochondria. calcitetrol the recommended trivial name for la,24R,25-trihydroxycholecalciferol. It is the inactivation product of calcitriol, from which it is formed by calcitriol 24-hydroxylase. See also vitamin D.

calcitonin or thyrocalcitonin a 3.4 kDa polypeptide hormone, that regulates the levels of calcium and phosphate in blood. In all species studied it consists of a single polypeptide chain of 32 amino-acid residues with a C-terminal prolinamide residue and an N-terminal seven-membered ring formed by a disulfide bridge between hemicystine residues at positions I and 7. The single letter code structure for the polypeptide is CGNLSTCMLGTYTQDFNKFHTFPQTAIGVGAP-NH z·

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calcitonin gene-related peptide Calcitonin is secreted by the Ccells, which in mammals occur primarily in the thyroid gland; in more primitive vertebrates they are found mainly in the ultimobranchial bodies and the lung. The hormone is also found to be concentrated in the hypothalamus of humans and some other vertebrates, and in the primitive brain of the chordate organism Ciona intestinalis. Calcitonin causes a rapid but short-lived drop in the level of calcium and phosphate in blood by promoting the incorporation of these ions in the bones. Overall its action is antihypercalcemic, opposing that of parathyrin. The response of plasma calcitonin to stimulation by administered pentagastrin or calcium may be used to screen for medullary cell carcinoma of the thyroid; the level rises to abnormally high values after stimulation, though normal in its absence. The precursor (human example below) and calcitonin gene-relat8d peptide precursor are formed by alternative splicing of the same gene: database code CALO_HUMAN, 141 amino acids (15.45 kDa); calcitonins have three motifs. calcitonin gene-related peptide abbr.: CGRP; a pleiotropic 3.8 kDa polypeptide of 37 amino-acid residues, found in parts of the nervous system and endocrine system, and in some other organs. It is a potent vasodilator and hypotensive agent, and is regarded as a neuromodulatory peptide. The mRNA is formed by alternative splicing of the transcript of the calcitonin gene, which has exons coding for a region common to both CGRP and calcitonin precursors together with specific calcitonin and CGRP exons. CGRP was the first peptide to be identified by a molecular approach in the absence of biological information; its existence was predicted, in 1983, on the evidence of a second, structurally distinct transcript resulting from calcitonin gene transcription. Initially a 12.5 kDa proCGRP is formed, from which a 55-residue 'amino terminal flanking peptide' is generated. The mature polypeptide has the structure (rat) SCNTATCVTHRLAGLLSRSGGVV KDNFVPTNVGSEAF-NH z, a form known as a-CGRP. Another form, known as ~-CGRP, is identical except for Lys instead of Glu at position 35, and is encoded by a separate gene related to the calcitonin/CGRP gene but lacking any exon encoding calcitonin. a-CGRP is found in the central nervous system in a distribution distinct from that of any other known neuropeptide; it is present in trigeminal and spinal sensory ganglion cells, in olfactory and gustatory systems, and at neuromuscular junctions. CGRP is also found in the endocrine system - in a subset of adrenal medullary cells and in small amounts in thyroid C cells - in bronchiolar cells, and in intestinal cells. Administration of synthetic rat CGRP causes a drop in blood pressure (CGRP is the most potent known hypotensive gene peptide), and increase in heart rate. In vitro it can relax arteries from many vascular beds taken from a variety of species, and is one of the most potent vasodilators known. It also inhibits gastrointestinal motility and causes catecholamine release and gastric hypoacidity. See also amylin. calcitonin gene-related peptide receptor any of several membrane proteins that bind calcitonin gene-related peptide (CGRP) and mediate its effects. CGRPI and CGRP z subtypes have been proposed; the antagonist CGRP s.37 is selective for CGRPI receptors, and [Cys(Acm)Z,7jCGRP for CGRP z receptor types. CGRP receptors are widely distributed in the nervous system, following the pattern of distribution of CGRP, except that receptor numbers are high in cerebellum. They are also widespread in the cardiovascular system, as well as in adrenal, pituitary, exocrine pancreas, kidney, and bone. CGRP receptor stimulation leads to cyclic AMP accumulation in a number of tissues (heart, liver, muscle, pancreatic acinar cells) indicating coupling to one or more G-proteins. calcitonin receptor any of the membrane proteins that bind calcitonin and mediate its effects. They are seven-transmembrane-helix receptors, normally coupled to G-proteins. In

calcium channel many systems they can activate both adenylate cyclase and the phosphatidylinositol cycle. In some systems, which second messenger system is activated depends entirely on conditions. For example in synchronized cells of a kidney cell line calcitonin activates adenylate cyclase during the G z phase, but activates the phosphoinositol cycle during S phase. Activation of the phosphatidylinositol cycle also causes activation of protein kinase C. In other systems, e.g. in brain, adenylate kinase is inhibited, but not through a G-protein. Example (precursor) from human ovarian small cell carcinoma: database code CALT_HUMAN, 490 amino acids (57.3 kDa). calcitrio' the recommended trivial name for la,25-dihydroxycholecalciferol. See cholecalciferol, vitamin D.

calcium symbol: Ca; an alkaline-earth metal of group 2 of the IUPAC periodic table; relative atomic mass 40.08, atomic number 20; it occurs naturally only in an ionized (Ca2+) or combined state, and is a mixture of stable nuclides of relative mass 40 (96.97 atom percent) and 44 (2.06 atom percent) with small proportions of nuclides of relative mass 43, 46, and 48. Calcium is the fifth most abundant element of the Earth's crust and is an essential component of all living material. It occurs in bone, shell, and teeth and low concentrations of ionic calcium play many important roles in the regulation of diverse cellular processes. The most abundant mineral in the human body, most of it is in the skeleton. It has especially important functions in bone, in the control of nervous, muscle, and other excitable tissue, and as a second messenger and regulator of enzyme activity. Calcium homeostasis depends on the action of: (1) parathyroid hormone, which increases tubular reabsorption of calcium, and releases calcium from bone, thereby having overall a hypercalcemic action; (2) vitamin D (calcitriol), which causes absorption of calcium from the gut and its release from bone, and also therefore has a hypercalcemic action; and (3) calcitonin, which reduces calcium resorption from bone. The range of plasma calcium in normal human adults is 2.2-2.6 mmol L-1. See also hypercalcemia, hypocalcemia. calcium-45 symbol: 45Ca; an artificial radioactive nuclide of calcium, with a half-life of 165 days. It emits ~--particles (i.e. electrons) of 0.252 MeV max. and no y-radiation. calcium-47 symbol: 47Ca; an artificial radioactive nuclide of calcium, with a half-life of 4.54 days. It emits ~--particles (i.e. electrons) of two energy ranges (1.98 and 0.67 MeV max.) and y-radiation of three energies (1.31, 0.815, and 0.49 MeV). calcium channel any of several proteins that permit the controlled (gated) passage of calcium ions through membranes. There are several types. L-type channels are involved in excitation-contraction coupling in muscle; they bind 1,4-dihydropyridine (DHP). The DHP receptor is a protein located in transverse (T-) tubules that specifically binds DHP compounds such as nifedipine. This modulates the slow L-type channel in skeletal muscle, neurons, and cardiac cells. N-type channels, identified only in neurons, participate in neurotransmitter release and are blocked by ro-conotoxin. T-type channels influence pacemaker activity in the heart and repeti-

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calcium-dependent regulator protein tive spike activity in neurons; they are blocked by octanol. Ptype channels, identified in some CNS neurons and prominent in Purkinje cells, are blocked by co-agatoxin, much less so by co-conotoxin. The L-type channel from skeletal muscle is heterooligomeric, consisting of five subunits: aI, database code CICLRABIT, 1873 amino acids (211.78 kDa); a2, database code CIC2_RABIT, 1106 amino acids (124.90 kDa); ~, database code CICB_RABIT, 524 amino acids (57.76 kDa); y, database code CICG_RABIT, 222 amino acids (25.03 kDa); and i5 (M r ~27 000). The largest subunit (al) is responsible for many of the functional features, including DHP binding and the voltage-gated pore. It is structurally similar to the Na+ channel a subunit, with four internal repeats of 200-300 amino acids exhibiting sequence homology. Each of these repeats contains six putative transmembrane segments, Sl to S6; segment S4 in all repeats has positively charged groups in -(K/R)XX- repeats (four to six K or R residues per segment), that have been implicated in sensing voltage changes; potential N-glycosylation sites (N residues 79 and 257, rabbit skeletal muscle) and seven potential cAMP-dependent phosphorylation sites (S residues 687, 1502, 1575, 1757, 1772, 1854, T residue 1552) have been identified on the aj protein. See also verapamil. calcium-dependent regulator protein or calcium-dependent modulator protein abbr.: CDR; former name for calmodulin. calcium ion ICa 2 +)·release channel another name for the ryanodine receptor. calcium pump any system that transports calcium ions across a biological membrane from a lower to a higher concentration with the consumption of energy. The term is used especially of the pump in the sarcoplasmic reticulum of muscle of which a transmembrane calcium-transporting ATPase is an integral part. calcium-regulated actin bundling protein a protein that is probably involved in the formation of filopodia. Example from Dictyostelium discoideum: database code ACTB_DICDI, 295 amino acids (33.31 kDa). calcium-transporting ATPase EC 3.6.1.38; an integral membrane protein that forms an essential component of the calcium pump in sarcoplasmic reticulum. It catalyses the hydrolysis of ATP to ADP and orthophosphate, simultaneously transporting two calcium ions from the cytosol into the sarcoplasmic reticulum for each ATP hydrolysed. Probably comprising 10 transmembrane domains, it is related to other metal-ion-transporting ATPases. A number of types exist. Example, SR/ER type from Drosophila melanogaster: database code ATCB_DROME, 1002 amino acids (109.47 kDa). calcium-trigger protein any of a group of small calciumbinding trigger proteins, including calmodulin, troponin C (see troponin), and parvalbumin. calculus (pl. calculi) a concretion of material that forms within the body. It often resembles a small pebble, hence is called a 'stone'. Calculi are most common in the gall bladder or kidney, and are composed variously of organic or inorganic salts, frequently of calcium; cholesterol calculi are gallstones of pure cholesterol. calcyclin other names: prolactin receptor associated protein, growth factor-inducible protein 2A9, S100 calcium-binding protein A6; a small protein that copurifies with prolactin receptor. It is induced in fibroblasts by growth factors and is overexpressed in acute myeloid leukemia. It binds specifically annexin XI. Example from human fibroblasts: database code SI06_HUMAN, 90 amino acids (10.18 kDa). caldecrin a pancreatic protein that lowers serum calcium. It also has chymotrypsin-like activity, which is not needed for the calcium-lowering effect. caldesmon an F-actin crosslinking protein in thin filaments in smooth muscle and in stress fibres in (nonmuscle) fibroblasts. It also binds myosin and tropomyosin. It appears to be a homodimer comprising two polypeptide chains each with a single actin-binding site and a single self-association site. It controls actin-myosin interactions and inhibits the actin-activated

calmodulin ATPase of myosin. Its action is attenuated by calciumcalmodulin and potentiated by tropomyosin. Caldesmon will interact with Ca 2 +-calmodulin (but not with calmodulin alone), an interaction that causes caldesmon to dissociate from F -actin. Example from Gallus gallus: database code CALD_CHICK, 756 amino acids (86.96 kDa). See also caldesmon kinase, caldesmon phosphatase. caldesmon kinase EC 2.7.1.120; the name given to a reaction now known to result from the autophosphorylation of caldesmon (by ATP) in the presence of calcium. This autophosphorylation abolishes the ability of caldesmon to bind actin. caldesmon-phosphatase EC 3.1.3.55; an enzyme that hydrolyses the phosphate from caldesmon phosphate. caldolysin an extracellular protease isolated from Thermus aquaticus strain T-35l, an extreme thermophile. It contains 13% carbohydrate by weight, and one atom of zinc; M r 21000. calelectrin see annexin IV, annexin V, annexin VI. calgizzarin an EF-hand Ca2 +-binding protein isolated from chicken gizzard smooth muscle. It is also abundant in rabbit lung and is found in other tissues. It has homology with annexin II light chain and is a homodimer (disulfide-linked). It is overexpressed in human colorectal tumours. Example from pig: database code ICAL_PIG, 713 amino acids (77.04 kDa). callose a linear (I,3)-fi-D-glucan insoluble in water but which dissolves in dilute alkali. The glucan chains form stable triple helices. Callose is a ubiquitous higher plant polysaccharide occurring as a component of specialized, and often transient, cell walls, especially in reproductive tissues and is a component of the cell plate. Callose is rapidly deposited on plasma membranes as drops, plugs, or plates on wounding or physiological stress. Callose deposits on cell walls stain specifically with Aniline Blue or its fluorochrome. Specific hydrolases, e.g. glucan endo-l,3-fi-D-glucosidase (EC 3.2.1.39) for callose and membrane-bound callose synthetase (EC 2.4.1.34) are found in plants. Functionally callose may act as a temporary wall matrix, as a special permeability barrier or as a wall strengthening agent. Other (1,3)-fi-D-glucans include yeast glucan, pachyman, lamarin, scleroglucan, curdlan, leucosin, mycolamarin, paramylon, chrysolamarin, and lentinan. callus 1 a mass of relatively unspecialized tissue that develops at wound sites in plants, forming a protective covering. Callus cells are used in tissue culture as the starting material for the propagation of plant clones. 2 tissue formed during the healing of broken bone. calmitine a mitochondrial Ca2+ -binding protein of fast-twitch muscle fibres with a characteristic 28-residue signal. The mature protein is identical to calsequestrin of the sarcoplasmic reticulum. calmodulin abbr.: CAM; a small, heat-stable, acidic, calciumdependent modulator protein that binds four calcium ions per molecule and is then able to stimulate a variety of eukaryotic enzymes or enzyme systems. These include brain adenylate cyclase, cytosolic cyclic nucleotide phosphodiesterase, myosin light-chain kinase, erythrocyte Ca 2+,Mg2+-ATPase, plant NAD+ kinase, and a number of calcium-dependent protein kinases including phosphorylase kinase (to which it contributes the i5 subunits); various other cellular processes such as membrane phosphorylation and microtubule disassembly also are stimulated. Calmodulin consists of a single-chain polypeptide of known sequence, aspartic or glutamic accounting together for about 30% of the total residues; it contains one residue of N 6 -trimethyllysine per mole but no cysteine, hydroxyproline, or tryptophan residues. Calmodulin appears to be ubiquitous within the animal and plant kingdoms, to be without species or tissue specificity, and to be almost invariant in structure, being conserved nearly perfectly throughout evolution; it has EF-hand domains and is similar to, but not identical with, troponin C from muscle. It was known previously by a variety of provisional names including modulator protein, phosphodiesterase activator protein, troponin C-like (modulator) pro-

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calmodulin-dependent protein kinase II tein, and calcium- (or Ca2+)-dependent regulator (or modulator) protein (CDR protein). Examples (I) from black rat: database code NRL_3CLN, 143 amino acids (16.13 kDa); 3-D structure known; (2) from human, rabbit, other rat species, Xenopus laevis, chicken, the sea urchin Arbacia punctulata, and Bos taurus: database code CALM_HUMAN, 148 amino acids (16.13 kDa). calmodulin-dependent protein kinase II recommended name: Ca 2+/calmodulin-dependent protein kinase, EC 2.7.1.123; other names: Ca2+-CAM kinase II; microtubuleassociated protein 2 kinase; multifunctional Ca 2 +-CAM kinase. An enzyme with broad specificity and activated by Ca2+ that catalyses the phosphorylation of Ser and Thr residues in proteins by ATP. It is involved in cell regulation. An oligomeric polypeptide, it is composed of various combinations of a (Mr 60 000) and ~ (Mr 55 000) subunits in a dodecahedral structure. On activation by Ca 2 +-CAM, autophosphorylation occurs as a result of which the enzyme converts to a Ca 2+-CAM-independent form. Substrates include synapsin I, tryptophan hydroxylase, skeletal muscle glycogen synthetase, and microtubule-associated proteins tau and MAP-2. A synthetic peptide substrate is PLSRTLSVSS. Examples from yeast: type I, database code KCCl_YEAST, 445 amino acids (50.08 kDa); type II (potentially autophosphorylation enzyme), database code KCC2_YEAST, 447 amino acids (50.36 kDa). calmodulin-like domain protein kinase abbr.: CDPK; EC 2.7.1.-; other name: Ca2+-binding Ser/Thr protein kinase. An enzyme that is subject to autophosphorylation and resembles calmodulin-dependent protein kinases. Example from soybean: database code CDPK_SOYBN, 508 amino acids (57.10 kDa). calnexin a calcium-binding protein of the endoplasmic reticulum. It appears to playa role in the processing of endoplasmic reticulum proteins, in monitoring assembly, and in retaining unassembled or incorrectly folded proteins. It has a single transmembrane helical region. Example from human (precursor): database code CALX_HUMAN, 592 amino acids (67.57 kDa); residues 1-20 are the signal, 21-592 calnexin. calomel electrode the mercury-mercurous chloride (mercurycalomel) (Hg;Hg 2CI 2, CI-) half-cell that is reversible to chloride ions. Because of its stability and simplicity, it is frequently used in conjunction with a saturated-KCI bridge as a reference electrode in pH meters, etc. calorie or (sometimes) gram calorie or small calorie symbol: cal; any of several units of heat or energy in the CGS system. A calorie originally represented the quantity of heat required to raise one gram of water through one degree centigrade (i.e. Celsius). However, the energy represented by a calorie varies slightly according to the initial temperature of the water. Hence, the International Table calorie (symbol: calIT) is now taken to equal 4.1868 J exactly, while the 15 °C calorie (symbol: callS) is equal approximately to 4.1855 J. Thermochemical calculations have often used a slightly different value; one thermochemical calorie (symbol: Calth) is now taken to equal 4.184 J exactly. In nutrition and physiology, the term 'calorie' is often used to mean the kilocalorie or Calorie (initial capital), equal to 10 3 cain. Use of all these units is now deprecated, the joule now being preferred. Calorie or (sometimes) kilogram calorie or large calorie the name used, especially in nutrition, for the kilocalorie, i.e. 10 3 cain. Compare calorie. calorific of, relating to, or generating heat. calorific value the amount of heat produced by the complete combustion of a given mass of a substance, such as a fuel or foodstuff. It is usually expressed in J kg- 1• calorigenesis the production or increased production of heat in an organism. -calorigenic adj. calorimeter an instrument for determining quantities of heat evolved, transferred, or absorbed.

calsequestrin calorimetry the measurement of the amount of heat evolved, transferred, or absorbed by a system. -calorimetric adj. calpactin see annexin. calpain EC 3.4.22.17; a Ca 2+-activated, neutral, thiol proteinase enzyme that preferentially cleaves the bonds: Tyr-IXaa, Met-I-Xaa, or Arg-I-Xaa with Leu or Val as the P2 residue. Calpains are cytoplasmic mammalian enzymes, of three main types; these have an identical small regulatory EFhand subunit and large catalytic subunit but differ in their sensitivity to Ca2+. Example (human) calpain II large subunit (responds to millimolar Ca2+): database code CAP2_ HUMAN, 700 amino acids (79.92 kDa). calpastatin a protein, found in liver and erythrocytes of several mammals, that is a specific calpain inhibitor. There are four characteristic domains involved in the inhibitory action. Example (precursor) from pig: database code ICAL_PIG, 713 amino acids (77.04 kDa). calphostin C one of a group of compounds isolated from Cladosporium cladosporioides having a unique structural feature in possessing a perylene quinone. It was identified in a search for inhibition of protein kinases. It inhibits protein kinase C by action on the regulatory domain and has a relatively high degree of specificity, but acts equally on all isoforms having the common regulatory domain. It is a highly potent and specific inhibitor (IC so = 50 nM) of protein kinase C. At higher concentrations it inhibits other kinases, including myosin light chain kinase, and cyclic GMP- and cyclic AMP-dependent kinases.

calphotin a Ca2 +-binding protein found in the cytoplasm of photoreceptor cells of Drosophila melanogaster. The C-terminal region contains a leucine zipper uninterrupted by prolines. The protein contains >50% proline, alanine, and valine. Database code CPN_DROME, 865 amino acids (84.78 kDa). calponin a thin filament-associated protein implicated in regulation and modulation of smooth muscle contraction. It is found as an actin-, calmodulin-, and tropomyosin-binding protein present in many vertebrate smooth muscles, and is related to troponin T in immunological and biochemical characteristics. Examples from rat; calponin HI: database code CLPI_RAT, 297 amino acids (33.31 kDa); acidic isoform: database code CLPA_RAT, 330 amino acids (36.39 kDa). calpromotin a cytoplasmic protein of red cells that activates Ca2+-dependent potassium transport. calregulin see calreticulin. calreticulin other names: calregulin; Crp55; CaBP3; HACBP; erp60; a Ca2+-binding protein of the endoplasmic reticulum lumen. Example (precursor) from human: database code CRTC_ HUMAN, 417 amino acids (48.09 kDa); amino acids 1-17 constitute the signal; the C terminus contains the KDEL sequence. calsequestrin a 44 kDa calcium-binding protein of low isoelectric point, found on the interior surface of the membrane of the sarcoplasmic reticulum of muscle. It acts as an internal calcium store in muscle and releases Ca 2 + at calcium channels. It has only a moderate affinity for calcium ions, but a high ca-

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calspectin Ca 2 +

Ca2 +

pacity (>40 ions per molecule); selective binding of in preference to other cations is promoted by ATP; it also exhibits protein kinase activity. Calsequestrin makes up some 19% of the protein of isolated sarcoplasmic vesicles, and is thought to assist in depleting the sarcoplasm of free calcium ions during relaxation. Example, human muscle isoform: database code CAQS_HUMAN, 390 amino acids (44.53 kDa), very acidic (47 Asp, 56 Glu; has a sequence of eight asparticacid residues at the C terminus). calspectin an alternative name for fodrin. calstorin a calcium-binding protein of the microsomal lumen of rat brain, similar to calsequestrin. caltractin or centrin an EF-hand Ca2+-binding protein of the centrosome of interphase and mitotic cells that plays a fundamental role in microtubule-organizing centre structure. It is present in the centrosome/basal body apparatus of the green alga Chlamydomonas reinhardtii. It contains four EF-hands, and belongs to the calmodulin/parvalbuminltroponin C superfamily. Example from the salt bush A triplex nummularia: database code CATR_ATRNU, 167 amino acids (19.22 kDa). caltrin abbr. for calcium transport inhibitor; other name: seminalplasmin; a small basic protein of male seminal vesicle fluids. It binds to calmodulin and inhibits Ca2 + uptake by epididymal spermatozoa. It has antimicrobial properties. Example (precursor, bovine): database code CALT_BOVIN, 80 amino acids (8.97 kDa). Calvin. Melvin (1911-97), US chemist and biochemist distinguished for pioneering the use of radioactive isotopes, especially carbon-14, as tracers in metabolism; Nobel Laureate in Chemistry (1961) 'for his research on the carbon dioxide assimilation in plants'. Calvin cycle see reductive pentose phosphate cycle. Cam symbol for the carbamoylmethyl group. CAM abbr. for 1 calmodulin. 2 crassulacean acid metabolism. CaM-BPso an alternative name for calcineurin. cAMP abbr. for cyclic AMP; see adenosine 3',5'-phosphate. campesterol (24R)-ergost-5-en-3p-ol; a sterol found in small amounts in rapeseed and other vegetable oils.

camphor 1,7,7-trimethylbicyclo[2.2.1 ]heptan-2-one; a compound obtained from the camphor tree, Cinnamomum camphora, which is indigenous to Taiwan. It is widely used in ointments and liniments. It is also used as a starting material in organic chemistry. cAMP receptor protein see catabolite (gene) activator protein. cAMP-regulatory protein see catabolite (gene) activator protein. canaline 04-aminohomoserine; 2-amino-4-(aminooxy)butanoic acid; HzN-O-[CHzh-CH(NHz)-COOH; a basic a-amino acid found as the L-enantiomer in the jack bean, Canavalia ensiformis, and in some other legumes containing L-canavanine. It is formed from canavanine by deamidination or transamidination. It inhibits pyridoxal-dependent enzymes.

cannabis canavalin a globular protein isolated from ripe seeds of the jack bean, Canavalia ensiformis. It is a storage protein, with sequence similarity to phaseolin, vicilin, and related proteins. See also concanavalin A. Example from Canavalia gladiata: database code CANA_CANGL, 445 amino acids (50.29 kDa). canavanase see arginase. canavanine d-guanidinohomoserine; 2-amino-4-(guanidinooxy) butanoic acid; a basic a-amino acid, occurring as the L-enantiomer in certain legumes esp. the jack bean, Canavalia ensiformis; an arginine antagonist. In seeds of the jack bean it constitutes up to 8% of their dry mass and forms their main storage compound for nitrogen. On germination of the seeds the nitrogen is released for synthetic purposes by hydrolysis of L-canavanine to L-canaline and urea, from each of which ammonium is then formed by further hydrolysis. See also canaline.

cancellate or cancellated or cancellous having a porous or spongy structure; meshlike or lattice-like. cancer any malignant neoplasm. Cancers are usually divided into carcinomas, derived from epithelial tissue, and sarcomas, derived from connective tissue. cancer-associated retinopathy protein see recoverin. candela symbol: cd; the SI base unit of luminous intensity, defined as the luminous intensity, in a given direction, of a source that emits monochromatic radiation of frequency 540 x 10 12 hertz and that has a radiant intensity in that direction of 1/683 watt per steradian. Candida a genus of (in many cases) dimorphic yeasts containing species of medical (c. albieans) and industrial importance: C. cylindrica is a source of lipases and is a rare example of a eukaryote with a non-standard genetic code for nuclear/cytoplasmic gene expression. cane sugar an old and common name for sucrose. cannabinoid any of about 30 derivatives of 2-(2-isopropyl-5methylphenyl)-5-pentylresorcinol found in the Indian hemp, Cannabis sativa, among which are those responsible for the narcotic actions of the plant and its extracts. The most important cannabinoids are cannabidiol, cannabinol, trans-L19tetrahydrocannabinol, trans-L18-tetrahydrocannabinol, and L19-tetrahydrocannabinolic acid. See also cannabis. cannabinoid receptor any of several membrane proteins that bind cannabinol and structurally similar compounds and mediate their intracellular action. Two types have been characterized, both of which are seven-transmembrane-domain G-protein-coupled receptors. CBI receptors are found in brain and testis. CB2 receptors are found in spleen and not in brain. For both types arachidonoylethanolamide (anandamide) is a putative endogenous ligand and both types are negatively coupled to adenylate cyclase decreasing intracellular cyclic AMP levels. Examples from Mus musculus: CBI, database code CBIR_MOUSE, 473 amino acids (52.94 kDa); CB2, database code CB2R_MOUSE, 347 amino acids (38.21 kDa). cannabinol see cannabinoid. cannabis the dried flowering or fruiting tops of Indian hemp, Cannabis sativa; numerous synonyms exist, including marijuana, bhang, and maconha. A resin, known variously as cannabin, hashish, or charas, is also obtained from the plant. Both preparations contain active principles, cannabinoids, and are used as recreational drugs, producing relaxation, euphoria, and enhanced awareness. Occasionally, anxiety or mental disturbance may result, and, rarely, loss of consciousness or even death. The major active ingredients are tetrahydrocannabinols. Cannabis is a controlled substance in the US Code of Federal Regulations.

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Cannizzaro reaction Cannizzaro reaction the base-catalysed dismutation of aldehydes with no a hydrogen atoms into the corresponding acids and alcohols: 2R-CHO + OH- ~ R-COO- + R-CHzOH. [After Stanislo Canizzaro (1826-1910).] canonical form or canonical structure an older name for contributing structure. canonical sequence a nucleotide or amino-acid sequence regarded as the archetype with which variants are compared. cap 1 or cap structure a structural feature present at the 5' end of most eukaryotic (ceIlular or viral) mRNA molecules and also of some virion mRNA molecules but not of bacterial mRNA molecules. It consists of a residue of 7-methylguanosine and a triphosphate bridge linking it 5'-5' to the end of the polynucleotide chain; in addition, the first one or two nucleotide residues in the chain may possess a 2'-O-methyl group and the first, if adenylyl, a 6-N-methyl group. The cap structure is thought to protect the 5' end of the mRNA from degradation by phosphatases or nucleases and to facilitate initiation of translation of mRNA by the eukaryotic (but not by the bacterial) ribosome. 2 a cluster or patch of aggregated proteins at one site on the surface of a cell, e.g. a lymphocyte. Surface components of the ceIl membrane are aggregated, e.g., by the action of polyvalent ligands, and may be swept to the posterior area of the ceIl when the ceIl moves, forming a cap at that site. 3 to form or place a cap on a molecule (or structure). CAP abbr. for 1 catabolite (gene) activator protein. 2 chloramphenicol (use deprecated, full name preferred). 3 Clostridium (histolyticum) aminopeptidase, EC 3.4.11.13. 4 cyclic AMP receptor protein; see CRP. capacitance or electric capacitance symbol: C; the ability of a system to store electric charge or a measure of this capacity for a particular system. C = QIU where Q is the quantity of charge stored to raise the system's potential by U volts. The SI derived unit of capacitance is the farad. capacitance minimization method a simple method for the determination of asymmetric surface potentials in lipid bilayers, based on the dependence of bilayer capacitance on transmembrane voltage. The capacitance is measured by rectifying the 90° component of an applied a.c. current signal. A superimposed slow triangular wave results in a hysteresis-like time course of capacitance. The centre of the hysteresis figure is shifted along the voltage axis by an amount equal to the capacitance minimization potential, the difference between the dipole plus surface-charge potentials on the two sides of the membrane. CAPB see calbindin. cap-binding protein any protein (e.g. a 24 kDa protein obtainable from rabbit reticulocytes) that specificaIly binds to the cap (def. I) of eukaryotic capped mRNA. Such proteins may facilitate the translation of capped mRNA molecules. CAP factor see catabolite (gene) activator protein. capillarity the phenomenon, resulting from surface tension, in which liquids rise up capillary tubes and which also causes them to form a concave or convex meniscus at their surface where it contacts a solid. capillary 1 of, or relating to, a hair or hairlike structure. 2 of, or relating to, a tube with a very fine bore. 3 any of the very fine blood vessels that form a network between the arterioles and the venules throughout the body. 4 a capillary tube. capillary column a chromatography column that has a very fine bore (0.1-0.25 mm), the inner surface of which may be coated with stationery phase or other support. Such columns are used in gas chromatography, supercritical fluid chromatography, or capillary electrophoresis. The column may be up to a few metres in length, coiled, and made of glass or fused silica. In high-performance liquid chromatography, columns of somewhat wider bore and shorter length are referred to as capillary columns. capillary electrophoresis abbr.: CE; a very-high-resolution

capsaicin method of electrophoresis, also known as capillary zone electrophoresis (abbr.: CZE) or high-performance electrophoresis. It is based on the use oflong (up to 100 cm), narrow ( Tyr-I-Xaa > Trp-I-Xaa > Leu-I-Xaa. It is a trypsin-like serine proteinase, and a homologue of chymotrypsin; it is found in mast cell granules (heart, lung, etc.). Example, human (precursor): database code MCPl_HUMAN, 247 amino acids (27.29 kDa). chyme the semifluid mass of partially digested food that passes through the pylorus of the stomach into the small intestine. chymopapain EC 3.4.22.6; other name: papaya proteinase II; the major endopeptidase enzyme of papaya (Carica papaya) latex; its specificity is similar to that of papain. The protein from that species is: database code PAP2_CARPA, 218 amino acids (23.66 kDa). chymosin or rennin EC 3.4.23.4; an aspartic proteinase enzyme that cleaves a single bond in K casein (Ser-Phe I05 -I-Met-Ala) and is responsible for clotting of milk. It is produced from a precursor in the mucosa of the fourth stomach of calves. It is now produced by eDNA technology. Example (bovine): database code NRL_ICMS, 323 amino acids (35.61 kDa); 3-D structure is known. (Note: use of the synonym rennin is now deprecated because of possible confusion with renin.) chymotrypsin a serine endopeptidase, EC 3.4.21.1, formed from the proenzyme chymotrypsinogen by the action of trypsin. In vertebrates, chymotrypsins are contained in pancreatic juice, and hydrolyse protein in the small intestine. Chymotrypsinogen is synthesized in the acinar cells of the exocrine pancreas and stored in zymogen granules until released. Several forms of chymotrypsin are found: Chymotrypsin A is formed from bovine and porcine chymotrypsinogen A. It will hydrolyse peptides, amides, and esters, preferentially at the carbonyl end of Tyr, Trp, Phe, and Leu residues. Chymotrypsin B, formed from chymotrypsinogen B, is homologous with chymotrypsin A. Chymotrypsin C, EC 3.4.21.2, is formed from porcine chymotrypsinogen C and from bovine subunit II of procarboxypeptidase A. It preferentially cleaves at the carbonyl end of Leu, Tyr, Phe, Met, Trp, GIn, and Asn residues. Enzymes homologous to and with similar specificities to chymotrypsin have been isolated from many species. Chymotrypsinogens are synthesized as a single 245-residue polypeptide chain cross-linked by five disulfide bonds. This is fully activated when the bond between Arg 15 and I1e 16 is cleaved by trypsin to yield 1t-chymotrypsin; subsequent autocatalytic cleavage of more peptide bonds (to remove 14-15, 147-148) converts it into a-chymotrypsin. Amino acids 1-13 form chymotrypsin A-chain, 16-146 form chymotrypsin Bchain, and 149-245 form chymotrypsin C-chain, the three chains being covalently linked by disulfide bonds, 1-122, 42-58, 136-201, 168-182, and 191-220. The mechanism involves a charge-relay system of His 57 , Asp 102, and Ser 195 . Chymotrypsin is more active than trypsin against certain esters, e.g. N-acetyl-L-tyrosine ethyl ester. Chymotrypsin binds ClIantitrypsin. Example (bovine): database code CTRA_BOVIN, 245 amino acids (25.64 kDa). 3-D structure known. chymotrypsinogen see chymotrypsin. chymotryptic of, or relating to, chymotrypsin; chymotryptic digestion is the partial hydrolysis of a protein by chymotrypsin. Ci symbol for curie. e/ or c1 symbol for lambda repressor. CI abbr. for Colour Index (especially as a prefix to the identifying number for a particular dye or stain). CIDNP abbr. for chemically induced dynamic nuclear polarization. CIE abbr. for counterimmunoelectrophoresis. ciliatine see phosphono+. cilium (pl. cilia) a specialized eukaryotic locomotor organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic mem-

circular chromosome brane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole. Compare flagellum. ciliary adj. cimetidine N-cyano-N' -methyl-N"-[-2-[[(5-methyl-l H-imidazol-4-yl)methyl]thio]ethyl]guanidine; a competitive antagonist of histamine H 2 receptors used clinically as an anti-ulcer drug; it inhibits gastric acid secretion and reduces the output of pepsin. One proprietary name is Tagamet.

clMP abbr. for cyclic IMP; see inosine 3'.5'-phosphate. ein4 the gene for the enzyme trans-cinnamate 4-monooxyganase found in many plants. cinchonine an alkaloid obtained from cinchona bark and possessing antimalarial properties. See also quinine. cinnamate the anion of 3-phenyl-2-propenoic acid; trans-cinnamate (3-phenyl-2E-propenoate) is a compound formed from phenylalanine by phenylalanine ammonia-lyase, EC 4.3.1.5; it is the precursor of ferulic and sinapic acids in the pathway for lignin synthesis. trans-einnamate 4-monooxvgenase abbr.: CA4H; EC 1.14.13.11; systematic name: trans-cinnamate,NADPH:oxygen oxidoreductase (4-hydroxylating); other names: cinnamic acid 4-hydroxylase; cinnamate 4-hydroxylase. An enzyme that catalyses a reaction between trans-cinnamate, NADPH, and dioxygen to form 4-hydroxycinnamate, NADP+, and H 2 0. It is an endoplasmic reticulum enzyme of high specificity - it does not act on amino acids, phenylacetate, or benzoate - and is the first enzyme in the pathway from cinnamate to lignin. Example from Catharanthus roseus: database code CRCIN4HX, 505 amino acids (58.21 kDa). cinoxacin azolinic acid; l-ethyl-l ,4-dihydro-4-oxo[1 ,3]diox010[4,5-g]cinnoline-3-carboxylic acid; a 4-quinolone antibiotic with activity against Gram-negative bacteria through the inhibition of DNA gyrase. ciprofloxacin a fluorinated 4-quinolone antibiotic active against both Gram-positive and Gram-negative bacteria although more so against the latter and also active against Chlamydia and mycobacteria. circadian describing biological activity (e.g. behavioural, physiological, metabolic) that exhibits an endogenous periodicity of approximately 24 hours independently of any daily variation in the environment. Compare diurnal, inlradian, ultradian. [From Latin circa, about, + dies, day.] Circe effect the phenomenon underlying any physicochemical description of the action of an enzyme upon a substrate. It refers to the strong attractive forces that bind the substrate into the active site of the enzyme, where it undergoes a radical transformation of form and structure. It is named after the sorceress, Circe, who according to Greek mythology transformed the men of Odysseus into beasts. circular birefringence the birefringence produced by left and right circularly polarized light. circular chromatography a technique of paper chromatography in which the substances to be separated are allowed to travel radially from the centre of a filter-paper disk. The material is applied to the centre of the disk from which a small sector is cut out and folded down to allow it to dip into the eluting solvent. circular chromosome a circular DNA duplex, the form taken by the chromosomes of some prokaryotic organisms, e.g. Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa.

circular dichroism

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circular dichroism abbr.: CD; the difference in absorption of left and right circularly polarized light. The shape and magnitude of the CD curve as a function of wavelength of solutions of proteins (and other macromolecules) are sensitive to changes in conformation of these solutes. See also Cotton effect, ellipticity, molecular ellipticity, optical rotatory dispersion. circular DNA any single- or double-stranded DNA molecule with a circular (but not necessarily geometrically circular) structure. If single-stranded, the circle is closed covalently, but if double-stranded, one or both strands may be open. See also covalent (closed) circle of DNA. circularly polarized light see polarized light. cis abbr.: c; conformational descriptor denoting synperiplanar (use not recommended); see conformation. cis- abbr.: CO; prefix (in chemical nomenclature) denoting that two specified substituents lie on the same side of a reference plane in the molecule. (cis means 'on this side'.) In systematic names it is denoted by the symbol Z. See cis-trans isomerism, E/Z convention. Compare trans-. cis-acting (in genetics) describing a regulatory genetic element whose effects are sensitive to its position relative to the gene being regulated, i.e. on the same molecule of DNA. Examples incl ude bacterial operators. cis configuration (in genetics) describing the configuration of two linked heterozygous genes in which both wild-type alleles occur on one of the paired homologous chromosomes while the mutant alleles occur on the other homologue; i.e. (++/ab). Compare trans configuration. cis isomer see cis-trans isomer. CISP abbr. for corticotropin-induced secreted protein; now called thrombospondin-2 (see thrombospondin). cisplatin cis-diammineplatinum(u) dichloride; cis-diaminedichloroplatinum; a substance that interacts with, and forms cross-links between, DNA and proteins. It is used as a neoplasm inhibitor to treat solid tumours, primarily of the testis and ovary. cisterna (pl. cisternae) 1 (in cytology) the flattened, saclike space enclosed between paired membranes of the endoplasmic reticulum and the Goigi apparatus. 2 (in anatomy) an enlarged space, such as the cisterna magna in the rear of the brain or the cisterna chyli between the crura of the diaphragm. -cisternal adj. cis-trans complementation test a genetic test to determine whether two gene mutations (a and b) occur in the same functional gene (or cistron). It involves comparison of heterozygotes in which the relevant mutations are in the same chromosome, i.e. in the cis configuration (++/ab), with heterozygotes in which the mutations are in separate chromosomes, i.e. the trans configuration (a+/+b). ci.....trans isomer or (sometimes) geometric isomer or geometrical isomer either of a pair of diastereoisomers that differ only in the positions of atoms relative to a specified reference plane in the molecules, in cases where these atoms are, or are considered as if they were, parts of a rigid structure. The two isomers are designated the cis isomer and the trans isomer when the two particular atomic groupings lie respectively on the same or on opposite sides of the reference plane. See also cis-trans isomerism. -cis-trans-isomeric adj. ci.....trans isomerism or (some times) geometrical isomerism the phenomenon of the existence of cis-trans isomers in general, or the occurrence of paired cis and trans isomers in a particular molecule. Atoms or groups are termed cis or trans to one another when they lie respectively on the same or on opposite sides of a reference plane identifiable as common among stereoisomers. For compounds containing only doubly bonded atoms the reference plane contains the double-bonded atoms and is perpendicular to the plane containing these atoms and those directly attached to them. For cyclic compounds the reference plane is that in which the ring skeleton lies or to which it approximates. See also flZconvention. cistron a unit of DNA sequence that codes for a single

citrate cleavage enzyme polypeptide or protein. It may be a smaller unit than the gene, which contains the unit of DNA determining a single character. Whether or not a cistron is the same as a gene can be determined by the cis-trans complementation test, hence the name cistron (cis means 'on this side'). Cit symbol for a residue of the a-amino acid L-citrulline. citraconate 1 the trivial name for methylmaleate, cis-I ,2propylenedicarboxylate, (Z)-2-methyl-2-butenedioate, the dianion of citraconic acid, (Z)-2-methyl-2-butenedioic acid. 2 any mixture of citraconic acid and its mono- and dianions. 3 any salt or ester of citraconic acid.

CH3

r=-o-p-o-(

CH 3

diisopropylphospho symbol: Dip; abbr.: DIP; the doubly esterified phosphoric acyl group, [(CH 3hCH-O-hP(O)-, derived from diisopropyl fluorophosphate by loss of a fluorine atom. dikaryon or dicaryon a living cell containing two nuclei, or a structure (e.g. a mycelium) composed of such cells. It may contain nuclei of the same genetic constitution (i.e. homokaryons) or of differing genetic constitutions (i.e. heterokaryons). -dikaryotic or dicaryotic adj. diketose any monosaccharide derivative containing two (potential) ketonic carbonyl groups. Compare ketose. dikinase either of the two enzymes belonging to the sub-subclass EC 2.7.9, comprising phosphotransferases with paired acceptors. For example, pyruvate,orthophosphate dikinase, EC 2.7.9.1, catalyses the reversible reaction: ATP + pyruvate + orthophosphate = AMP + phosphoenolpyruvate + pyrophosphate. dil. abbr. for dilute (def. 2). dilate to expand or cause to expand; to make larger or wider; e.g. of the pupil of the eye or a chamber of the heart. -dilation or dilatation n. dilatometer any instrument for measuring small changes in the volume of liquids. One design consists of a (glass) bulb fitted with a graduated hollow stem in which changes in volume may be observed. In another design, the (glass) bulb is fitted with a stopper through which runs a capillary tube so that any increased volume of the contained liquid may escape; the change in mass of the bulb and its contained liquid may then be determined. -dilatometry n. diluent a diluting agent; see dilute (def. I). dilute 1 a to lower the concentration of a solute in a solution (or of particles in a suspension). b to mix one fluid with another thereby lowering the concentration of the first. 2 abbr.: dil.; describing a solution (dispersion or mixture) having a relatively low concentration (of a specified solute, type of dispersed particle, or component). Compare concentrated (def. I). diluted (of a solution or suspension) lowered in concentration and increased in volume by addition of solvent or other diluent. Compare concentrated (def. 2). dilution 1 the act or process of making more dilute (def. 2). 2 a diluted solution or suspension. 3 the (specified) extent to which a solution or suspension has been diluted. dilution end-point analysis the determination of the concen-

tration of antibody in a solution by allowing a given amount of antigen to react with increasing dilutions of the antibody. The most dilute solution that produces a detectable effect, e.g. precipitation, is taken as the end point. dilution law see Ostwald dilution law. dilution quenching the lowering of counting efficiency of a liquid scintillation counter by the addition of solvent to the contents of the scintillation vial. See also quenching. dilution rate symbol: D; the rate, F, at which existing medium is replaced with fresh medium in a continuous culture, divided by the volume, V, of the culture: D = FIV. Under steady-state conditions the dilution rate numerically equals the specific growth rate of the culture. See also auxostat, chemostat. dilution value of a buffer symbol: (~pH)\f,; the change in pH that occurs when a buffer solution is diluted with an equal volume of water. dimer 1 any molecular structure of any size in which two initially identical chemical entities have become covalently combined. 2 any macromolecular structure in which two (either identical or nonidentical) subunits are noncovalently associated. See also heterodimer, homodimer. -dimeric adj. dimercaprol or British anti-lewisite (abbr.: BAL); 2,3-dimercaptopropanol; an antidote to the arsenical war gas, lewisite, that is also useful as a chelating agent and detoxicant for heavy-metal ions and as a protective agent for sulfhydryl groups in enzymes, coenzymes, or the like. dimerize or dimerise cause a dimer to be formed. -dimerization or dimerisation n. dimerizer hypothesis or dimeriser hypothesis an unsubstantiated model of facilitated diffusion proposed to explain the rates of entry of sugars into human erythrocytes from various mixtures of sugar species. According to this hypothesis, permeation occurs as a result of pairs of sugar molecules interacting with a membrane component, followed by the association of the sugars into dimers, a form in which a reduced number of free hydrogen-bond-forming groups would be available. dimethoxytrityl abbr.: DMT; 4,4'-dimethoxytriphenylmethyl; a group used for protecting hydroxyl groups (especially the 5'hydroxyl groups of nucleosides) during chemical synthesis or other procedures. It is usually introduced by reaction with dimethoxytrityl chloride, 4,4-dimethoxytriphenylmethyl chloride. Compare trityl.

OCH3 4,4-dimethoxytriphenylmethyl chloride

dimethylallyl transtransferase EC 2.5.1.1; systematic name: dimethylallyl-diphosphate:isopentenyl-diphosphate dimethylallyltranstransferase; other names: prenyltransferase; geranyldiphosphate synthase. An enzyme that catalyses the reaction of dimethylallyl diphosphate with isopentenyl diphosphate to form pyrophosphate and geranyl diphosphate. It participates in the pathway for the formation of polyprenyl groups, sesquiand higher terpenes, and cholesterol. dimethylaminoazobenzene isothiocyanate see DABITe. dimethylaminoazobenzene sulfonyl chloride see dabsyl.

dimethylaminobenzaldehyde dimethylaminobenzaldehyde see Ehrlich's reagent. dimethylaminonaphthalene sulfonyl chloride see dansyl, dansylate. dimethylformamide see DMF. dimethyltryptamine N,N-dimethyltryptamine; 3-[2-(dimethylamino)ethyljindole; a hallucinogenic agent extracted from several plant species including Piptadenia peregrina. It is also a metabolite of 5-hydroxytryptamine. It is a controlled substance under the US Code of Federal Regulations.

dimorphism 1 the existence of a chemical compound in two distinct physical forms, e.g. two different crystalline forms. 2 the existence of individuals belonging to two distinct forms within the same species of organism; e.g. in sexual dimorphism the males and females of the same species are markedly different. 3 the occurrence in certain plants of two distinct forms of leaves or other parts in the same individual. -dimorphic or dimorphous ad). dinactin see nonactin. dinitrofluorobenzene abbr.: DNFB; a (less correct) name for fluorodinitrobenzene. See Sanger's reagent. dinitrogen systematic name for the diatomic compound N z, commonly termed (molecular) nitrogen. dinitrophenate the strongly yellow-coloured anion, (NO zh-C 6H r O-, formed from dinitrophenol. dinitrophenol abbr.: DNP; 2,4-dinitrophenol; a pale-yellow crystalline solid. It is a powerful uncoupler of oxidative phosphorylation, and hence toxic. dinitrophenyl symbol: Dnp; the group formed by loss of the phenolic hydroxyl group from 2,4-dinitrophenol. See Sanger's method. dinitrophenylate to introduce a dinitrophenyl group into a compound. -dinitrophenylation n. dinoprost a generic name for prostaglandin F Za' See prostaglandin. dinor+ prefix (in chemical nomenclature) indicating shortening of a carbon chain or contraction of a ring by two methylene groups. See also nor+. Dintzis procedure a procedure for investigating the direction and rate of biosynthesis of a polypeptide. It requires the addition to a protein-synthesizing system in vitro, at a given time, of a pulse of a labelled form of an amino acid, of which there are several residues at different positions in the structure of the polypeptide. After various periods of elapsed time, within the time required for synthesis of a complete chain, completed molecules of the polypeptide are isolated, and the extents of incorporation of the labelled amino acid into them are determined for each position in which a residue occurs naturally. Over all the samples, a gradient of radioactivity (increasing from the N terminus to the C terminus of the chain) is found, indicating that the pulse tends to enter the more C-terminal positions and that the more N-terminal region has already been synthesized. By these means it was clearly shown for the first time that polypeptide chains are assembled from amino acids on a template and that synthesis takes place from its N terminus. [After Howard Marvin Dintzis (1927- ), US biochemist, who conceived the procedure and described its use in 1961.) dinucleotide 1 any oligonucleotide consisting of two mononucleotides in 3'-5' phosphodiester linkage. 2 any nucleotide coen-

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2,5-diphenyloxazole zyme in which either of the mononucleotides adenosine 5'phosphate or adenosine 2',5'-bisphosphate is in 5'-5' diphosphate (Le. phosphoric anhydride, pyrophosphate) linkage with nicotinamide mononucleotide or riboflavin 5'-phosphate. dinucleotide fold an alternative name for nucleotide binding fold. diode 1 a semiconductor device, containing one p-n junction, used in circuits to rectify alternating current to a direct current: semiconductor diode. 2 a thermionic valve containing an anode and a cathode and functioning in a similar manner: thermionic diode. dioestrus see estrous cycle. diol any organic compound (or portion of such a compound) containing two hydroxyl groups. diol lipid any of various neutral lipids that are fatty-acid esters of dihydroxy alcohols (i.e. are not glycerides). They occur in small amounts in seed oils; e.g. l-palmitoleoyl-2-trans-vaccenoyl-erythro-butane-2,3-diol, which is found in seeds of Coix lachrima. dioxin receptor see ARNT. dioxygen systematic name for the diatomic compound O 2, commonly termed (molecular) oxygen. Compare trioxygen. dioxygenase any oxidoreductase enzyme of the sub-subclass EC 1.13.11. Such enzymes catalyse reactions involving the incorporation of both oxygen atoms of dioxygen into a second substrate; see e.g. ethylene-forming enzyme, benzoate t,z-dioxygenase. Dip symbol for the diisopropylphospho group. DIP abbr. for the diisopropylphospho group. dipentene a racemic mixture of the (+) and (-) enantiomers of limonene. dipeptide any oligopeptide consisting of two (usually, 12'-) amino-acid residues. dipeptide mimic any synthetic dipeptide that inhibits angiotensin-converting enzyme. An example is captopril. dipeptidyl-peptidase abbr.: DPP; any member of a group of enzymes belonging to the sub-subclass EC 3.4.14, dipeptidylpeptide and tripeptidylpeptide hydrolases, that release an N-terminal dipeptide from an oligo- or polypeptide. Dipeptidyl-peptidase I (or cathepsin C), EC 3.4.14.1, is a lysosomal cysteine-type peptidase that acts on polypeptides, but not if the terminal amino-acid residue is Arg or Lys, and not if either of the adjacent residues is Pro. Example from Rattus norvegicus: database code CATC_RAT, 462 amino acids (52.38 kDa). Dipeptidyl-peptidase II, EC 3.4.14.2, is a lysosomal serine-type peptidase that acts preferentially on tripeptides. DipeptidyJpeptidase III, EC 3.4.14.4 (other names: red cell angiotensinase; enkephalinase B), is a cytosolic serine-type peptidase that acts on tetra- or longer peptides. Dipeptidyl-peptidase IV, EC 3.4.14.5 (other names: dipeptidyl aminopeptidase IV; Xaa-Prodipeptidyl-aminopeptidase; Gly-Pro naphthylamidase; postproline dipeptidyl aminopeptidase IV), catalyses the release of an N-terminal dipeptide, Xaa-Xbb-j-Xcc, from a polypeptide, preferentially when Xbb is Pro, provided Xcc is neither Pro nor hydroxyproline. The protein is a serine proteinase, type II transmembrane glycoprotein; it is a homodimer: database code DPP4_HUMAN, 766 amino acids (88.22 kDa); T-cell activation antigen CD26. Dipeptidyl-dipeptidase, EC 3.4.14.6, is a thiol-activated peptidase from Brassica oleracea that acts preferentially on tetrapeptides. dip-F symbol for diisopropyl fluorophosphate. DIPF abbr. for diisopropylphosphofluoridate. See diisopropyl fluorophosphonate. diphenylamine reaction the reaction of an acidic solution of diphenylamine with deoxypentoses to give a blue colour. It is used in the quantitative determination of DNA, and alone or in combination with other reagents as a detection reagent. 2,S-diphenyloxazole abbr.: PPO; a compound used as a primary scintillant in scintillation counting. See scintillation counter. See also scintillation cocktail.

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dipyridamole

diphosphate

N-N

fYZo>-D 2,5-diphenyloxazoie

diphosphate 1 the tetravalent anion, P 20 74-, derived from diphosphoric acid (earlier known as pyrophosphoric acid), heptaoxodiphosphoric(v) acid, (HObPO-O-PO(OHh 2 any mixture of free diphosphoric acid and its anions. see also inorganic diphosphate, pyrophosphate. 3 any (partial or full) salt or ester of diphosphoric acid. 4 any organic compound containing two phosphoric residues linked by an oxygen atom. 5 name of the univalent group -0-PO(OH)-0-PO(OH)2 (irrespective of its state of ionization). 6 formerly, any organic compound containing two independent phosphoric residues attached to different parts of the molecule; now incorrect, use bisphosphate. l+)diphospho+ 1 prefix to (or infix in) a chemical name indicating the presence in ester (or diester) linkage of a diphosphoric residue. 2 formerly, prefix to a chemical name indicating the presence of two independent phosphoric residues in ester linkages; now incorrect, use bisphospho+. diphosphoglycerate former name for 1 2.3-bisphospho-D-glycerate. 2 3-phospho-D-glycerovl phosphate. diphosphoglycerate pocket abbr.: DPG pocket; see bisphosphoglycerate pocket. diphosphoinosotide former name for phosphatidylinositol 4phosphate. diphosphopyridine nucleotide (oxidized) abbr.: DPN; obsolete name for the oxidized form of nicotinamide adenine dinucleotide; see NAD+. diphosphopyridine nucleotide (reduced) abbr.: DPNH; obsolete name for the reduced form of nicotinamide adenine dinucleotide; see NADH. diphosphoric symbol: PP or (in the one-letter convention for nucleotides) pp; general name for a residue of diphosphoric acid, (HOhPO-O-PO(OHb, whether singly or multiply attached through oxygen to other groups and whether or not any residual hydroxyl groups are dissociated. diphthamide a modified histidine residue on EF-2. See elongation factor.

diphtheria toxin an enzyme toxin produced by strains of Corynebacterium diphtheriae which are lysogenic for corynephage, whose genome contains the tox structural gene (carried by phage ~tox+). The toxin has the activity of EC 2.4.2.36; recommended name: NAD+ -diphthamide ADP-ribosyltransferase; systematic name: NAD+:peptide-diphthamide N-(ADP-D-ribosyl)transferase. It catalyses the reaction between NAD+ and peptide diphthamide to form nicotinamide and peptide N-(ADP-D-ribosyl)diphthamide. The toxin molecule is a proenzyme comprising a single polypeptide chain of ~62 kDa; the toxin is lethal for susceptible animals at around 100 ng per kg of body mass. On cleavage of one peptide bond

and one disulfide bond, the toxin splits into an N-terminal fragment, A (2 l.l 5 kDa), the enzyme that specifically inhibits protein synthesis by catalysing transfer of the ADP-ribosyl moiety of NAD+ to eukaryotic EF-2 (see elongation factor) in the cytoplasm, and a C-terminal fragment, B (~40 kDa), that is required for recognition of specific surface receptors on sensitive cell membranes. Fragment B is necessary for the toxicity of fragment A because it enables the latter to cross the plasma membrane. Example (precursor) from phage ~: database code DTX_CORBE, 567 amino acids (61.53 kDa); fragment A, amino acids 33-225; fragment B, amino acids 226-567. dipicolinate 2,6-pyridinedicarboxylate; a substance that is abundant (10%) in bacterial spores. Its production is a striking feature of sporulation and it may playa part in making spores resistant to heat.

n

HOOC::""N

COOH

dipicolinic acid

diplochromosome a 'double chromosome', compnsmg the arms of two daughter chromosomes attached to a single centromere. It arises due to failure of the centromere to divide following duplication of a chromosome. diploid describing a cell or nucleus having two sets of homologous chromosomes; i.e. containing twice the haploid number. diploidy n. diploid state the chromosome state of a cell in which each type of chromosome, except for the sex chromosomes, is always represented twice. diplotene the fourth phase of prophase I in meiosis. dipolar bond or coordinate bond or coordinate covalence or coordinate link or dative bond or semipolar double bond a covalent bond formed (actually or conceptually) between two initially uncharged moieties by coordination (def. 2). The consequent generation of opposing charges on the linked structures creates a dipole; e.g. R 3N: +Q: ~ R 3N+-Q:-. The term is preferred to the alternatives, which are now either obsolescent or obsolete. Compare polar bond. dipolar correlation time time taken for an atomic spin system to rotate through one radian from its previous orientation, the rotation being caused by interactions with other, neighbouring spins. dipolar interaction the interaction between two magnetic moments due to the effect of the magnetic field of one on the other. dipolar ion or zwitterion a molecule containing ionic groups of opposite charge in equal numbers. Compare amphion. dipole a pair of equal and opposite electric charges or magnetic poles (especially in a molecular entity) separated by a, usually, small distance. -dipolar ad). dipole moment or electric dipole moment symbol: p or p; a vector quantity equal to the product of the absolute magnitude of either charge in a dipole (the two are equal in an uncharged molecule) multiplied by the distance separating them. If a molecule possessing a dipole moment is placed in a uniform electric field, it will be subject to torque tending to line it up in the direction of the field. p = r.Q;r; coulomb metres, where Qi is the charge and ri is the position vector. dipyridamole an inhibitor of cyclic AMP phosphodiesterase and 5-lipoxygenase, used as a coronary vasodilator.

180

diradical

disperse phase

dipyridamole diradical an alternative term for biradical. direct current abbr.: d.c. or DC; an electric current that flows in only one direction. directional selection any genetic selection that shifts the population mean in the direction desired by the breeder. dis+ prefix indicating 1 reversal. 2 deprivation. exclusion, or lack. 3 negation. 4 removal or release. dis2 a gene in fission yeast that is the equivalent of DIS2 51 in budding yeast. disabled strain any strain of organism, especially a microorganism, that because of some character, e.g. a nutritional requirement, is unable to reproduce in the normal environment, including the normal host, and can only survive in laboratory conditions. disaccharidase any enzyme within sub-subclass EC 3.2.1 that hydrolyses a disaccharide to its constituent monosaccharides. disaccharidase deficiency see lactase deficiency. disaccharide any oligosaccharide consisting of two monosaccharide residues. It may be a nonreducing disaccharide or a reducing disaccharide, depending on the mode of linkage between the residues. disalicylidenepropanediamine abbr.: DSPD; N,N'-disalicylidene-I,3-diaminopropane; an inhibitor of photosynthetic electron flow at the ferredoxin level.

disassociation a variant form of dissociation (def. I). disc a variant spelling (esp. Brit.) of disk. discharge 1 (in physics) the release of an electric charge, e.g. from a condenser or a battery, or the equalization of an electric potential difference. 2 (in physics) the intermittent or continuous flow of electricity through a gas by the formation of electrons and ions. 2 (in medicine) an abnormal secretion from a body cavity, or the secretion from a wound. discoidin any of a group of endogenous carbohydrate-binding proteins (lectins) produced by cells of the slime mould Dictyostelium discoideum during differentiation. Similar to pallidin, they may be concerned in cell adhesion. Examples (all from D. discoideum): discoidin I, A chain: database code DISA_ DICDI, 253 amino acids (28.24 kDa); Band C chains: database code DISC_DICDI, 253 amino acids (28.39 kDa). discontinuous epitope an immunological determinant (i.e. epitope) on an antigen that comprises different sections of a protein molecule brought together by folding of the polypeptide chain. Compare continuous epitope. discriminator 1 any (electronic) device that gives an output signal only when the input signal is above a certain preset level

or has certain preset characteristics. 2 any criterion used in sorting objects, experimental results, signals, etc. disease any anatomical abnormality or impairment of the normal functioning of an organism or of any of its parts other than one arising directly from physical injury. It may be caused by environmental factors (e.g. malnutrition, toxic agents, etc.), infective agents (bacteria, viruses, etc.), inherent defects in the organism (e.g. genetic disease), or any combination of these factors. disequilibrium assay any radioimmunoassay in which the reagents are not added at the same time and are not allowed to reach thermodynamic equilibrium. Compare equilibrium assay. disinfection the destruction or removal of all organisms capable of giving rise to infection. Compare sterilize (def. 1). disintegration or nuclear disintegration any process of nuclear decay involving a splitting into more nuclei or the emission of particles (either spontaneously or as a result of a collision). disintegration constant or decay constant symbol: Jc; for a radionuclide, the probability of the nuclear decay of one of its nuclei in unit time. It is given by: Jc := -(l/t)ln(AIA o), where A o is the radioactivity at zero time and A is the activity at time t. See also average life. disintegrin any of a group of compounds that act as inhibitors of platelet-fibrinogen interaction and other aggregations. They are found in certain snake venoms. Example, disintegrin CTF-I1CTF-II from Trimeresurus flavoviridis: database code DISC_TRIFL, 75 amino acids (8.32 kDa); two motifs. Example, from Agkistrodon rhodostoma (Malayan pit viper) venom: database code DISCAGKRH, 68 amino acids (7.32 kDa). disjunction the separation of chromosomes at anaphase during nuclear division. disk or (esp. Brit.) disc 1 a circular, flattened structure, or any object having or resembling such a shape. See also retinal rod. 2. (in computing) a disk-shaped device on which files are stored electromagnetically. disk (gel) electrophoresis a technique of separation by electrophoresis in which a tube is loaded first with the sample, applied in a gel support (usually polyacrylamide), followed by a spacer gel and finally by the running gel, in which separation occurs. The gels are so formed as to give a gradient of progressively smaller pore size, and a discontinuous buffer system is used. This arrangement causes the separating components of the applied mixture to stack as a series of very thin bands and permits very high resolution. dismembrator an ultrasonic device for rapidly disrupting cells in bacteriological and cytological studies. It consists of a probe oscillating at ~20 kHz and an acoustical power of up to 150 W that is dipped into a cell suspension, contained in either a stainless-steel or glass beaker. dismutase see superoxide dismutase. dismutation a chemical reaction in which a single compound serves both as an oxidizing agent and as a reducing agent; e.g. the reaction of two molecules of pyruvate and one of water giving rise to one molecule each oflactate, acetate, and carbon dioxide. Compare disproponionation. disodium chromoglycate see cromolyn. disodium etidronate see etidronate. disome a polysome in which two ribosomes are attached to a strand of messenger RNA. Compare monosome, nucleodisome. Dispase proprietary name for a highly stable neutral metalloproteinase obtained from Bacillus polymyxa. It is so named from its use, alone or with collagenase, for gentle enzymic disaggregation and dispersal of animal tissues into separated cells for primary cell culture and for redispersal of cells on subculturing. See also Chaotropase, Pronase. disperse phase or dispersed phase the phase in a two-phase sys-

181

dispersion tem that consists of the particles in a colloid, emulsion, or suspension. dispersion 1 the selective separation of an inhomogeneous emission according to some criterion (especially frequency, particle mass, speed, or energy); e.g. the separation of heterochromatic light into its components. 2 any system in which particles of any nature (e.g. solid, liquid, gas, or composite) are dispersed in a solid, liquid, or gas of different composition. 3 (in statistics) the extent to which values of a statistical frequency distribution are scattered around a mean or median value. dispersion force or London force a long-range attractive interaction occurring between atoms or molecules whether or not they have permanent charges or dipole moments. Since the electrons in an atom or molecule are moving, an instantaneous dipole moment is induced in the atom or molecule; this averages to zero over a short time. This instantaneous dipole moment will induce an oppositely oriented dipole moment in a neighbouring atom or molecule in a manner that does not time-average to zero. This interaction energy, V(R), is given approximately by: V( R) = _ ~ ( hpAPB ) aAaB ..1 2 PA + PB (47teo) R6 where PA and PB are the approximate frequencies of the first electron transitions of entities A and B, aA and as are their polarizabilities, eo is the permittivity of vacuum, h is the Planck constant, and R the distance between the entities. [After Fritz London (1900-54), German-born US physicist.) dispersive replication of DNA see replication of DNA. displacement binding a technique in which the displacement of radioligand bound to a population of receptors is measured as the concentration of an unlabelled ligand, which binds to the same receptors, is increased. It is used to distinguish different affinity states of the receptor population or receptor selectivity of the radioligand. displacement chromatography an analytical chromatographic technique in which a mixture is applied to a chromatographic column and the components of the mixture are then successively displaced by elution with a solution containing another substance of higher affinity for the column material than that of the most firmly held component. The relative proportions of the components of the mixture are determined by frontal analysis of the eluate. displacement electrophoresis an alternative term for isotachophoresis. displacement loop an alternative name for D-Ioop. displacement reaction a chemical reaction in which an atom or group is displaced from its covalent attachment to a central (frequently a carbon) atom following an attack by either an electrophile or a nucleophile. disproportionation any chemical reaction of the type: A+ A~A'+ A", where A, A', and A" are different chemical species. Compare dismutation. DIS2 $1 a gene of budding yeast encoding protein phosphatase I (its equivalent in fission yeast is disZ). In the absence of gene function mitosis is arrested. The product in Saccharomyces cerevisiae is: database code YSCDIS2S1A, 312 amino acids (35.93 kDa). dissimilation a less common alternative term for catabolism. Compare assimilation. -dissimilatory adj. dissimilatory nitrate reduction see nitrate reduction. dissociation 1 or disassociation a reversible splitting of a chemical substance into simpler entities; compare association. In this sense, the term may be applied to: a the heterolysis of a covalent bond, yielding, in the case of an initially uncharged molecule, positively and negatively charged ions: ionic dissociation; b the disaggregation of a macromolecular homopolymer or heteropolymer into its constituent units (i.e. protomers), usually by a stepwise process through components of interme-

disulfide bond diate size (i.e. oligomers) and without rupture of covalent bonds; c the breakdown of an enzyme-substrate complex, which mayor may not involve cleavage of a covalent bond; or d the separation of a complex of two or more molecules into the constituent molecules. 2 a splitting of a chemical substance by the homolysis of a covalent bond, yielding radicals. 3 translocation between a large chromosome and a small supernumerary one, in effect splitting the large chromosome into two chromosomes. 4 separation (induced or spontaneous) of the nuclear components of a heterokaryotic dikaryon. -dissociated, dissociable, dissociative adj.; dissociate vb. dissociation constant symbol: Kdiss or K d ; the equilibrium constant for the reversible breakdown of a complex or a chemical compound into two or more simpler entities; the reciprocal of the association constant, Kass • In some cases, an apparent dissociation constant (K'd) is determined (for the distinction see equilibrium constant). It is also known as the ionization constant in cases where a substance dissociates into ions. For a dissociation (or ionization) of the general type AB ...... A + B, the dissociation (or ionization) constant is given by: Kdiss = [A)[B)/[AB) = lIKass • dissociation energy symbol: D; the enthalpy (per mole) required to break a given chemical bond in a specified chemical entity by homolysis. distal situated furthest from an origin, central line, or point of attachment. distal protein a protein that binds late in the assembly of complex structures, such as ribosomes. Compare proximal protein. distil or (US) distill to undergo, to subject to, to purify, or to separate by distillation. distillate the liquid (or solid) product of distillation. distillation the act or process of evaporating a liquid by boiling so that its components, which are vaporized at different temperatures or at different rates, can be separated and condensed back to a liquid (or solid). It is used to purify one liquid from a mixture of liquids or from (dissolved) solids. See fractional distillation. distribution 1 (in chemistry) an alternative term for partition. 2 (in biochemistry) the pattern of occurrence of a substance within or between cells or tissues, or within a group of organisms, taxa, etc. 3 (in biology) the geographical range or pattern of occurrence of a particular taxon or genetic variant. 4 (in statistics) the frequency of occurrence of a variable at each of a number of discrete values. See also normal distribution. distribution coefficient 1 an alternative term for partition coefficient. 2 in gel chromatography, the fraction of the stationary phase that is available for diffusion of a given solute species. distribution law an alternative /lame for partition law. distributive 1 of, relating to, or characterized by distribution. 2 (in molecular biology) or nonprocessive describing (the action of) any enzyme or catalytic complex that progressively synthesizes or degrades a biopolymer by effecting several or many cycles of the same type of reaction or reaction sequence and dissociates from the template or intermediate product after each catalytic event. Compare processive. -distributively adv. disulfide or disulphide (in organic chemistry) any compound containing two bivalent sulfur atoms linked by a covalent bond and each attached to a carbon atom. disulfide bond or disulfide bridge or disulfide link a covalent bond between two sulfur atoms. Such bonds in biomolecules are usually formed by the oxidation of sulfhydryl groups in two neighbouring cysteine molecules or residues. Disulfide bonds may link two half-cystine residues in the same polypeptide chain, as in ribonuclease, or in different peptide chains, as in insulin or oxidized glutathione, and they often are important in maintaining the three-dimensional structure of polypeptides and proteins. They may also be reversibly formed in oxidation~reduction reactions as in the interconversion of

182

disulfide interchange Iipoamide and dihydroIipoamide. Also: disulphide bond or disulphide bridge or disulphide link. disulfide interchange or disulphide interchange any chemical reaction in which there is an interchange in the groups attached to two or more disulfide bonds; e.g.: R-S-S-X + Y-S-S-Z ~ R-S-S-Y + X-S-S-Z, where R, X, Y, and Z are different polypeptide chains or other SH-bearing molecules. See also protein disulfide isomerase. disulfide knot or disulphide knot a region at the centre of a fibrinogen molecule where the six polypeptide chains are linked together by eight disulfide bonds. Compare cystine-knot. disulfiram trivial name for tetraethylthiuram disulfide; bis(diethylthiocarbamoyl) disulfide; a drug used to deter alcohol abuse in the treatment of alcoholism. Alcohol ingestion after disulfiram causes vasomotor disturbances, nausea, vomiting, and even unconsciousness and death. It acts by inhibiting the enzyme acetaldehyde dehydrogenase and hence slows the removal of acetaldehyde. It occurs naturally in the otherwise edible fruit body of the agaric mushroom Coprinus atramentarius. One proprietary name is Antabuse.

DIT abbr. for diiodotyrosine. dithioerythritol abbr.: DTE; erythro-I,4-dimercapto-2,3-butanediol; both this and dithiothreitol are known as Cleland's reagent. It has similar properties to dithiothreitol but is less often used. dithiothreitol abbr.: DTT; threo-I,4-dimercapto-2,3-butanediol; both this and dithioerythritol are known as Cleland's reagent. A water-soluble solid compound which, because of its low redox potential (-0.33 Y, pH 7.0), is capable of maintaining monothiols completely in the reduced state and of reducing disulfides quantitatively, so becoming oxidized to a cyclic disulfide; it has little tendency to be oxidized directly by air. diuresis increased or excessive flow of urine. diuretic 1 producing an increase in the volume of urine. 2 any agent that increases the volume of urine. diurnal 1 occurring during the day. 2 repeating every day; having a periodicity of approximately 24 hours. Compare circadian. Diuron see DCMU. divergent evolution or divergence biological evolution that tends to produce an increasing difference in some characteristic(s) between initially similar groups of, e.g., organisms or gene products. Compare convergent evolution. divergent transcription the transcription of adjacent genes from opposite strands of duplex DNA and in opposite directions. dixenic see synxenic. Dixon plot a graphical method for the presentation of enzyme-kinetic data by which a Michaelis constant, Xm (see Michaelis kinetics), or an inhibitor constant, Xi, may be determined. The method is primarily used as a means of readily obtaining Xi' The reciprocal of the initial velocity (i.e. II V) is plotted against a series of inhibitor concentrations [I], at constant substrate concentration, [S]. When this is done for a number of values of [S], the resulting lines intersect at a point corresponding to Xi' The value of [I] at which this occurs is to the left of the ordinate (for competitive inhibition) and corresponds to -Ki . For non-competitive inhibition the lines meet on the abscissa. [After Malcolm Dixon (1899-1985), British enzymologist, who described it in 1972.]

DNA

dizygotic describing twin offspring formed from two separate ova fertilized by two separate sperms. Compare monozygotic. DL prefix (in chemical nomenclature) denoting an equimolar mixture of D and L enantiomers. See D/L convention. dl· prefix (in chemical nomenclature) formerly used to denote racemic; now obsolete, use (±)-, racemo-, or rac-. D/L convention a convention of symbols used to designate the absolute configuration around a chiral element in a-amino acids, cyclitols, monosaccharides, and derivatives of these classes of compounds. Within these classes it can be applied to any molecule of the type R j CHXR 2 that can be oriented in a Fischer projection with the most highly oxidized atom at the top; then if X is on the right the configuration is designated by the prefix D-, whereas if X is on the left the configuration is designated by the prefix L-, relative to D-( +)- or L-(-)-glyceraldehyde. Racemic (i.e. equimolar) mixtures of D and L enantiomers are designated by the prefix DL-. a-Amino acids are designated Dor L- according to the configuration at the a-carbon atom. Cyclitols are designated D- when the formula is drawn in such a way that the substituent on the lowest-numbered asymmetric carbon atom is above the plane of the ring and the numbering is anticlockwise, and L- when it is clockwise; the locant of the defining centre should precede the prefix D- or L-, e.g. ID-I-Omethyl-myo-inositol. For monosaccharides the highest-numbered chiral centre (i.e. carbon atom) is the reference atom determining whether the monosaccharide is D or L. When a compound contains more than one class of residue the configuration designators are Ds or Ls if they apply to an amino-acid residue, Dc or Lc to a cyclitol residue, and Dg or Lg to a monosaccharide residue (the subscript s denoting the reference aamino acid serine, the subscript c denoting cyclitol, and the subscript g denoting the reference monosaccharide glyceraldehyde). The absolute configurations of chiral compounds of classes other than those listed are designated by application of the sequence rule. Compare ambo-, do, 1-, dl-, isomerism. D-Ioop or displacement loop a DNA structure generated when an additional strand of DNA is taken up by a DNA duplex, so that one strand of the original duplex is displaced, forming a D-shaped loop. Formation of a D-loop is favoured in negatively supercoiled DNA and can occur spontaneously. Such Dloops are formed in covalently closed mammalian mitochondrial DNA, and are prominent as intermediates in genetic recombination, in which their formation is catalysed by strand-exchange enzymes, the best characterized of which is the RecA protein of Escherichia coli. DMF or DMFA abbr. for N,N-dimethylformamide; a neutral liquid of low melting point (-61°C) and a reasonably high boiling point (153°C), miscible with water and with most common organic solvents, hence sometimes termed the universal solvent. DMSO abbr. for dimethylsulfoxide (use discouraged, Me2S0 preferred). DMT abbr. for the dimethoxytrityl group. dna symbol for any of various bacterial genes that are involved in DNA replication. For example, dnaG is the gene for DNA primase in Escherichia coli. DNA abbr. and common name for deoxyribonucleate (def. I), or deoxyribonucleic acid; one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one. Compare RNA. The absence of a 2' -hydroxyl group on each deoxyribose moiety renders these phosphodiester linkages resistant to hydrolytic attack by alkali, in contrast to those of RNA. A DNA strand, unless circular, has polarity, with one 5' end and one 3' end, the two strands in duplex DNA having opposed polarities. Two purines, adenine and guanine, and two pyrimidines, cytosine and thymine, are the major bases present. The linear sequence of the purine and pyrimi-

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DNAase dine bases carries genetic information, whereas the deoxysugar and phosphoric residues playa structural role; the ba.se sequence is written in the 5'-43' direction. See als~ double helix. Specific forms, functions, molecules, or preparatIOns of DNA may be designated by prefixes or suffixes, thus: A-DNA or DNA-A, Aform of DNA; amDNA, anti-messenger DNA; B-DNA or DNA-B, Bform of DNA; cDNA, complementary DNA; cccDNA, covalently closed circular DNA; C-DNA or DNAC, Cform of DNA; ctDNA, chloroplast DNA; dsDNA, doublestrand(ed) DNA (see duplex DNA); iDNA, intercalary DNA; msDNA, multicopy single-strandled) DNA; mtDNA, mitochondri~1 DNA; nDNA, nuclear DNA; pDNA, plasmid DNA; rDNA, ribosomal DNA; recDNA, recombinant DNA; rfDNA, replicative-form DNA; rtDNA, recombinant DNA; scDNA, single-copy DNA; ssDNA, single-strand(ed) DNA; tDNA, transfer DNA; T-DNA, transfer DNA of the Ti plasmid. See full entry for T-DNA. Z-DNA or DNA-Z, Zform of DNA. DNAase or DNAse abbr. sometimes used for deoxyribonuclease; DNase is more usual. DNA-binding protein FIG see matrin. DNA blot transfer see blot-transfer technique. DNA chip see SOH. DNA cloning see molecular cloning. DNA cycle see cell-division cycle. DNA-dependent DNA polymerase see DNA polymerase. DNA-dependent RNA polymerase see RNA polymerase. DNA-directed DNA polymerase recommended name for DNA polymerase, EC 2.7.7.7. DNA-directed RNA polymerase recommended name for RNA polymerase, EC 2.7.7.6. . DNA fingerprinting a term sometimes used to refer to genetic profiling. IDNA) glycosylase or DNA glycosidase any of a group .of glycohydrolases that initiate repair of DNA by hydrolysmg Nglycosyl bonds linking deoxyribose residues "Yit? !ll?di~ied ~r incorrect bases to generate apurinic or apynmldmlc sites m the DNA and release the bases. They include DNA-3-methyladenine glycosidase I (EC 3.2.2.20), DNA-3-methyladenine glycosidase II (EC 3.2.2.21), and formamidopyrimidine-DNA glycosidase (EC 3.2.2.23). The enzymes form part of the pathway of base-excision repair, which acts on oxidative or nonoxidative damage, as determined by the specificity of individual enzymes. Sequences tend to be related; examples from Escherichia coli: DNA-3-methyladenine glycosidase I is constitutive and specific to the named base: database code 3MGI_ECOLl, 187 amino acids (21.08 kDa); DNA-3-methyladenine glycosidase II is inducible and releases any of 3-methyladenine, 3-methylguanine, 7-methylguanine, 0-2methylthymine, and 0-2-methylcytosine: database code 3MG2 ECOLl, 282 amino acids (31.36 kDa). DNA gyrase see type II DNA topoisomerase. DNA helicase an enzyme that catalyses unwinding of the DNA double helix during DNA replication and repair. It requires ATP. Example, rep gene product from Escherichia coli: database code REP_ECOLl, 673 amino acids (76.85 kDa). . (DNA) joinase an alternative name for DNA ligase. DnaK or heat-shock protein 70 abbr.: hsp70; a heat-shock protem that plays an essential role in the initiation of DNA repli~a­ tion in lambda phage and, in combination with Dnal protem, acts to release proteins 0 and P. Example from Escherichia coli: database code DNAK_ECOLl, 637 amino acids (68.98 ill~. . DNA ligase or (DNA) joinase or DNA repair enzyme either of two enzymes that restore broken phosphodiester bonds in deoxyribonucleic acids. (I) DNA ligase (ATP) EC 6.5.1.1; ~ys­ tematic name: poly(deoxyribonucleotide):poly(deoxynbonucleotide) ligase (AMP-forming); other names: polynucleotide ligase; DNA repair enzyme; (DNA) joi.nase; former name: sealase. An enzyme that catalyses the reactIOn: ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m =

DNA polymerase AMP + pyrophosphate + (deoxyribonucleotide)n+m' Example from phage T4: database code DNLCBPT4, 487 amino acids (55.23 kDa). (2) DNA ligase (NAD+) EC 6.5.\.2; systematic name: poly(deoxyribonucleotide) :poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming); other names: polynucleotide ligase (NAD+); DNA rep~ir enzyme; (DNA) joinase. An enzyme that catalyses the reaction: NAD+ + (deoxyribonucleotide)n + (deoxyribonucleotide)m = AMP + nicotinamide mononucleotide +(deoxyribonucleotide)n+m' Example from Escherichia coli: database code DNLJ_ECOLI, 671 amino acids (73.61 kDa). DNA-like RNA abbr.: D-RNA or dRNA; a minor fraction of eukaryotic cellular RNA that has a base composition much closer to that of DNA than the bulk of RNA. It is mainly of high molecular mass, short half-life, and confined to the nucleus, and is probably the same as giant messenger-like RNA and pre-messenger RNA. DNA-3-methyladenine glycosidase see (DNA) glycosylase. DNA methylase either of two enzymes involved in modification and other roles. (I) Site-specific DNA-methyltransferase (adenine-specific) EC 2.1.\.72; other names: N-6 adeninespecific DNA methylase; modification methylase; restrictionmodification system; it catalyses the reaction: S-adenosyl-L-methionine + DNA-adenine = S-adenosyl-L-homocysteine + DNA-6-methylaminopurine. Example from Escherichia coli: database code DMA_ECOLl, 278 amino acids (32.06 kDa); it recognizes the base sequence GATC and is part of the system for postreplicative mismatch repair. (2) Site-specific DNA-methyltransferase (cytosine-specific) EC 2.\.\.73; other names: C-5 cytosine-specific DNA methylase; modification methylase; restriction-modificati.on system; it catalyses the reaction between S-adenosyl-L-methlOnine and DNA-cytosine to form S-adenosyl-L-homocysteme and DNA-5-methylcytosine. Example from E. coli: database code DCM_ECOLl, 472 amino acids (53.40 kDa); it recognizes the base sequence CCWGG and methylates both strands. IDNA) nicking-closing enzyme or nicking-and-closing enzyme alternative names for type I DNA topoisomerase. DNA nucleotidylexotransferase recommended name for terminal deoxynucleotidyltransferase. DNA photolyase EC 4.1.99.3; recommended name: .deo:,"yribodipyrimidine photo-lyase; other name: photoreactlvatmg enzyme. An enzyme that splits cyclobutadipyrimidine ~in DNA) into two pyrimidine residues (in DNA), thereby repairing the DNA after light-induced pyrimidine dimer formation. It is light dependent, requiring the cofactors reduced flavin and either (in different enzyme types) a folate coenzyme or a modified flavin. Example, Escherichia coli enzyme required for 'light repair': database code PHR_ECOLl, 472 amino acids (53.61 kDa); four motifs. DNA polymerase common name for either of two categories of enzymes that catalyse the synthesis of DNA from ?eoxt ribonucleoside triphosphates in the presence of a nucleic-acid primer. Based on structural similarities, DNA polymerases have been grouped in two families. In family A are Escherichia coli and various other bacterial polymerases I, Thermus aquaticus Taq polymerase, some bacteriophag~ polymerases, and yeast mitochondrial polymerase y. In family B are many polymerases of higher eukaryotes, yeast polymerases I to I!I, and polymerase REV3, E. coli polymerase II, archaebactenal polymerases, and many viral polymerases. (I) DNA-directed DNA polymerase ~C 2.7.~.7.; othe~ name: DNA nucleotidyltransferase (DNA-directed); It IS reqUired for DNA replication and repair and has 3'-exonuclease activity (see proofreading). Eukaryotic DNA-directed DNA polymerases are of five types: (a) DNA polymerase-a (also called DNA polymerase I or Kornberg enzyme) is a high-molecular-mass (>100 kDa) en-

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DNAprimase zyme that was first detected in E. coli; in association with DNA primase it is replicative. Example (human): database code DPOA_HUMAN, 1462 amino acids (165.67 kDa) belongs to polymerase family B, with six conserved regions, four of which are involved in substrate binding. Several DNA viruses have type B polymerases; examples include adenoviruses and herpesviruses. (b) DNA polymerase-~ (or DNA polymerase II) is a low-molecular-mass «50 kDa) enzyme recovered almost entirely in nuclear extracts. (c) DNA polymerase-y (or DNA polymerase III) is an enzyme of high molecular mass (>100 kDa) that copies synthetic polyribonucleotides with high efficiency, but does not copy DNA well. Examples from E. coli: a chain: database code DP3A_ECOLl, 1160 amino acids (129.76 kDa); ~ chain: database code DP3B_ECOLl, 366 amino acids (40.54 kDa); e chain: database code DP3E_ECOLl, 243 amino acids (27.07 kDa). The protein at database code DP3X_ECOLl, 643 amino acids (71.06 kDa) represents e and ,; the production of the two protein products from this region is due to programmed ribosomal frameshifting. (d) DNA polymerase-o is a zinc finger protein with both polymerase and 3'-exonuclease activities; it is a heterodimer of 125 kDa and 50 kDa subunits. (e) DNA polymerase-mt is the mitochondrial DNA polymerase. E. coli has three DNA polymerases: (a) pol I, database code DPOI_ECOLl, 928 amino acids (103.00 kDa); this has 5'- and 3'-exonuclease activities; the 5'-exonuclease activity is involved in DNA replication; the polymerase activity is employed during DNA repair; 3-D structures are known for parts of the enzyme (database codes NRL_IDPIl and NRL_ I DPI2). (b) pol II, database code DP02_ECOLl, 782 amino acids (89.82 kDa); is regulated by lexA and belongs to family B (above). (c) pol III, the major replication polymerase, has an a subunit with polymerase activity, database code DP3A_ ECOLl, 1160 amino acids (129.76 kDa) and a total subunit composition of (a,E,eh-'2-(y,o,o',,,,,xh-~4'The complex (a,E,e), the 'core', is assembled first. (2) RNA-directed DNA polymerase is the EC recommended name for reverse transcriptase. DNA primase a DNA-directed RNA polymerase (EC 2.7.7.-) of the bacterial primosome. It associates transiently with the primosome and synthesizes short RNA primers for the Okazaki fragments on both template strands at replication forks. Example from Escherichia coli: database code PRIM_ECOLl, 581 amino acids (65.49 kDa). DNA print the pattern formed by denaturing the DNA in colonies of bacteria grown on a support and fixing the DNA to the support. DNA provirus see provirus. DNA repair enzyme any of the various enzymes involved in the different stages of DNA repair. Three steps are involved, each catalysed by a different set of enzymes: (l) the altered portion of DNA is removed by repair nucleases; (2) DNA polymerase fills the gap with a complementary copy; (3) the break is sealed by DNA ligase. There are two other related repair pathways, called (base-)excision repair and nucleotide-excision repair. See a/so repair enzyme. DNA replication see replication of DNA. DNA-RNA hybrid a double helix consisting of one DNA chain and one complementary RNA chain, the two chains being held together by hydrogen bonds between the complementary base pairs. DNA-RNA hybridization or DNA-RNA hybridisation the formation of a duplex (def. 2) nucleic-acid structure that occurs when DNA and RNA molecules that have complementary base sequences are brought together. This phenomenon is exploited in a technique used to localize genes in a chromosome that depends on allowing radioactively labelled RNA to hybridize with denatured, single-stranded DNA from which the

dNTP RNA was transcribed and then determining the position on the DNA where hybridization has taken place by autoradiography. It also forms the basis of Northern blotting. DNase usual abbr. for deoxyribonuclease. Compare DNAase. (DNA) sealase an alternative name for polynucleotide ligase (def. 1). DNA sequencing determination of the order in which bases occur in DNA. Usually the DNA is cut with restriction enzymes and subjected to either the chemical cleavage method or the chain-termination method. DNA superhelix see supercoil. (DNA) swivelase a former name for type I DNA topoisomerase. DNA topoisomerase any enzyme that alters superhelix density in supercoiled DNA. Topoisomerases are found in all cell types, from microorganisms to those of humans, and in some viruses e.g. bacteriophage T4 and vaccinia. All topoisomerases isolated so far have the ability to relax negatively supercoiled DNA, converting it to a less supercoiled form. They have been divided into type I, which make a transient single-strand break, and type II, which make a transient double-strand break. Type I DNA topoisomerase, EC 5.99.1.2; other names: DNA topoisomerase, relaxing enzyme, untwisting enzyme, swivelase, nicking-closing enzyme, ro-protein; it catalyses the ATP-independent breakage of a single strand of DNA, which may be followed by passage (i.e., in the case of duplex DNA, transfer of the unbroken strand through the broken strand) and rejoining. This has the effect of relaxing one negative supercoil. Example from Escherichia coli: database code TOPI_ECOLl, 864 amino acids (97.29 kDa). This enzyme can relax only negatively supercoiled DNA, whereas some enzymes, e.g. that from calf thymus, can relax both negatively and positively supercoiled DNA. Type II DNA topoisomerase, EC 5.99.1.3; other name: DNA topoisomerase (ATP-hydrolysing); it catalyses ATP-dependent breakage, passage (in this case, of a double-strand through a double-strand break) and rejoining of the double-stranded DNA. This enzyme can thus decatenate circular duplex DNA. All type II enzymes can relax both positively and negatively supercoiled DNA. Bacterial DNA gyrase is a special example of this class of enzyme. In addition to the properties of the other type II enzymes, it catalyses the ATP-dependent introduction of negative superhelical turns into a closed circular DNA. It is an A 2B2 tetramer. The energy-free topoisomerase activity of the A subunit, which breaks the DNA, is inhibited by 4-quinolone antibiotics such as nalidixic acid and ciprofloxacin. The energy-transducing activity of the B subunit is inhibited by novobiocin and other coumarin antibiotics. Example, subunit A: database code GYRA_ECOLl, 875 amino acids (96.85 kDa); subunit B: database code GYRB_ECOLl, 803 amino acids (89.72 kDa). The breaking and rejoining of DNA is catalysed by the A subunit; the B subunit is the ATPase. A distinctive property of this particular enzyme is that it can introduce negative superhelical turns into a closed circular DNA molecule with the coupled hydrolysis of ATP. See a/so linkage number, supercoil, winding number, writhing number. (DNA) untwisting enzyme an alternative name for (DNA) swivelase. DNA virus or deoxyribovirus any virus in which the genome consists of DNA, either double-stranded (in class I viruses) or single-stranded (in class II viruses). See Baltimore classification of viruses. DNFB abbr. for (2,4- )dinitrofluorobenzene. See Sanger's reagent. Dnp symbo/for dinitrophenyl group. DNP abbr. for 1 (2,4-)dinitrophenol. 2 deoxyribonucleoprotein (use deprecated). Dns symbol for 5-(dimethylamino)naphth-I-ylsulfonyl; see a/so dansy!. dNTP abbr. for any deoxynucleoside (5'-)triphosphate (the deoxynucleoside being eithe,r unspecified or unknown).

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DOC DOC abbr. for (use discouraged) 1 deoxycholate (see deoxycholic acid). 2 deoxycorticosterone. doca or DOCA abbr. for deoxycorticosterone acetate (see deoxycorticosterone) . Docetaxel a proprietary name for a semisynthetic analogue of taxol. docking the binding of any macromolecule or part of such a molecule to its specific harbouring site on another molecular structure. See also signal recognition particle receptor. docking protein another name for signal recognition particle receptor. docosa+ or (before a vowel) docos+ prefix indicating twentytwo or twenty-two times. docosadienoic acid any straight-chain fatty acid having 22 carbon atoms and two double bonds. The (5Z,13Z)-form has been reported to occur in Limnanthes douglasii. docosahexaenoic acid any straight-chain fatty acid having 22 carbon atoms and six double bonds. Only the (all-Z)4,7,10,13,16,19-isomer, of the n-3 family, occurs naturally, being present in substantial amounts (10-15% of total fatty acids) in fish oils, and in variable amounts (a few percent of total) in animal glycerophospholipids. It can be formed metabolically from a-linolenic acid. docosanoic acid or behenic acid a straight-chain saturated fatty acid having 22 carbon atoms that occurs as a constituent of cerebrosides and some seed oils (especially of Lophira spp.); in some of the latter it accounts for 20-30% of total fatty acids. docosapentaenoic acid any straight-chain fatty acid having 22 carbon atoms and five double bonds. The (all-Z)4,7,1O,13,16-isomer is a member of the n-6 family and can be formed metabolically from linoleic acid; it is a constituent of animal glycerophospholipids. The (all-Z)-7, 10, 13, 16,19-isomer, of the n-3 family, can be formed metabolically from alinolenic acid; it is a precursor of 4,7,10,13,16, 19-docosahexaenoic acid, and is present in small amounts (a few percent) in animal glycerophospholipids and in larger amounts (up to 10%) in fish oils. docosatetraenoic acid any straight-chain fatty acid having 22 carbon atoms and four double bonds. Adrenic acid is found in animal glycerophospholipids, especially in brain and heart of animals fed sunflower or corn oil, and is presumed to be the (all-Z)-7, 10,13, 16-isomer. docosatrienoic acid any straight-chain fatty acid having 22 carbon atoms and three double bonds. The (all-Z)-7, 10,13-isomer occurs in animal lipids, especially during essential fatty acid deficiency. docosenoic acid any straight-chain fatty acid having 22 carbon atoms and one double bond. The (IIZ)-isomer, cetoleic acid, occurs in marine oils and rapeseed oil. The (l3Z)-isomer, erucic acid, is an important constituent of rapeseed and other oils of plants belonging to the family Cruciferae. The possibility that it may be harmful has prompted efforts to breed crop varieties that yield oils containing low levels or none of this fatty acid. Dod symbol for the dodecy1 group. dodeca+ or (before a vowel) dodec+ prefiX indicating twelve. dodecandrin a type I ribosome-inactivating protein. dodecanoic acid systematic name for lauric acid, a straightchain saturated fatty acid having 12 carbon atoms. See also laurate. dodecanoyl symbol Lau; systematic name for lauroyl. dodecenoic acid any straight-chain fatty acid having 12 carbon atoms and one double bond. dodecenoyl the acyl group derived from any dodecenoic acid. dodecenoyl-CoA .A-isomerase EC 5.3.3.8; systematic name: dodecenoy1-CoA LJ3-cis-LJ2-trans-isomerase; other names: LJ3_ cis-.d 2-trans-enoyl-CoA isomerase; acetylene-allene isomerase; 3,2 trans-enoy1-CoA isomerase. An enzyme that is involved in unsaturated fatty acid oxidation; it catalyses the isomerization of 3-cis-dodecenoyl-CoA to 2-trans-dodecenoyl-

dolichyl-diphosphooligosaccharide-protein CoA, thereby producing a substrate for enoyl-CoA hydratase. Example from rat: database code 521091, 298 amino acids (32.86 kDa). See also peroxisomal bifunctional enzyme. dodecyl symbol: Dod; preferred name for the alkyl group, CH 3-[CH 2lto-CH r (also known as lauryl), derived from dodecane. n-dodecyl-N,N-dimethylglycine lauryldimethylbetaine; a zwitterionic betaine detergent, CMC 1.6-2, I mM, Proprietary name: Empigen BB. n-dodecyl-j3-D-glucopyranoside a water-soluble nonionic detergent, CMC 0.13 mM. n-dodecyl-j3-D-maltoside a water-soluble nonionic detergent, aggregation number 98, CMC 0.1-0,6 mM. dodecylsulfate the CHdCH 2]JQ-CH r O-S0 3 anion. See sodium dodecyl sulfate. doghouse configuration (of a cyclobutadipyrimidine) see pyrimidine dimer. Doisy, Edward Adelbert (1893-1986), US chemist, biochemist, and endocrinologist remembered for the isolation of the female sex hormones estradiol, estriol, and estrone, and especially for his isolation (from putrified fish meal) of a second antihemorrhagic principle named vitamin K 2 (now termed menaquinone) (see also Dam) and for his subsequent structural characterization of vitamins K] and K 2; Nobel Laureate in Physiology or Medicine (1943) 'for his discovery of the chemical nature of vitamin K' [prize shared with H. C. P. Dam]. dolichol the recommended term for any 2,3-dihydropolyprenol derived from four or more linked isoprene units, of general structure i.e. any prenol derivative H-[-CHrC(CH3)=CH-CHrln-CHrCH(CH3)-CH2-CH2-0H where n is greater than 3; in naturally occurring dolichols n is commonly in the range 13-23, (Note: Because the isoprene unit carrying the hydroxyl group is saturated in dolichols, they are not true prenols or polyprenols, though often classed as such. It is therefore recommended that, unless qualified, these collective terms are not used to include dolichols,) The phosphoric esters of dolichol (dolichol phosphate or phosphodolichol or dolichyl phosphate) and the diphosphoric esters (dolichol diphosphate or diphosphodo1icho1 or dolichyl diphosphate) function in eukaryotes as carriers of mono- and oligosaccharide residues in the glycosylation of lipids and proteins within intracellular membranes. First, glycosyl groups are transferred from soluble nucleoside-diphosphosugars such as GDPmannose, UDP-N-acetylglucosamine, UDPglucose, or UDPxylose to form dolichyl phospho- or diphosphosugars. Then dolichyl diphosphooligosaccharides are built up from these by stepwise transfer of additional sugar residues. Finally the completed oligosaccharide moiety is transferred to a lipid or to a growing polypeptide chain with release of dolichyl diphosphate. dolichol kinase EC 2,7,1.108; an enzyme that catalyses the formation of dolichyl phosphate from CTP and dolichol with release of CDP. Dolichyl phosphate is a precursor of dolichyl diphosphooligosaccharides, dolichyl phosphoglucose, and dolichyl phosphomannose, intermediates in N-linked glycoprotein oligosaccharide biosynthesis. Example from yeast: database code SC59_YEAST, 519 amino acids (58,84 kDa). dolichol o-acyltransferase EC 2.3.1.123; an enzyme that catalyses the formation of dolichyl palmitate from palmitoylCoA and dolichol with release of CoA. Acylated dolichols are found in some cell membranes, though their function is obscure. dolichyl the alkyl group derived from a dolichol by loss of its hydroxyl group, dolichyl diphosphooligosaccharide a precursor for the transfer of N-linked oligosaccharide chains to protein in the synthesis of glycoproteins. It consists of dolichol esterified to diphosphate with an oligosaccharide chain linked to the diphosphate by the C-1 of the sugar at the reducing end of the chain. dolichyl-diphosphooligosaccharide-protein glycosyl·

dolichyl-phosphate ~-D-glucosyltransferase transferase EC 2.4.1.119; an enzyme that catalyses the reaction of dolichyl diphosphooligosaccharide with protein L-asparagine to form a glycoprotein with the oligosaccharide chain attached by glycosylamine linkage to protein L-asparagine, with release of dolichyl phosphate. Example from chicken: database code GSBP_CHICK, 508 amino acids (56.90 kDa). dolichyl-phosphate /3-o-glucosyltransferase EC 2.4.1.117; an enzyme that catalyses the reaction of UDPglucose with dolichyl phosphate to form dolichyl ft-o-glucosyl phosphate (an intermediate in the biosynthesis of N-linked glycoprotein oligosaccharides) and UDP. It is a type II membrane protein of the endoplasmic reticulum involved in the glycosylation pathway. Example from yeast: database code ALG5_YEAST, 334 amino acids (38.30 kDa). dolichyl-phosphate-mannose-protein mannosyltransferase EC 2.4.1.109; an enzyme that catalyses the reaction of dolichyl phosphate o-mannose with protein to form O-o-mannosylprotein and dolichyl phosphate. Two examples from yeast: database code PMTLYEAST, 817 amino acids (92.57 kDa); and database code PMT2_YEAST, 758 amino acids (86.75 kDa). See also dolichyl-phosphate p-o-mannosyltransferase. dolichyl-phosphate p-D-mannosyltransferase EC 2.4.1.83; an enzyme that catalyses the formation of dolichyl o-mannosyl phosphate, an intermediate in the biosynthesis of N-linked glycoprotein oligosaccharides, from GDPmannose and dolichol phosphate with release of GDP. Example (precursor of isoenzyme I) from yeast: database code DPMl_YEAST, 267 amino acids (30.33 kDa). See also dolichyl-phosphatemannose-protein mannosyltransferase. domain 1 any topological region having specific characteristics, contained within certain limits, andlor under individual control. 2 or structural domain a compact, globular region in the structure of a single protein molecule, which may consist of several such globular regions held together by more flexible parts of the polypeptide chain. It has been suggested that the word be reserved for large subassemblies that would be stable if the polypeptide chain connecting them to the rest of the protein molecule were to be cleaved and that the term folding unit be used to define small assemblies of secondary structure segments in a protein molecule. 3 a region of a protein molecule delimited on the basis of function without knowledge of and relation to the molecular substructure, as, e.g., the part of a protein molecule that binds to a receptor, that binds a substrate and possesses a catalytic function forming a catalytic domain, or that, in a membrane protein, passes through the membrane from one face to the other, forming a transmembrane domain. Such a region may contain more than one structural domain (see def. 2) 4 a poorly characterized length of chromosomal DNA, of the order of 50-200 kilo base pairs, that comprises all the (coding or noncoding) sequences required for the formation of mRNA for anyone (specified) protein. 5 a zone within a cellular membrane consisting of one class of component, e.g. lipid. 6 a diverse set of cellular events, processes, and metabolic reactions controlled or affected by a specific agent, e.g. a hormone or another messenger. See metabolic code. 7 a mathematical aggregate to which a variable is confined. 8 (in physics) any region in a ferromagnetic solid in which all the atoms have the spins of their unpaired electrons aligned in the same direction: magnetic domain. See also Appendix E. domain of bonding the two linked binding sets through which a pair of associated protomers are associated. dominant (in genetics) describing a gene that produces the same character whether present in the homozygous state or in the heterozygous state (i.e. together with a different specified allele). The ineffective heterozygous allele is described as recessive to the dominant one. Dominant inherited diseases fall into one of three categories: (1) 'change of function' in which the abnormal protein acquires a novel activity that is deleterious to the cell, (2) 'dominant negative' in which the abnormal

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dopamine protein forms heterooligomeric complexes with the protein from the normal allele thereby knocking out the function of the entire protein complex, (3) 'haplo-insufficiency' in which a single copy of the gene has lost function and the 50% of the normal amount of protein that is produced from the nonmutated allele is not adequate to preclude clinical symptoms. Examples: type (1), sodium channel disorders; type (2), mutations in collagen genes which lead to osteogenesis imperfecta; type (3), loss of function in one copy of the low-densitylipoprotein receptor gene resulting in familial hypercholesterolemia. Donnan effect or Dounan (membrane) equilibrium the effect of the presence of charged macromolecules upon one side of a semipermeable membrane on the distribution of small, permeable ions across the membrane. At equilibrium, the small counterions will be more concentrated on the macromolecules' side of the membrane and the small ions of the same charge as the macromolecules will be less concentrated there, whereas on the side of the membrane with no macromolecules the concentrations of the small ions of opposite charge will be equal. It can be shown that, if the small ions are A + and B-,

=

=

[A+h/ [A +](2) [B-](2)1 [B-](l) r D , where r D is the Donnan ratio and the subscripts 1 and 2 indicate the two sides of the membrane. [After Frederick George Donnan (l870-1956), British physical chemist.] donor (in chemistry) any chemical species that is able to donate one or more electrons, atoms, or groups to another species, the acceptor. donor atom 1 an atom that supplies two electrons in forming a dipolar bond. 2 an atom, added as an impurity to a semiconductor, that provides additional electrons in the conduction band. See also electron donor. donor cell any living cell that contributes genetic information to another, recipient cell. See conjugation (def. 3), transduction, transformation. dopa or DOPA abbr. for 3-hydroxytyrosine; 3,4-dihydroxyphenylalanine; 2-amino-3-(3,4-dihydroxyphenyl)propanoic acid; the naturally occurring enantiorner is 3-hydroxY-L-tyrosine (abbr.: L-dopa, also known as levodopa because it is levorotatory; [a]~~6 "" 13.0). L-Dopa is formed from L-tyrosine by tyrosine 3-monooxygenase, EC 1.14.16.2, and is an immediate metabolic precursor of the neurotransmitter dopamine and other catecholamines. L-Dopa is used in the treatment of Parkinson's disease.

dopac or DOPAC abbr. for dihydroxyphenylacetate. dopachrome A-isomerase EC 5.3.3.12; systematic name: dopachrome ALA2-isomerase; an enzyme that catalyses the conversion of dopachrome (2-carboxy-2,3-dihydroindole-5,6quinone) to 5,6-dihydroxyindole-2-carboxylate. Dopachrome is formed non-enzymatically from dopaquinone, the product of monophenol monooxygenase. These are reactions in the pathway of melanin synthesis. A deficiency in the enzyme results from a mutation in mice known as slaty. The enzyme contains zinc. Example from Mus musculus: database code TYR2_MOUSE, 517 amino acids (58.57 kDa). dopa decarboxylase see aromatic-L-amino-acid decarboxylase. dopamine an alternative name for 3,4-dihydroxyphenylethylamine; 3-hydroxytyramine; 3,4-dihydroxyphenylethylamine; 4-(2-aminoethyl}-1,2-benzenediol; a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase, EC 4.1.1.28, from 3,4-dihydroxY-L-phenylalanine. A metabolic

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dopamine p-hydroxylase precursor of norepinephrine and epinephrine, it is found in dopaminergic nerves in the brain and in the adrenal medulla. See also Parkinson's disease.

dopamine /3-hydroxylase EC 1.14.17.1; recommended name: dopamine ft-monooxygenase; systematic name: 3,4-dihydroxyphenethylamine,ascorbate:oxygen oxidoreductase (ft-hydroxylating). An enzyme that catalyses hydroxylation of dopamine to norepinephrine in aminergic neurons releasing norepinephrine and epinephrine; ascorbate is simultaneously oxidized to dehydroascorbate. The enzyme is a copper protein, stimulated by fumarate. It is absent from dopaminergic neurons. Example, homotetramer, human precursor, database code DOPO_HUMAN, 603 amino acids (67.62 kDa). dopamine JJ-monooxygenase see dopamine JJ-hydroxylase, dopamine receptor any of several membrane proteins that bind dopamine and mediate its intracellular effects. Types D j to D s have been recognized; D j and D s (also called D jA and D jB ) comprise one subfamily; D z, D 3. and D 4 (also called D ZA , D 2B , and D 2d comprise a second subfamily. D 3 receptors seem to be insensitive to guanine nucleotides and regulate conductance of Ca 2+. All are seven-transmembrane-domain receptors that couple to G-proteins. D j and D s elevate cyclic AMP, but vary in binding characteristics; D 2 has a short and a long form originating from alternative splicing; in humans, the short form (D 2S ) has 414 amino acids, and the long form (D 2d has 443 amino acids. D z lowers cyclic AMP levels and regulates ion channels, opening K+ and inhibiting Ca z+ channels. D 3 and D 4 have binding characteristics similar to, but distinct from D z; their action is not mediated by G-protein interaction with adenylate cyclase. Examples, all human; D I: database code DADR_HUMAN, 446 amino acids (49.29 kDa); D z: database code D2DR_HUMAN, 443 amino acids (50.62 kDa); D 3: database code D3DR_HUMAN, 400 amino acids (44.22 kDa); D 4 : database code D4DR_HUMAN, 387 amino acids (40.89 kDa); D s: database code DBDR_HUMAN, 477 amino acids (52.95 kDa). dopaminergic describing a nerve that is activated by dopamine. The term is applied to nerves that act by releasing dopamine at their nerve endings. Compare adrenergic, aminergic, cholinergic, peptidergic, purinergic, serotonergic. Doppler effect the apparent change in the frequency of acoustic or electromagnetic waves due to relative motion between the source and the observer. The frequency appears to increase when the source and the observer move towards each other, and to decrease when they move away from each other. [After Christian Johann Doppler (1803-53), Austrian mathematician and physicist.] dorsal protein embryonic developmental morphogenetic nuclear protein; a protein whose concentration in the nucleus of a cell during the blastoderm stage of development determines the cell's lateral or ventral identity. It is similar to the product of the vertebrate proto-oncogene corel. Example from Drosophila melanogaster: database code DORS_DROME, 678 amino acids (75.39 kDa). dose 1 a measured quantity of a drug, microorganism, radiation, etc. administered to an organism, often at specified intervals. In experimental pharmacology, the units and routes of administration should be specified and the quantity of the drug expressed per unit of animal mass, e.g. mol kg-I, mg kg-I, mg min-I kg-I. 2 to prescribe or administer a dose or doses. dosage n. dose equivalent symbol: H; a measure of the biological effects of ionizing radiation upon humans (or other mammals)

double helix used in radiation dosimetry and health physics. It is usually equal to the absorbed dose multiplied by the quality factor. In the case of radiation arising from radioactive material within a person's body, the absorbed dose must be multiplied also by a distribution factor (normally unity, but in certain instances given a value of 5) in order to take account of any nonuniform distribution of radioactivity. The CGS unit of dose equivalent is the rem; the corresponding SI derived unit is the sievert (def. I). dose rate in radiation dosimetry, the amount of ionizing radiation (expressed in grays, rads, rems, rontgens, or sieverts) received or receivable by an irradiated object or organism in unit time. For personnel, it is usually expressed in sieverts per hour. (There is no separately named unit of dose rate.) dose ratio an older name for concentration ratio. dose-response curve any graphical representation of the relationship between the size of an administered dose and the extent of the response of the organism, or other test system, to the dose. The response may be some biochemical or physiological change in one or more organisms, tissue samples etc., or the proportion of organisms in a group that show a response. dosimeter or dose meter an instrument for measuring the quantity of ionizing radiation administered to an organism or an object, or the intensity of a source of such radiation. dosimetry the process of measuring administered quantities of ionizing radiation, drugs, microorganisms, etc. dot hybridization or dot hybridisation or dot blotting a development of blotting or blot transfer, in which as little as I pg of a specific nucleic-acid sequence, bound to nitrocellulose as a small spot, can be detected using a 32P-labelled probe as a 'dot blot'. double-antibody method any technique in which a specific antibody, used to detect or measure its corresponding antigen, as in immunoassay, is isolated from the reaction mixture by combination with heterologous antibody to the specific antibody. Compare antiglobulin test. double-beam spectrophotometer a spectrophotometer in which the incident light beam is split into two halves, one half passing through the sample and the second half passing through the reference so that direct measurement of the difference in absorption can be made. In one type the two emergent beams fall on different detectors and the resulting signal is a direct current; in another type the incident beam passes alternately through the sample and the reference, and the two emergent beams fall on the same detector resulting in an alternating current signal. double-blind testing a method of evaluating the efficacy of a substance (e.g. a drug) in which neither the subjects nor the experimenter knows the identity of the samples at the time of the evaluation. double bond a covalent bond that consists of two electron pairs shared by two atoms. double-displacement (enzyme) mechanism or ping-pong mechanism or substituted-enzyme mechanism any enzymic mechanism in which an enzyme reacts with one substrate to give a covalently modified enzyme together with the release of one product, and the modified enzyme then reacts with the second substrate with the subsequent release of the second product and the return of the enzyme to its initial state. double helix or Watson-Crick model of DNA; the main features of this model are that DNA consists of two antiparallel helical polynucleotide chains coiled around the same axis to form a double helix. Deoxyribose-phosphate backbones are on the outside of the helix and purine and pyrimidine bases lie approximately at right angles to the axis on the inside of the helix. The diameter of the helix is 2.0 nm and there is a residue on each chain every 0.34 nm. The angle between each residue on the same chain is 36°, so that the structure repeats after 10 residues (3.4 nm) on each chain. The two chains are held together by hydrogen bonds between pairs of bases, each mem-

188

double immunodiffusion ber of the pair belonging to a different polynucleotide chain. Adenine is always paired with thymine and guanine with cytosine. The two chains are therefore complementary. double immunodiffusion or double diffusion a technique of immunodiffusion in which both the antibody and the antigen diffuse towards each other through a gel to form lines of precipitation. See Ouchterlony technique. double labelling an experimental strategy in which either a single chemical compound is labelled with two different nuclides or two compounds are each labelled with a different nuclide. It is used to follow the simultaneous transformations of two substances or two parts of one substance, or to distinguish identical molecules synthesized at different times. -doubly labelled adj. double layer see electric double layer. double membrane see unit membrane. double-reciprocal plot a plot of IIx versus lIy, where x and yare two variables. If the plot of y versus x has the shape of a rectangular hyperbola the corresponding double-reciprocal plot will be a straight line. Note: The x and y axes are not the asymptotes of the rectangular hyperbola. The Lineweaver-Burk plot is a double-reciprocal plot. See also hyperbolic kinetics curve. double refraction see birefringence. double refraction of flow see flow birefringence. double-sector cell a cell (def. 2), used in analytical ultracen-

trifugation experiments, with two radial sector-shaped cavities, allowing the concentration distribution of a solute in one sector to be related to that of the solvent alone in the other sector: i.e. the second sector provides a reference for the first. double-sieve hypothesis a hypothesis invoked to account for the unexpectedly low level of error (misreading) observed in protein biosynthesis. According to this hypothesis, the discrete synthetic and hydrolytic sites that exist on certain aminoacyl-tRNA synthetases provide a two-stage stereochemical sorting mechanism - likened in action to a pair of sieves for the elimination of inappropriate amino acids. The synthetic site first rejects amino acids larger than that genetically specified; the hydrolytic site then preferentially destroys reaction products of amino acids smaller than, or isosteric with, the one specified. The second process has also been termed editing or proofreading. Such a mechanism would have particular importance in discriminating between a pair of very similar amino acids such as isoleucine and valine. Compare kinetic

dpm nuclei or mitochondria. [After Alexander Latham Dounce, US biochemist (1909- ).] Dowex proprietary name for a group of synthetic ion-exchange resins made by Dow Chemical Company. See also cholestyramine resin. down regulation

1 a decrease in response of a cell to a hormone brought about either by a decrease in receptor number or by the uncoupling of an effector component. 2 a decrease in the activity of an enzyme or the amount of a protein resulting from the action of an effector molecule on gene expression or protein synthesis. --down-regulated adj. Down's syndrome or (formerly) mongolism a type of mental abnormality frequently associated with trisomy of chromosome 21. The condition is characterized by a small stature, a rounded head with obliquely slanted ('Mongol-like') eyes and high cheekbones, a fissured tongue with enlarged papillae, and a characteristic palmprint. The degree of mental defect varies considerably. [First described in 1866 by John Langdon Haydon Down (1828-96), British physician.] downstream 1 (in molecular biology) that part of a strand of DNA lying towards the 3' end from the recognition sequence for a particular restriction enzyme. 2 towards the end of a multistage process, or at a stage nearer to the endpoint of the process than a key stage or one under consideration. Compare upstream. doxorubicin a cytotoxic anthracycline antibiotic from Streptomyces peucetius var. caesius; its carbohydrate is daunosamine. It intercalates with DNA and prevents the actions of type II DNA topoisomerase. It also inhibits reverse transcriptase and acts on cell membranes. It has anti-tumour activity and has

been used to treat some forms of cancer.

OH

proofreading. double-stop terminator two consecutive termination codons in

a molecule of mRNA. double-stranded or double-strand describing a duplex form of a nucleic acid. See double-stranded RNA, duplex DNA. double-stranded RNA abbr.: dsRNA; a structure that occurs

when complementary base sequences in single-stranded RNA form a duplex (def. 2). The RNA may fold back on itself to generate an antiparallel duplex structure, known as the stem, with a loop of unpaired bases at the end. The loop and stem together are called a hairpin. The two complementary sequences can result from an inverted repeat. See also palin-

doxycycline 5-hydroxy-6-deoxytetracycline;

an antibiotic having a wide range of activity against both Gram-positive and Gram-negative organisms. It is closely similar to tetracycline in structure and mechanism of action. One proprietary name is Vibramycin.

drome. doublet 1 any sequence of two nucleotides in a polynucleotide

strand. 2 a closely spaced pair of spectral lines or peaks. Compare twin. doubling dilution a serial dilution effected so that the concentration in each tube of the particular cell, substance, etc. of interest is half that in the preceding tube of the series. doubling time the average time taken for the number of cells in a population to double. It will equal the generation time only if every cell in the population is able to form two daughter cells and there is no cell lysis. Dounce homogenizer or Dounee homogeniser a hand-operated tissue homogenizer, usually of glass, consisting of a ball that is operated as a piston in a tube. The clearance is adjusted to give a fine particle size reduction without damage to cell

DPG or 2,3-DPG abbr. for (2,3-)diphosphoglycerate (former name for 2,3-bis{phospho)-n-glycerate). DPG pocket abbr. for diphosphoglycerate pocket. See bisphosphoglycerate pocket. dpm or d.p.m. abbr. for disintegrations per minute.

189 Dpm Dpm see Azpm. DPN abbr. for diphosphopyridine nucleotide when its oxidation state is unknown or unspecified (obsolete; NAD now used). DPN+ abbr. for diphosphopyridine nucleotide (oxidized) (obsolete name for NAD+). DPNH abbr. for reduced diphosphopyridine nucleotide (obsolete; NADH now used). DPP abbr. for dipeptidyl peptidase. Dpr see Azpr. dps abbr. for disintegrations per second. DPT abbr. for 2-diazophenylthioether, the short name of the group -O-CHz-CH(OH)-CHz-O-[CHzl4-0-CHz-CH(OH)CHz-S-C6H4-N/, used to introduce reactive diazonium groups into cellulose or paper, forming DPT-cellulose or DPT-paper. These are used in blottransferof proteins or nucleic acids. DPT is formed by diazotization of 2-aminophenylthioether (abbr.: APT) groups previously coupled to the support.

D region the (third) hypervariable region occurring between the V region and the J region in the heavy chains (but not in the light chains) of immunoglobulin molecules. It is coded for by the D (for 'diversity') gene segment. dRib symbol for the monosaccharide deoxyribose, 2-deoxY-Dribose. Drk abbr. for 1 a small protein that bears SH2 domains (see SH domain) and acts as a link between sevenless protein and son of sevenless protein in the Drosophila photoreceptor system (downstream of receptor kinases). 2 Drkl a mammalian integral membrane protein forming a voltage-dependent potassium channel of the delayed rectifier class. The voltage sensor, probably segment S4, is characterized by a series of positively charged amino-acid residues at every third position. Example from rat: database code CIKA_RAT, 853 amino acids (95.17 kDa). D-RNA or dRNA abbr. for DNA-like RNA. dropping-mercury electrode an electrode used in polarography in which mercury drops from a reservoir through a capillary tube into the solution under study. It has the advantage of constantly presenting a clean, un polarized mercury surface to the solution. Drosophila a genus of small dipterous insects that includes the fruit fly, D. melanogaster, also known as vinegar fly or banana fly. This is much used in genetic research because of the giant chromosomes, which occur in the cells of its salivary glands, and because of its short life cycle. Drude equation an equation describing the variation of optical rotation with wavelength of light. It is useful in the interpretation of measurements of optical rotatory dispersion, when it may be expressed in the form: z [m'] = 96nNA x ~ Z -l hc A - A6 where N A is the Avogadro constant, h is the Planck constant, c is the speed of light, R is the rotational strength, AQ is the wavelength of the centre of an absorption band, A is the wavelength of the observation, and [m']-l is the reduced mean residue rotation at that wavelength, as defined at molar optical rotation. See also Moffitt-Yang equation. [After Paul Karl Ludwig Drude (1863-1906), German physicist, noted for, inter alia, his work on refraction of light.]

Dubnoff shaker drug any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease. drug-metabolizing enzyme or xenometaboJic enzyme any enzyme that acts on a drug or other foreign compound but is not known to have any action on a normal metabolite. Many enzymes previously included in this category have subsequently been found to act also on normally occurring substrates. drug resistance the relatively enhanced resistance of an organism to the action of a drug. It may be caused by induction of an enzyme acting on the drug, by mutation, or by the acquisition of a plasmid coding for drug resistance. dry ice solid carbon dioxide. It is a convenient cooling agent because, at ordinary atmospheric pressures, heat converts it directly to the gaseous form (sublimation point 194.65 K at 101 325 Pa; -78.5 °C at 760 Torr). DsbA a 21 kDa protein that is the bacterial functional equivalent in Escherichia coli of protein disulfide-isomerase in eukaryotes. There is little similarity in the primary structure of the two proteins. The structure of DsbA has been determined by X-ray crystallography and part of the structure shown to be similar to thioredoxin. DSC abbr. for differential scanning colorimetry or differential scanning calorimeter. dsDNA abbr. for double-strand(ed) DNA (see duplex DNA). DSPD abbr. for disalicylidenepropanediamine. dsRNA abbr. for double-strand(ed) RNA. DSS abbr. for 2,2-dimethylsilapentane 5-sulfonic acid; a compound used as a water-soluble reference substance in nuclear magnetic resonance spectroscopy. dsx abbr. for the doublesex gene in Drosophila melanogaster. Alternative splicing of the same transcript yields the male-specific protein (database code DSXM_DROME, 549 amino acids (57.35 kDa»; and the female-specific protein (database code DSXF_DROME, 427 amino acids (44.72 kDa». They are transcription factors that bind to the fat body enhancer. dT symbol for a residue of the deoxynucleoside thymidine (alternative to dThd). dTDP abbr. for deoxyribosylthymine diphosphate or thymidine diphosphate, the common names for 2'-deoxyribosylthymine5'-diphosphate; thymidine 5'-diphosphate; 5'-thymidylyl phosphate; thymine 2'-deoxyriboside 5'-diphosphate. DTE abbr. for l,4-dithioerythritol. dThd symbol for a residue of the deoxynucleoside thymidine; 2'-deoxyribosylthymine; thymine 2'-deoxyriboside (alternative to dT). dThd5'P symbolfor thymidine 5'-phosphate. dThd5'PP symbol for thymidine 5'-diphosphate (alternative to ppdT). dThd5'PPP symbol for thymidine 5'-triphosphate (alternative to pppdT). dTMP abbr. for deoxyribosylthymine monophosphate or thymidine monophosphate, the common names for 2'-deoxyribosyl thymine 5'-phosphate, thymidine 5'-phosphate, 5'thymidylic acid, thymine 2'-deoxyriboside 5'-phosphate. DTNB abbr. for 5,5'-dithiobis(2-nitrobenzoic acid); see Ellman's reagent. DTT abbr. for 1,4-dithiothreitol. dTTP abbr. for deoxyribosylthymine triphosphate or thymidine triphosphate, the common names for 2'-deoxyribosylthymine 5'-triphosphate; thymidine 5' -triphosphate; 5'-thymidylyl diphosphate; thymine 2'-deoxyriboside 5'-triphosphate. dU symbolfor a residue of the deoxynucleoside 2'-deoxyuridine (alternative to dUrd). dual specificity mitogen-activated protein kinase kinase see MAP kinase kinase. Dubnoff shaker a controlled-temperature water bath with a uniformly oscillating load platform and facilities for main-

Duboscq colorimeter taining a controlled atmosphere. It is used for studies of the metabolism of tissues and microorganisms and for enzyme and blood-coagulation studies. [After Jacob William Dubnoff (1909- ), US biochemist.] Duboscq colorimeter an early, accurate visual colorimeter for determination of small quantities of substances in solution, in which the intensities of colour of two solutions, standard and unknown, were compared by varying the pathlengths of light passing through them from a single source until their apparent colours matched. This was achieved by placing the solutions in flat-bottomed vessels (termed cups) and adjustment of their positions in relation to two identical, fixed, transparent plungers through which the light passed, via prisms, to a divided-field eyepiece. The path-length in each solution was then read from a vernier scale. [After Jules Duboscq (1817-86), French optician.] Duchenne muscular dystrophy see dystrophin. ductless gland an alternative name for endocrine gland. dUDP abbr. for deoxyuridine diphosphate, the common name for 2'-deoxy-5'-uridylyl phosphate; 2'-deoxyuridine 5'-diphosphate; uracil 2'-deoxyriboside 5'-diphosphate. Duffy system symbol: Fy; a blood-group system for which the antigenic determinant depends on the structure of an erythrocyte membrane glycoprotein, of molecular mass 35-55 kDa, the structural details of which are lacking. Dulbecco, Renato (1914- ), Italian-born US virologist notable for demonstrating how certain viruses are able to transform some cells into a cancerous state; Nobel Laureate in Physiology or Medicine (1975) jointly with D. Baltimore and H. M. Temin 'for their discoveries concerning the interaction between tumour viruses and the genetic material of the cell'. dulcitol another (older) name for galactitol. dUMP abbr. for deoxyuridine monophosphate, the common name for 2'-deoxyuridine 5'-phosphate; 2'-deoxy-5'-uridylic acid; uracil 2'-deoxyriboside 5'-phosphate. duodenum that part of the small intestine extending from the pylorus of the stomach to the jejunum. In mammals it lies around the head of the pancreas and receives the duct from the exocrine pancreas and the gall bladder. -duodenal adj. Duolite proprietary name for a group of ion-exchange resins. It includes those formerly known by the names Biodeminrolit, De-Acidite, Zeo-Karb, and Zerolit. duplex 1 having two parts or elements, especially of similar form or function. 2 describing a molecular structure (or part of one) in which two polynucleotide strands lie side by side in a head-to-tail orientation and are linked together along their length; see duplex DNA. 3 describing a telegraphic system, computer channel, etc. that permits two messages to be sent simultaneously in opposite directions. duplex DNA double-stranded DNA in which the two polynucleotide chains are linked together by hydrogen bonds between complementary base pairs along their lengths, with the 3'-.075' phosphodiester bonds of the two chains running in opposite directions. Such a molecule is usually coiled into a double helix and it mayor may not be covalently closed into a circular molecule andlor formed into superhelical DNA (see supercoil) See also double helix. duplicate (in biology) to reproduce by division into two equal parts; see binary fission. duplication see gene duplication. dUrd symbol for a residue of the deoxynucleoside deoxyuridine; 2'-deoxyribosyluracil; uracil 2'-deoxyriboside (alternative to dU). dUrd5'P symbol for deoxyuridine 5'-phosphate. dUrd5'PP symbol for deoxyuridine 5'-diphosphate (alternative to ppdU). dUrd5'PPP symbol for deoxyuridine 5'-triphosphate (alternative to pppdU). dUTP abbr. for deoxyuridine triphosphate, the common name for 2'-deoxyuridine 5'-triphosphate; 2'-deoxy-5'-uridylyl diphosphate, uracil 2'-deoxyriboside 5'-triphosphate.

190

dynactin dUTPase EC 3.6.1.23; recommended name: dUTP pyrophosphatase; systematic name: dUTP nucleotidohydrolase; other name: deoxyuridine-triphosphatase. An enzyme of nucleotide metabolism in eukaryotes that prevents the incorporation into DNA of deoxyuridylyl residues from dUTP by catalysing the hydrolysis of the latter to dUMP and pyrophosphate. Genes for dUTPase are found in several viruses, e.g. herpes simplex type I: database code DUT_HSVII, 371 amino acids (39.08 kDa). Duve see de Duve. du Vigneaud, Vincent (1901-78), US biochemist distinguished for the synthesis of the posterior pituitary hormones oxytocin and vasopressin, for establishing the structure of biotin, and for his contributions to the synthesis of penicillin; Nobel Laureate in Chemistry (1955) 'for his work on biochemically important sulphur compounds, especially for the first synthesis of a polypeptide hormone'. dwarfism underdevelopment of the body due to hyposecretion of somatotropin. Affected humans typically attain adult heights of less than 1.25 m. Dy symbol for dysprosium. dyad 1 two units treated as one. 2 a meiotic chromosome in which the two homologous members of the tetrad have separated. 3 a pair of cells resulting from the first meiotic division. 4 a bivalent atom, molecule, or group. See also dyad symmetry. dyad axis a twofold rotation axis. dyad-related describing a phenomenon that occurs at a specific position with respect to a dyad axis. dyad symmetry 1 the type of symmetry occurring in molecular structures in which there is repetition after every 180 0 rotation around a dyad axis. 2 (in molecular biology) the formal description of a palindromic sequence in which the axis of symmetry is at the centre of the palindromic sequence. See palindrome. dye a natural or synthetic substance that strongly absorbs certain wavelengths of visible or near ultraviolet light and is used to colour material by becoming firmly attached to it. See also stain. dye-exclusion test a test for cell viability based on the phenomenon that living cells exclude some dyes, e.g. Eosin and Trypan Blue, whereas dead cells take them up and become stained. dye-laser a device for obtaining high-intensity light of chosen wavelength by passing the monochromatic emission beam of a laser through a stream of liquid containing a fluorescent dye, and then passing the emitted broad-band fluorescent light through a monochromator. By variation of the dye employed a wide range of wavelengths of high-intensity light can be obtained from the single-wavelength laser emission. The light obtained by this device is necessarily of longer wavelength than that of the laser emission. dye-ligand chromatography or pseudo-affinity chromatography or pseudo-ligand affinity chromatography a technique similar to affinity chromatography in which the immobilized ligand is anyone of certain reactive dyes (coupled usually to cross-linked agarose), the dye commonly being a triazinyl compound, e.g. Reactive Blue 2 or Reactive Red 120. The technique is thus sometimes referred to (inappropriately) as triazine-dye affinity chromatography. The fixed dye molecules selectively bind particular enzyme or other protein molecules; the specificity of the interaction varies widely with both protein and dye, although frequently the dye appears to mimic a natural ligand of the protein. Examples of use are the isolation of nucleotide-requiring enzymes (see also nucleotide-binding fold) and the removal or purification of albumin from serum. The underlying mechanism is not fully understood but appears to involve both hydrophobic (Le. apolar) and strongly ionic interactions. Many uses may in reality be examples of affinityelution chromatography. dynactin the largest protein component of the dynactin com· plex, a 20S multiprotein assembly of total mass about 1.2

191 dynamic

MDa, that activates dynein-based activity in vivo. A large structural component of the complex is an actin-like 40 nm filament composed of actin-related protein, to which other components attach. Vertebrate dynactin is a ubiquitously expressed cytoplasmic protein; several isoforms of mass ranging from 117 kDa to 160 kDa are produced by alternative splicing. It has a high degree of homology with the product of the Drosophila gene glued, essential during embryogenesis, some mutations of which kill homozygous embryos. Example from rat: database code DYNA_RAT, 1325 amino acids (146.05 kDa). dynamic of, or concerned with, motion or force, or with dynamics. dynamics 1 the branch of a science, especially mechanics, concerned with the motions of objects and the forces that produce such motions. It includes kinetics. 2 those forces that produce change or movement in a system or molecule; the motions (e.g. of residues within a macromolecule) so resulting. dynamic state of body constituents the phenomenon, discovered in the early 1940s, that body components, especially proteins, are in a state of continuous degradation and resynthesis (i.e. of dynamic equilibrium). It was subsequently found to be applicable to other body constituents, although genomic DNA is a notable exception. dynamin a microtubule-associated protein able to bind and hydrolyse GTP. The dynamin family includes two types, neuron-specific dynamin 1, and the widely expressed dynamin 2, which exhibit a high degree of sequence similarity in the 300 amino acid N-terminal region containing the GTP-binding site, but show divergence in a 100 amino acid proline-rich Cterminal region that in dynamin 1 but not dynamin 2 is a site for regulation of GTPase activity by phosphorylation-dephosphorylation. Dynamins are activated by protein kinase C and have a pleckstrin homology domain which binds acidic (especially inositol-) phospholipids with activation of the GTPase activity. Dynamins are involved in formation of microtubule bundles and in vesicular trafficking; purified dynamin 2 in solution forms helical structures that in vivo may facilitate the pinching off of vesicles budding from the plasma membrane and accelerate endocytic recycling. The Drosophila protein (a dynamin 2) is a product of shibire, a gene known to be involved in endocytosis. Examples, rat dynamin 1: database code DYNLRAT, 851 amino acids (95.93 kDa); Drosophila product of shibire: database code DYN_DROME, 883 amino acids (98.54 kDa). dyne symbol: dyn; the CGS unit of force, defined as the force required to give one gram an acceleration of one centimetre

dystrophy

per second per second. A gram weight thus represents a force of about 980 dyn. 1 dyn = 10- 5 N. dynein a large, multisubunit protein complex with ATPase activity, that is associated with micro tubules and functions as a molecular motor to drive the movement of a diverse range of intracellular structures, such as endosomes, Iysosomes, and mitochondria, along micro tubules towards the centrosome. It is also attached to the peripheral fibrous components of eukaryotic flagella and cilia and is responsible for their movement; it may also playa role in the separation of chromosomes at cell division. The complex consists of two heavy chains (",500 kDa), three or four intermediate chains ("'70 kDa) and four light chains ("'50 kDa). Example: cytoplasmic dynein heavy chain (MAP-l C) from rat: database code RATDYNEINC, 4644 amino acids, (531 kDa); intermediate chain from Chlamydomonas reinhardtii: database code DY06_ CHLRE, 567 amino acids (63.52 kDa). dynorphin an opioid tridecapeptide of high potency found in pig brain, duodenum, and pituitary, having the structure Tyr-Gly-Gly-Phe-Leu-Arg-Arg-Gln-Phe-Lys-Val-Val-Thr, the N-terminal pentapeptide sequence of which is identical with [5-leucine]enkephalin. It is synthesized as preprodynorphin (also called preproenkephalin B), from which its precursor protein prodynorphin (also called ~-neoendorphin or proenkephalin B), a 236-residue polypeptide, is formed. See also endorphin. dys+ prefix indicating abnormal, diseased, impaired, painful, or difficult. dysfunction any abnormality or disturbance in the function of an organ, tissue, cell, or part of a cell. -dysfunctional ad). dysgenic genetically deleterious. dystroglycan a protein precursor yielding a 43 kDa transmembrane glycoprotein and an extracellular 156 kDa dystrophinassociated glycoprotein in skeletal muscle; the 156 kDa component binds laminin, acting as a laminin receptor that links the extracellular matrix and sarcolemma in skeletal muscle. Example (precursor) from human: database code DSGl_ HUMAN, 1049 amino acids (113.59 kDa). dystrophin a protein present in small amounts in normal muscle but absent or abnormal in patients with Ducbenne muscular dystrophy. It may playa role in anchoring the cytoskeleton to the plasma membrane. Example from human: database code OMD_HUMAN, 3685 amino acids (426.19 kOa). See also dystroglycan, utropbin. dystrophin-related protein (abbr ORP) see utrophin. dystrophy any disorder, sometimes genetic, of the structure and functions of an organ or a tissue, as of muscle or bone. dystrophic ad).

Ee e symbol for 1 electron; it may be written as e- to indicate its charge; e+ denotes a positron. 2 (in mathematics) the transcendental number equal to the limiting value of the series [1 + (lin!)] for n = I to infinity; its value is 2.718 281 82846. It is used as the base of natural (Napierian) logarithms. 3 equatorial; see conformation. e' symbol for pseudo-equatorial; see conformation. e symbol for 1 elementary charge (or proton charge) 2 efficacy (of a drug). E symbol for 1 a residue of the a-amino acid L-glutamic acid (alternative to Glu). 2 elimination reaction. 3 electromeric effect (in electron displacement). 4 exa+ (SI multiplicative prefix denoting 10 18 ). lEl o or [Elt or IElstoich (in enzyme kinetics) symbolfor the total or stoichiometric concentration of active (catalytic) centres. E, abbr. for estrone. Ez abbr. for estradiol. E74 a protein, expressed during development of Drosophila, that correlates with an ecdysone-induced activity of puff 74EF. It is encoded by Drosophila EIP74Ej, an ecdysone-inducible gene that encodes two ETS-related protein products, E74A and E74B, that differ mainly in their N-terminal regions, and have substantial poly-Ala, poly-Asn, poly-Gin, poly-Gly, and poly-Ser domains. E symbol for 1 (in chemical nomenclature) a specific configuration around a double bond; see Ell convention. 2 electromotive force. 3 electric potential difference (of a galvanic cell). 4 energy; kinetic energy and potential energy may be denoted by the symbols E k and E p respectively. 5 extinction coefficient (no longer recommended). 6 (bold italic) electric field strength (see electric field). IE)- prefix (in chemical nomenclature) denoting a geometric isomer in which the highest priority ligands according to the Cahn-Ingold-Prelog rules (see sequence rule) are located on opposite sides of a double bond. See also Ell convention. -E conformational descriptor denoting the envelope conformation of a monosaccharide or monosaccharide derivative. ED or E-e- symbol for standard electrode potential. ED' or E-e-, symbol for standard electrode potential at a specified pH. E. or EA symbol for (Arrhenius) activation energy. E•• symbol for electron affinity (def. 2). Eadi&-Hofstee plot a graphical representation of enzyme kinetic data in which the reaction velocity divided by the substrate concentration, vl[S], is plotted as ordinate against the reaction velocity, v, as abscissa. If a straight line is obtained, the intercept on the abscissa gives the maximum velocity, V, and that on the ordinate VIKm • The slope is -l/Km . [After George Sharpe Eadie (1895-1976) and Barend Hendrik Jan Hofstee (1912-80). US biochemists, who independently described it in 1942 and 1952, respectively.] Eagle's medium any of various growth or maintenance media used in tissue culture and essentially comprising a balanced salt solution, usually Earle's balanced salt solution or Hanks's balanced salt solution, supplemented with amino acids, vitamins, serum, and antibiotics. EAR·3 see COUP. Earle's balanced salt solution a solution used in tissue culture to provide a normal ionic, pH, and osmotic environment for cell growth. It contains, per 100 ml distilled water, 0.68 g NaCl, 0.04 g KCI, 0.02 g CaCl z, 0.02 g MgS0 4 '7H zO, 0.0125 g NaH zP0 4 -H zO, 0.22 g NaHC0 3, 0.1 g glucose, and 0.002 g Phenol Red; it has a pH of 7.6-7.8. early enzyme an enzyme that is transcribed from an early gene (def. 2) of a virus. Compare late enzyme. early gene 1 or immediate gene any of a number of genes in-

volved in the earliest responses of cells to factors that initiate the transition from quiescence to proliferation. Early genes include those that encode transcription factors, such as the cJUN, c-FOS, and c-EGR genes, and those coding for structural proteins such as actin. Early genes are further subdivided into immediate-early and delayed-early genes. 2 any viral gene that is transcribed early after the virus infects a host cell. Such genes probably code for proteins that are necessary for viral nucleic acid replication. Compare late gene. early growth response protein any of a family of proteins that are expressed early in response to growth factors and function as transcriptional regulators, binding to the DNA sequence 5'-CGCCCCCGC-3'. Example, early growth response protein 1 from human (other names: krox24, TF ETR103): database code EGRI_HUMAN, 543 amino acids (57.51 kDa). early protein a protein that is transcribed from an early gene (def. 2) of a virus. Compare late protein. early quitter any incomplete polypeptide formed in an in vitro translation system. Easson-Stedman model a model to explain the differences in biological activity of two enantiomeric molecules; it assumes that three of the groups attached to an asymmetric carbon atom in an agonist (or substrate) are involved in its attachment to a specific receptor (or enzyme), one enantiomer will therefore be a better agonist (or substrate) than the other. The concept is similar to, but considerably pre-dates, that developed by Ogston (see Ogston concept). EBV or ED virus abbr. for Epstein-Barr virus. EC abbr. for 1 Enzyme Commission; it is used as a prefix in the numerical designation of an enzyme (see enzyme classification). 2 electron capture. 3 enterochromaffin (as in EC cell). EC so abbr. for half effective concentration; the molarity of an agonist that produces 50% of the maximal possible effect of that agonist. Other percentage values (EC zo , EC 4o , etc.) can be specified. The action of the agonist may be stimulatory or inhibitory. EC cell abbr. for enterochromaffin cell. Eccles, (Sir) John Carew (1903-97), Australian neurophysiologist; Nobel Laureate in Physiology or Medicine (1963) jointly with A. L. Hodgkin and A. F. Huxley 'for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cell membrane'. eccrine 1 describing a secretory cell that discharges its product without loss of cytoplasm. 2 describing a gland made up of such cells. Compare apocrine, holocrine, merocrine. ECD abbr. for 1 electron capture detector. 2 electrochemical detection. See polarography. ecdysis the periodic shedding of the exoskeleton and construction of a new cuticle, as in insects and crustaceans, or the shedding of the outer layer of the skin, as in reptiles. -ecdysial ad). ecdysone 1 ex-ecdysone (22R)-2P,3P,14,22,25-pentahydroxycholest-7-en-6-one; the ecdysteroid that is synthesized in and

193

ecdysone receptor

secreted by the pro thoracic glands of immature insects and the ovaries of the adult females. First isolated from the silkworm moth (Bombyx mori), it is the inactive prohormone of the moulting hormone ecdysterone; it may also have intrinsic hormonal activity at other stages of insect development. 2 13ecdysone an alternative name for ecdysterone. 3 a former name for ecdysteroid. ecdysone receptor a receptor for ecdysone, located in the cell nucleus and related to the steroid/thyroid/retinoic acid family of nuclear hormone receptors. It consists of a heterodimer of a subunit named EcR (ecdysone receptor) and another named USP (ultraspiracle), the insect homologue of vertebrate retinoid X receptor. The heterodimer binds ecdysone with high affinity, and the ternary complex binds to DNA. Example: database code ECR_DROME, 878 amino acids (93.85 kDa). ecdysteroid or (formerly) ecdysone any of a group of polyhydroxylated ketosteroids of which a-ecdysone is the parent substance for the purpose of nomenclature (see ecdysone). They are almost invariably C 27 steroids, differing only in the number and/or steric arrangement of their hydroxyl groups. Ecdysteroids are ubiquitous in insects and other arthropods, in which they initiate postembryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females. They have been found also in annelids, molluscs, and nematodes. Cognate substances, often known as phytoecdysones, have been identified in plants. The principal ecdysteroids in insects are a-ecdysone (see ecdysone (def. 1)) and ecdysterone. ecdysterone or 13-ecdysone or crustecdysone or (insect) moulting hormone 20-hydroxyecdysone; (22R)-2{i,3{i,14,20,22,25hexahydroxycholest-7-en-6-one; the ecdysteroid isolated both from insects and from crustaceans. In insects, ecdysterone is formed in peripheral tissues from a-ecdysone through the action of ecdysone 20-monooxygenase (EC 1.14.99.22). The hormone causes puffing of polytene chromosomes, and initiates moulting of larval and pupal forms by stimulating the epidermal cells to enlarge, divide, and secrete degradative enzymes that dissolve the protein and chitin components of the cuticle. Moreover, in the adult females of certain insects, e.g. mosquitoes (Aedes spp.) and Drosophila melanogaster, ecdysterone formed from a-ecdysone in the ovaries stimulates vitellogenin synthesis in the fat body.

ECF abbr. for extracellular fluid. ECG or (US) EKG abbr. for 1 electrocardiograph. 2 electrocardiogram. echinochrome A 2-ethyl-3,5,6,7,8-pentahydroxy-l,4-naphthalenedione; a red pigment of sea urchin eggs.

H O W :0O H

-::r I

HO

I

~ OH

CH3

OH 0

EDso echinoderm any of the phylum Echinodermata of marine invertebrates that contains sea urchins, sea cucumbers, starfish, etc. They are more or less radially symmetrical, with calcareous skeletal plates in their skin and a well-developed coelom. Locomotion and gaseous exchange are accomplished by means of retractable tube feet. They are related to the same ancestral stock that gave rise to the vertebrates. eclipsed conformation see torsion angle. eclosion hormone any peptide hormone that programmes the death of certain muscles and neurons during metamorphosis of insects. ecology the branch of biology dealing with the relations of living organisms to their surroundings. -ecological adj.; ecologically adv.; ecologist n. ecomone any non trophic molecule that ensures a flux of information between organisms in an ecosystem. ecosystem a unit of the environment together with the organisms it contains. There is a constant interchange between living organisms and their chemical and physical environment. ecotin a monomeric periplasmic protein of Escherichia coli that inhibits the pancreatic serine proteases chymotrypsin, trypsin, and elastases, enabling the organism to survive in the presence of these enzymes. It also inhibits blood coagulation factors Xa and XIIa and kallikrein, thereby having anticoagulant effects. Example from E. coli: database code ECOT_ECOLI, 162 amino acids (18.17 kDa). ECP abbr. for eosinophil cationic protein. ecstasy see 3.4-methylenedioxymethamphetamine. ECTEOLA cellulose abbr. for a weakly basic (pK ""7.5) anionexchange material of uncertain structure, prepared by the condensation of epichlorhydrin, triethanolamine (hence e,c + t,e,ola), and cellulose. It is useful for separations of proteins, nucleoproteins, and nucleic acids. ecto+ comb. form indicating external, outer. ectocrine describing or relating to a metabolite that, when released from the organism in which it was made, differentially affects other organisms of the same or a different species. Such a metabolite might be harmful to some members of a community and beneficial to others. The term includes allomone, ectohormone, kairomone, and pheromone. Compare endocrine (def. 1), exocrine (def. 1). ectoenzyme any enzyme that is attached to the external surface of the plasma membrane of a cell. ectohormone any ectocrine substance whose production and release benefits either the organism producing it or other members of the same species. Compare endohormone. ectoparasite any parasite that lives on the exterior of its host organism. ectopic occurring in an unusual place or in an unusual form or manner. For example, an ectopic protein is a protein produced by a neoplasm derived from a tissue that does not normally produce that protein. An example is the production of vasopressin and corticotropin by small cell lung cancer. Ectopic pregnancy occurs when the fertilized ovum implants outside the uterus e.g. in a fallopian tube. Compare entopic. ectoplasm the outer, relatively rigid part of the cytoplasm. Compare endoplasm. -ectoplasmic adj. ectoplast the part of the plasma membrane of a plant cell that is in contact with the cell wall. ectoprotein any individual protein found on the exterior of cells. Such proteins may function, e.g., as mediators of cell-cell or cell-surface interactions, or as receptors for substances with regulatory actions on cells. ectosymbiont a partner in a symbiotic relationship that remains outside the tissues and cells of the other partner, often occupying a body cavity; e.g. one of the cellulose-metabolizing microorganisms occurring in the digestive tract of ruminants. Compare endosymbiont. See also symbiosis. ED llO abbr. for median effective dose; i.e. the dose of a drug or other agent that produces, on average, a specified all-or-none response in 50% of a test population, or, if the response is

194

edeine

EF·'

graded, the dose that produces 50% of the maximal response to that drug or agent. edeine any of several pentapeptide-amide antibiotics elaborated by a strain of Bacillus brevis and effective against Gram-positive and Gram-negative bacteria, some fungi and other eukaryotic cells, and some neoplastic cells. Edeine AI, NU[( JV2-{JV2-[N-(f3- tyrosyl)isoseryl]-2, 3-diaminopropiony I} -2,6diamino-7-hydroxyazela-9-yl)glycyl]spermidine, and its NW_ amidinospermidine analogue, edeine Bj, are highly active; their respective constitutional isomers, edeines A2 and B2 , have low intrinsic activity. In intact bacteria, low concentrations of edeine reversibly inhibit DNA synthesis and enhance RNA synthesis but do not affect protein synthesis. In cell-free systems, edeine Al interacts with both ribosomal subunits (preferentially the smaller one) and strongly inhibits translation. OH

17

~ I

NH

o

OH

~ ~s./"o... ~

HN-

~

1I

NH2

H

Iro~NH

./"0...

~

COOH

H

N~N~

NH2

o

edeineA,

Edelman, Gerald Maurice (1929- ), US biochemist; molecular biologist, and neuroscientist; Nobel Laureate in Physiology or Medicine (1972) jointly with R. R. Porter 'for their discoveries concerning the chemical structure of antibodies'. edema or (esp. Brit.) oedema swelling of an organ or tissue due to the accumulation of fluid. -edematous or (esp. Brit.) oedematous ad). edestin a 300 kDa globulin obtained from hemp seed, castoroil beans, and certain other seeds. It readily forms polymorphic crystals and will support the growth of animals in the absence of other dietary proteins. [From Greek edestos, edible.} edetate see EDTA. EDF abbr. for erythroid differentiation protein; see activin. editing 1 the process or act of altering or adapting erroneous molecular structures, especially nucleotide sequences in polynucleotides, so as to preserve fidelity in the transfer and expression of genetic information. For example, the 3' ~5' exonuclease activity of DNA polymerase I has an editing function in DNA polymerization by removing mismatched residues at the primer terminus of the growing chain. Another editing function is shown by aminoacyl-tRNA synthetases. In the presence of ATP and the 'wrong' amino acid, these enzymes do not catalyse the formation of the incorrect aminoacyl-tRNA but act as ATP pyrophosphatases, hydrolysing ATP to AMP and pyrophosphate. The term is applied also to the processes of conversion of RNA precursors, e.g. hnRNA, to the mature form, mRNA. 2 the insertion, deletion, or substitution of nucleotides within nascent RNA transcripts to produce RNA molecules with sequences that differ from those coded genomically. Most examples have been found in organelle-encoded RNAs, e.g. mitochondrial RNAs, and include

ApoB, several glutamate receptor mRNAs, and Wilms tumour susceptible gene mRNA. In the case of ApoB, a cytidine residue is deaminated to a uridine residue so that the codon for glutamine (CAA) becomes a stop codon (UAA); hence, translation results in a shortened form of the protein. editosome a macromolecular complex involved in the editing of RNA transcripts. Specific ribonucleotide complexes include guide RNA (see gRNA), which specifies the edited sequence. Edman degradation a procedure used in sequencing (poly)peptides in which amino-acid residues are removed stepwise from the N terminus by reaction with phenylisothiocyanate, C 6H s-N=C=S, to form the phenylthiocarbamyl-peptide (abbr.: PTC-peptide). This is then cleaved in anhydrous acid (which favours attack by the sulfur atom on the carbonyl carbon of the terminal peptide) to give a thiazolinone intermediate and the release of the remainder of the peptide chain. The thiazolinone intermediate is hydrolysed to the phenylthiocarbamyl derivative of the N-terminal amino acid, which then cyclizes to form the phenylthiohydantoin derivative (abbr.: PTH-amino acid). The PTH-amino acid is extracted into organic solvents and identified by chromatography. These derivatives have a strong UV-absorption at about 259 nm, which permits them to be visualized against a fluorescent screen using an ultraviolet light source. As the remainder of the peptide chain is liberated intact, the procedure may be repeated up to about ten amino-acid residues may be sequenced in this way, or more in favourable cases. The procedure may be automated, e.g. in a sequenator. [After Pehr Victor Edman (191677), Swedish protein chemist, who described the method in 1956.] Edman reagent phenylisothiocyanate; C6 H s-N=C=S. See Edman degradation. EDR abbr. for equi-effective dose ratio. EDRF abbr. for endothelium-dependent releasing factor (see nitric oxide). EDTA ethylenediaminetetraacetate; edetate; any anion or salt, esp. the (hydrated) disodium salt, of edetic acid, ethylenediamine- N, N. N', N' -tetraacetic acid, (ethylenedinitrilo)tetraacetic acid. Commonly used as the disodium salt, it is a powerful chelating agent for divalent metal ions.

ethylenediaminetetraacetic acid

EEDQ abbr. for N-ethoxycarbonyl-2-ethoxy-I,2-dihydroquinoline; an agent for peptide condensation that causes little or no racemization; it is useful in coupling ligands to insoluble polymers. It also causes progressive and irreversible inhibition of mitochondrial F,-ATPase.

eEF-2 a eukaryotic elongation factor that is equivalent to the prokaryotic EF-G. EET (formerly) abbr. for epoxyeicosatetraenoate. EF abbr. for elongation factor. EF·1 see EF-T, elongation factor.

195

EFE EFE abbr. for ethylene-forming enzyme. effective dose see EDSQ. effective theoretical plate number symbol: N; a number indicative of chromatographic column performance when resolution is taken into account: N = l6R s 2/(l - a)2, where R s is the peak resolution and a the separation factor (i.e. the ratio of the distribution ratios or coefficients for the two substances being resolved when measured under identical conditions); by definition a is greater than unity. Compare height equivalent to an effective theoretical plate. See also theoretical plate. effectomer the part of a two-component agonist that brings about the biological effect but only when bound to a haptomer, which enables it to interact with the cell membrane and exert its toxic action on intact cells. For example, the A fragment of diphtheria toxin can only exert its toxic effects on a target cell when bound to the B fragment. effector 1 or modifier or modulator (in molecular biology) any small molecule or ligand that interacts with an enzyme thereby changing its catalytic behaviour but that is not itself changed during the enzyme action. A positive effector enhances catalytic activity while a negative effector reduces it. See also allosteric effector. 2 (in physiology) a cell or organ that produces a physiological response when stimulated by the nervous system. effector site or regulatory site any site on an enzyme molecule that binds an effector. efferent 1 conveying outwards from a part, organ, or centre; e.g. of a blood vessel, nerve, or duct. 2 an efferent part, e.g. a blood vessel or nerve. Compare afferent. efficacy symbol: e; a quantitative index of drug action related to the magnitude of a tissue response generated at a given level of receptor occupancy with (full) agonists (of high efficacy) generating the maximum possible response. Drugs with lower efficacy that cannot generate a maximal response even when all receptors are occupied are known as partial agonists; antagonists have an efficacy of zero. The overall response to a drug will be a function of its efficacy and receptor binding affinity, which determines the proportion of receptors occupied at a given concentration of drug. It may be formulated as the combination of an agonist with its receptors that results in a signal or a stimulus, S, equal to the product of the efficacy of the agonist, eA, and the proportion of receptors occupied, PAR; i.e. SA = eAPAR' See also intrinsic efficacy, maximal agonist effect. efficiency the ratio of the useful output of a machine, device, system, etc. to the input, whether in terms of thermal, mechanical, or radiation energy, or of biological or chemical conversions. efficiency of counting see counting efficiency. efficiency of plating abbr.: EOP; a quantification of the relative efficiencies with which different cells can be infected by viruses, and support viral replication. It is the ratio of the plaque count to the number of virions in the inoculum. efflux see Ilux. EF-G or translocase abbr. for an elongltion lactor of Escherichia coli that promotes the GTP-dependent translocation of the nascent protein chain from the A-site to the P-site of the ribosome. Database code EFG_ECOLI, 703 amino acids (77.36 kDa). An equivalent factor in eukaryotes is named eEF-2. EF·hand a helix-turn-helix motif that binds Ca 2 +; it is found in many Ca2+-binding membrane proteins and also in certain others, e.g. myosin light chain. It was first recognized in parvalbumin, in which it involves helices E and F. To envisage the motif, use the right hand with thumb and forefinger extended at "'90 0 with the remaining three fingers clenched. The thumb will then point towards the C terminus of helix F and the forefinger will point along helix E in the N-terminal direction, the clenched fingers tracing the course of the E-F loop about the bound calcium ion. Two apposed right-hands, representing the E and F and the C and D helices of the molecule, are related by a 2-fold axis of symmetry. efrapeptin or efrastatin or A23871 a hydrophobic peptide fun-

Ehlers-Danlos syndrome gal antibiotic that inhibits oxidative phosphorylation by binding to the soluble component, F b of mitochondrial W-tran.porting ATP synthase. EF-T or transfer factor a cytoplasmic protein of Escherichia coli and other prokaryotes which functions in protein synthesis to promote the GTP-dependent binding of aminoacyl-tRNAs to the A-site of the ribosome during protein chain elongation. EF-T can be dissociated into two polypeptides, EF-Tu (EFlA) and EF-Ts (EF-IB), the complex being the main form in bacterial cells. These are so described since on their initial isolation one was heat-labile, or unstable, (Tu) and one was heatstable (Ts). Only Tu functions directly in the GTP-dependent binding of the aminoacyl-tRNA to the A-site of the ribosome but Ts is required for regenerating Tu·GTP after the binding reaction which results in the hydrolysis of GTP to GDP. The factors were originally isolated from both E. coli and Pseudomonas fluorescens. The structures from E. coli are known, database code EFTS_ECOLI, 283 amino acids (30.39 kDa), EFTU_ECOLI, 393 amino acids (43.13 kDa). The 3-D structure of Tu shows high alpha-helix content with identified binding sites for GTP and aminoacyl-tRNA. The Tu from E. coli is also a subunit of RNA polymerase of phage Q~ (Q beta). See also elongation Ilctor. EF-Ts now designated EF-IB; see EF-T. EF-Tu now designated EF-IA; see EF-T. egasyn an amphipathic glycoprotein, found in microsomal (i.e. endoplasmic reticulum) membranes of mouse liver, that forms a complex with microsomal (but not lysosomal) P-D-glucuronidase (EC 3.2.1.31) and thereby anchors it to the microsomal membranes. It may similarly anchor other polar proteins. It hydrolyses carboxylic esters to an alcohol and carboxylic anion. It has a C-terminal consensus sequence, HXEL, that retains the proteins in the endoplasmic reticulum. Example from Mus musculus: database code A55281, 562 amino acids (61.51 kDa). [From e (endoplasmic) + g (glucuronidase) + Greek syn, with.] EG cell or L cell an enteroglucagon-producing endocrine cell. Such cells are found in the basal part of the mucosal glands in the lower intestine; the highest concentrations occur in the terminal ileum and colon. They contain large, dense, secretory granules and are easily distinguishable from other endocrine cells in the same area. EGF abbr. for epidermal growth factor. egg the reproductive structure of certain animals, e.g. reptiles, birds, and insects, consisting of an ovum together with nutritive and protective tissues, and from which, when fertilized, a young offspring emerges. egg albumin the common name for ovalbumin. egg cell an alternative name for ovum. egg white the white part of an egg (especially a bird's egg) surrounding the yolk. Its principal organic constituent is egg albumin (see ovalbumin). EGTA abbr. for ethylene glycol-O,-O'-bis(2-amino-ethyl)N,N, N',N'·tetraacetic acid, [ethylenebis(oxyethylenetrinitrilo)]tetraacetic acid; also for any anion or salt thereof. It is a chelating agent with a high affinity for Ca 2+ ions.

Ehlers-Danlos syndrome a heterogeneous group of inherited human disorders sharing many phenotypic features. Classically the clinical picture includes hyperelastic, fragile skin, poor wound healing, hyperextensible joints, and easy bruising. Seven distinct genetic forms have been described. Type I,

Ehrlich which is severe, is inherited as an autosomal dominant; the biochemical lesion is unknown. Types II and III are inherited as autosomal dominants; the biochemical lesions are unknown. Type IV is inherited as an autosomal dominant, but X-linked inheritance is not excluded; patients lack type III collagen and analysis has shown that skin collagen from these patients lacks a peptide of about 100 amino-acid residues that is characteristic of type III collagen. Type V shows X-linked inheritance and fibroblast cultures from a patient show a diminished Iysyl oxidase activity, both in the cells and the medium. Type VI is inherited as an autosomal recessive, and collagen from such patients is deficient in hydroxylysine; fibroblast cultures from these patients contain an abnormal lysyl hydroxylase (EC 1.14.11.4). Type VII is presumed to be inherited as an autosomal recessive and the biochemical lesion is a deficiency of procollagen peptidase, with a consequent failure to normally convert procollagen to collagen. [After Edvard Ehlers (1863-1937), German dermatologist, and Henri Alexandre Danlos (1844-1932), French dermatologist, whose respective descriptions of the disorders were published in 190 I and 1908.] Ehrlich, Paul (1854-1915), German medical scientist famous for his work in chemotherapy, especially for his demonstration of the efficacy of synthetic arsenicals in spirochaetal infections, and notable also for his studies of the interaction of dyes with living tissues, for his work on the assay of antisera, and for advancing the side-chain theory of immunity; Nobel Laureate in Physiology or Medicine (1908) jointly with 1. I. Mechnikov 'in recognition of their work on immunity'. Ehrlich's reagent a solution of p-dimethylaminobenzaldehyde in cone. HC!. It forms coloured complexes with a number of compounds, such as indoles, aromatic amines, ureides, and hydroxyproline, and is useful in the detection and estimation of these compounds. EIA abbr. for enzyme immunoassay. eicosa+ or (before a vowel) eicos+ a variant spelling (esp. US) of icosa+ (comb. form denoting twenty or twenty times). This spelling is universally used in naming eicosanoids, although not officially recommended (but see Appendix B). eicosadienoic acid any straight-chain fatty acid having twenty carbon atoms and two double bonds per molecule. The all-Z-(8,11)-isomer is a normally minor metabolite of oleic acid in mammals, but is important as an intermediate in the pathway synthesizing all-Z-eicosa-5,8,II-trienoic acid (Mead acid) during essential fatty acid deficiency. The (5,1 I)-isomer occurs in gymnosperms, and several others have been synthesized. The (IIZ,14Z)-isomer occurs as an intermediate in the synthesis of arachiodonate from linoleate via dihomo-y-linolenate, but this is not the major pathway for this biosynthesis. eicosanoic acid the systematic name for arachidic acid. eicosanoid any of various agents that are C 20 polyunsaturated fatty acids, commonly arachidonic acid (see eicosatetraenoic acid), or an eicosapentaenoic acid, or their skeletal derivatives. They include the leukotrienes and the prostanoids and are noted for their widespread biological activity, such as contraction or relaxation of smooth muscle, platelet aggregation, and the inflammatory response. eicosapentaenoic acid any straight-chain fatty acid having twenty carbon atoms and five double bonds per molecule. The most noteworthy is the all-Z-(5,8,11, 14, 17)-isomer, which occurs in animal phospholipids, especially those of many marine species; fish oils are a good source, with eicosapentaenoic acids often representing up tc 10% of total fatty acids. Eicosapentaenoic acids act as precursors of the PG 3 series of prostaglandins. The suggestion has been made that a higher than normal content of this acid in the diet can protect against heart disease. eicosatetraenoic acid any straight-chain fatty acid having twenty carbon atoms and four double bonds per molecule. The all-Z-(5,8,11,14)-isomer is arachidonic acid. The (8,11,14,17)isomer is an important intermediate in the formation of long-

196

elafin chain n-3 fatty acids from (9,12, 15)-linolenic acid, being formed from that acid by de saturation at C-6 and chain elongation. The (5,11,14, 17)-isomer is another naturally occurring form. eicosatetraynoic acid any straight-chain fatty acid having twenty carbon atoms and four triple bonds per molecule. eicosa-5,8, It, 14-tetraynoic acid (abbr.: ETY A) is a relatively nonspecific inhibitor of reactions involving arachidonate, including phospholipase A 2 , prostaglandin-endoperoxide synthase, and Iipoxygenase. eicosatrienoic acid any straight-chain fatty acid having twenty carbon atoms and three double bonds per molecule. The all-Z-(5,8, II )-isomer (Mead acid) is synthesized in mammals in essential fatty-acid deficiency. The all-Z-(8, II, 14)-iso mer, known also as dihomo-(6,9, 12)-linolenic acid (or dihomoy-linolenic acid), is a precursor of arachidonic acid and of the PG 1 series of prostaglandins. The (5,l1,14)-isomer has been found in higher plants and algae, cats, marine organisms, and insects. eicosatriynoic acid any straight-chain fatty acid having twenty carbon atoms and three triple bonds per molecule. 5,8,II-eicosatriynoic acid (abbr.: ETI) is an agent that selectively inhibits 5- and 12-lipoxygenase without inhibiting prostaglandin-endoperoxide synthase. eicosenoic acid any straight-chain fatty acid having twenty carbon atoms and one double bond per molecule. The 9E-isomer is gadelaidic acid (see gadelaidate); the 9Z-isomer is gadoleic acid (see gadoleate), a constituent of fish oils; and the II Z-isomer is gondoic acid, present in seeds and fish oils. EID abbr. for electroimmunodiffusion. elF abbr. for eukaryotic initiation factor (see initiation factor). Eigen, Manfred (1927- ), German physical chemist noted for developing techniques for the study of rapid reactions and applying them to problems of molecular biology; Nobel Laureate in Chemistry (1967), the prize being shared with R. G. W. Norrish and G. Porter 'for their studies of extremely fast chemical reactions, effected by disturbing the equilibrium by means of very short pulses of energy'. eigenfunction a solution of a differential equation that has solutions only for particular values of some parameters. eigenvalue anyone of the possible values for a parameter of an equation for which the solution will be compatible with the boundary conditions. Eijkman, Cbristiaan (1858-1930), Dutch physician, bacteriologist, and nutritionist noted for observing that unpolished rice grains contained an antiberiberi principle (later recognized as a vitamin and named vitamin B) or thiamine) and for being the first to produce a dietary deficiency disease experimentally; Nobel Laureate in Physiology or Medicine (1929) 'for his discovery of the antineuritic vitamin' [prized shared with F. G. Hopkins]. einstein a non-SI unit used to express the energy associated with one mole of photons during a photochemical reaction. I einstein = N Ahf/, where N A is the Avogadro constant, h is the Planck constant, and f/ is the particular frequency of the electromagnetic radiation effecting the reaction. Einstein, Albert (1879-1955), German-born Swiss then US patent examiner and mathematical physicist famous above all for his formulation of both the special theory of relativity (in 1903) and the general theory of relativity (in 1916); Nobel Laureate in Physics (1921) 'for his services to Theoretical Physics, and especially for his discovery of the photoelectric effect'. Einstein-Sutherland relation a relation between the diffusion coefficient at infinite dilution, Do, and certain molecular parameters. Do = kTlf, where T is the thermodynamic temperature, k is the Boltzmann constant, andfis the frictional coefficient of the diffusing particle. EKG abbr. (US) for 1 electrocardiograph. 2 electrocardiogram. elafin another name for SKALP. [From elastase f inhibitor. The

197

elaidate

'r was inserted to avoid confusion with elastin and gives an association to the Latinfinire, to terminate.] elaidate 1 numerical symbol: 18:1(9); the trivial name for (E)octadec-9-enoate; CHrlCH 2h-CH=CH-[CH 2h-COO- (trans isomer); the anion derived from elaidic acid, (E)-octadec-9enoic acid, a monounsaturated straight-chain higher fatty acid. 2 any mixture of free elaidic acid and its anion. 3 any salt or ester of elaidic acid. Compare oleate. elaidinization or elaidinisation the cis to trans isomerization of mono- and polyunsaturated fatty acids, as in the isomerization of oleic acid to elaidic acid brought about by treatment with nitrous acid or by the action of rumen bacteria. elaidoyl the trivial name for (E)-octadec-9-enoyl; CHr[CHzh-CH=CH-[CHzh-CO- (trans isomer); the acyl group derived from elaidic acid, (E)-octadec-9-enoic acid. It occurs in acylglycerols to an appreciable extent in the body fats of ruminants, possibly having arisen from oleic acid by elaidinization. Compare oleoyl. elaioplast any oil-storing leukoplast that occurs in plant cells. ELAM abbr. for endothelial leukocyte adhesion molecule; i.e. Eselectin (see selectin). elasmobranch 1 any member of the subclass Elasmobranchii, comprising fishes with cartilaginous skeletons such as sharks, skates, and rays. 2 of, pertaining to, or relating to the Elasmobranchii. elastase historically, any proteinase that hydrolyses elastin. However, the name is now applied to a group of enzymes that vary in specificity. Pancreatic elastase, EC 3.4.21.36 (other names: pancreatopeptidase E; pancreatic elastase I), catalyses the hydrolysis of proteins, including elastin, with preferential cleavage at Ala-I-Xaa. Example (domestic pig): database code NRL_3EST, 240 amino acids (25.88 kDa); 3-D structure known. Pancreatic elastase II, EC 3.4.21.71, preferentially cleaves the carbonyl side of Leu, Met, and Phe. Leukocyte elastase EC 3.4.21.37 (other names: lysosomal elastase; neutrophil elastase; bone marrow serine protease; medullasin), catalyses the hydrolysis of proteins, including elastin, with preferential cleavage at Val-I-Xaa > Ala-I-Xaa. Pancreatic elastase and leukocyte elastase, in common with most elastases, are serine proteinases, but others, e.g. elastase (EC 3.4.24.26) from Pseudomonas aeruginosa, are zinc-containing metalloproteinases. Elastase III is pancreatic endopeptidase E (EC 3.4.21.70; other name: cholesterol-binding proteinase); it shows preferential cleavage at Ala-I-Xaa, but does not hydrolyse elastin. elastatinal a peptide produced by actinomycetes that inhibits serine proteineases, particularly elastase.

o

H~. .H L-Gln-L-Alaninal

HI" O~

l L-Leu

N):=NH NH

elastic (of a body or a substance) capable of returning to its original shape after deformation. -elasticity n. elasticity coefficient symbol: e~; for a metabolic system in a steady state. the fractional change in the velocity. v, of an enzyme step caused by a fractional change in substrate, effector, or product concentration, S. It is given by:

s(aV)

_

eV alnv s - ~ as y,z.... - alnS Since the elasticity coefficient is defined as the partial derivative of a velocity, v, with respect to S (multiplied by the scaling factor, SII,) all other variables that are able to influence the rate through the enzyme are held constant. There are, for any

electricity

reaction. as many elasticity coefficients as there are metabolites and effectors that interact with the enzyme in question. See also controllability coefficient, response coefficient. sensitivity coefficient. elastin a major structural protein of mammalian connective tissues. especially elastic fibres, and found at sites such as the aorta, nuchal ligament. and lung. Glycine makes up one third of the amino-acid residues in elastin; glycine. proline, alanine, and valine together account for over 80% of its residues. The polymeric chains are cross-linked together into an extensible 3-D network, lysinonorleucine and desmosine cross-links being formed between allysine and lysine residues. A soluble precursor of elastin, proelastin, has been isolated from copperdeficient pigs in which the formation of allysine is blocked. Example (precursor) from human: database code ELS_ HUMAN, 730 amino acids (63.19 kDa). elastonectin a protein, M, 120 000, from human skin fibroblasts and associated with adhesion of mesenchymal cells to elastic fibres. elective theory of immunity an alternative name for selective theory of immunity electrical coupling the phenomenon of ion transport across a membrane, in the absence of a cation-anion cotransport system, when the movement of anions and cations, following the law of electroneutrality, is governed only by the passive permeabilities of the membrane to the ions in question. electric birefringence a form of birefringence, also known as the Kerr effect, caused by the alignment of (macro)molecules in an electric field. electric capacitance see capacitance. electric cell an apparatus consisting of two reversible electrodes dipping into the same solution, or into separate solutions electrically connected through an electrolyte bridge. It is used to generate an electromotive force, for electrolysis, or to measure the chemical activity of a chemical species in one of the solutions. See also half-cell. electric charge or quantity of electricity symbol: Q or q; the attribute of certain elementary particles that is responsible for electric phenomena. Electric charge may be of two kinds, positive or negative. which interact electromagnetically such that like charges repel one another while unlike charges are attracted one to another. The SI derived uni t of electric charge is the coulomb. See also charge (def. 3). electric conductance or conductance symbol: G; a measure of the readiness with which an electric current can flow through a given component of a circuit. For a direct-current circuit it is equal to the reciprocal of the resistance; for an alternatingcurrent circuit it is equal to the resistance divided by the square of the impedance. The SI derived unit of conductance is the siemens. See also mho. electric current or current symbol: I or i; one of the seven SI base physical quantities - flow of electric charge through a conductor. The magnitude of a current is given by the amount of charge flowing per unit time. The SI base unit of electric current is the ampere. electric dichroism the form of dichroism (def. I) caused by orientation of (macro)molecules in an electric field. electric dipole moment see dipole moment. electric double layer an alternative name for electrochemical double layer. electric field a field in which a stationary electric charge, Q, experiences a force, F, proportional to the magnitude of the charge. The electric field strength, E, is given by: E = FIQ; it is expressed in V m- 1• If the field is produced by other stationary charges it is called an electrostatic field. Compare Coulomb's law. electricity 1 any of the forms of energy associated with moving or stationary electrons, protons, or other charge-bearing entities (whether molecular or otherwise). Static electricity is associated with stationary charges, current electricity with moving charges. 2 the science dealing with electricity.

198

electric potential electric potential or potential symbol: V or I{>; the work done in bringing unit electric charge from infinity to a specified point in an electric field. The SI derived unit of electric potential is the volt. electric potential difference or potential difference symbol: E or U or ~Vor ~¢; abbr.: pd; the work done when a unit electric charge is moved between two points having different electric potentials. If the points are joined by a conductor an electric current will flow between them. The SI derived unit of electric potential difference is the volt. Compare electromotive force. electric resistance or resistance symbol: R; the impediment to the flow of an electric current through a component of a circuit, a medium, or a substance. The Sf derived unit of resistance is the ohm. electro+ or (sometimes before a vowel) electr+ comb. form indicating electric, electrically, electrolytic. electroblot see electrophoretic transfer. electroblotting an alternative name for electrophoretic transfer. electrochemical analysis or electrochemical assay a chemical analysis or assay performed by means of electrolysis or electrodeposition. electrochemical double layer any double layer of charges formed in a solution by the adsorption of a layer of ions of opposite charge at the surface of another charge-carrying phase, e.g. the walls of the vessel or the surface of a macromolecule. electrochemical equivalent the mass of an ion deposited or liberated by the passage of I coulomb of electricity. In grams it is 1/96487 of the chemical equivalent. electrochemical potential symbol: Ii; the change in free energy occurring when a charged solute is transported either up or down a concentration gradient. It is the sum of the free energy changes due both to the concentration gradient and to the electric poten tial. It is expressed in J mol-I. electrochemical series an alternative name for electromotive series. electrochemistry the branch of science concerned with the study of electrolysis, electrolytic cells, and the applications and properties of ions in solution. -electrochemical adj. electrochromatography the form of chromatography in which separation of the constituents of a mixture is due to the effect of a constant electric field. See also zone electrophoresis. electrochromism any reversible change in optical absorption or emission spectra of a molecule in the condensed phase due to an external electric field. Compare photochromism, thennochromism. -electrochromic adj. electrocortin the former name for aldosterone (before establishment of its structure). electrocrystallization or electrocrystallisation electrodeposition that results in crystal formation. electrode any conductor, such as metal, metal covered with one of its salts, carbon, or a thin glass or other membrane, used to establish electric contact with a solution or other nonmetallic part of an electric circuit. The potential assumed by the electrode may depend on the (thermodynamic) activity of one of the solutes in the solution with which it is in contact. See also anode, calomel electrode, cathode, enzyme electrode, hydrogen electrode, ion-selective electrode, oxygen electrode, quinhydrone electrode, reference electrode. electrodecantation or electrophoresis convection a technique for separating and fractionating proteins and other sols that exploits local differences in concentration and density that may occur during electrodialysis. Under the influence of gravity such density differences lead to large-scale separation of sols of high and of low concentrations. This results in a gradual increase in the concentration of a sol in the lower layers of the solution and a decrease in the upper layers. electrodeposition the deposition of material from a dissolved or suspended state onto an electrode by the application of an electric field; it includes electrocrystallization. electrode potential symbol: E; the electric potential between

electrolytic conductivity a reversible electrode and the solution in which it is immersed. It may be due to the loss or gain of electrons, if the solution

contains a redox couple, or to the formation of ions from unchanged atoms or of atoms from ions, if the solution contains ions of a chemical element present as uncharged atoms in the electrode. electrodialysis a form of dialysis conducted in the presence of an electric field across the membrane(s). It is useful for quickly removing ionic microsolutes from a solution containing nondiffusible material. electroelution a technique in which application of an electric potential causes biomolecules to be transferred from an electrophoresis gel to a membrane during blotting procedures. See also transfer membrane. electroendosmosis a former term for electroosmosis. -electroendosmotic ad}. electrofocusing a newer name for isoelectric focusing. electrofuge (in chemistry) a leaving group in a reaction that does not carry away the bonding electron pair. electrogenesis the generation of an electrochemical potential gradient, esp. across a membrane. electrogenic pump any biological system that generates an electrochemical potential across a membrane by pumping one ion across the membrane without the concomitant movement of another ion of the same charge in the opposite direction. electroimmunoassay the original name for rocket immunoelectrophoresis. electroimmunodiffusion abbr.: EID; any technique for the analysis of antigenic macromolecules in which a combination of electrophoresis and immunodiffusion is employed. Four types may be distinguished: (I) one-dimensional single, i.e. rocket immunoelectrophoresis; (2) one-dimensional double, i.e. counter immunoelectrophoresis; (3) two-dimensional single, i.e. crossed immunoelectrophoresis; and (4) two-dimensional double, not so far individually named or much used. electroimmunodiffusogram the immunoprecipitation pattern produced by any type of electroimmunodiffusion. electrokinetic potential or zeta potential symbol: (; the potential drop across the mobile part of an electrochemical double layer that is responsible for electrokinetic phenomena. The electrokinetic potential is positive if the potential increases from the bulk of the liquid phase towards the interface. electrolectin a lectin of the galaptin family from Electrophorus electricus, and the name of a group of p-D-galactoside-binding lectins found in teleosts, amphibians, and mammals. Example from E. eIectricus: database code LEG_ELEEL, 129 amino acids (14.44 kDa). electrolysis the chemical change produced by passing a direct electric current through a solution of an electrolyte, or through a fused electrolyte. Positively charged ions (cations) move towards the cathode and negatively charged ions (anions) move towards the anode, thus carrying the electric current. At the electrodes the positively charged ions gain electrons and negatively charged ions give up electrons, forming uncharged atoms, molecules, or radicals, which may either be deposited on the electrode or react with the electrode, the solvent, or each other. Alternatively, atoms of the electrode material may ionize and go into solution. electrolyte any substance that, when in solution or molten, can undergo (partial or complete) dissociation into ions and hence is able to conduct an electric current by the movement of the ions. electrolyte balance (in physiology) the sum total of the reactions and processes concerned with the maintenance of a constant internal environment in the body with respect to the distribution of ions between the various fluid compartments and excretions. electrolytic 1 of, pertaining to, or produced by electrolysis. 2 of or pertaining to an electrolyte. electrolytic conductivity or (formerly) specific conductance symbol: K; the ability of an electrolyte to permit the flow of

electromagnetic

199

electric current, defined by the equation: /( = j/ E, where j is the electric current density and E is the electric field strength. In SI units, /( is in S m I, j in A m- z, and E in V m- I . Electrolytic conductivity is usually measured in a rigid conductivity cell whose cell constant has been determined by means of a reference potassium chloride solution. electromagnetic 1 of, relating to, or involving both electricity and magnetism; having both electrical and magnetic properties. 2 of or relating to electromagnetic radiation. 3 a of, relating to, containing, or operated by an electromagnet. b of or relating to electromagnetism. electromagnetic radiation abbr.: emr or EMR; radiation consisting of transverse waves of energy with associated electric and magnetic fields that can be represented by vectors at right angles to each other and to the direction of its propagation. The radiation results from the acceleration of electric charges and can be propagated through free space (i.e. it requires no supporting medium). The characteristics of the radiation vary with the frequency (or the wavelength) of the wave motion, the range of possible frequencies constituting the electromagnetic spectrum. From the low-frequency end of the spectrum to the high end are ranged: radiofrequency radiation, infrared radiation, visible radiation or light, ultraviolet radiation, Xrays, and gamma-radiation. Radiation of all frequencies travels at the same velocity through space. The speed of light in vacuum, Co, is defined as 299 792 458 m SI. electromagnetic unit abbr.: emu or EMU; any of the electrical units based on the magnetic properties of electric currents. The force, F, between two magnetic poles of strength mJ and mz placed a distance d apart in a medium of permeability j.l is given by F = mlmz/j.ld2. If F, j.l, and d each be unity and if ml = mz = m, then m, and mz are poles of unit strength. Units based on this definition of m are electromagnetic units and are denoted by the prefix 'ab+'. electromeric effect an obsolescent term for a molecular polarizability effect occurring by intramolecular electron displacement characterized by the substitution of one electron pair for another in the same atomic octet of electrons. electrometer any instrument of very high input impedance that is used for detecting or measuring (changes in) the magnitude of an electric potential difference or electric charge esp. if of small value. Hence it is useful also for the (indirect) measurement of a very low electric current or a very high electric resistance, and for the detection or measurement of ionizing radiation. -electrometric adj. electrometric titration 1 an alternative name for potentiometric titration. 2 a name sometimes used generically for conductometric titration and potentiometric titration. electromotive force abbr.: emf or EMF; symbol: E; the energy supplied by a source of electric current in driving unit electric charge through an electric circuit. The SI derived unit of electromotive force is the volt. Compare electric potential difference. electromotive series or electrochemical series a series in which the metals are arranged in decreasing order of their tendency to form cations by a reaction of the type: M"""'" M+ + e-. electromyogram abbr.: EMG; the tracing produced by an electromyograph. electromyograph an instrument for detecting and recording the electrical activity of a muscle or group of muscles. electron 1 symbol: e or e- or 13-; a negatively charged elementary particle of rest mass, me, ~9.1 09 39 x 10- 31 kg and electric charge 1.602 177 33(49) x 10- 19 C. It is sometimes termed a negatron, especially to distinguish it from its antiparticle, the positron. Electrons are present orbiting in all atomic nuclei and are involved in the formation of bonds between atoms. Specific designations of electrons in atoms and molecules include: u-electrons, which participate in single bonds; n-electrons, which participate in double or triple bonds; and p-electrons, which participate in unshared electron pairs. 2 (sometimes) either a negatron (i.e. electron (def. I)) or a positron. See also beta-particle.

electron equivalent electron acceptor 1 any substance to which an electron may be transferred. 2 an alternative name for Lewis acid (use discouraged). Compare electron donor. electron affinity 1 the degree to which any molecular entity attracts one or more additional electrons. 2 symbol: E ea ; the minimum energy, expressed in joules, needed to remove an electron from a negatively charged molecular entity, or the reciprocal of the energy required to introduce an electron into a molecular entity. electron-affinity spectroscopy a sensItIve ionization method for the qualitative analysis of small quantities of organic compounds separated by gas chromatography, based on the differences in electron-capture ability that exist between the principal classes of organic compounds. The substances to be detected are passed through an ionized gas; the detector is sensitive to the resulting reduction in current. electron capture 1 or K-capture abbr.: EC; a mode of decay of radionuclides in which an electron from an inner orbit of a decaying atom is absorbed into its nucleus, wherein a proton is converted to a neutron. Rearrangement of the orbital electrons then leads to the emission of characteristic X-radiation (see X-radiation). Generally the captured electron is derived from the K-shell, hence the alternative name. 2 see electronaffinity spectroscopy. electron-capture detector abbr.: ECD; the type of detector used in electron-affinity spectroscopy. electron carrier any molecular entity that serves as an electron acceptor and electron donor in an electron transport system. electron-dense describing any structure, material, or compound that scatters an impinging electron beam, thus becoming apparent in electron microscopy, etc. electron-dense label any atom group or substance (e.g. ferritin) that is electron-dense and that has been or may be attached in a specific manner to compounds or structures so as to show them up by electron microscopy, etc. electron density the electron probability distribution in any molecular entity. If P(x,y,z) is the electron density at the point with coordinates x,y,z, then the probability of finding an electron in the volume element dxdydz is P(x,y,z) dxdydz. In, e.g., X-ray scattering experiments the scattering at this position is proportional to this probability. The term is often wrongly applied to negative charge density. electron-density map a three-dimensional representation of the structure of a molecule or substance derived from X-ray diffraction data and made by the superposition of the electron-density contours of a series of imaginary parallel planes through the specimen being examined. electron diffraction an effect observed when a narrow beam of electrons passes through a layer of material, e.g. a crystal, and is deflected by this material. The effect is due to the wavelike nature of electrons. electron donor 1 any substance that is able to transfer an electron to another chemical species. 2 an alternative name for Lewis base (use discouraged). Compare electron acceptor. See also donor atom. electron donor-acceptor chromatography see charge-transfer chromatography. electron donor-acceptor complex (sometimes) an alternative name for 1 charge-transfer complex (use not recommended). 2 Lewis adduct (use not recommended). electronegative 1 describing an atom or a group of atoms that tends to attract electrons, especially in the formation of a covalent bond. 2 describing any chemical or other entity that carries a negative charge and hence tends to move to the anode in electrophoresis. electronegativity a measure of the power of an atom or group of atoms to attract electrons to itself from other parts of the same molecular entity. electron equivalent the equivalent of any oxidizing (or reducing) agent that is equivalent to one entity of electrons.

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electroneutrality condition electroneutrality condition the condition that in any solution the sum of the negative electric charges on ions must be equal to the sum of the positive charges on ions. electron-exchange resin any synthetic resin containing groups able to undergo reversible oxidation-reduction reactions; such resins are useful as insoluble oxidizing or reducing agents. electron gun a device used in electron microscopes, mass spectrometers, and other instruments to generate a beam of highvelocity electrons. It consists of a white-hot tungsten filament, as the electron source, and an anode kept at a potential of several tens of kilovolts above that of the filament. The electrons are accelerated towards the anode, which contains a small orifice through which some of the fastest electrons pass to form the electron beam. electron hole the hole in the valency structure of an atom created by the absence of an electron when the energy level of an electron is raised from the valency band to the conduction band. The hole has a great tendency to recapture an electron. See also hole. electronic 1 of or relating to an electron or electrons. 2 of, relating to, or operated by electronics (def. 2). electronics 1 (functioning as sing.) the branch of science and technology concerned with electronic devices and circuits and with their development and applications. 2 (functioning as pl.) the circuits, devices, and equipment that function by the passage of electrons through semiconductors, transistors, and thermionic valves. electronic transition the passage of an electron in a chemical entity from one energy level to another. electron lens any arrangement of coils andlor electrodes producing a magnetic andlor an electric field used to focus an electron beam, e.g. in an electron microscope. electron micrograph any photograph of an object taken with an electron microscope. electron microscope abbr.: EM or e.m.; an instrument in which a magnified image of a sample is produced using a beam of high-energy electrons. The electrons are accelerated by means of an electron gun, using voltages in the range 40-100 kV, and the apparatus is evacuated to minimize electron scatter by air. In the transmission electron microscope (abbr.: TEM) the electron beam is focused onto a thin sample by a combination of magnetic and electric lenses and, after passing through the sample, the electrons are focused onto a fluorescent screen or photographic plate. The resolving power can be as great as 0.2-0.5 nm. In cryoelectron microscopy, lightly fixed frozen sections are employed. If these are used for the detection of antigens with antibodies coupled to colloidal gold, the technique is called cryoimmunoelectron microscopy. In the scanning electron microscope (abbr.: SEM) a narrow beam of electrons is made to scan to and fro across the sample by a varying field, and emitted secondary electrons are focused onto a screen to produce an image of the specimen. The specimen may be thicker than in the transmission electron microscope and, though resolution is lower with the scanning instrument, the depth of field is greater and the image gives a three-dimensional effect. electron multiplier an electronic device for detecting, and counting, electrons, using secondary emission. It consists of an evacuated tube containing a series of electrodes, each held at a higher positive electric potential than the preceding one. When an electron hits the first electrode two or more secondary electrons are emitted; these are accelerated to the second electrode, where more electrons are produced, and so on. electron nuclear double resonance abbr.: ENDOR; a phenomenon in nuclear magnetic resonance spectroscopy in which saturation of an electron resonance by the simultaneous application of a microwave field causes, under appropriate conditions, an improvement of the resolution of nuclear hyperfine structures. electron optics the branch of science concerned with the effects of electric and magnetic fields on the movement of elec-

electron trap trons, especially with the focusing and deflection of electron beams in cathode-ray tubes, electron microscopes, and similar devices. electron paramagnetic resonance spectroscopy an alternative name for electron spin resonance spectroscopy. electron probe X-ray microanalysis a highly sensitive technique for elemental microanalysis based on the frequencies and/or intensities of the characteristic X-rays emitted by each element present in a sample when it is excited by a beam of accelerated electrons. electron sink or electron trap an electrophilic atom or group of atoms that can capture an electron from another part of a molecular system. electron spectroscopy for chemical analysis abbr.: ESCA; see photoelectron spectroscopy. electron spin see spin (def. 3). electron spin-echo spectroscopy a technique giving precise values for electron spin relaxation times, in which intense microwave pulses at a frequency satisfying the resonance condition are applied to a paramagnetic sample in a magnetic field. Phase coherence in the spins is lost through relaxation when the pulse is switched off but can be restored by a second pulse 180 0 out of phase. The restoration of phase coherence gives rise to a nuclear induction signal (the echo). electron spin-lattice relaxation time (in electron spin resonance spectroscopy) a measure of the time taken for the spin population to return to its equilibrium value by interaction with the fluctuating internal electric fields surrounding it. electron spin resonance spectroscopy abbr.: ESR (spectroscopy); a technique, also called electron paramagnetic resonance spectroscopy (abbr.: EPR (spectroscopy)) and analogous to nuclear magnetic resonance spectroscopy, that is used to investigate paramagnetic centres in the system under study; only electrons whose spin is not paired with the oppositely directed spin of another electron give an ESR signal. Useful information is obtained by this technique about certain transitionmetal ions (notably Cu 2 +), (free) radicals, and free electron centres such as may be produced by X-irradiation of (macro) molecules. A probe (def. 2) giving an ESR signal may be incorporated into membrane lipids or attached to proteins to enable otherwise inaccessible systems to be studied by this technique. electron spin-spin relaxation time (in electron spin resonance spectroscopy) a measure of the time taken for phase coherence to be lost and equilibrium to be re-established through interaction with neighbouring spins. It is inversely proportional to the line width of the signal. electron-transfer flavoprotein or electron-transferring flavoprotein abbr.: ETF; a protein containing flavin adenine dinucleotide (FAD) that together with an acyl-CoA dehydrogenase (EC 1.3.99.3) forms a system that oxidizes an acyl-CoA molecule and reduces ubiquinone and other acceptors in the mitochondrial electron transport system. electron-transferring flavoprotein dehydrogenase abbr.: ETF dehydrogenase EC 1.5.5.1; an enzyme that catalyses the oxidation of reduced ETF by ubiquinone to form ETF and ubiquinol. The ubiquinol is then oxidized by ubiquinol-eytochrome c reductase. It is an iron-sulfur flavoprotein involved in coupling the beta-oxidation system to the respiratory chain. See also electron-transferring flavoprotein. electron-transferring fluoroprotein see azurin. electron transport 1 respiratory electron transport; the process by which pairs of electrons derived from intermediates of the tricarboxylic-acid cycle and other substrates flow down the respiratory chain to dioxygen, the ultimate electron acceptor in respiration. 2 photosynthetic electron transport; the process by which pairs of electrons are transported from H 20 to NADP+ in the light phase of photosynthesis during noncyclic photophosphorylation. electron-transport chain an alternative name for respiratory chain. electron trap an alternative name for electron sink.

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eleetronvolt electronvolt or electron volt symbol: eV; a non-SI unit of energy equal to the kinetic energy acquired by an electron when accelerated through an electric potential difference of I volt. I eV = e x V ~ 1.602 18 x 10- 19 J, where e is the elementary charge and V is the volt. electroosmosis or (formerly) electroendosmosis the motion of a liquid through a membrane (or plug or capillary) consequent upon the application of an electric field across the membrane. A similar phenomenon may occur in electrophoresis, where many of the supporting media used, e.g. paper or agar, acquire negative charges during electrophoresis at alkaline pHs and, since the medium cannot move, H 30+ ions move towards the cathode, giving the effect of an osmotic movement of solvent towards the cathode and making electrically neutral molecules appear to be cationic. -electroosmotic adj. electropherogram a variant spelling of electrophoretogram. electrophile or electrophilic reagent any chemical species that is preferentially attracted to a region of high electron density in another species during a chemical reaction. Such reagents normally are positively charged or contain electron-deficient chemical groups. They tend to react with electron-rich or negatively charged chemical species. Compare nucleophile. electrophilic 1 of, pertaining to, or being an electrophile; having or involving an affinity for regions of high electron density in a chemical reactant. 2 describing a chemical reaction in which an electrophile participates. electrophilic catalysis catalysis by a Lewis acid, i.e. any chemical species that abstracts an electron pair from the reactant. electrophilic displacement an alternative term for electrophilic substitution reaction. electrophilicity the relative reactivity of an electrophile, measured by the relative rate constants of different electrophiles towards a common reactant. electrophilic reagent an alternative name for electrophile. electrophilic substitution reaction or electrophilic displacement a chemical reaction in which an electrophile effects heterolytic substitution in another reactant, both bonding electrons being supplied by that other reactant. electrophoresis 1 the phenomenon of the movement of ions (including macromolecular ions) or charged particles or ions through a fluid under the influence of an electric field applied to the fluid. A number of different media have been used as the fluid support, including paper, cellulose acetate, starch gel, and polycrylamide gel. Ions or particles bearing a net positive charge tend to move towards the negative pole of the electric field and vice versa, the rate of movement of a particular variety of ion or particle depending, inter alia, on its charge-to-mass ratio. The phenomenon has been widely applied in separating proteins, nucleic acids, and other charged molecular species for analytical or preparative purposes, and also in the analytical or preparative fractionation of heterogeneous populations of dispersed cells or other types of macroscopic particles. 2 the act or process of causing ions or charged particles so to migrate; any technique based upon such a phenomenon, e.g. continuous flow electrophoresis, immunoelectrophoresis, moving boundery electrophoresis, paper electrophoresis, polycrylamide gel electrophoresis, zone electrophoresis. See also electrodecantation. -electrophoretic adj. electrophoresis convection an alternative term for electrodecantation. electrophoretic effect the phenomenon of decreased electrophoretic mobility of a charged macromolecule caused by the movement of counter ions andlor solvent molecules in the opposite direction to that of the macromolecule. electrophoretic mobility symbol: u; the electrophoretic velocity, v, of a charged particle expressed per unit field strength; hence, u = viE, where E is the field strength. The value of u is positive if the particle moves towards the pole of lower potential and negative in the opposite case. The electrophoretic mobility depends only on molecular parameters.

eleetrostrietion electrophoretic molecular sieving (sometimes) an alternative term for polyacrylamide (gell electrophoresis. electrophoretic titration curve the pH-mobility curve of an ampholyte, e.g. a protein, generated by subjecting a zone of it to electrophoresis in a gel slab at right angles to a preformed, stationary pH gradient. Compare isoelectric focusing. electrophoretic transfer or electro blotting a development of the technique of blot transfer, in which proteins or nucleic acids are transferred from a separation gel to nitrocellulose or diethylaminoethyl- (DEAE-)cellulose membranes or to diazobenzyloxymethyl- (DBM)- or diazophenylthioether- (DPT-) paper by electrophoresis, rather than by capillary flow, with a consequent decrease in the time required for the transfer. The membrane or paper bearing a resultant pattern of separated substances has been termed an electroblot. See blotting. electrophoretic velocity symbol: v; the velocity of a charged particle during electrophoresis. It is normally proportional to the electric field strength. Compare electrophoretic mobility. electrophoretogram or electropherogram the result of a zoneelectrophoretic separation, either directly visible or after staining or processing to produce a graph. electrophysiology the part of physiology concerned with the electrical phenomena associated with bodily processes, such as nervous and muscular activity. electroporate to create momentary pores in the membranes of living cells, without loss of their viability, by exposing them to a sequence of brief electrical pulses of high field strength. The reversible breakdown of the cell membranes thus caused enables treated cells to take up exogenous material (e.g. drugs or foreign DNA). -electroporated adj.; electroporation n. electroporator an apparatus or device for effecting electroporation. electropositive 1 describing an atom or group of atoms that tends to give up electrons, especially in the formation of a covalent bond. 2 describing any chemical or other entity that carries a positive charge and hence tends to move to the cathode in electrophoresis. electropositivity a measure of the power of an atom or group of atoms to give up electrons to other parts of the same molecular entity. electrospray a technique used in mass spectrometry in which a dilute acidic solution of the macromolecule is sprayed from a metal syringe needle maintained at +5000 V, forming fine highly charged droplets from which the solvent rapidly evaporates. electrostatic of or pertaining to static electricity or electrostatics. electrostatic bond any valency linkage between atoms arising from the transfer of one or more outer-shell electrons of one atom to the outer shell of another atom, leading to more complete outer shells in both atoms. The dissociation of an electrostatic bond leads to the production of ions. electrostatic field any electric field produced by stationary charges. electrostatic interaction any of the attractive or repulsive forces between atoms and/or groups of atoms and/or molecules that are due to the presence of ionized chemical entities and to the electronegative and electropositive properties of these atoms, groups, or molecules. Compare electric field. electrostatic precipitation the removal of small particles suspended in a gas by electrostatic charging followed by precipitation onto a highly charged collector. electrostatics the branch of physics concerned with static electricity. electrostatic units abbr: esu or ESU; a system of electrical units, used in the cgs system, based upon the electrostatic unit of electric charge, i.e. the quantity of electricity that will repel an equal quantity of electricity, I em distant from it in a vacuum, with the force of I dyne. electrostriction the reversible change in dimensions of a dielectric when an electric field is applied to it. For example, the

electrotaxis

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electrostatic field associated with a dissolved electrolyte causes a shrinkage in the volume occupied by the solvent. electrotaxis the directional movement of an organism in an electric field. -electrotactic adj. electrotropism any orientation response of a sessile organism to an electrical stimulus. electrovalency or (esp. US) electrovalence 1 the type of valencv characterized by the transfer of one or more electrons from one atom to another atom, with the formation of ions. 2 the number of negative or positive charges acquired by an atom by the respective gain or loss of electrons. -electrovalent adj.; electrovalently adv. electrovalent bond an alternative term for ionic bond. electroviscosity the, usually minor, change in viscosity that occurs when an electric field is applied to some polar liquids. eledoisin a tachvkinin with the structure Glp-Pro-Ser-Lys-AspAla-Phe-Ile-Gly-Leu-Met-NH 2; it is obtained from the posterior salivary glands of small octopus (Eledone spp.). It is more potent than phvsalaemin and substance P in some assay systems. It is useful as a lachrymal and salivary secretagogue and in the study of receptors for substance P. element any basic and distinct component of matter that is not resolvable into simpler components with differing chemical properties. Each consists exclusively of atoms with the same unique proton number (although such atoms may not necessarily have the same nucleon number or relative atomic mass). Ninetythree chemical elements are known to occur naturally, either in the free state or in combination with others; to date, a further 16 have been produced artificially. -elemental or elementaryad). elementary analysis any quantitative chemical analysis of the amounts of different chemical elements present in a sample. elementary charge or proton charge symbol: e; a fundamental physical constant representing the electric charge on one electron (or proton). Its recommended value is 1.602 177 33 (49) x 10- 19 C. elementary particle 1 or fundamental particle any of the particles that form the base units of which all matter is composed. The stable elementary particles are protons, electrons, and neutrinos; they combine with neutrons to form stable atoms. Other, short-lived elementary particles are known. 2 or Fernandez-Moran particle or oxysome or stalked particle any of the knoblike structures, 8-9 nm in diameter, seen in the electron microscope on the inner surface of the inner membrane of unfixed mitochondria negatively stained with phosphotungstate. elementary rest mass symbol: me; the mass of an electron, it is a fundamental atomic constant, 9.109 389 7(54) x 10-31 kg. eleostearate 1 numerical symbol: 18:3(9,11,13); the trivial name for octadeca-9, II, 13-trienoate; CH r [CH 2h-[CH= CHh-[CH 2h-COO-; the anion derived from eleostearic acid, octadeca-9, 11, 13-trienoic acid, a triunsaturated straight-chain higher fatty acid. It is a constitutional isomer of (6,9,12)linolenate with conjugated double bonds. 2 any mixture of free eleostearic acid and its anion. 3 any salt or ester of eleostearic acid. See also eleostearovl. eleostearoyl symbol: eSte; the trivial name for octadeca9,11,13-trienoyl; CHr[CH 2h-[CH=CHh-[CH 2h-CO-; the acyl group derived from eleostearic acid. The 92, liE, 13E-isomer occurs naturally as acylglycerols in some seed oils, especially tung oil. ELF1 a gene encoding transcription factors, related to the protooncogene ETS and named from E74-like factor (see E74), a Drosophilia protein that binds a regulatory element of the dopa decarboxylase gene. Example from Drosophila melanogaster: database code ELFLDROME, 1063 amino acids (116.15 kDa). elimination reaction a chemical reaction in which two groups are removed from a molecule of an organic compound without being replaced by other groups. In most such reactions the groups are lost from adjacent carbon atoms: one of the groups

ellipticity eliminated is commonly a hydron and the other a nucleophile, and the elimination results in the formation of a multiple bond. The reverse process is an addition reaction. Elion, Gertrude Belle (1918-99), US chemist, biochemist, and pharmacologist distinguished for her introduction, largely in collaboration with her colleague G. H. Hitchings, of a range of widely used synthetic drugs designed as antimetabolites, including the antifolate bactericidal agent co-trimoxazole, the immunosuppressants mercaptopurine and its derivative azathioprine, and the antiviral compound acvcloguanosine; Nobel Laureate in Physiology or Medicine (1988) jointly with J. W. Black and G. H. Hitchings 'for their discoveries of important principles for drug treatment'. ELISA abbr. for enzyme-linked immunosorbent assay. Elk a family of cell-surface proteins similar to those encoded by the protooncogene ETS and with presumed similar function (named from Eph-like kinase); they are protein tyrosine kinases, restricted to brain and testis, having a single transmembrane domain and two fibronectin-like domains. Example from rat (precursor): database code KELK_RAT, 984 amino acids (109.88 kDa). Elk-1 a gene-regulating protein, found in lung and testis, that binds to DNA at purine-rich sites. It is a substrate for a MAP kinase in the phosphorylation cascade originating with activated protein kinase C or Ras; on phosphorylation it forms with the transcription factor SRF a ternary complex, which binds to the serum response element of DNA, turning on FOS transcription. Example (human): database code ELK! HUMAN, 428 amino acids (44.86 kDa). ellagic acid 4,4',5,5',6,6'-hexahydroxydiphenic acid 2,6,2',6'dilactone; a commonly occurring plant polyphenol that inhibits glutathione S-transferase. OH OH

OH

ellipse any closed plane figure whose perimeter is the locus of a point that moves so that the sum of its distances from two fixed points, the foci, is constant. An ellipse has two axes of symmetry, the major axis at the furthest distance between opposing points on its circumference and the minor axis at the nearest distance. ellipsoid any surface or solid figure whose plane sections are all either ellipses or circles. -ellipsoidal adj. ellipsoid of rotation or ellipsoid of revolution a solid figure generated by the rotation of an ellipse about one of its axes. If the rotation is about the major axis the ellipsoid of revolution is said to be prolate, whereas if the rotation is about the minor axis it is said to be oblate. See also equivalent ellipsoid of rotation, spheroid (def. 2). ellipsosome a compartment in the retinal cones of fish that contains cytochrome-like pigment. elliptical of, relating to, or having the shape of an ellipse or ellipsoid. -elliptically adv. elliptically polarized or elliptically polarised describing light (or other electromagnetic radiation), whose electric vector appears to follow an elliptical path when viewed along the light beam. See also polarized light. ellipticity 1 the ratio of the lengths of the major to the minor axis of an ellipse or ellipsoid. 2 the arc tangent of the ratio of the lengths of the minor to the major axis of an ellipse. See also circular dichroism, Cotton effect, molecular ellipticity.

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Ellman's reagent Ellman's reagent 5,5'-dithiobis(2-nitrobenzoic acid) (abbr.: DTNB); a reagent used for labelling thiol (SH) groups in protein side-chains. The reagent reacts quantitatively with thiol groups, forming mixed disulfides and releasing the anion 5sulfido-2-nitrobenzoic acid; this absorbs light at 412 nm, thus permitting the determination of the number of thiol groups in the protein sample. [After George Leon Ellman (1923- ).]

elongase any of the long-chain fatty-acyl-coenzyme A elongating enzymes, found in mammalian microsomes, that act on saturated and unsaturated fatty-acyl derivatives having 16 or more carbon atoms per molecule of fatty acid. elongation factor abbr.: EF; any of a group of soluble proteins required for chain elongation during polypeptide synthesis at the ribosome. In Escherichia coli there are three elongation factors: EF-Tu, EF-Ts (see EF-1), and EF-G. EF-Tu helps to bind aminoacyl-tRNA, via a tertiary complex, aminoacyl-tRNA'EF-Tu'GTP, to the ribosomal A-site. After EF-Tu-dependent GTP hydrolysis, the EF-Tu·GDP complex dissociates from the ribosome and is recycled to EF-Tu'GTP, probably via an EF-Tu'EF-Ts intermediate. E. coli EF-Tu and GTP form ternary complexes with all aminoacyl-tRNAs except the initiator, tRNA~etEF-G catalyses the GTP-dependent movement of the ribosome and the codon-anticodon-linked mRNA'peptidyl-tRNA complex relative to each other, resulting in the removal of a deacylated tRNA and the location of peptidyl-tRNA from the ribosomal A-site to the P-site. In eukaryotes three proteins, EF-Ia, EF-I~, and EF-2, are required for the elongation events. EF-Iu, which occurs in different tissues as aggregates of varying size of a polypeptide chain of M r 53 000, functions during chain elongation, like EF-Tu, to bring the aminoacyl-tRNA to the ribosomal A-site in a reaction in which GTP is hydrolysed. EF-I~, of M r 30000, functions as EF-Ts. EF-2, like EF-G, catalyses the translocation of the peptidyl-tRNA from the ribosomal A-site to the P-site in a GTP-dependent reaction. Rat liver EF-2 has an M r of 110000, while wheatgerm EF-2 has an M r of 70000. Compare initiation factor, release factor. Eison-Morgan reaction a colorimetric reaction for the estimation of combined and free hexosamines. The specimen is heated in alkaline solution with acetylacetone to form a pyrrole derivative, which then gives a red colour with p-dimethylaminobenzaldehyde on acidification. [After Leslie Alderman Elson and Walter Thomas James Morgan (1900- ), British biochemist, who together described the reaction in 1933.] eluant a variant spelling of eluent. eluate 1 (in chromatography) the solution flowing from a chromatographic column; the desired material in such a solution. 2 (in immunology) a solution of material derived from an insoluble or particulate antigen-antibody complex, e.g. by heating or by treatment with an appropriate buffer solution. eluent or eluant, a liquid used in elution, particularly in chromatography. eluent strength function (in chromatography) the order of an eluotropic series defined as the adsorption energy per unit area of standard activity of the solvent: log K = log Va + a(SO - A,eO), where K is the distribution coefficient in mass/volume of adsorbent and is independent of the solute concentration, Va is the adsorbent surface volume, a is an adsorbent function proportional to the average surface energy of the adsorbent, So is a solute parameter equivalent to the adsorption energy of the

emetine solute from solution, A, the area of absorbant occupied by solvent, and eO is a solvent strength parameter; the larger eO, the stronger the solvent. efuotropic series a series of solvents arranged in the order of their relative abilities to effect elution. elute to wash out or extract retained material, particularly from a chromatography column. eluting 1 of or relating to elution, e.g. an eluting solvent. 2 the process of carrying out an elution. elution the process of washing out or extracting adsorbed material from a chromatographic column. elution volume (in chromatography) the volume of mobile phase that must pass through a chromatographic column, after sample application, to produce a peak in the concentration of a particular solute in the effluent or eluate. elutriation the process of separating and purifying particles in a powder or suspension according to their rates of sedimentation. It may be effected by repeatedly washing, decanting, and settling, or by allowing a liquid or gas containing the particles to flow upwards (against gravity), when particles whose sedimentation rates are less than the rate of upward flow are washed away from the larger, heavier particles. Compare centrifugal elutriation, electrodecantation. elutriator a device for grading finely divided material according to the sizes and weights of the particles by means of a stream of liquid or gas. elymoclavine an ergot alkaloid produced by Claviceps purpurea and other fungi. em+ prefix; a variant of en+ (sometimes before b, m, and p). EM or e.m. abbr. for electron microscope (or electron microscopy). Embden-Meyerhof pathway or Embden-Meyerhof-Parnas pathway alternative names for glycolytic pathway. [After Gustav Embden (1874-1933) and Otto Meyerhof (1884-1951), German biochemists, and Jacob Karol Parnas (1884-1949), Polish biochemist.] EMBL abbr. for European Molecular Biology Laboratory; an international research facility based at Heidelberg in Germany. The initials are also used as the name of a major database of nucleic acid and protein sequences maintained by EMBL. EMBO abbr. for European Molecular Biology Organization. embolus (pl. emboli) a thrombus fragment that is transported in the circulation to distant tissues, where it can cause ischemic tissue damage. embryo the structure that develops from a zygote, up to the time of birth or hatching in eutherian animals, or of germination in plants. In mammals the term is restricted to the structure present in the early part of gestation that develops into a fetus. -embryonic adj. embryogenesis or embryogeny the formation of an embryo from an ovum and the processes of its development. -embryogenic adj. embryology the branch of biology concerned with the study of embryos and their development. -embryological or embryologic adj.; embryologically adv.; embryologist n. embryonated differentiated into, or having an embryo, e.g. an embryonated hen's egg. embryonic stem cell abbr.: ES cell; a totipotent cell that can be cultured from an early embryo. embryonin another name for bovine «Xl-macroglobulin. emerimicin see peptaibophols. Emerson enhancement the phenomenon in photosynthesis in which the quantum yield of light in the far-red region of the spectrum is enhanced by weak background illumination with shorter wavelength light. Compare enhancement spectrum. [After Robert Emerson (1903-59).] emetic 1 having the power to cause vomiting. 2 any compound with emetic properties. emetine 6',7', 10,11-tetramethoxyemetan; an alkaloid from Cephaelis ipecacuanha that is a gastrointestinal irritant and

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emf potent emetic and used as an expectorant and antiamoebic agent. It inhibits protein synthesis by preventing translocation of peptidyl-tRNA from the A- to the P-site on the ribosome.

emf or EMF abbr. for electromotive force. EMG abbr. for electromyogram. +emia or (esp. Brit.) +aemia suffix denoting blood, especially some abnormal condition of the blood. emilin abbr. for elastin microfibril interface located protein; an extracellular matrix glycoprotein, gp115. It is a component of elastin fibres, preferentially located at the elastin-microfibril interface. emiocytosis a process whereby a secretory substance is released from a cell; a form of exocytosis. A secretory granule moves to the cell surface, where the membrane sac enclosing the granule fuses with the plasma membrane, ruptures, and liberates the granule into the extracellular space. emission (in physics) the release of energy in the form of radia tion or particles. emission spectrophotometry or emission photometry the processes of measuring an emission spectrum, either photometrically or photographically. emission spectroscopy the spectroscopy of an emission spectrum. This differs from emission spectrophotometry in being a generic term. Thus measurement may be photometric or photographic, for example. emission spectrum any spectrum of emitted electromagnetic radiation produced by a sample after its atoms or molecules have been put into excited states by the absorption of energy, each line in the emission spectrum being produced by the decay of a particular species of excited atom or molecule to some lower energy level. The exciting energy may be supplied as heat, bombardment by particles, or irradiation with other electromagnetic radiation. Compare absorption spectrum, excitation spectrum. EMIT abbr. and trademark for enzyme-multiplied immunoassay technique; see homogeneous enzyme immunoassay. emodin 1,3,8-trihydroxy-6-methylanthraquinone; a compound found (as its rhamnoside) in rhubarb root and other plants.

EMPIGEN BB proprietary name for dodecyl-N,N-dimethylglycine. EMR abbr. for 1 equi-effective molarity concentration ratio. 2 or emr electromagnetic radiation. emu or EMU abbr. for electromagnetic unit. emulsifier 1 an alternative name for emulsifying agent. 2 a machine for making emulsions. emulsify to form or to convert into an emulsion. -emulsifiable or emulsible adj.; emulsification n.

enantiomorph emulsifying agent or emulsifier any amphiphile or surfactant, such as a phospholipid or a soap, small quantities of which promote the formation of, and stabilize, an emulsion. emulsin a ferment (i.e. an enzyme preparation) obtained from sweet or bitter almonds and originally studied in 1837 by the German chemists Justus von Liebig (1803-73) and Friedrich Wohler (1800-82) for its ability to degrade amygdalin. Together with invertin, it played an important role in Fischer's work on enzyme specificity leading to his lock and key model. In modern terms, it was an enzyme mixture containing mainly /3glucosidase activity (EC 3.2.1.21). emulsion 1 a temporary or permanent dispersion of an oil or other hydrophobic material in an aqueous solution, or vice versa, forming an oil-in-water emulsion or a water-in-oil emulsion respectively. 2 short for photographic emulsion. en+ or (sometimes before b, m, and p) em+ prefix 1 (forming verbs) put in or into, e.g. encapsulate, encode; surround or cover with, e.g. enmesh; to make into a certain condition, e.g. enrich. 2 (forming nouns and adjectives) in, into, e.g. endemic. enalapril (S)-I-[N-[ 1-(ethoxycarbonyl)-3-phenylpropyl]-Lalanyl]-L-proline; an inhibitor of angiotensin converting enzyme (ACE) and a valuable antihypertensive drug. It has the advantage over captopril that it is more easily absorbed and has fewer side effects, and also that enalaprilate, to which it is converted after absorption by removal of the ethyl ester group, is a much more potent ACE inhibitor than captopril. ACE inhibitors were developed from compounds such as succinylproline, an early inhibitor. Conversion of the free succinyl carboxyl group to a sulfhydryl, and addition of a methyl group, yielded captopril with greatly enhanced binding properties. In enalaprilate there was addition of further binding affinity by a phenylethyl group, restoration of carboxyl in place of sulfhydryl and introduction of a secondary amino group. These drugs lower angiotensin II levels which lowers blood pressure, both because of a reduction in direct action of angiotensin as a vasoconstrictor and also by reducing its actions in stimulating aldosterone and norepinephrine release, both of these latter substances having hypertensive effects.

enamel the hard, white, calcified material that forms the outer covering of the crown of a tooth. enamilin see tuftelin. enamine or alkenylamine any organic molecule having the general structure RIR2NCR3=CR4R 5 (where the R groups may be any hydrocarbyl group or H, and the same or different). enanthate see heptanoate. enantiomer either of a pair of stereoisomers whose molecules as a whole display chirality, i.e. are mirror images of each other and thus not superposable. They are sometimes referred to as optical isomers or optical antipodes; these terms are not recommended. See also enantiomorph (def. 2), racemate (def. 1). Compare diastereoisomer. enantiomeric of, or pertaining to, an enantiomer; pertaining to the phenomenon of, or displaying enantiomerism. Chiral groups that are mirror images of one another are termed enantiomeric groups. See also enantiomorphic, racemic. enantiomeric purity a measure of the proportion of one enantiomer in an enantiomeric mixture expressed as either a fraction or a percentage. Distinguish from optical purity. enantiomerism the phenomenon of the existence of enantiomers in general, or the existence of enantiomeric molecules in a particular instance; it includes optical isomerism. enantiomorph 1 either of two objects, especially crystals, that

205 enantiomorphic are mirror images of each other and thus are not superposable. 2 either of the two crystalline forms exhibited by a pair of enantiomers. Use of the term to mean enantiomer is deprecated. enantiomorphic or enantiomorphous of, or pertaining to, an enantiomorph; pertaining to the phenomenon of, or displaying enantiomorphism. The term is often used synonymously with enantiomeric (enantiomeric molecules frequently form enantiomorphic crystals). enantiomorphism the phenomenon of being related as between an object and its nonsuperposable mirror image. The term is used especially in relation to enantiomorphic crystals. enantiomorphous see enantiomorphic. enantiotopic 1 when chemically-like ligands in constitutionally equivalent locations (generally the two a ligands in Caabc) are related by a centre or plane of symmetry, or by an alternating axis of symmetry (but not by a simple axis of symmetry), they are enantiotopic. The two ligands are in a stereochemically different, mirror-image environment. If each a ligand of Caabc is replaced separately by a different, achiral ligand, d, the products are the two enantiomers of Cab cd. Example: the methylene hydrogens of ethanol are enantiotopic; if ethanol is written as a Fischer projection structure with OH at the top, H-C-H in the middle, and CH 3 at the bottom, the left-hand hydrogen of the central methylene is Hoi', while that at the right is H R (see pro-Rlpro-S convention). Replacement of IH R by 2H yields (+)-(R)-[1-2Htlethanol and the same replacement of IH s yields the enantiomer, (-)-(S)-[1- 2HtlethanoI. In another important compound, citric acid, the two CH 2COOH groups are also enantiotopic. 2 the two faces of a double bond or of a planar cyclic ring system that are related by a symmetry plane but not by a C2 axis (i.e., a two-fold axis of symmetry) are enantiotopic; the two faces show stereochemically different, mirror-image related environments. Separate addition of the same achiral reagent to the two faces (see RefS; convention) gives enantiomeric products. Example: the simple addition of HCN to CH 3-CHO yields a racemic mixture of the (R) and (S) cyanohydrins, CHrCH(OH)-CN, with both faces of C=O being involved. The reduction of the c=o bond of CHrCHO to form ethanol by alcohol dehydrogenase requires addition of a hydride ion from NADH at the C atom and a hydron at the 0 atom. Thus, reduction of CHrCHO with NAD2H at its A face (see diastereotopic (def. 2» yields (R)-[I2Htlethanol and reduction of CH r C2HO with A-NADH yields (S)-[1-2HIlethanoI. The enzymatic reduction is stereospecific and only one of the enantiotopic faces of C=O is attacked; it is the same one (the Re face) in both of these situations. Compare diastereotopic. encapsidate to surround (a particle of viral nucleic acid) with a capsid. -encapsidation n. encapsis the association of myofibrils into bundles and the further association of these bundles into larger bundles, etc. encephalin a variant spelling of enkephalin. encephalitis inflammation of the brain. 3' end the end of a linear polynucleotide strand at which the 3'hydroxyl group of the terminal nucleoside residue is normally not phosphorylated. 5' end the end of a linear polynucleotide strand at which the 5'hydroxyl group of the terminal nucleoside residue is normally phosphorylated. end+ a variant form of endo+ (sometimes before a vowel). end capping (in chromatography) the blocking of residual silanol groups on the surface of silica where these remain exposed after the bonding of C I8 or other alkyl chains to the silica in the formation of reversed-phase stationary phases for column chromatography. For this purpose hydrocarbyl silanes (see silane (def. 3» having small alkyl (usually methyl) groups are used so that they can penetrate between the main bonded-phase groups. endemic present in or peculiar to a more or less localized area, e.g. an endemic disease. Compare enzootic.

endohydrolysis endergonic describing a process or reaction on which work must be done, i.e. one requiring an energy input, for it to take place. At constant pressure and temperature the free energy content of such a system increases. Compare exergonic. [From endo+ plus Greek ergon, work.] end group any residue at an extremity of a branched or linear macromolecule. end-group analysis determination of both the nature and the number of terminal groups in a macromolecule, e.g. in proteins, the N- and C-terminal amino-acid residues; in polynucleotides, the 3'- and 5'-terminal nucleotide residues. endo+ or (sometimes before a vowel) end+ comb. form meaning within, inner, absorbing, containing. Compare exo+. See also intra+. endo- prefix (in chemical nomenclature) denoting insertion (of the additional constituent(s) specified) into the structure of (a named compound); e.g. endo-4a-glycine-[5-leucine]enkephalin; endo-Gl y4a-[Leu 5]enkephalin; Tyr-Gly-G1y-Phe-Gly-Leu; a synthetic polypeptide in which a glycine residue has been inserted between residues 4 and 5 of [5-leucine]enkephalin. endo- prefix (in stereochemistry). See conformation. endoamylase any amylase that hydrolyses nonterminal glycosidic linkages; it is a subcategory of endoglycosidase. endocrine 1 describing or relating to any gland or other group of cells that synthesizes hormones and secretes them directly into the blood, lymph, or other intercellular fluid. 2 describing or relating to a secretion of endocrine tissue. 3 a secretory product of endocrine tissue; a hormone. Originally known as internal secretion. Compare exocrine. endocrine gland or ductless gland any of the ductless glandular structures that secrete (one or more) hormones directly into the bloodstream. endocrinology the science concerned with the endocrine organs, their products, and the effects of these products. endocrinological adj. endocytic 1 situated within a living cell but not belonging to the cell itself; intracellular. 2 an alternative term for endocytotic (see endocytosis). endocytosis the uptake of external materials by cells through the mechanism of phagocytosis or pinocytosis. The term is often used interchangeably with pinocytosis. Compare exocytosis, transcytosis. See also internalize, viropexis. -endocytic or endocytotic adj.; -endocytose vb. endocytotic vesicle see pinocytotic vesicle. endodeoxyribonuclease see deoxyribonuclease. endoenzyme 1 any intracellular enzyme. Compare ectoenzyme, exoenzyme (def. I). 2 any enzyme that catalyses endohydrolysis. It may be an endoglycosidase, an endonuclease, or an endopeptidase. Compare exoenzyme (def. 2). endogenous arising or developing within an organism, tissue, or cell, and excluding any consequences of externally added agents or materials. -endogenously adv. endoglin a major glycoprotein of vascular endothelium that may be important in the binding of endothelial cells to integrins. It forms a heteromeric complex with the signalling receptors for transforming growth factor P (TGF-P). It has an RGD integrin-recognition motif and is a homodimer of disulfidelinked subunits. Example (precursor) from Sus scrofa: database code EGLN_PIG, 653 amino acids (70.20 kDa). endoglycosidase any enzyme within subclass EC 3.2, glycosidases, that hydrolyses nonterminal glycosidic linkages in oligo- or polysaccharides. Many activities of this type are known, e.g. from Flavobacterium meningosepticum. endohormone any hormone acting within the individual organism that produces it. Compare ectohormone. endohydrolysis the hydrolysis, esp. by an endoenzyme, of any linkage between residues in a biopolymer. For example, endopeptidases attack neither the C-terminal nor the N-terminal peptide linkages of an oligo- or polypeptide, and endoglycosidases attack the terminal glycosidic linkages at either the reducing or nonreducing end of an oligo- or polysaccharide.

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endolyn-78 endolyn-78 a glycoprotein, M r 78 000, present in substantial amounts in membranes of endosomes and Iysosomes, but occurring only at low levels in plasma membrane and the peripheral tubular endosomal compartment. endomembrane system a hypothetical integrated membrane system of eukaryotic cells, proposed by Morn: and Mollenhauer, that represents a developmental and functional continuum. It comprises the endoplasmic reticulum, nucleus, Golgi apparatus and vesicles, plasmalemma, tonoplast, and outer membranes, but not the inner membranes of the mitochondria and chloroplasts. endometrium the mucous membrane that lines the uterus. It becomes progressively thicker and more glandular in the later stages of the estrous (menstrual) cycle, which prepares it for embryo implantation. If pregnancy occurs the endometrium becomes the decidua, which is shed after birth. If pregnancy does not occur the endometrium returns to its original state; in primates, including humans, much of the endometrium breaks down and is lost in menstruation. -endometrial ad). endomitosis the replication of chromosomes without cellular or nuclear division. It is a form of polyploidization that is fairly common in differentiated or differentiating tissues. It is characterized by an increase in nuclear DNA content. endonuclease any enzyme of a large group of phosphoric diester hydrolases, forming sub-subclasses EC 3.1.21-31, that catalyses the hydrolysis of nonterminal diester linkages in polynucleotides to yield oligonucleotides. Examples include certain of the deoxyribonucleases and ribonucleases. Compare exonuclease. See also restriction endonuclease. endopeptidase or endoproteinase or (formerly) proteinase any enzyme within subclass EC 3.4, peptide hydrolases, that hydrolyses nonterminal peptide linkages in oligopeptides or polypeptides, and comprising any enzyme of sub-subclasses EC 3.4.21-99. They are classified according to the presence of essential catalytic residues or ions at their active sites. Four distinct sub-subclasses are: (I) serine proteinases (EC 3.4.21); (2) cysteine proteinases (EC 3.4.22); (3) aspartic proteinases (EC 3.4.23), and (4) metalloproteinases (EC 3.4.24). There are two major families of serine proteinases, the chymotrypsins and the subtilisins. Aspartic proteinases contain two aspartic residues at their active site. The metalloproteinases contain metal ions, usually zinc. The proteinases can be distinguished by inhibitors, which are usually specific for a particular class or type. endopeptidase La the enzyme EC 3.4.21.53; other names: ATP-dependent serine proteinase; ATP-dependent protease La; a serine proteinase that catalyses the hydrolysis of large proteins such as globin, casein, and denatured serum albumin in the presence of ATP. It is seemingly the sole member of its own superfamily. Example from Escherichia coli: database code JN0303, 784 amino acids (87.35 kDa). endoperoxide a cyclic peroxide formed from a long-chain polyunsaturated fatty acid, especially arachidonic acid, through the action of prostaglandin-endoperoxide synthase. endoplasm the inner, relatively fluid, part of the cytoplasm. Compare ectoplasm. -endoplasmic ad). endoplasmic reticulum abbr.: ER; the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached). When cells are disrupted by homogenization, the cisternae of rough ER break up into small closed vesicles called rough microsomes. Similarly the smooth ER may give smooth microsomes . The functions of the two forms of the ER differ. The ribosomes attached to the rough ER are the site of translation of the mRNA for those proteins which are either to be retained within the cisternae (ER-resident proteins), the proteins of the Iysosomes, or the proteins destined for export from

endosymbiotic infection the cell. Glycoproteins also undergo their initial glycosylation within the cisternae. The smooth ER has several distinct roles. It is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex (see Goigi apparatus), the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The major membrane phospholipids are phosphatidylcholines, phosphatidylethanolamines, phosphatidylserines, and sphingomyelins. The ER also produces cholesterol, triacylglycerols, and ceramides. The membranes of the smooth ER also contain enzymes that catalyse a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER. endoproteinase or (formerly) proteinase an alternative name for endopeptidase. ENDOR abbr. for electron nuclear double resonance. endorphin any endogenous peptide with morphine-like activity. The term was originally applied to a general class of substances of morphine-like activity postulated to occur in the brain; 'endogenous opioid' is now used to denote any peptide, found in higher organisms, that has morphine-like activity. The group includes the pentapeptide enkephalins, but the term is most often applied to the endogenous opioid peptides of the pituitary gland, including a-endorphin, which has the structure Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-ProLeu-Val-Thr; y-endorphin has the same structure but with an additional Leu at the C terminus; ~-endorphin has the same structure as a-endorphin with additionally -Leu-Phe-Lys-AsnAla-Ile-Ile-Lys-Asn-Ala-His-Lys-Lys-Gly-Gln-OH at the C terminus. Endorphins have the same N-terminal tetrapeptide sequence as the enkephalins. Tissue endorphins are larger polypeptides (about 7 kDa) found in pancreas, placenta, and adrenal medulla. The members of this group of pep tides originate from large precursor molecules: preproopiomelanocortin is the precursor of ~-endorphin, both in brain and other tissues, and [Met 5]enkephalin; preprodynorphin (preproenkephalin B) is the precursor of dynorphin; [Leu 5]enkephalin is formed from preproopiomelanocortin and from preproenkephalin A. Compare exorphin. [From endo(genous) + morphine.] endo-a-sialidase EC 3.2.1.129; other names: endo-N-acetylneuraminidase; endoneuraminidase; poly(a-2,8-sialosyl) endoN-acetylneuraminidase; an enzyme that catalyses the endohydrolysis of a-2,8-sialosyl linkages in oligo- or poly(sialic) acids. Example from bacteriophage kif: database code ENAN_ BPKIF, 919 amino acids (101.77 kDa). endoskeleton any skeleton lying within an organism, such as the axial skeleton of vertebrates. Compare exoskeleton. endosmosis the osmotic flow of water or of an aqueous solution into a cell, organism, or vessel from a surrounding aqueous medium. Compare exosmosis. -endosmotic ad). endosome a membrane-bound organelle in animal cells that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation. endosperm the nutritive tissue, found in the seeds of most angiosperms, that surrounds and nourishes the embryo. endosperm albumin the proteins occurring in the endosperm of, e.g. barley; see protein Z. endospore 1 an asexual spore formed within a cell, especially one produced by some bacteria and algae. 2 or endosporium the innermost coat of the wall of a spore or pollen grain. endosymbiont a partner in a symbiotic relationship that penetrates the tissues or cells of the other partner; e.g. any of the nitrogen-fixing species of bacteria that occur in the root nodules of legumes. See symbiosis. Compare ectosymbiont. endosymbiotic infection an infection of cells by viruses that replicate without cytopathic effect.

207 endothelial leukocyte adhesion molecule endothelial leukocyte adhesion molecule abbr.: ELAM; another name for selectin. endothelin abbr.: ET; anyone of three 21-residue peptides, called endothelins I, 2, and 3 (abbr.: ET-l, ET-2, ET-3). Endothelins 2 and 3 are so named because of homology with ET-I, which is known to be made by the endothelial cell. ET-I is the most potent vasopressor compound yet discovered, being ten times more potent than angiotensin II. All three compounds have two disulfide bridges, between cysteine residues I and 15, and 3 and II; these hold the structure in a conical spiral shape. The amino-acid sequence of ET-I is {bicyclic(l ~ 15, 3~ II)} [Cysl-Ser-Cys3-Ser-Ser-Leu-Met-Asp-Lys-Glu-CysllVal-Tyr-Phe-Cys I5-His-Leu-Asp-Ile-Ile-Trp]; ET-2 differs in having -Trp-Leu- at positions 6,7; ET-3 has the substitutions (position in parentheses) Thr(2), Phe(4), Thr(5), Tyr(6), Lys(7), and Tyr(l4). The endothelins are products of three distinct genes, and are synthesized as part of a large precursor molecule, preproendothelin (prepro-ET), which is then proteoIytically processed. The 2.2 kb mRNA for human prepro-ET-I is encoded in five exons, the 5'-flanking region containing response elements for phorbol ester (Fos/Jun-inducible) and nuclear factor I (TGF-~-induced expression; see transfonning growth factor), and its expression is stimulated by vasopressor hormones such as epinephrine, angiotensin II, and arginine vasopressin, as well as TGF-~ (from aggregating platelets), thrombin, and interleukin-l. Prepro-ET-I is a 203-residue peptide, which is cleaved to the 92-residue pro-ET (big endothelin), from which ET-I is formed by endothelin converting enzyme. Related peptides are vasoactive intestinal contractor and sarafotoxin, a peptide produced by Atractaspsis engaddensis. Only ET-I is detected in vascular endothelial cells; it is also expressed in nonvascular cells in other tissues, including brain, kidney, and lung. ET-2 and ET-3 are expressed in tissues such as brain, kidney, adrenal, and intestine. endothelin receptor any of several membrane proteins that bind endothelins and mediate their intracellular effects. They are G-protein-coupled seven-transmembrane-domain receptors. The structures of two types have been predicted from human, rat, and bovine cDNA. ETA (human, 427 amino acids) has affinity ET-I ;;. ET-2 $> ET-3, while ET B (human, 442 amino acids) is equipotent for all three. endothelium the single layer of thin, flattened cells of mesoblastic origin that lines the blood vessels and some body cavities, e.g. those of the heart. Compare epithelium, mesothelium. -endothelial adj. endothelium-derived relaxing factor abbr.: EDRF; see nitric oxide. endothermic describing a process or reaction that absorbs heat, i.e. a process or reaction for which the change in enthalpy, AH, is positive at constant pressure and temperature. Compare exothennic. endothiapepsin EC 3.4.23.22; other name: Endothia aspartyl proteinase. An enzyme that catalyses the hydrolysis of proteins with broad specificity similar to that of pepsin A; it prefers hydrophobic residues at PI and PI', but does not cleave the Ala-Leu linkage in the B chain of insulin or the protected dipeptide Cbz-Glu-Tyr; it clots milk. Example from Cryphonectria parasitica (Endothia parasitica; chestnut blight fungus): database code NRL_4APE, 330 amino acids (33.76 kDa); 3-D structure known; it is similar to other aspartic proteases. endotoxin any microbial toxin that cannot easily be separated from the structure of the cell. Compare exotoxin. end point or endpoint the point in a titration that should (but may not always) correspond to the theoretical equivalence point. end product the final chemical substance formed in a sequence of metabolic (or chemical) reactions. end-product inhibition the inhibition of a sequence of metabolic reactions by the end product of the sequence, usually by action on a reaction which is often at the beginning of the sequence.

engrailed end-window counter a Geiger counter or proportional counter so constructed that its base is relatively transparent to the radiation to be detected. +ene suffix (in chemical nomenclature) indicating the presence of one or more carbon-carbon double bonds in an organic compound. enediol any acyclic organic compound in which there is a hydroxyl group attached to each of two carbon atoms that are linked by a double bond. Compare enol. energy symbol: E; the capacity of a system for doing work. There are various forms of energy - potential, kinetic, electrical, chemical, nuclear, and radiant - which can be interconverted by suitable means. The SI unit of energy is the joule. energy balance the algebraic balance of the various energy inputs versus energy outputs of a system; it is positive if energy is released and negative if it is absorbed. In physiology it is the relation of the amount of energy taken into the organism to the amount used for internal work, external work, and for the growth and repair of tissues. energy barrier see potential energy barrier. energy charge see adenylate energy charge. energy coupling the coupling of ATP synthesis to electron transport in the respiratory chain. energy diagram a diagram representing the energy contents of various states of the reactants, activated complexes, and products in a chemical reaction; or of the nuclear energy levels of an atom; or of the electronic energy levels of an atom or molecule. energy flow (in ecology) the transfer of energy between organisms in an ecosystem. energy level any of the stable energy states that a molecular entity can take up. In quantum mechanics only certain discrete energy levels are possible and continuous variation of the energy level of a molecular entity is excluded. energy metabolism the metabolic reactions of a cell or organism concerned with energy transformations. energy of activation see activation energy. energy-poor term sometimes used to describe 1 a compound whose hydrolysis under standard conditions manifests a small negative free energy change. See also low-energy compound. 2 a chemical group with a low group potential. 3 the linkage of such a chemical group to some other group. energy requirement the amount of energy needed to maintain a cell or organism. energy sink a molecule or a group in a molecule that is able easily to accept energy transferred to it from another component of the system. energy transduction see transduction (def. 2). energy transfer the transfer of excitation energy from one chromophore or one molecular entity to another by a process not involving radiation; the energy may then be dissipated in a variety of ways, e.g. by fluorescence. Such energy transfer is very dependent on the distances involved and is useful in studies of structural relationships between groups on a macromolecule. energy trapping the processes by which energy released in a catabolic reaction is coupled to the synthesis of another compound, often a nucleoside triphosphate such as ATP. engineered 1 (of a cell or organism, or a strain of cells or organisms) colloquial term for genetically engineered. 2 (of a nucleotide sequence) jargon term, usually followed by 'into' artificially inserted (into a longer sequence, such as a vector). 3 (of a protein) jargon term describing an altered protein synthesized by a cell or organism (or a strain of cells or organisms) whose genetic material has been manipulated to that end. engrailed any of various protein products of the homeotic gene engrailed; in Drosophila this is a segment-polarity gene. Examples: engrailed-I and engrailed-2 (human) respectively: database codes HMELHUMAN and HME2_HUMAN, 391 amino acids (40.00 kDa) and 332 amino acids (34.12 kDa); en-

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enhancement grailed chain C, Drosophila melanogaster, database code NRL_IHDDC, 57 amino acids (6.94 kDa); 3-D structure of complex with DNA known; one motif. enhancement 1 the improvement of the effects of ionizing radiation on tissue by dioxygen or other chemical agents. 2 the increased yield of one virus from cells infected by another virus; the term is often used when the mechanism of the process is not known. Compare complementation (def. 2), interference. 3 see Emerson enhancement. 4 see fluorescence enhancement. enhancement of fluorescence an alternative term/or fluorescence enhancement. enhancement spectrum a spectrum showing the enhancement of photosynthetic quantum yield from that produced at a fixed-wavelength background illumination to that produced by illumination with a variable-wavelength beam. Such spectra show peaks that can sometimes be reasonably well identified with specific pigments in the system. Compare Emerson enhancement. enhancer (in molecular biology) a eukaryotic control element that can increase expression of a gene. Enhancers may be located some distance from the gene and may be either upstream or downstream. enhancesome a disclike structure, formed by a 180 bp loop of DNA and dimers of the Xenopus transcription factor xUBF, that is involved in rRNA transcription. enkephalin any pentapeptide endorphin with the sequence TyrGly-Gly-Phe-Xaa. There are two similar naturally occurring enkephalins, present in brain, spinal cord, and gut; their recommended trivial names are: [5-leucine]enkephalin (abbr.: [Leu 5]enkephalin or [Leu]enkephalin), Tyr-Gly-Gly-Phe-Leu (I); and [5-methionine]enkephalin (abbr.: [Met 5]enkephalin or [Met]enkephalin), Tyr-Gly-Gly-Phe-Met (II). (II has the same sequence as residues 61-65 of ~-Iipotropin.) The common precursor of I and II, proenkephalin - itself formed from preproenkephalin by removal of the signal peptide - contains four copies of II and one each of I, the heptapeptide [Met 5]enkephalinyl-Arg-Phe, and the octapeptide [Met 5]enkephalinyl-Arg-Phe-Leu. (Note: Designations such as Leu-, leucyl-, or leucine-enkephalin have commonly been given to I, with corresponding terms for II, but all of these incorrectly imply N-terminal extension with a residue of leucine or methionine, respectively.) enkephalinase see carboxypeptidase H. enkephalin convertase a specific carboxypeptidase that converts enkephalin precursors into enkephalin in adrenal chromaffin granules. It is now known as carboxypeptidase H. enniatin any of various antibiotics from Fusarium spp. that function as ionophores. They are cyclodepsipeptides (see depsipeptide). enol any acyclic organic compound with a hydroxyl group attached to either of two carbon atoms that are linked by a double bond. Compare enediol. See also keto-enol tautomerism. enolase EC 4.2.1.11; recommended name: phosphopyruvate hydratase; other name: 2-phosphoglycerate dehydratase. An enzyme that catalyses the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and H 20; magnesium is a cofactor. Example from Saccharomyces cerevisiae: database code NRL_7ENL, 436 amino acids (46.58 kDa); 3-D structure known; six motifs. enology or (esp. Brit.) oenology the study of wines. 5-enolpyruvylshikimate-3-phosphate phospholyase see chorismate synthase. eNOS see nitric-oxide synthase. enoyl an acyl group derived from any alkenoic acid. enoyl-[acyl-carrier protein] reductase (NADPH, A-specific) EC 1.3.1.39; other name: acyl-ACP dehydrogenase; an enzyme of the fatty acid synthase complex in liver. It catalyses the reduction by NADPH of trans-2,3-dehydroacyl-[acyl-carrier protein] to form acyl-[acyl-carrier protein] and NADP+ . enoyl-CoA hydratase 1 EC 4.2.1.17; systematic name: (3S)-3-

enteroglucagon hydroxyacyl-CoA hydro-lyase; other names: enoyl hydrase, unsaturated acyl-CoA hydratase; an enzyme of the beta-oxidation system, present in mitochondria and peroxisomes. It catalyses the hydration of (3S)-3-hydroxyacyl-CoA to trans-2( or 3)-enoyl-CoA. It is a mitochondrial matrix protein, a homohexamer; a characteristic transit peptide sequence is found in the precursor. Example (precursor) from rat: database code ECHM_RAT, 290 amino acids (31.48 kDa). 2 EC 4.2.1.74; recommended name: 10ng-chain-enoyl-CoA hydratase; an enzyme that catalyses a similar reaction to the above; it does not act on crotonoyl-CoA. See also beta-oxidation system. enoyl-CoA isomerase see dodecenoyl-CoA Llo-isomerase. 3,2-trans-enoyl-CoA isomerase see dodecenoyl-CoA .ll-isomerase. enrich to increase in content or abundance; e.g. to increase the abundance of one (usually stable) nuclide of an element above its naturally occurring level; to increase the content in a foodstuff of one or more specific nutrients (such as vitamins or minerals) above the natural level. -enrichment n. enrichment medium a selective culture medium that favours the growth of a desired microorganism. entactic describing an enzyme poised for catalytic action in the absence of substrate. entactin or nidogen a sulfated Ca 2+-binding protein occurring in basement membrane and involved in cell adhesion; it binds laminin and type IV collagen. The protein has two globular domains, an EF-hand domain, EGF-like domains and a thyroglobulin type I domain. Example (precursor) from human: database code NIDO_HUMAN, 1247 amino acids (136.34 kDa). enteric or enteral of or pertaining to the intestine or gut. enteric-coated describing a drug or medicament that is prepared in a form enabling it to pass through the stomach unaltered and be released in the intestine. entero+ or (before a vowel) enteH comb. form denoting the intestine. enterobactin or enterochelin N',N',N"-tris(2,3-dihydroxybenzoyl)-2,6, 1O-trioxo-l ,5,9-trioxacyclododecane-3,7, Il-triamine; a siderochrome of the catechol-derivative variety produced by certain members of the Enterobacteriaceae, e.g. Escherichia coli, Salmonella spp. It is the cyclic self-triester (trilactide) of N-(2,3-dihydroxybenzoyl)-L-serine, and a product of the shikimate pathway. enterochelin an alternative name for enterobactin. enterochromaffin cell abbr.: EC cell; any gut endocrine cell containing biogenic monoamines that gives a positive chromaffin reaction and displays a characteristic yellow formaldehydeinduced fluorescence. Such cells may be divided immunocytochemically and ultrastructurally into functionally distinct types. enterocrinin a putative peptide hormone, crystallizable from extracts of intestine of certain mammals, that is held to stimulate duodenal and jejunal secretion of digestive enzymes. enterocyte any of the columnar epithelial cells on the luminal surface of the villi of the small intestine. Enterocytes are immature in the crypts, mature in the middle of the villi, and senile at the exfoliation area at the villous tips. They have numerous microvilli on their luminal surface (the brush border) and are responsible for the synthesis of digestive enzymes and for the absorption of materials from the gut. enterogastrone the putative hormone from the duodenum that inhibits gastric activity. Some or all of the actions attributed to enterogastrone are probably due to glucose-dependent insulinotropic peptide. enterogastrone effect see gastric inhibitory peptide. enteroglucagon a collective term for a small family of peptides derived from proglucagon by post-translational processing in the L cells (or EG cells) of the distal small intestine and colon. One component is GLP-J7 37 (see GLlP). enteroglucagon or glucagon-37 or oxyntomodulin a peptide isolated from porcine jejuno-ileum that interacts with glucagon receptors and activates adenylate cyclase in hepato-

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enterohepatic recirculation cytes. It has a specific action on the acid-secreting area of gastric mucosa. It has 37 residues, of which the sequence of the N-terminal 29 is identical with that of pancreatic glucagon. enterohepatic recirculation the cycle of secretion from the gall bladder into the upper intestinal tract with reabsorption in the lower tract and transport to the liver followed by resecretion. See bile acids. entero-insular axis the interrelationship of endocrine function between the gastrointestinal tract and the pancreatic islets in which signals arising in the gut after ingestion of nutrients effect endocrine responses by the islets. enterokinase a former name for enteropeptidase. enteropeptidase or (formerly) enterokinase the enzyme EC 3.4.21.9; a serine proteinase enzyme of the brush border of the upper small intestine that activates trypsinogen by the selective cleavage of the Lys6_I_IIe 7 bond in the latter. Example (precursor) from Bos taurus: database code ENTK_BOVIN, 1035 amino acids (114.89 kDa); residues 1-800 form the non-catalytic heavy chain, 801-1035 the catalytic light chain. enterotoxin any bacterial exotoxin, whether ingested or produced within the intestine, that has an action upon the intestinal mucosa, usually giving rise to diarrhoea and other unpleasant symptoms. Cholera toxin is an example. Other enterotoxins are produced by Escherichia coli and some Staphylococci. Of the E. coli enterotoxins, L T (from labile, i.e. heat-labile, toxin) is similar in structure to cholera toxin and has a similar mode of action. ST (from heat-stable toxin) has an effect similar to atrial natriuretic peptide, activating guanylate cyclase. It has 13 amino acids. Other enterotoxins produced by E. coli include hemolysin and vero toxin, a Shiga-like toxin similar to that of Shigella dysenteriae that has N-glycosidase activity, and cleaves an adenine residue from the 288 rRNA of the 60S ribosome subunit. enthalpimetry the measurement of the enthalpy of a body or system. enthalpy or heat content symbol: H; a physical quantity and a thermodynamic property defined as the sum of the internal energy of a system, U and the product of the volume, V, multiplied by the pressure, p, i.e. H = U + p V. Enthalpy is related to the Gibbs energy, G, by the equation G = H - TS, where T denotes the thermodynamic temperature and S denotes entropy. Entne.....Doudoroff enzyme the 'catabolic' o-glucose-6-phosphate dehydrogenase (EC 1.1.1.49) from Pseudomonas fluorescens. It is a 220 kDa protein composed of four, apparently identical, polypeptide chains. See also Entner-Doudoroff pathway. Entne.....Doudoroff pathway a metabolic pathway occurring in Pseudomonas spp. in which o-glucose 6-phosphate is first oxidized to 6-phospho-o-gluconate, which is then acted on by 6-phosphogluconate dehydratase (EC 4.2.1.12) to form 2-dehydro-3-deoxy-6-phospho-o-gluconate. This is then split by 2dehydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) to give pyruvate and o-glyceraldehyde 3-phosphate. [After Nathan Entner (1920- ) and Michael Doudoroff(l911- ).] entomology the science of the study of insects. entopic occurring in the usual place. Compare ectopic. ENTREZ a suite of computer programs accessible via the Internet that links MEDLINE with genome and sequence databases. entropic union a polymerization, or other reaction, resulting from an energetically unfavourable interaction of a surface of the molecule in question with water molecules; the polymerization causes the removal of water from the molecules' surfaces and a hence a decrease in the free energy content of the system. entropy symbol: S; a physical quantity and a thermodynamic property indicating the amount of disorder in a system; i.e. the amount of energy in a system that is unavailable for doing work. In any irreversible process the total entropy of all systems concerned is increased. In a reversible process the total increase in entropy in all systems concerned is zero, while the increase in entropy, dS, of any individual system, or part of a

enzyme I system, is equal to the heat that it absorbs, dqrev' divided by the thermodynamic temperature, T; i.e. dS = dqre)T. Entropy is related to Gibbs energy, G, and enthalpy, H, by the equation G = H - TS. The SI unit for entropy is J K-l -entropic adj. entry exclusion the phenomenon in which a resident plasmid interferes with the entry of genetic material to a cell by (bacterial) conjugation (def. 4). enucleate 1 to remove the nucleus from (a cell). 2 (of a cell) deprived of its nucleus. -enucleation n. enuresis the involuntary passing of urine. -enuretic adj. enva viral gene for envelope protein. envelope 1 any covering or enclosing structure, e.g. a membrane, capsule, shell, or skin. 2 the cell membrane of a bacterium, together with all the structures external to it including the cell wall and, sometimes, the capsule. 3 or peplos an outer lipoprotein coat of a virion that occurs in an enveloped virus. 4 see nuclear envelope. envelope conformation any confonnation of a nonplanar fivemembered saturated ring compound when four of its ring atoms lie in one plane and the remaining atom lies outside that plane. For a monosaccharide or monosaccharide derivative the conformational descriptor -E may be added to its name. enveloped virus any virus in which a nucleoprotein core is surrounded by a lipoprotein envelope consisting of a closed bilayer of lipid derived from that of the host cell's membrane(s), with glycoprotein on the outside and matrix protein or nucleocapsid protein on the inside. Enveloped viruses include herpesviruses, negative-strand RNA viruses, retroviruses, and togaviruses. envelope protein any protein (usually a glycoprotein) of the envelope of a virus. Example: envelope polyprotein gpl60 precursor of human immunodeficiency virus (HIV) type I; database code ENV_HVIA2, 855 residues (97.33 kDa). Residues 1-29 are the signal peptide; 30-509 form exterior membrane glycoprotein gp120; 510-855 form transmembrane glycoprotein gp41. The variable (very rapidly evolving) antigenic regions of HIV are in the gpl20 sequence. envelysin EC 3.4.24.12; other names: sea-urchin-hatching proteinase; hatching enzyme; an enzyme so named because it dissolves (lyses) the fertilization envelope of the sea-urchin embryo. It is a metalloendopeptidase that catalyses the preferential cleavage of proteins on the amino side of bulky hydrophobic residues, Leu, lie, Phe, and Tyr. The enzyme requires zinc and calcium. Example (precursor) from the sea urchin Paracentrotus lividus: database code HE_PARLI, 587 amino acids (65.14 kDa). Enzacryl the proprietary name for a group of synthetic carriers for the immobilization of enzymes and other organic biomolecules that are copolymers of acrylamide and various derivatives of N,N' -methylene diacrylamide. enzootic present in or peculiar to animals in a more or less localized area; e.g. an enzootic disease. Compare endemic. enzyme any naturally occurring or synthetic macromolecular substance composed wholly or largely of protein, that catalyses, more or less specifically, one or more (bio)chemical reactions at relatively low temperatures. The action of RNA that has catalytic activity (see ribozymel is often also regarded as enzymic. Nevertheless, enzymes are mainly proteinaceous and are often easily inactivated by heating or by protein-denaturing agents. The substances upon which they act are known as substrates, for which the enzyme posseses a specific binding or active site. See also enzyme classification, isoenzyme. [From German enzym, possibly from modern Greek enzumos, leavened, or more probably from Greek en, in, + zume, leaven, yeast.] -enzymic or enzymatic adj. enzyme I EC 2.7.3.9; enzyme I of the phosphotransferase system; phosphoenolpyruvate-protein phosphotransferase; systematic name: phosphoenolpyruvate:protein-L-histidine Nn_phosphotransferase. A soluble bacterial enzyme, part of a system for the transport of hexoses across the cell membrane, that cata-

enzyme II

210

lyses the phosphorylation by phosphoenolpyruvate of a low M" heat-stable protein, HPr. Compare enzyme II (def. I). enzyme II 1 EC 2.7.1.69; enzyme II of the phosphotransferase system; protein-N"-phosphohistidine-sugar phosphotransferase; systematic name: protein-N"-phosphohistidine:sugar N"-phosphotransferase. Any of a group of related membranebound bacterial enzymes, part of the system for the transport of hexoses across the cell membrane, that catalyse the phosphorylation of hexoses by phospho-HPr (see enzyme I). Enzyme II is responsible for the specificity of the transport process with respect to the sugar. 2 a former name for acyl-carrier protein. enzyme-activated irreversible inhibitor an alternative name for suicide inhibitor. enzyme activation the generation of a catalytically active enzyme from an inactive or poorly active form or from a biosynthetic precursor (proenzyme). Activation may be by enzymic or chemical covalent modification or by addition of a specific activator. enzyme adaptation see inducible enzyme. enzyme cascade see cascade sequence. enzyme classification the systematic arrangement and naming of enzymes by the Enzyme Commission. Each enzyme is denoted by the abbreviation EC followed by a set of four numbers separated by stops. The first number denotes one of the six main divisions: EC I, oxidoreductases; EC 2, transferases; EC 3, hydrolases; EC 4, Iyases; EC 5, isomerases; and EC 6, ligases. The second number denotes the subclass, the third number denotes the sub-subclass; the fourth number is the serial number of the particular enzyme. The most recent edition of the classification, Enzyme Nomenclature 1992 (IUB/Academic Press; San Diego, London), lists 3196 enzymes. enzyme cluster or (sometimes) multienzyme cluster 1 any physiologically significant system of two or more enzymes in physical (i.e. noncovalent) association. The term embraces any enzyme complex, multienzyme complex, or membrane-bound enzyme array. Clustered enzymes usually display different kinetic and/or regulatory features from their un associated counterparts; they may be encoded in a cluster-gene. See also multienzyme system. 2 an alternative term for cluster (def. 2). Enzyme Commission or the International Commission on Enzymes; a body established in 1956 by the International Union of Biochemistry (IUB) to consider the classification and nomenclature of enzymes and coenzymes, their units of activity and standard methods of assay, together with the symbols used in the description of enzyme kinetics. The Commission, which worked closely with the Biological Chemistry Nomenclature Commission of the International Union of Pure and Applied Chemistry (IUPAC), was dissolved in 1961 and its work has been carried on in turn by the Standing Committee on Enzymes of IUB, by the IUPAC/IUB Joint Commission on Biochemical Nomenclature (JCBN), by an Expert Committee on Enzymes, and most recently by the Nomenclature Committees of IUB (NC-IUB) or the International Union of Biochemistry and Molecular Biology (NC-IUBMB). See also enzyme classification. enzyme complex an operational term for any structural and functional entity composed of a number of dissociable enzymes that catalyse a sequence of closely related chemical reactions. Compare multienzyme. enzyme detergent any detergent preparation incorporating an enzyme to assist its cleansing action. The enzymes used in such detergents are usually proteinases of high thermal and alkaline stability, e.g. Alcalase. enzyme differentiation the process whereby, during the development of an organism, each tissue acquires its own characteristic quantitative pattern of enzymes, which underlies the physiological functions and morphological features of the tissue. From a fairly uniform enzymic make-up in the cells of the early embryo, the enzyme patterns of different tissues become progressively more differentiated as development into the mature organism proceeds.

enzymic activity enzyme electrode any electrode, incorporating an enzyme into its structure, that responds to the concentration of one of the substrates or products of the reaction catalysed by the enzyme. The enzyme is trapped within a gel matrix surrounding the electrode or is kept in contact with the electrode by a semipermeable membrane. enzyme engineering or enzyme technology the branch of biomolecular engineering concerned with processes designed to produce, isolate, purify, and immobilize enzymes and to use them for the catalysis of specific chemical reactions. enzyme immunoassay or enzymoimmunoassay abbr.: EIA; any immunoassay in which an enzyme-catalysed reaction is used as the indicator. See also heterogeneous immunoassay, homogeneous immunoassay. enzyme induction the synthesis of an enzyme in a cell or organism at a markedly increased rate in response to the presence of an inducer. The inducer is thought to combine with a repressor thereby preventing the latter from blocking an operator, which controls the translation of the structural gene for the enzyme. enzyme-inhibition immunoassay a variation of enzyme immunoassay in which the inhibition of an enzyme-catalysed reaction is used as the indicator. enzyme labelling a method used to detect or locate (and sometimes estimate) an antigen in, e.g., a tissue section. The section is exposed to a complementary antibody that has been covalently linked to an enzyme; the antibody binds to the antigen, and its location (and its amount) is determined by an assay dependent on the catalytic activity of the linked enzyme. See also enzyme immunoassay. enzyme-linked immunosorbent assay abbr.: ELISA; a form of quantitative immunoassay based on the use of antibodies (or antigens) that are linked to an insoluble carrier surface, which is then used to 'capture' the relevant antigen (or antibody) in the test solution. The antigen-antibody complex is then detected by measuring the activity of an appropriate enzyme that had previously been covalently attached to the antigen (or antibody). enzyme membrane any (semipermeable) membrane to which an enzyme has been covalently bound. Such membranes are useful in constructing enzyme electrodes. enzyme-multiplied immunoassay technique abbr. and proprietary name: EMIT; an alternative name for homogeneous enzyme immunoassay. enzyme-paper graft an enzyme immobilized on (filter) paper, which is frequently impregnated with indicators. It is useful for making analytical devices. enzyme reactor a device for using immobilized enzymes or enzyme systems for synthetic or other processing reactions, especially on an industrial scale. enzyme recruitment the exploitation of substrate-ambiguous enzymes or transport proteins in the evolution of new biochemical pathways. enzyme repression inhibition of the formation of an enzyme by a compound formed in or taken in by a cell or organism. enzyme specificity see specificity. enzyme-Bubstrate complex abbr.: ES; the stoichiometric complex of an enzyme molecule and a substrate molecule bound at the enzyme's active site. enzyme technology an alternative term for enzyme engineering. enzyme unit symbol: U; abbr.: EU; an obsolete unit of activity of enzymes, defined as the amount of enzyme that will catalyse the transformation of one micromole of the substrate per minute under standard conditions. It has now been superseded by the kata!. enzymic or enzymatic by, of, involving, or relating to an enzyme or enzymes; catalysed by an enzyme or by enzymes. enzymically or enzymatically adv. enzymic activity the rate of reaction of substrate that may be attributed to catalysis by an enzyme. The concept is now obsolete, having been superseded by catalytic activity. The unit of

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epidermal growth factor receptor

enzymic cycling enzymic activity was initially the enzyme unit and subsequently the katal (as originally defined). The derived quantity concentration of enzymic activity was defined as activity divided by volume and was expressed as katals per litre. See also catalytic activity concentration, molar (enzymic) activity, specific (enzymic) activity. enzymic cycling a form of catalytic assay in which there is no coupled indicator reaction; instead, the regenerating system is allowed to cycle for a set time, after which the reactions are stopped by destruction of all enzymes and the most easily determined product is measured in a separate assay. The coupled system thus acts as a chemical amplifier in the determination of the intermediate catalyst. enzymo+ comb. form denoting an enzyme or enzymic activity. enzymoimmunoassay an alternative name for enzyme immunoassay. enzymology the science of the study of enzymes and enzymecatalysed reactions. -enzymological adj.; enzymologist n. enzymolysis the enzyme-catalysed splitting of a chemical compound into smaller ones. The term commonly refers to enzymic hydrolysis. -enzymolytic adj. eobiogenesis the first occurrence of the formation of living matter from nonliving material. eobiont any system showing some characteristics of living systems but not enough to be generally accepted as living. eosin any of a number of similar red acidic dyes, derivatives of fluorescein, especially Eosin Y (yellowish), 2',4',5',7'-tetrabromofluorescein disodium salt, Acid Red 87 (CI 45380), or Eosin B (bluish), 4',5'-dibromo-2',7'-dinitrofluorescein disodium salt, Acid Red 91 (CI 45400). They are widely used as stains in histology and hematology.

Br

Br

2',4',5',7'-tetrabromofluorescein eosinophil(el 1 or eosinophil leukocyte or eosinophilic leukocyte a polymorphonuclear leukocyte, present in blood and other connective tissues, that has numerous large cytoplasmic granules that stain readily with eosin. The granules contain numerous hydrolytic enzymes including acid phosphatase, arylsulfatase, cathepsins, glucuronidase, peroxidase, and ribonuclease. The relative number of eosinophils in the blood, normally low, rises markedly in certain allergic conditions and parasitic infections but their function is poorly understood. 2 any cell whose cytoplasm stains readily with eosin, especially an eosinophilic cell of the anterior pituitary that secretes prolactin and somatotropin. eosinophil cationic protein abbr.: ECP; a highly basic zinccontaining ribonuclease that binds avidly to negatively charged surfaces and is particularly effective at damaging the tegument of schistosomes. eosinophilic having an affinity for eosin. eosinotactic having an attractive or repulsive action on eosinophils. [A contraction of eosinophil + chemotactic.] eosome the suggested primary particulate biogenetic precursor, via the neosome, of the ribosome. Eosomes of Escherichia coli have an average sedimentation coefficient of 14S. EPA abbr. for 1 eicosapentaenoic acid. Normally indicating the (all-Z)-5,8,11,14,17 isomer. 2 erythroid potentiating activity (see TlMP).

EpETrE abbr. for epoxyeicosatrienoate. EPH a gene encoding a subfamily of protein tyrosine kinases. It is named from erythropoietin-producing hepatocellular carcinoma cell line, from which the probe used to isolate the gene was obtained. Related proteins are Elk (Eph-like kinase), Eek (Eph and Elk-related kinase), Eck (epithelial cell kinase), and Erk (Elk-related kinase). Overexpressed EPH has tumorigenic potential; the ligand of Eph is unknown; database code for the expressed protein: KEPH_HUMAN, 984 amino acids (108.80 kDa); residues 1-23 are the signal 24~984 Eph. ephedrine (I R,2S)-I-phenyl-l-hydroxy-2-methylaminopropane; an alkaloid obtained from several species of gymnosperm shrubs belonging to the genus Ephedra. A structural analogue of epinephrine, it mimics central and peripheral effects of noradrenergic and adrenergic neurons through direct and indirect actions, hence its CNS-stimulant effects and its use as a decongestant in upper respiratory tract infections.

epi+ or (before a vowel) ep+ prefix denoting lon, upon, above, over, beside, near, close to, in addition to. 2 a chemical compound or group related in some way to a specified chemical compound or group, e.g. an epimer. 3 a chemical compound or group distinguished from a specified chemical compound or group by having a bridge connection in the molecule, e.g. an epoxide. epiarginase see epiprotein. epichlorohydrin 3-chloropropylene oxide; chloromethyloxirane; l-chloro-2,3-epoxypropane; a colourless liquid widely used in industry as a solvent and an intermediate in the manufacture of glycerol, glycerol ethers and epoxy resins. In the presence of potassium hydroxide it reacts with compounds containing alcoholic hydroxyl groups to form diethers of glycerol and hence finds application in the manufacture of crosslinked derivatives of polysaccharides such as the proprietary materials Sephacel, Sephadex, and Sepharose. epidemic 1 describing a disease that affects many persons simultaneously in a more or less restricted area. 2 the widespread occurrence of a disease in a human population. Compare endemic. epidemiology the study of the nature and spread of a disease in a human population. epidermal growth factor abbr.: EGF; any member of a group of heat-stable, hormonal, =6 kDa proteins that consist of a single polypeptide chain of 49-53 residues with three intrachain disulfide bonds; they are classified as cytokines. One form (mEGF), originally known as tooth-lid factor, can be isolated from submaxillary glands of the male mouse (see nerve growth factor). A similar protein (hEGF), extracted from human pregnancy urine and named urogastrone, is now known to be highly homologous to EGF (37 of 53 residues identical, disulfide bonds preserved). The main effects of EGF in vivo are to stimulate the growth of epidermal and epithelial cells, and to inhibit the secretion of gastric acid. It also has a potent mitogenic action on many types of cultured mammalian cells and displays a number of insulin-like properties towards them (see insulin-related growth factors). It is synthesized as a large preprotein, EGF membrane glycoprotein precursor, which contains, as well as the mature EGF protein, nine EGF-like repeats and urogastrone. Example (precursor) from human: database code EGF_HUMAN, 1207 residues (133.79 kDa). The action of EGF is mediated by the epidermal growth factor receptor. epidermal growth factor receptor or EGF receptor the mediator of the biological signal of epidermal growth factor (EGF)

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and also of transforming growth factor-a (TGF-a). It is a membrane protein with a single transmembrane domain, and a tyrosine kinase activity in the cytoplasmic domain; the extracellular domain, which binds EGF, is highly glycosylated. The v-erbB oncogene codes for a protein highly homologous to a truncated EGF receptor, and the gene that codes for the receptor is now regarded as the protooncogene c-erbB (see erbS). Binding of EGF to the receptor leads to the induction of tyrosine kinase activity, and formation of dimers, as a result of which autophosphorylation occurs; stimulation of cell DNA synthesis and cell proliferation follows. Internalization of the EGF-receptor complex occurs subsequent to binding EGF. Example (precursor) from human: database code EGFR_ HUMAN, 1210 amino acids (134.14 kDa). epidermis the outermost layer of cells of an animal or plant. epidermal adj. epienzymatic control a form of control of arginine metabolism, occurring in some Saccharomyces spp., in which arginases bind stoichiometrically to ornithine carbamoyltransferase (EC 2.1.3.3), inhibiting the latter's activity but without substantially modifying the arginase activity. See also epiprotein. epigenesis the concept that an organism develops from an originally undifferentiated mass of living material through the appearance of structures and functions not originally present. epigenetic describing any of the mechanisms regulating the expression and interaction of genes, particularly during the development process. These include changes that influence the phenotype but have arisen as a result of mechanisms such as inherited patterns of DNA methylation rather than differences in gene sequence: imprinting is an example of this. epigenetics the branch of biology dealing with the analysis of the mechanisms causing phenotypic effects to be produced by the genes of a genotype. epiligrin an extracellular matrix protein, secreted by cultured epidermal keratinocytes. It is found in epithelial basement membranes but not membranes of endothelia, nor in muscle or nerve cells. It is a ligand for cell adhesion via imegrins, with three chains linked by disulfide bonds, and is also an adhesive ligand for T lymphocytes. Example from the gene sequence of human epiligrin a3: database code HUMLAMAB, 145 amino acids (15.77 kDa). See also laminin. Epilim a proprietary name for sodium valproate (see valproic acid). epimer (in stereochemistry) either of two diastereoisomers that differ in configuration at only one chiral centre. The term includes anomer. epimerase any enzyme within subclass EC 5.1, that catalyses epimerization (note that subclass EC 5.1 also includes racemases). Some epimerases, e.g. UDParabinose 4-epimerase (EC 5.1.3.5), contain tightly bound NAD, which undergoes oxidation and reduction during the reaction. epimeric of or relating to an epimer or the chiral centre that specifies an epimer. epimerization or epimerisation the process of converting an epimer into its diastereoisomer by altering the configuration at the epimeric chiral centre. -epimerize or epimerise vb. epimino+ an alternative term for imino+ (def. 2). epinephrine or adrenaline (-)-I-(3,4-dihydroxyphenyl)-2(methylamino)ethanol; a hormone secreted by the adrenal medulla and a neurotransmitter secreted by neurons in the brainstem. It is synthesized by the methylation of norepinephrine. It is an agonist for adrenoceptors, through which it has powerful glycogenolytic and lipolytic effects (both of which are mediated by cyclic AMP) and also affects the activity of smooth muscle (notably of the cardiovascular system and bronchi) and glandular tissue. Its mode of action critically depends on whether it acts through a or ~ adrenoceptors.The BP official name for this substance is Adrenaline; the USP official name for this substance is Epinephrine; Adrenalin is a USA trademark name. It was named adrenalin by Takamine in 1901.

epoxyeicosatrienoate

HQ:~/CH3 I~ ~

OH

OH

epinephrine

epiphase the upper, less dense layer of a two-phase system. Compare hypophase. -epiphasic ad). epiplasm a membrane skeleton of certain protists, that contributes to cell shape and patterning of the species-specific cortical architecture. This cytoskeleton contains proteins known as articulins. epiprotein a specific protein, produced in certain circumstances in some Saccharomyces cerevisiae strains, that binds stoichiometrically to ornithine carbamoyltransferase (EC 2.1.3.3), thereby inhibiting its activity. It has subsequently been shown to have arginase activity and so is sometimes known as epiarginase. See also epienzymatic control. episemantic molecule any molecule that is synthesized under the control of a tertiary semantide. All molecules built by enzymes in the absence of a template are included because, although they do not express extensively the information contained in the semantide, they are a product of this information. See also asemantic molecule. episome 1 a genetic element that is sometimes found in cells, especially those of bacteria, and that can replicate either when integrated into or independently of the host chromosome. 2 any fragment of DNA that exists in a cell as an extrachromosomal element. This DNA mayor may not be replicated and passed to daughter cells. The plasmid is an example of an episome. DNA elements that use transposases involved in phage lambda integration are also examples of episomes. epithelium 1 (in animal anatomy) a sheet of closely packed cells, arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube (except the blood vessels, heart, and serous cavities). Compare endothelium, mesothelium. 2 (in plant anatomy) any of certain layers of parenchymal cells that line an internal cavity or tube. epithelial adj. epitope any immunological determinant group of an antigen. -epitopic ad). epitype any class or group of related epitopes. epoprostenol international nonproprietary name for prostaglandin 12; see prostacyclin. epothilone see taxo!. epoxidation the formation of an epoxide by addition of an oxygen atom as a bridge across the double bond of an alkene. epoxide any compound where molecules contain an epoxy group attached to adjacent carbon atoms to form a saturated three-membered ring system. epoxy+ prefix (in chemical nomenclature) indicating the presence in a molecule of an oxygen atom directly attached (by single covalent bonds) to two (adjacent or nonadjacent) carbon atoms of a carbon chain or ring system. Epoxy compounds are cyclic ethers. epoxyeicosatrienoate abbr.: EpETrE or (formerly) EET; any of various metabolites of arachidonate that contain an epoxy group. They are formed by the action of cytochrome P450 - this occurs in numerous tissues and has a high degree of stereospecificity. The products are predominantly present esterified to membrane-bound phosphatidylcholine. They have a wide spectrum of biological activities, including stimulation of peptide hormone release, inhibition of Na+,K +-ATP-

213

equilin

epoxy resin ase, mobilization of microsomal Ca2+, and inhibition of prostaglandin-endoperoxide synthase. Examples are (al1-Z)5S,6R-epoxyeicosa-8, 11, 14-trien-l-oate and (al1-Z)-ll S, 12Repoxyeicosa-5,8,14-trien-l-oate. EpETrEs can be further metabolized to vic-diols, diepoxides, and other products.

taen-17-one; a weakly estrogenic steroid hormone isolated from the urine of pregnant mares. Compare equilin.

HO

CH 3 (a 11-2)-5S,6R-epoxyeicosa-8.11,14-trien-1-oate

(all-2)-11 S,12R-epoxyeicosa-5,8.14-trien-1-oate

epoxy resin or epoxide resin any of a class of synthetic resins, containing ether linkages and epoxy groups, formed by the copolymerization of an epoxide (e.g. l-chloro-2,3-epoxypropane) and a polyphenol (e.g. 2,2-bis(4-hydroxyphenyl)propane). When mixed with certain accelerators, e.g. an amine or an anhydride, such resins produce hard, clear, resistant, thermosetting polymers that are used as adhesives and coatings and for embedding materials for microscopy, especial1y electron microscopy. Eppendorf pipette any of a range of push-button, plunger-operated, precalibrated, dispensing micropipettes with disposable polypropylene tips. [After the name of the manufacturer.] EPPS an alternative name for Hepps. EPR or epr abbr. for electron paramagnetic resonance spectroscopy (see electron spin resonance spectroscopy). epsilon symbol: 8 (lower case) or E (upper case); the fifth letter of the Greek alphabet. For uses see Appendix A. epsilon chain or E chain the heavy chain of IgE immunoglobulin molecules. EPSP abbr. for 5-enolpyruvylshikimate phosphate; an intermediate in aromatic amino-acid biosynthesis by the shikimate pathway (see shikimate). EPSP synthase an alternative name for 3-phosphoshikimate 1-carboxyvinyltransferase. See also shikimate. Epstein-Barr virus human (gamma) herpesvirus 4; a DNA virus, first isolated from specimens of tumour tissue obtained from African children affected by Burkitt's lymphoma, that causes infectious mononucleosis (glandular fever) in young adult humans. [After (Sir) Michael Anthony Epstein (1921- ), British pathologist and immunologist, and Yvonne M. Barr.] eq. or Eq. abbr. for equivalent (def. 4). equation of state any equation connecting the pressure, volume, and temperature of a substance or a mixture. equatorial 1 of, relating to, or being an equator; located at or near an equator. Compare axial (def. 1). 2 (in stereochemistry) symbol: e; see conformation. equi+ comb. form denoting equal or equality. equi-effective dose ratio abbr.: EDR; the ratio of the doses of test and reference substances that produce the same biological effect (whether activation or inhibition). equi-effective molarity ratio abbr.: EMR; the ratio of the molarity of test and reference substances that produce the same biological effect (whether activation or inhibition). equilenin the trivial name for 3-hydroxyestra-1 ,3,5,7 ,9-pen-

equilibrate to bring to equilibrium, or cause (something) to be in equilibrium (with some other thing), especial1y with the environment or with a (specified) system. -equilibration n. equilibrium 1 a state of balance between or among opposing forces or processes that results in the absence of net change. 2 (in chemistry) a state of dynamic balance in a reversible chemical reaction when the reaction velocities in both directions are equal. equilibrium assay a type of radioimmunoassay in which the reagents used are al10wed to reach thermodynamic equilibrium. Compare disequilibrium assay. equilibrium constant symbol: K; an expression of the position of the equilibrium (def. 2) of a reversible chemical reaction under specified physical conditions (e.g. temperature, pressure, nature of solvent, ionic strength, etc.). For a reaction of the generalized form: aA + bB +... """" mM + nN + ... when the thermodynamic activity of each of the components A, B, M, N, etc. is written as (A), (B), (M), (N), etc., and a, b, m, n, etc. are the respective numbers of molecular entities participating in the reaction, the equilibrium constant is given by: K:= [(M)m(N)n ... ]/[(A)a(B)b ... ]

Frequently in biochemical systems it is not possible to evaluate the activities of al1 the components; the concentration equilibrium constant (symbol: K a) rather than the true or thermodynamic equilibrium constant is then calculated, K being expressed in terms of the molarities of each of the components in place of their activities. When the specified concentration of a component includes more than one chemical species (e.g. ionized plus un-ionized forms, or chelated plus unchelated metal ion) in unknown proportions, an apparent (concentration) equilibrium constant (symbol: K') constrained with respect to certain variables (e.g. pH, or total concentration of metal ion), is written. See also affinity constant, association constant, dissociation constant, pK. equilibrium density-gradient centrifugation a method for the separation of cel1s, cel1 organel1es, macromolecules, or other particles of different densities by centrifugation in a solution that increases in solute concentration, and hence in density, from the top to the bottom of the centrifuge tube. At equilibrium, particles of the same density are found as a band or zone in the density gradient. Compare differential centrifugation. equilibrium dialysis a technique used to measure the binding of a microsolute or ions to a macrosolute. A solution of the macrosolute is placed inside a dialysis bag (through which the macromolecules wil1 not pass); this represents phase a. The bag is suspended in a solution containing the microsolute (phase 13). At equilibrium, any excess concentration of the microsolute in phase a is taken as evidence for binding. From a measurement of the excess concentration of the microsolute and knowledge of the concentration of the macrosolute the extent of the binding may be determined. equilin the trivial name for 3-hydroxyestra-1 ,3,5(1 0), 7-tetraen17-one; a weakly estrogenic steroid hormone isolated from the urine of pregnant mares. Compare equilenin.

214 equimolar equimolar of equal molarity. equimolecular containing equal numbers of molecular entities. equine of, relating to, or being a member of the family Equidae (horses, zebras, and asses); of, belonging to, characteristic of, obtained from, or relating to, a horse or horses; resembling a horse. equiv. abbr. for equivalent (def. 3). equivalence 1 the state of being equal, equivalent, or interchangeable. 2 equivalency. 3 the point or zone in a precipitin test at which antigen and antibody are present in optimal proportions for combination and precipitation. equivalence factor symbol (for a chemical species X): feq(X); a number pertaining to a given reacting component of a specified titrimetric reaction derived from consideration of the overall stoichiometry of the reaction. For a reaction of the following type: pA + pB ~ products, where pA and pB are the respective numbers of reacting entities, then the equivalence factor of species B is given by: feq(B) = pBI pA. When pA > pB and feq(A) is taken as unity, then feq(B) is unity or less than unity. In the case of a reaction that can be clearly identified as acid-base or oxidation-reduction, the equivalence factor must be related to one entity of titratable hydrons or of transferable electrons, respectively. equivalence point or stoichiometric point or theoretical end point the point in a titration at which the amount of titrant added is chemically equivalent to the amount of substance titrated. equivalency or equivalence 1 the state of having equal valencies. 2 the state of having equal equivalence factors. equivalent 1 equal or interchangeable in amount, importance, meaning, or value. 2 (in chemistry) having equal valencies. 3 something that is equivalent (to something else). 4 (in chemistry) a abbr.: equiv. or eq. or Eq.; a unit of amount of substance, defined as the entity of a chemical species that in a specified reaction would combine with, displace, or in any other appropriate way be equivalent to, one entity of titratable hydrons (in an acid-base reaction) or one entity of electrons (in an oxidation-reduction reaction). It is the arithmetic product of the molar mass of the chemical species and its equivalence factor. b (formerly) equivalent weight. equivalent activity a measure of the radiation output of a real radiation source containing a particular radionuclide, defined as being equal to the activity (def. 1b) of a hypothetical point source of the same radionuclide that would give the same exposure rate at the same distance frolll the centre of the source. It is customarily used to express the' strengths of most sources emitting high-energy gamma radiation. equivalent ellipsoid of rotation the ellipsoid of rotation having the same volume as an actual hydrodynamic unit of a macromolecule in solution (which consists of the macromolecule and tightly bound solvent). equivalent weight abbr.: equiv. wt.; an obsolete term defined as the weight in grams of an element, compound, or group that, in a specified reaction, will combine with or displace 8 grams of oxygen, or the equivalent weight of another chemical species. See also equivalent (def. 4). ER abbr. for endoplasmic reticulum. erbA an oncogene (v-erbA) originally found in avian erythroblastosis virus; the corresponding protooncogene (c-erbA) encodes thyroid hormone receptor. Example, product of v-erbA from avian erythroblastosis virus: database code ERBA_ AVIER, 385 amino acids (43.98 kDa); it requires the activity of other oncogenic agents for tumorigenesis. See also erbS. emB an oncogene (v-erbB) from avian erythroblastosis virus; the corresponding protooncogene (c-erbB) encodes the epidermal growth factor receptor. In tumours the extracellular ligandbinding domain and the C terminus are deleted, contributing to a system with a constitutively active receptor protein. Example of protein product of v-erbB from avian erythroblastosis virus: database code ACBERBBH, 31 amino acids (3.50 kDa). The erb oncogene system is complicated; the transform-

er 9 0 + ing protein from the virus is a polyprotein product from gag, erbA, and erbB. ercalcidiol or (formerly) 25-hydroxyergocalciferol the recommended trivial name for (52,7E,22£)-(3S)-9, 10(l9),22-ergostatetraene-3,25-diol; a secosteroid with vitamin 0 activity. It is formed in the liver from ercalciol and converted to ercalcitriol in the kidney. ercalciol or ergocalciferol the recommended trivial name for calciferol, vitamin D 2, (52,7E,22E)-(3S)-9,1 0-seco-5,7,10(19),22ergostatetraen-3-01; a secosteroid with vitamin 0 activity, obtained synthetically by UV-irradiation of ergosterol. It is the form of vitamin D most commonly used as a dietary supplement and for treatment of vitamin D deficiency. International nonproprietary name: ergocalciferol.

ercalcitriol or (formerly) la,25-dihydroxyergocalciferol the recommended trivial name for (52,7E,22£)-(lS,3R)-9,10-seco5,7, 1O(19),22-ergostatetraene-l ,3,25-triol; a secosteroid with vitamin 0 activity. It is the biologically active metabolite of ercalcidiol and ercalciol.

ERE abbr. for estrogen response element (see response element). erepsin a once-supposed single enzyme secreted by the mucosa of the small intestine and thought to be responsible for completing the breakdown in the gut of partially digested pro-teins into amino acids. It is now known to be a mixture of peptidases. erg the cgs unit of work, defined as the work done by a force of 1 dyne acting over a distance of 1 cm; equivalent to 10-7 J. ERG a gene encoding a family of transcription factors and related to the protooncogene ETS; it is named from 'ETSrelated gene'. It is expressed in some tumour-derived cell lines. Database code for expressed protein: ERG_HUMAN, 462 amino acids (52.03 kDa). ergastoplasm a term formerly applied to the basophilic, fibrillar structures seen especially in pancreatic secretory cells; now termed rough endoplasmic reticulum. +ergic suffix (in pharmacology) indicating agonist activity on a receptor in a neuron. See, e.g., adrenergic. ergo+ (comb. form) 1 or (before a vowel) erg+ denoting work. 2 or (before a vowel) ergot+ denoting obtained from ergot or derived from a substance occurring naturally in ergot.

215

erythro+

ergocalciferol ergocalciferol the alternative recommended trivial name and the international nonproprietary name for ercalciol. ergoflavin the major pigment from ergot. ergometrine see ergonovine. ergonovine D-Iysergic acid L-2-propanolamide; ergometrine; an ergot alkaloid noted for inducing sustained uterine contractions and used in the treatment of postpartum hemorrhage.

ergosome (sometimes) a polyribosome. ergosterol trivial name for (22E)-ergosta-5,7,22-trien-3jJ-ol; (22E)-(24R)-24-methylcholesta-5,7,22-trien-3jJ-ol; a sterol found in ergot, yeast, and moulds. It is usually obtained industrially from yeast, which synthesizes it from simple sugars. It is the most important of the provitamins D. On irradiation with ultraviolet light it is converted to ercalciol (vitamin D z).

ergot the common name for the sclerotial phase of the fungus Claviceps purpurea, which parasitizes the ovaries of cereals such as rye, and other grasses, leading to ergot-contaminated seeds. Ergot yields various medically useful alkaloids, including ergotamine and ergometrine, and is a source of lysergic acid. However, ingestion of contaminated seeds by livestock or humans can result in poisoning (ergotism). ergot alkaloid any of a group of about 30 indole alkaloids obtainable from ergot. All are derivatives of Iysergamide and are biosynthesized from L-tryptophan. ergotamine 12'-hydroxy-2'-methyl-5'a-(phenylmethyl)ergotaman-3',6',IS-trione; an ergot alkaloid with vasoconstrictor activity, used in the treatment of migraine.

quently) known as MAP kinases. Examples (all human): ERKI (or insulin-stimulated MAP2 kinase) phosphorylates MAP2 and myelin basic protein; database code ERKl_HUMAN, 379 amino acids (43.09 kDa); ERK2 (or mitogen-activated protein kinase 2 or MAP kinase 2) is similar; database code ERK2_ HUMAN, 360 amino acids (41.34 kDa); ERK3 (or MAP kinase isoform p63) has similar activity; database code ERK3_ HUMAN, 557 amino acids (62.55 kDa). ER mannosidase EC 3.2.1.-; other name: Man(9)-a-mannosidase; a glycoprotein enzyme of the N-glycosylation pathway of the endoplasmic reticulum that catalyses the removal of just one mannose residue from the core oligosaccharide of glycoproteins (Man(9» to produce a specific isomer of Man(S)G1cNAc. Example (precursor) from human: database code MAN9_ HUMAN, 625 amino acids (70.74 kDa). See mannosidase. Ernst, Richard Robert (1933- ) Swiss physical chemist noted for the application of pulsed radiofrequency radiation in nuclear magnetic resonance spectroscopy and the resultant extension of the technique to biological macromolecules; Nobel Laureate in Chemistry (1991) 'for his contributions to the development of the methodology of high resolution nuclear magnetic resonance (NMR) spectroscopy'. erp60 see calreticulin. ER-resident protein any protein that is retained by the endoplasmic reticulum. Their retention is regulated by the heterotetramer of a phosphoprotein (calnexin), a phosphoglycoprotein (see Ssra), and two glycoproteins (see Ssr13). See also KDEL. 'error catastrophe' hypothesis a hypothesis stating that since the protein synthetic machinery of the cell is itself made of protein, any imprecision in protein synthesis will lead to the formation of protein synthetic machinery oflowered accuracy, which will lead in turn to the production of even less precise machinery. If this positive feedback of error into the protein synthetic machinery is sufficiently high it will cause instability and an accelerating deterioration of the cell, resulting in cell death or loss of function. error-prone repair the processes of DNA repair, following damage, that give rise to 'fixed' mutations. Whether or not a particular damaged site will eventually lead to a mutation is dependent both on the genetic constitution of the cell and on environmental factors. It has been suggested that such mutations are due to errors in filling gaps in daughter DNA strands. erucic acid the trivial name for (Z)-docos-13-enoic acid (22: 1 n-9).

ERYF1 see GAlA-1. erythritol i-erythritol; meso-erythritol; ms-l,2,3,4-tetrahydroxybutane; erythro-l,2,3,4-butanetetrol; a polyol configurationally isomeric with (active) threitol but optically inactive through internal compensation. It occurs in certain fungi (where it appears to act as a storage carbohydrate), and is found also (as an ester of orsellinic acid) in some green algae and lichens. It is about twice as sweet as sucrose. Brythro- the configurational prefix to the systematic name of a polyhydric alcohol, especially of a monosaccharide, used to indicate the particular stereochemical configuration of a set of two contiguous CHOH groups that occurs in D- or L-erythrose; e.g. D-erythro-2-pentulose for D-ribulose. Compare threD-.

CHO I H-y-OH H-C-OH

Hy-oH H-C-OH

D-erythrose

D-erythro

i CH20H

ERIC abbr. for enterobacterial repetitive intergenic consensus sequence; any of a number of highly conserved partly palindromic sequences. They are reminiscent of REPs but are longer (120 bp) and are in extragenic sites. ERK abbr. for from extracellular signal-regulated kinase; any of a sub-subclass (EC 2.7.-), protein kinases, also (more fre-

I

I

erythro+ or (before a vowel) erytbr+ or (sometimes) eryth+ comb. form 1 indicating red-coloured. 2 pertaining to red blood cells.

216

erythroblast erythroblast any of the nucleated red blood cells that are intermediates in the formation of a nonnucleated erythrocyte from a hemocytoblast. -erythroblastic adj. erythrocruorin any of a group of respiratory pigments of invertebrates in the range of 0.4-6.7 MDa and containing 30-400 heme groups per molecule. erythrocuprein an alternative name for superoxide dismutase. erythrocyte a mature red blood cell; in mammals it is non-nucleated and lacks mitochondria. Erythrocytes contain, but are no longer capable of synthesizing, hemoglobin and they function in the transport of oxygen. Mammalian erythrocytes obtain energy from anaerobic glycolysis and also metabolize glucose via the phosphogluconate pathway. -erythrocytic adj. erythrocyte sedimentation rate abbr.: ESR; the rate at which erythrocytes sediment as measured under defined conditions. An increased ESR is almost always indicative of organic disease and is associated with an increased concentration of fibrinogen, y-globulin, u2-macroglobulin, or y,-macroglobulin in the plasma. erythrodextrin any of the larger dextrins that give a red colour with diiodine. erythrogenesis an alternative term for erythropoiesis. erythro-,6-hydroxyaspartic acid an amino acid formed by post-translational modification of an aspartyl residue at position 41 of the light chain of protein C. erythroid 1 red or reddish in colour. 2 of or relating to erythrocytes or their precursors. erythroid differentiation factor see inhibin. erythrolabe a pigment that is sensitive to red light (570 nm) and is found in some retinal cones of the mammalian eye. It is lacking in subjects with red-blindness but is present in those with green-blindness. Compare chlorolabe, cyanolabe. erythromycin any of several wide-spectrum macrolide antibiotics obtained from Streptomyces erythreus. Three components, A, B, and C, are produced during fermentation, the major component being erythromycin A. They inhibit protein synthesis in prokaryotes by binding to the 50S ribosomal subunit and inhibiting translocation. erythromycin resistance factor any of several proteins that confer resistance to the antibiotic erythromycin. There are three mechanisms of resistance: (I) erythromycin esterase (EC 3.1.1.-), which is itself of two types (I and II); (2) a transmembrane export system (e.g. erm genes of Arthrobacter and certain Gram-positive bacteria); (3) rRNA (adenine-N6-) -methyltransferase (EC 2.1.1.48), an enzyme that catalyses the reaction between S-adenosyl-L-methionine and rRNA to form S-adenosyl-L-homocysteine and rRNA containing N6- methyladenine; example from Staphylococcus aureus: database code MLS2_STAAU, 244 amino acids (28.83 kDa); this protein produces a dimethylation of the adenine residue at position 2058 in 23S rRNA, resulting in reduced affinity between ribosomes and all macrolide, lincosamide, and streptogramin Btype antibiotics. erythron a collective term for the circulating erythrocytes and their precursors. erythrophore a type of chromatophore, coloured red and found especially in some fishes and crustaceans. The pigment, a carotenoid, is contained in bright red granules, which normally are dispersed throughout the cytoplasm, but which aggregate rapidly in response to epinephrine leading to near discoloration of the cell. erythropoiesis or erythrogenesis the formation of red blood cells, in bone marrow or elsewhere. -erythropoietic or erythrogenetic adj. erythropoietin a 46 kDa mammalian glycoprotein cytokine, formed in the kidneys and liver of mammals, that stimulates cellular differentiation of bone-marrow stem cells at an early stage of erythropoiesis, accelerates the proliferation and maturation of terminally differentiating cells into erythrocytes, and maintains a physiological level of circulating erythrocyte mass. The protein is now prepared from cDNA expressed in

essential CRO cells and other cells. It is now established as the accepted treatment of chronic renal failure. Its receptor is a type I membrane protein. Examples (precursors, human): erythropoietin, database code EPO_HUMAN, 193 amino acids (21.28 kDa); erythropoietin receptor, database code EPOR_HUMAN, 508 amino acids (55.00 kDa). erythrose the trivial name for the aldotetrose erythro-tetrose; it has D and L enantiomers, which are respectively diastereoisomeric with those of threose. See erythro- for structure. erythrosome an artificial membrane preparation in which detergent-extracted, glutaraldehyde-fixed erythrocyte ghosts are coated with phospholipid. erythrulose the trivial name for the ketotetrose glycero-tetrulose; it has D and L enantiomers. ES abbr. for enzyme-substrate complex. esc a regulatory gene in Drosophila that controls expression of BX-C genes in embryos. It is named from extra sex combs. ESCA abbr. for electron spectroscopy for chemical analysis. See photoelectron spectroscopy. ES cell abbr. for embryonic stem cell. Escherichia a genus of Gram-negative, rod-shaped, usually motile, chemoorganotrophic bacteria belonging to the family Enterobacteriaceae. It contains a single species, the colon bacillus, Escherichia coli. [After Theodor Escherich (18571911), German physician, who (in 1885) isolated the colon bacillus and gave it its original name of Bacterium coli commune.) Escherichia coli or colon bacillus abbr.: E. coli; the sole member of the bacterial genus Escherichia and arguably the most widely used experimental cell system in biochemistry and molecular biology. The cells are straight, round-ended rods, commonly 0.5-1 l-lm x 1-4 l-lm, and usually occurring singly or in pairs. The organism is present in the intestinal tract of humans and other animals and is common in soil and water. The numerous strains, some of which are enteropathogenic, are commonly distinguished serologically by their 0, K, and H antigens. Strain 0157 is a life-threatening enteropathogen with genes seemingly derived (at least in part) from Shigella spp. It produces both hemolysin and enterotoxin. E. coli takes part in bacterial conjugation and other forms of genetic transfer, and can be infected with some bacteriophages and plasmids. See also toxin. Eschweiler-Clarke reaction see reductive ami nation. esculetin 6,7-dihydroxycoumarin; an agent that selectively inhibits 5- and 12-lipoxygenase, without inhibiting prostaglandin-endoperoxide synthase.

E-selectin see selectin. eserine an alternative name for physostigmine. E-site the deacylated tRNA binding site in ribosomes; in bacteria this involves ribosomal proteins of the large subunit and 23S rRNA. ESQL abbr. for embedded SQl; a computer language that allows SQL to interface with other programming languages, e.g. FORTRAN and C. ESR or esr abbr. for 1 electron spin resonance. 2 erythrocyte sedimentation rate. essential 1 of or being the essence of something; inherent. 2 absolutely necessary, basic, fundamental, indispensable, vitally important. 3 necessary for the normal growth of an organism but either not synthesized by that organism or synthesized at an inadequate rate. 4 (in pathology) describing a clinical condition or disorder that is not attributable to any discernible cause; idiopathic (def. 1). 5 relating to or derived from an extract of a plant, especially as an essence.

217

estramustine

essential amino acid essential amino acid any amino acid that cannot be synthesized by a cell or an organism in an amount corresponding to need. The extent to which a particular amino acid is essential in anyone species of organism depends on the stage of development of the subject and its physiological state. The following L-amino acids are nutritionally essential for the maintenance of nitrogen equilibrium in an adult human: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. In addition, arginine and histidine are essential in growing children. The initial letters of the L-amino acids needed for optimal growth of infants or rats may be remembered using the mnemonic 'Many Very Hairy Little Pigs Live In The Torrid Argentine'. Compare nonessential amino acid. essential fatty acid any polyunsaturated fatty acid that cannot be synthesized by a cell or an organism in an amount corresponding to need or from any dietary precursor. For mammals, linoleic acid (see linoleate) and (9,12,15)-linolenic acid (formerly collectively known as vitamin F) are nutritionally essential. Compare nonessential fatty acid. essential fatty acid deficiency a condition that arises from the absence of essential fatty acids in the diet. A deficiency of fatty acids of the fI-6 family (e.g. linoleic acid) in the diet of young animals results during growth in decreased body weight and, after some months, in increased skin permeability and capilliary fragility, and dermatitis. If prolonged into adulthood, poor litter sizes (e.g. in rats) and infertility can result. Deficiency of fatty acids of the n-3 family, in the presence of n6 fatty acids, does not result in such obvious manifestations, partly because these fatty acids are tenaciously retained in tissues, and partly because n-6 fatty acids (e.g. 22:5 n-6) not normally present in significant amounts are synthesized and appear to compensate for the deficiency of n-3 fatty acids of similar length and degree of unsaturation. That the effects of deficiency are not solely due to lack of substrates for prostanoid synthesis is indicated by the ability of columbinic acid to relieve some of the effects. essential fructosuria a relatively rare, hereditary, asymptomatic metabolic disorder characterized by the presence of fructose in the urine. In humans it is probably inherited as an autosomal recessive trait. Fructosuria occurs only after ingestion of fructose, which can also cause vomiting and aversion to sweet foodstuffs; long-term consequences can include failure to thrive, renal tubular dysfunction, and cirrhosis. Fructose metabolism involves formation of fructose I-phosphate by ketohexokinase (EC 2.7.1.3); fructose I-phosphate is then an (alternative) substrate for fructose-bisphosphate aldolase (EC 4.1.2.13) (I). Of the three isoenzymes of! (A, B, and C), B is much more active than A and C with fructose I-phosphate as substrate. In essential fructosuria, the B isoenzyme of I is deficient and as a result there is a failure to metabolize fructose. essential oil any of a group of volatile, odorous, natural oils obtained from plants. Such oils are usually benzene derivatives or terpenes, and are useful as flavouring agents or perfumes. essential pentosuria see pentosuria. EST abbr. for expressed sequence tag. EST1 a gene involved in telomere maintenance, possibly coding for telomerase. It is named from 'even shorter telomeres'. It encodes a DNA-binding protein with RNA-directed DNA polymerase activity. Yeast gene product: database code ESTL YEAST, 699 amino acids (81.62 kDa). established cell line cultured cells of a single origin that have the potential to be subcultured indefinitely whilst maintaining stable characteristics. eSte symbol for the eleostearoyl group, CHr[CHzlJ-

either an alcohol or a phenol. Esters formed by condensation of one, two, or three molecular proportions of alcohol or phenol with one of a tribasic oxoacid may be termed monoesters, diesters, or triesters, respectively. esterase any enzyme that catalyses the hydrolysis of an ester. Esterases form subclass EC 3.1 of the class EC 3, hydro lases, and are divided according to the nature of their substrates into the following sub-subclasses: EC 3.1.1, carboxylic ester hydrolases; EC 3.1.2, thiolester hydrolases; EC 3.1.3, phosphatases, phosphoric monoester hydro lases; EC 3.1.4, phosphodiesterases, phosphodiester hydrolases, phosphoric diester hydrolases (other than nucleases; see EC 3.1.11-3.1.31 below); EC 3.1.5; triphosphoric monoester hydrolases; EC 3.1.6, sulfatases, sulfuric ester hydrolases; EC 3.1.7, pyrophosphatases, diphosphoric monoester hydro lases; EC 3.1.8, phosphoric triester hydrolases; EC 3.1.11, exodeoxyribonucleases producing 5'-phosphomonoesters; EC 3.1.13, exoribonucleases producing 5'-phosphomonoesters; EC 3.1.14, exoribonucleases producing other than 5'-phosphomonoesters; EC 3.1.15, exonucleases active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters; EC 3.1.16, exonucleases active with either ribo- or deoxyribonucleic acids and producing other than 5'-phosphomonoesters; EC 3.1.21, endodeoxyribonucleases producing 5'-phosphomonoesters; EC 3.1.22, endodeoxyribonucleases producing other than 5'-phosphomonoesters; EC 3.1.25, endodeoxyribonucleases specific for altered bases; EC 3.1.26, endoribonucleases producing 5'phosphomonoesters; EC 3.1.27, endoribonucleases producing other than 5'-phosphomonoesters; EC 3.1.30, endonucleases active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters; EC 3.1.31, endonucleases active with either ribo- or deoxyribonucleic acids and producing other than 5'-phosphomonoesters. esteratic of, by means of, or having the activity of an esterase. esterification the act or process of forming an ester from an oxoacid by condensing it with an alcohol or a phenol, or vice versa. esterify to effect or to undergo esterification. ester value an alternative term for saponification number. 1713-estradiol or (esp. Brit.) 1713-oestradiol 1,3,5-estratriene3,17P-diol; the most potent of the major estrogens. It is synthesized by the ovary, from which it is secreted directly into the circulation. Its formation depends on the presence of both luteinizing hormone and FSHRH; it is synthesized from testosterone by the aromatase complex, which is localized in ovarian granulosa cells, and is stimulated by follitropin; lutropin, on the other hand, stimulates production of testosterone, the aromatase substrate, by ovarian thecal cells. Apart from being important during development in inducing female characteristics, 17p-estradiol is important during the first half of the menstrual cycle (i.e. before ovulation) in stimulating proliferation of the epithelial and stromal layers of the endometrium in preparation for ovulation; it also stimulates production by the liver of proteins that bind steroids and thyroxine. During pregnancy, synthesis of estrogens is greatly increased, most of this increase being due to synthesis by the fetal adrenal gland of the precursors dehydroepiandrosterone and 16-hydroxydehydroepiandrosterone.

HQ

[CH=CHlJ-[CHz17~CO-.

ester any organic compound formed, either actually or formally, by the elimination of the elements of water between a hydroxyl group of an oxoacid (def. I) and a hydroxyl group of

estramustine or (esp. Brit.) oestramustine estradiol 3-bis(2chloroethyl)carbamate; an ester formed between estradiol and

218

ethereal sulfate

estriol the carbonic-acid analogue of nitrogen mustard (mustine); it has antineoplastic activity. OH

o ::::,.

A /'...

o

N-

~CI

~

~CI

estriol or (esp. Brit.) oestriol 16a-estradiol; 1,3,5-estratriene3,16a,17p-triol; a relatively weak estrogen produced mainly during pregnancy. It is synthesized by the placenta from 16ahydroxydehydroepiandrosterone sulfate, which is formed in fetal liver from dehydroepiandrosterone sulfate secreted by the fetal adrenal gland. Urinary estriol is measured to monitor fetal well-being in high-risk pregnancies. Low levels are also associated with the inherited X-linked disorder, placental sulfatase deficiency.

HO

estrogen or (esp. Brit.) oestrogen any substance, natural or synthetic, that produces changes in the female sexual organs similar to those produced by 17p-estradiol, the principal hormone of the vertebrate ovary. Naturally occurring estrogens are CIs-steroid hormones; they are produced also by the placenta, adrenal cortex, and testis, as well as by many species of plants. Compare androgen. -estrogenic or oestrogenic adj. estrone or (esp. Brit.) oestrone 1,3,5-estratrien-3-01-17-one; a major estrogen, also called folliculin, synthesized and secreted by the ovary, in which it is formed from androstenedione by the aromatase complex. However, estrone is mainly synthesized in peripheral tissues, from androstenedione taken up from the circulation. Its actions are similar to those of 17fJestradiol.

estrone sulfotransferase EC 2.8.2.4; an enzyme involved in the inactivation of estrogens. It catalyses the reaction of 3'phosphoadenylylsulfate with estrone to form the inactive estrone 3-sulfate with release of adenosine 3',5'-bisphosphate. Example from Bos taurus: SUOE_BOVIN, 295 amino acids (34.60 kDa). estrophile (sometimes) estrogen receptor. estrous cycle or (esp. Brit.) oestrous cycle the hormonally controlled cycle of activity of the reproductive organs of ilOn-

pregnant, sexually mature females of many species of mammal. It may be continuous or seasonal, depending on species. There are four principal phases. (1) Follicular phase or estrusovarian Graafian follicles mature, estrogen secretion by the ovary is at its highest, and the endometrium proliferates; the phase culminates in ovulation; in seasonal animals it is the time of sexual receptivity. (2) Luteal phase or metestrus - the corpus luteum develops in the ovary, estrogen secretion diminishes, and progesterone secretion reaches its maximum. (3) Diestrus - the corpus luteum and endometrium regress, new follicular growth begins, and progesterone secretion diminishes. (4) Proestrus - the corpora lutea involute, Graafian follicles re-emerge, and gonadal hormone secretion is at its lowest. The cycle then recommences. estrus or (esp. Brit.) oestrus the first phase of the estrous cycle. -estrous or (esp. Brit.) oestrous adj. esu or ESU abbr. for electrostatic unit. Et symbolfor the ethyl group, CHrCH z-. ET abbr. for endothelin. eta 1 symbol: 11 (lower case) or H (upper case); the seventh letter of the Greek alphabet. For uses see AppendixA. 2 (in chemical nomenclature) a less common alternative name for hapto. ETF abbr. for electron-transfer flavoprotein or electron-transferring flavoprotein. ethambutol (+ )-N,N' -bis( I-hydroxymethylpropyl)ethylenediamine; an antitubercular drug. ethanol or (formerly) ethyl alcohol CHrCHz-OH; a colourless, water-miscible, flammable liquid. It is produced by alcoholic fermentation and is thereby probably the single most important product of bioindustry in economic terms. However, most ethanol (not destined for human consumption) is now manufactured from ethylene as a by-product in the petroleum industry. Commonly known as alcohol. ethanolamine-phosphate cytidylyltransferase EC 2.7.7.14; other name: phosphorylethanolamine transferase; an enzyme that catalyses the reaction of CTP and ethanolamine phosphate to form CDPethanolamine with release of pyrophosphate. ethanolaminephosphotransferase EC 2.7.8.1; an enzyme of the pathway for de novo synthesis of phosphatidylethanolamines. It catalyses the reaction of CDPethanolamine with 1,2-diacylglycerol to form phosphatidylethanolamine with release of CMP. Example from yeast: database code EPTl_YEAST, 391 amino acids (44.51 kDa). Compare phosphatidylserine decarboxylase. ethanol fermentation an alternative term for alcohol fennentation. ethanolic of, containing, or derived from ethanol; dissolved in pure or aqueous ethanol. ethanolysed cellulose a powdered and highly purified form of cellulose, formerly in use as a supporting medium in preparative zone electrophoresis of proteins, e.g. serum proteins. It is prepared by heating fibrous cotton (cotton wool) under reflux for approximately 24 h with acid-ethanol (absolute ethanol made I molar with respect to HCI either by introduction of dry hydrogen chloride gas or by reaction with acetyl chloride). By this means, partial alcoholysis of the cellulose occurs and acidic groups are neutralized by esterification, the cotton fibres being partially degraded into nonclumping particles; at the same time, light-absorbing and other interfering impurities are extracted from the cellulose. ether 1 any anhydride, of general formula RI_O-Rz, formed between two (identical or nonidentical) organic hydroxy compounds. 2 the common name for diethyl ether (or ethyl ether or ethoxyethane), CzHs-O-CzH s. ethereal (in chemistry) of, containing, or dissolved in an ether, especially diethyl ether. ethereal sulfate an obsolete term for any biogenic half-ester of sulfuric acid with an aromatic hydroxy compound. Ethereal sulfates are found in the urine as end products of sulfur metabolism and metabolism of some aromatic compounds.

219 ether lipid ether lipid any lipid that contains (normally) one fatty alcohol in ether linkage to one of the carbon atoms (normally Col) of glycerol. They are found in low concentrations in glycerophospholipid fractions, the constituent at C-2 of the glycerol moiety then being an acyl group. Platelet-activating factor is an important physiologically active ether glycerophospholipid. Ether linkages in neutral acylglycerols are known, and contain one fatty alcohol linked to glycerol by an ether linkage (usually at Col), with fatty acids in ester linkage at the other two positions. The ether linkage resists hydrolysis, and typical hydrolysis products are the glyceryl ethers such as batyl alcohol, chimyl alcohol, and selachyl alcohol. ethidium the 3,8-diamino-5-ethyl-6-phenylphenanthridinium cation, usually used as the bromide salt. It binds by intercalation to double-stranded regions of DNA and RNA molecules with marked enhancement of fluorescence. It is used as a trypanocide and to reveal double-stranded DNA and RNA in gel electrophoresis.

eu+ vesicle-mediated transport and transport from the endoplasmic reticulum to the Golgi stack. Example from Chinese hamster: database code SCI8_CRIGR, 744 amino acids (82.44 kDa). See also SNAP (def. 3). ethynylestradiol see ethinylestradiol. ETI see eicosatriynoic acid. etidronate any anion of etidronic acid, (l-hydroxyethylidene)bisphosphonic acid, an analogue of diphosphoric acid in which the latter's bridging oxy group is replaced by a l-hydroxyethylidene group. Disodium etidronate is useful clinically for reducing the turnover rate of bone, e.g. in osteoporosis or in Paget's disease of bone.

o CH 0

3"

" I Ho-P-C-P-OH I I I OH OH OH etidronic acid

etiology or (esp. Brit.) aetiology the cause or causes of disease and their study. Etn symbol for a residue of ethanolamine, H2N~CHrCHrO-. EtO or OEt symbol for the ethoxy group, CH 3-CH 2-O-. ES cell abbr. for embryo-derived stem cell. Etoposide a semisynthetic lignan derivative prepared from podophyllotoxin. It is useful as an antitumour agent in multidrug therapies, exerting its effect probably through interaction with topoisomerase II, which it inhibits; it also inhibits nucleoside transport in mammalian cells. ethinylestradiol the international nonproprietary name for ethynylestradiol; l7a-ethynyl-l ,3,5(10)-estratriene-3, l7P-diol]; (l7a)-19-norpregna-l ,3,5(10)-trien-20-yne-3, l7-diol; a synthetic steroid with potent estrogenic activity, commonly used in oral contraceptive preparations. ethionine S-ethyl-L-homocysteine; a synthetic, carcinogenic analogue of methionine. Its toxicity is due to the fact that it competes with methionine for the enzyme methionine adenosyltransferase, with the result that S-adenosylmethionine is formed. This leads to a deficiency of ATP. ethoxy symbol: OEt or Eto; the alkoxy group, CH3~CHrO-, derived from ethanol by loss of a hydrogen atom. ethyl symbol: Et; the CH r CH 2- alkyl group, derived from ethane. ethyl alcohol the former name for ethanol. ethylene CH 2=CH 2; a colourless gas and the first member of the olefin (or alkene) series of hydrocarbons. It occurs naturally as a phytohormone, with a number of physiological effects, the most important being stimulation of ripening of fleshy fruit and stimulation of abscission of leaves. See also ethylene-forming enzyme. ethylenediaminetetraacetate see EDTA. ethylene-forming enzyme abbr.: EFE; other name: 1aminocyclopropane-l-carboxylate (ACe) oxidase. An enzyme component of the biosynthetic pathway for the formation of the plant hormone ethylene; it catalyses a reaction between 1aminocyclopropane-l-carboxylate and O2 to form ethylene, HCN, CO 2, and two molecules of 2H 2 0; iron and ascorbate are cofactors. The enzyme is a dioxygenase but structurally unrelated to other examples of these. Example from tomato: database code ACCl_LYCES, 316 amino acids (35.93 kDa). ethylenic containing one or more aliphatic carbon~carbon double bonds, as in ethylene. ~ethylmaleimide abbr.: NEM; an agent that reacts irreversibly with thiol groups in proteins; it is useful as an inhibitor in transport studies and of thiol enzymes. N-ethylmaleimide-sensitive fusion protein abbr.: NSF protein; a homotetrameric cytoplasmic protein required for

ETS abbr. for expression tagged site; a jargon phrase from genome mapping projects, etc. meaning a DNA database code (usually short) corresponding to an actively transcribed gene (i.e. cDNA from mRNA) of known sequence but, in general, of unknown function. Large ETS libraries are used in the Human Genome Project and similar projects on other organisms. ETS a protooncogene related to v-ets, one of the oncogenes of the acutely transforming avian erythroblastosis virus E26; is named from 'E twenty-six specific'. It encodes a family of transcription factors: Ets 1 activates stromelysin and collagenase genes and binds to the enhancer sequence of the TCRa gene; it is expressed in tumours of the peripheral nervous system and in Ewing's sarcoma; Etsl and Ets2 are kinase substrates. Example of expressed protein: database code ETSl_ HUMAN, 441 amino acids (50.41 kDa). ETYA 5,8,11,14-eicosatetraynoic acid (see eicosatetraynoic acid). eu+ prefiX 1 indicating well, pleasant, good. 2 indicating normal, true, typical. In medicine, sometimes used interchangeably with normo+.

e.u.

220

e.u. symbol for entropy unit. Eu symbol for europium. EU abbr. for enzyme unit (obsolete). Eubacteria a name suggested for one of three major lineages of cellular organisms, the others then being Archaebacteria and eukaryotes, defined when organisms are classified on the basis of sequence homologies of their ribosomal RNA. It comprised all typical bacteria, the major subdivisions being the cyanobacteria, the Gram-positive bacteria, and the Gram-negative bacteria. This classification has now been superseded: see Archaea, Bacteria, and Eukarya. eucaryon a variant spelling of eukaryon. eucell any cell of a eukaryote. euchromatin the dispersed less dense form of chromatin in the interphase nucleus. It exists in at least two forms, about 10 per cent being in the form of transcriptionally active chromatin which is the least condensed, while the rest is inactive euchromatin which is more condensed than active chromatin but less condensed than heterochromatin which represents about 10 per cent of the chromatin in the interphase nucleus. eucollagen 1 a highly modified form of collagen that can be easily and completely transformed into gelatin. 2 a hypothetical limiting structure for collagen in which Gly occurs at intervals of three residues and Hyp at intervals of ten residues; it is considered to be responsible for the 28.6 repeat distance in the X-ray diffraction pattern. eugenics (functioning as sing.) the study of methods of improving the hereditary characters of the human race, especially by selective breeding. -eugenic ad). Euglena a genus of fusiform, photosynthetic protozoa (sometimes classified as algae) of the division Euglenophyta. They are useful in biochemical research as unicellular photosynthetic organisms. euglobulin any 'true' globulin of blood plasma that is soluble in isotonic salt solutions, insoluble at low ionic strengths (or in pure water), and precipitated by addition of saturated ammonium sulfate solution to a final concentration of 33%. Compare pseudoglobulin. euglycemia or normoglycemia the condition or state in which the blood glucose level is within the normal range. See also glycemia. -euglycemic adj. Eukarya one of the three major kingdoms of cellular organisms, the others being Archaea and Bacteria. The eukarya are characterized by the presence of a eukaryon. eukaryon or (sometimes) eucaryon (pl. eukarya or eucarya) the type of cell nucleus bounded by a nuclear membrane and containing true chromosomes. It is characteristic of all multicellular and unicellular organisms except bacteria, actinomycetes, and cyanobacteria. Compare prokaryon.-eukaryous or eucaryous ad}. eukaryosis or (sometimes) eucaryosis the condition of possessing a eukaryon. -eukaryotic or eucaryotic ad). eukaryote or (sometimes) eucaryote any organism whose cells contain a eukaryon (or eukarya) and undergo meiosis. Compare prokaryote. eukaryotic porin see porin. Euler 1 Hans Karl August Simon von EuJer-Chelpin (18731964), father of U.S. von Euler (see von Euler (def. 2)) and generally known as Hans von Euler or Euler, German-born Swedish chemist and biochemist distinguished for his work on the enzymic mechanism of fermentation and in particular for his isolation, naming, and study of the chemical nature and functions of cozymase (now known as NAD); Nobel Laureate in Chemistry (1929), the prize being shared with A. Harden 'for their investigations on the fermentation of sugar and fermentative enzymes'. 2 VIC Svante von Euler see von Euler (def. 2). Euler·Chelpin see Euler (def. 1). eumelanins see melanin. eupeptide a name suggested for any physiologically active gastrointestinal polypeptide. eupeptide bond a name suggested for a peptide bond formed

excimer specifically between C-I of one amino-acid residue and N-2 of another residue. Compare isopeptide bond. euploid having a chromosome number that is an exact multiple of the monoploid number; i.e. each chromosome of the set is present in the same number. Compare aneuploid. -euploidy n. euthyroid having a normally functioning thyroid gland and normal levels of thyroid hormones. eutopic binding (sometimes) an alternative term for productive binding. eutrophic describing a habitat, esp. a lake or other mass of water, that contains abundant nutrients, both organic and inorganic, and hence favours excessive growth of aerobic plants and microorganisms. Such growth results in depletion of dissolved dioxygen and, ultimately, extinction of aerobic life. Compare dystrophic (def. 2), oligotrophic. eutrophication the process of becoming or rendering eutrophic. eV symbolfor electronvolt. event marker a feature of some chart recorders by means of which a mark is made on the chart to record the occurrence of a specifiable event or series of events, e.g. the stepwise operation of a fraction-collecting device. evolution 1 (in biology) the process of cumulative change occurring in the form and mode of existence of a population of organisms in the course of successive generations related by descent. 2 (in chemistry) the liberation of a gas, or of heat, in the course of a chemical reaction. -evolutionary or evolutional ad). evolve 1 to develop gradually; to cause to develop. 2 (in biology) to undergo evolution (def. I). 3 (in chemistry) to give off a gas or heat. ex+ 1 prefiX indicating out of, away from, outside of; without, lacking; former. 2 comb. form a variant of exo+ (sometimes before a vowel). exa symbol: E; the SI prefiX denoting 10 18 times. EXAFS abbr. for extended X-ray absorption fine structure (spectroscopy). excelsin a crystallizable globulin of z290 kDa obtained from the seed of the brazil-nut tree, Bertholettia excelsa. It structurally resembles arechin, edestin, and glycinin. exchange 1 to cause two different objects to change places with each other. 2 the act or process of exchanging. 3 (in genetics) the reciprocal exchange of chromatid segments between chromosomes at meiosis or mitosis that results in genetic recombination. exchange diffusion the exchange of ions or molecules across a (biological) membrane; it can be by simple diffusion or be carrier-mediated. exchange labelling the catalysed exchange of one nuclide for another radioactive or stable nuclide of the same element in a chemical compound in order to produce an isotopically labelled form. The procedure is useful esp. in the preparation of tritium-labelled compounds. exchanger a substance upon which, or a device by which, an exchange (def. 2) can be effected; e.g. an ion exchanger, or a heat exchanger. exchange reaction a chemical reaction that results in the production of a substance that is chemically identical with the starting material. It is not detectable by traditional chemical analysis but (often) is demonstrable with the help of (radio)isotopes. excimer an adduct formed between a molecular entity that has been excited by a photon and an identical unexcited molecular entity; the adduct exists until it fluoresces by emission of a photon. An excimer is recognized by the production of a new fluorescent band at a longer wavelength than that of the usual emission spectrum. Its formation is distinguishable from resonance energy transfer in that the excitation spectrum is identical with that of the monomer. excitation: A + photon ~ A* excimer formation: A* + A ~ D* excimer fluorescence: D* ~ A + A + photon

221

excinuclease excinuclease a DNA-repair endonuclease. An example is the ABC excision nuclease of Escherichia coli; this comprises three subunits, named from the corresponding uvr genes. UvrA is an ATPase and DNA-binding protein that preferentially binds single-stranded or UV-irradiated double-stranded DNA; it belongs to the ABC transporter family; database code UVRA_ ECOLI, 940 amino acids (103.75 kDa). UvrB stimulates the activities of UvrA; database code UVRB_ECOLI, 673 amino acids (76.14 kDa). UvrC is a nuclease component; database code UVRC_ECOLI, 588 amino acids (65.64 kDa). excisase an enzyme involved in lambda phage induction. See integrase. excise to cut out or remove, as of a tumour, organ, or part of a linear polymer. excision 1 the act or process of excising, especially the enzymic removal of an oligonucleotide segment from a nucleicacid molecule. 2 (in genetics) the separation of one or more replicons from a cointegrate. excisionase see Xis protein. excision repair one of the intracellular mechanisms for the repair of DNA lesions (single-strand breaks, damaged bases, etc.). It occurs in the following stages: (I) recognition of the damaged region; (2) removal of the damaged oligonucleotide by two enzymic nucleolytic reactions (excision); (3) synthesis by DNA polymerase of the excised oligonucleotide using the second (intact) DNA strand as template; and (4) covalent joining by DNA ligase of the newly synthesized segment to the existing ends of the originally damaged DNA strand. The process is light-independent. Compare photoreactivation, postreplication repair. See also short-patch repair. excitability proteins a collective name for intrinsic membrane proteins that are ion channels, receptors, and ion pumps. excitable capable of responding to a stimulus; used especially of a biological membrane, neuron, or other living matter. -excitability n. excitable membrane any biological membrane capable of responding to a specific chemical or physical stimulus. Such membranes are commonly characterized by: (I) the presence of a highly specific, integral protein receptor; (2) the occurrence of a conformational change in the receptor in response to the specific stimulus with a consequential change in membrane permeability or in the activity of a membrane-bound enzyme; and (3) reversibility of the alterations in conformation of the receptor and functional activity of the membrane. excitation-contraction coupling a general term often used to refer to the coupling of an excitatory stimulus to the contraction of muscle; the process by which the fibres of a muscle are caused to contract by the stimulation of a neuron. excitation spectrum any spectrum of electromagnetic radiation that, when applied to a sample, causes the atoms and molecules of the sample to become excited by the absorption of energy and, when reverting to their normal energy levels, to emit radiation of different frequencies to that of the absorbed radiation. Compare absorption spectrum, emission spectrum. excitatory able to excite; stimulatory. excitatory amino-acid receptor a receptor for any excitatory amino-acid in the central nervous system. These comprise two main groups: ionotropic, regulating an intrinsic ion channel, or metabotropic, coupled to either the cAMP or inositol phospholipid second messenger systems. The three main types of ionotropic receptors all have four transmembrane domains and are characterized pharmacologically by selective agonists: N-methyl-D-aspartate (NMDA), a-amino-3-hydroxy-5-methylisoxazole (AMPA), and kainate. NMDA receptors have a further binding site for glycine, which modulates receptor activation. All such ionotropic receptors regulate Na+ and K+ conductance; NMDA receptors additionally regulate Ca2+ conductance. Seven subtypes of metabotropic receptor have been cloned, all with seven transmembrane domains (mGlul to mGlu7): mGlul and mGlu5 modulate inositol phospholipid

exocytic turnover while mGlu2, mGlu3, mGlu4, mGlu6, and mGlu7 are all negatively coupled to adenylate cyclase. excite 1 to raise a molecular entity from its ground state to an excited state by the input of energy. 2 to cause an increase in activity or other response in an organism or part of an organism. -excitation n. excited state any state of a molecular entity that has a higher energy level than its ground state. exciter any device that excites, or raises a substance to an excited state. exciton any nonconducting nonlocalized neutral entity that occurs in semicrystalline semiconductors, consisting of an excited electron bound to a positive hole, the combination forming a concentration of energy with certain properties characteristic of a particle. exciton splitting the splitting of electronic absorption bands of a population of identical chromophores that are arranged in space such that sets of two or more are in close proximity. The splitting arises from electronic interactions between excited and nonexcited chromophores within the sets. exclusion chromatography an alternative name for permeation chromatography. exclusion limit an attribute of a specific gel used in gelpermeation chromatography. It is the relative molecular mass of the largest molecule of a particular shape that can be effectively fractionated by its use. exclusion principle see Pauli exclusion principle. exclusion reaction the reaction of a phage-infected bacterium that prevents the entry of additional phages. It is brought about by the strengthening of the bacterial cell envelope. exclusion volume the volume of solvent retained by the column bed in gel-permeation chromatography that is outside the gel particles. Compare void volume. excrete to eliminate waste materials (from a body or organism). -excretion n.; excretive or excretory adj. exendin any of several peptides belonging to the glucagon family that have been isolated from Heloderma spp., exendin-I (or helospectin 1), exendin-2 (or helodermin) and exendin-4 from Heloderma suspectus and exendin-3 from Heloderma horridus horridus. They have biological activity similar to vasoactive intestinal peptide and secretin. Exendin-4 shares 53 per cent similarity in its primary structure with glucagon-like peptide I (GLP-I) (7-36) amide. The latter binds to exendin receptors on pancreatic acinar cells, and exendin (9-39) (from exendin-3 or -4) is a GLP-l receptor antagonist which blocks the inhibitory effect of GLP-l on food intake of fasted rats. Exendin-4 is HGEGTFTSDLSKQMEEEAVRLFIEWLKNGGPSSGAPPPS (database code EXE4_HELSU, 4.188 kDa); exendin-3 is similar except for residues 1-3 which are HSD. exergonic describing any process or reaction that can produce work; i.e. one that, at constant pressure and temperature, results in a negative change in free energy content. Compare endergonic. exhaustive methylation the maximal methylation of all groups in a substance that are capable of being methylated; it is useful in structural studies of carbohydrates, alkaloids, etc. exo+ or (sometimes before a vowel) ex+ comb. form indicating outside, external, outer. Compare endo+. See also exo-. exo- prefix (in stereochemistry) see conformation. exocellular describing cellular components that are external to the cell membrane but attached to its outer surface. Compare extracellular. exocrine 1 describing or relating to a gland or other group of cells that discharges its secretion through a duct. 2 relating to a secretion of exocrine tissue. 3 a product of exocrine tissue. Compare endocrine. exocytic 1 situated outside a living cell and not belonging to

exocytose

222

the cell itself; extracellular. 2 an alternative term for exocytotic (see exocytosis). exocytose to effect exocytosis. -exocytosed adj. exocytosis the discharge by a cell of intracellular materials to the exterior by emiocytosis or reverse pinocytosis. Compare endocytosis, transcytosis. See also externalize. -exocytic or exocytotic adj. exodeoxyribonuclease see deoxyribonuclease. exodeoxyribonuclease I EC 3.1.11.1; other names: exonuclease I; Escherichia coli exonuclease I. An enzyme that catalyses exonucleolytic cleavage of DNA in the 3'- to 5'- direction, releasing 5'-phosphomononucleotides. It shows a preference for single-stranded DNA. Database code EX1_ECOLI, 475 amino acids (54.44 kDa). exodeoxyribonuclease V EC 3.1.11.5; other names: exonuclease V; Escherichia coli exonuclease V; RecBC. An enzyme that catalyses exonucleolytic cleavage of DNA (in the presence of ATP), in either the 5'- to 3'- or the 3'- to 5'-direction, to yield 5'-phosphoo1igonuc1eotides. Database codes of the subunits (products of genes recA, recB, and recC): RecA: EX5A_ ECOLI, 608 amino acids (66.89 kDa); RecB: EX5B_ECOLI, 1180 amino acids (133.81 kDa); RecC: EX5C_ECOLI, 1122 amino acids (128.70 kDa). exodeoxyribonuclease VII EC 3.1.11.6; other names: exonuclease VII; Escherichia coli exonuclease VII. An enzyme that catalyses exonucleolytic cleavage of DNA, in either the 5'- to 3'- or the 3'- to 5'-direction, to yield 5'-phosphomononucleotides. exodeoxyribonuclease (phage SP3-inducedl EC 3.1.11.4; other names: phage SP3 DNase; DNA 5'-dinucleotidohydrolase. An enzyme that catalyses exonucleolytic cleavage of DNA in the 5'- to 3'-direction to yield 5'-phosphodinucleotides. exoenzyme 1 any enzyme that occurs attached to the outer surface of a cell (i.e. an ectoenzyme) or in the periplasmic space, or one that is secreted by a cell into the medium. Compare endoenzyme (def. I). 2 any enzyme that cleaves a linkage to the terminal residue of a biopolymer. Compare endoenzyme (def. 2). exogenous originating outside an organism, tissue, or cell, e.g. nutrients; of or pertaining to external factors that affect an organism, e.g. light. -exogenously adv. exomorphin see casomorphin. exon 1 any coding or messenger sequence of deoxynucleotides; Le. any intragenic region of DNA in eukaryotes that will be ultimately expressed in (mature) mRNA or rRNA residues. An arrangement of exons alternating with introns constitutes a transcriptional unit. 2 ordinary title of any of the four most junior officers of the Yeomen of the Guard (Beefeaters, Warders of the Tower of London, appointed by the monarch) who in turn act as resident commanders in the absence of superior officers. -exonic adj. exon shuffling the recombination of different coding regions of eukaryotic structural genes (i.e. exons) through crossingover, a mechanism proposed to explain the mosaic structure of eukaryotic genes. Such a mechanism is also responsible for the generation of, e.g., antibody diversity. exonuclease any enzyme of a group of phosphoric diester hydrolases, forming sub-subclasses EC 3.1.11-16, that catalyses the hydrolysis of terminal diester linkages in polynucleotides to yield mononucleotides, the degradation of the chain occurring sequentially from one end. Compare endonuclease. See also deoxyribonuclease, nuclease, ribonuclease. exopeptidase any enzyme of a group of peptide hydrolases within subclass EC 3.4 that catalyses the hydrolysis of peptide bonds adjacent to the terminal amino or carboxyl group of an oligo- or polypeptide. They include: EC 3.4.11, aminopeptidases; EC 3.4.13, dipeptidases; EC 3.4.14, di- and tripeptidyl peptidases; EC 3.4.15, peptidyldipeptidases; EC 3.4.16, serinetype carboxypeptidases; EC 3.4.17, metallocarboxypeptidases; EC 3.4.18, cysteine-type carboxypeptidases; and EC 3.4.19, omega peptidases.

exponential

exophthalmic goitre or Graves' disease a form of hyperthyroidism characterized by enlargement of the thyroid gland and protrusion of the eyeballs. exopolysaccharide any of a range of extracellular homo- or heteropolysaccharides produced by microorganisms, either as insoluble capsules or as soluble slimes. They serve for protection and possibly also in recognition by host organisms. exoribonuclease see ribonuclease. exorphin any peptide with morphine-like activity (see opioid peptide) that originates from outside the body. Such substances occur, e.g., in proteolytic digests of certain dietary proteins. Compare endorphin. exo-a-sialidase EC 3.2.1.18; other names: sialidase; neuraminidase; N-acylneuraminate glycohydrolase; a-neuraminidase; an enzyme that catalyses the hydrolysis of a-2,3-, a-2,6-, and a-2,8-glycosidic linkages joining terminal nonreducing Nor O-acylneuraminyl residues to galactose, oligosaccharides, glycoproteins or glycolipids. Examples: hemagglutinin-neuraminidase from measles virus (strain aik-c) (subacute sclerosing panencephalitis virus): database code HEMA_MEASA, 617 amino acids (69.24 kDa); sialidase (neuraminidase) from Clostridium perfringens: database code NANH_CLOPE, 382 amino acids (42.76 kDa). exoskeleton any skeleton covering the outside of an organism or lying in the skin, such as the hard chitinous cuticle of an arthropod or the shell of a mollusc. Compare endoskeleton. exosmosis the osmotic flow of water or of an aqueous solution from a cell, vessel, or organism into the surrounding aqueous medium. Compare endosmosis. -exosmotic adj. exosome a fragment of exogenous DNA that, when taken up by a cell, is not readily integrated into the chromosome but can replicate, and be expressed. exothermic describing a process or reaction that is accompanied by the evolution of heat; i.e. a process or reaction for which the change in enthalpy, I1H, is negative at constant pressure and temperature. Compare endothermic. exotic describing an introduced (i.e. foreign), nonendemic, nonacclimatized organism. exotoxin any toxin formed by a microorganism and secreted into the surrounding medium. Compare endotoxin. exp (in mathematics) symbol for exponential; see exponential function. expansin any of a group of proteins, located within the cell walls of plants (both dicotyledons and grasses), that play an essential role in loosening cell walls during cell growth. They are hydrophobic, nonglycosylated proteins of M r ~30 kDa. experiment abbr.: expt.; 1 any procedure or series of procedures, carried out in defined conditions and designed to obtain new information about substances, materials, organisms, or natural phenomena, or to test or confirm a hypothesis. 2 an alternative term for experimentation. 3 to carry out an experiment or experiments. -experimenter n. experimental abbr.: expt1.; 1 of, relating to, or based on the results of, an experiment or experimentation. 2 describing a disease produced deliberately in laboratory plants or animals for the purposes of study or as a model for the natural disease condition. 3 any particular object or system in an experiment that includes, or is subjected to, one of the variables. Compare control (def. 1). -experimentally adv. experimentation the act, process, or practice of carrying out an experiment or experiments. explant 1 to transfer a piece of living tissue from its normal situation to a culture medium. 2 any piece of tissue treated in this way. -explanted adj. exponent or index (in mathematics) any number (or expression, or symbol for a number) indicating the power to which another number (or expression or symbol) is raised; e.g., in the expression an, n is the exponent, indicating that a is multiplied by itself n times. exponential (in mathematics) 1 of, containing, or involving one or more exponents, e.g. an exponential equation. 2 de-

223

exponential function scribing something approximately expressible by an exponential equation. exponential function (in mathematics) any function of the type eX or AeaX, where A and a are constants, e is an irrational number that is the base of natural logarithms, and x is a variable; eX is sometimes written exp x. exponential growth an alternative term for logarithmic growth. exponential phase an alternative term for logarithmic phase. export informal term describing a substance synthesized in, and then secreted from, a cell or type of cell in a multicellular organism; e.g. export protein. exposure 1 (in photography or radiography) the act or process of exposing sensitized photographic material, e.g. a film or plate, to light or to ionizing radiation. 2 (in photography) a a measure of the amount of light admitted into a photographic device expressed in terms of the lens aperture (f number) and time. b or light exposure symbol: H; a physical quantity equal to the product of the illuminance and the time, At, for which the area is exposed. The SI unit is the lux second. 3 (in radiation dosimetry) a measure of the amount of X- or gamma radiation to which a subject or object is exposed, expressed in terms of the quantity of electric charge of the ions of one sign produced when all the electrons of both signs liberated in a volume of air of unit mass are completely stopped. The SI unit is C kg-I, which has replaced the rontgen. Compare absorbed dose. express 1 (in genetics) a to allow or cause the information in a gene to become manifest. b to activate the cellular functions involved in gene expression. c (in cDNA technology) to effect the synthesis of protein from the corresponding cloned gene using an expression vector in an expression system. 2 (in mathematics) to indicate by means of a symbol, formula, or equation. 3 to force or squeeze out a liquid from an object. expressed sequence tag abbr.: EST; a partial sequence of a clone picked at random from a cDNA library and used in the identification of genes being expressed in a particular tissue. The technique exploits recent advances in automated DNA sequencing and sequence data handling, and a remarkably high number of ESTs turn out to represent previously unknown genes. These are identified by the predicted primary structure of the proteins that would be expressed and their relation to proteins of known structure. ESTs have proved extremely valuable in mapping the human genome, and there has been controversy surrounding attempts to patent them. expression 1 the act or process of allowing information to become manifest. See gene expression, expression vector, expression system. 2 (in mathematics) a variable function or some combination of constants, variables, andlor functions. 3 the act or process of forcing or squeezing fluid from or out of something. expression system a cell system into which an expression vector has been introduced and that contains all the enzyme systems needed for translation of messenger RNA. Ideally, it also contains the enzymes needed for post-translational modification of the synthesized protein. Expression in Escherichia coli or other bacterial cells may be inadequate for eukaryotic protein expression, but expression in mammalian cell lines may be inconvenient. Use of a baculovirus expression vector in insect cells is one technique that has been used successfully for eukaryotic protein expression. expression tagged site see ETS. expression vector (in cDNA technology) a vector that promotes transcription of a cloned gene, leading to synthesis of protein in a suitable expression system. An expression vector carries a promoter, e.g. EcoRI(UV5), which includes the regulatory region of the lac operon and the UV5 mutation, so that the system is insensitive to catabolite repression. expressor a chemically undefined positive regulator of eukaryotic gene expression. expt. abbr. for experiment (def. I). exptl. abbr. for experimental (def. I, 2). extein a peptide counterpart of an exon. See intein, splicing.

extracellular space extended X-ray absorption fine structure (spectroscopy) abbr.: EXAFS (spectroscopy); a method for determining short-range order and local structure around specific atoms in noncrystalline materials. In this technique the X-ray absorption spectrum of the material is measured over an extended energy range near the absorption edge of one particular element in the material and structural details may be obtained from the observed modulation of the X-ray absorption on the highenergy side of the absorption edge. It is useful for elucidating the environment of metal ions in biological macromolecules. extensin a glycoprotein found in plant cell walls in association with pectin. It resembles collagen of animal cells in being rich in trans-4-hydroxy-L-proline residues, and it contains Larabinofuranose and D-galactopyranose residues attached in oligosaccharide units to the hydroxyl groups of the protein. extension sequence a terminal sequence of amino-acid residues that is present in a nascent polypeptide as generated by translation of mRNA but is absent from any mature polypeptide or protein formed from it. An N-terminal extension sequence may be a signal sequence. extensive property any of the properties of a substance or object that depend on the amount of the substance or the size of the object being considered, e.g. internal energy, mass, volume. Compare intensive property. externalize or externalise to render external, especially to secrete a substance from a cell or organism. -externalization or externalisation n. external standard any standard that is added to a sample at some point in an assay and serves as a reference by which the unknown being investigated can be quantified or identified. external-standard method of quench correction or external standardization a method for correcting for quenching in liquid scintillation counting in which a source of gamma radiation external to the sample is brought into proximity with it after the sample has been counted and the sample is then counted again. The observed increase in count rate is correlated with that obtained using a set of differently quenched standards and the appropriate correction to the sample-count rate obtained. The method is simple and can be automated but on its own is less accurate than other methods. Compare internal-standard method of quench correction. extinction an older term (no longer recommended) for absorbance. extinction angle in flow birefringence between concentric cylinders, with polarizer and analyser at right angles, the angle between the cross of isocline and the cross formed by the polarizer and the analyser. It ranges from 45° (no orientation) to zero (complete orientation). extinction coefficient symbol E; an alternative term (no longer recommended) for molar (decadic) absorption coefficient. See absorption coeflicient. extra+ prefix signifying outside or beyond. extra arm or variable arm the base-paired segment of variable length in the cloverleaf model of some tRNA molecules. See transfer RNA. extracellular present outside a cell, expelled from a cell, or happening outside a cell. Compare exocellular, intracellular. extracellular fluid abbr.: ECF; the portion of the total liquid content that occurs outside the cells, esp. as distinct from intracellular fluid. In higher animals it comprises the interstitial fluid, the lymph, and the blood plasma. In a 70 kg man the volume of ECF is approximately 15.5 L and it represents approximately 22% of body mass. Compare intracellular fluid. extracellular matrix a layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying cells such as endothelial and epithelial cells. The constituent substances are secreted by cells in the vicinity, especially fibroblasts. extracellular space that part of a multicellular organism outside the cells proper - usually taken to be outside the plasma membranes - and occupied by fluid.

224 extrachromosomal extrachromosomal describing structures, including DNA molecules, that are not part of a chromosome, or processes that proceed outside the chromosomes. extrachromosomal inheritance inheritance controlled by extrachromosomal genes, such as those in mitochondrial or chloroplast DNA or in plasmids. extract I to remove from or separate; to obtain a substance from a material, mixture, organism, or part of an organism by some chemical and/or physical process. 2 something extracted; a solution containing an active principle that has been extracted from plant or animal material. extraction I the act or process of extracting. 2 something that has been extracted. Compare extract (def. 2). extra piece an alternative name for signal peptide. extrapolate (in mathematics) to estimate a value or the value of a function beyond the data values already obtained by either extending a graph or by calculation. Compare interpolate. -extrapolation n. extremophile an organism that requires extreme physicochemical conditions for its optimum growth and proliferation. Such organisms include thermophiles or psychrophiles, halophiles, alkalophiles or acidophiles, osmophiles, and barophiles, based on their growth at extremes of temperature, salt concentration, pH, osmolarity, or pressure, respectively. extrinsic originating or acting from the outside. -extrinsically adv. extrinsic factor a former name for vitamin B12 . extrinsic fluorescence fluorescence caused by a molecule of a fluor of small molar mass attached by either chemical coupling or simple binding to a (macro)molecule under study. extrinsic pathway lof blood coagulation) see blood coagulation. extrinsic protein an alternative name for peripheral (cell membranel protein. extrude to squeeze or force out; used especially of a solid or semisolid material. -extrusion n. extrusome an organelle excreted as an anterior vacuole by a parasitic protist. It contains substances used for penetration of host cells. ex vivo describing any biological process, reaction, or experiment in which the nature or magnitude of a change occurring

ezrin in living tissues in intact organisms is subsequently measured in vitro following the excision of affected tissues. Compare in vivo [Latin, meaning from life.] eye (in molecular biology) a region of DNA undergoing replication, in which the separated strands give the appearance of an eye. E/Z convention a convention of stereochemical descriptors for an unsaturated compound showing cis-trans isomerism that indicate unequivocally the steric relations around a (given) double bond. The sequence rule is applied in turn to the pair of atoms or groups attached to one of the doubly bonded atoms and to the pair attached to the other doubly bonded atom, and the order of preference in each case is established. If the two preferred atoms or groups are on opposite sides of the reference plane of the molecule the arrangement is called E [from German entgegen, opposite], and if they are on the same side of the plane it is called Z [from German zusammen, together]. For use as a prefix (in chemical nomenclature) the descriptor is placed in parentheses and connected with a hyphen, e.g. (E)butenedioate and its stereoisomer (Z)-butenedioate (the respective systematic names for trans-I,2-ethylenedicarboxylate (= fumarate) and for cis-I,2-ethylenedicarboxylate (= maleate». When a molecule of an unsaturated compound contains more than one double bond the prefix is composed of multiple symbols, each preceded if appropriate by the lowernumbered locant of the relevant double bond; e.g. (2E,4Z)2,4-hexadienoate. The convention is now generally preferable to that using the structural prefixes cis- and trans-, especially for olefinic compounds having more than two substituents at a double bond (where it avoids possible ambiguity as to which pair of substituents is being designated). See also pro-E.pro-Z convention. ezrin or cytoviIlin or viIlin-2 or PSI a protein involved in connections of major cytoskeletal structures to the plasma membrane, having domains in common with talin. It undergoes tyrosine phosphorylation after activation of specific growth factor receptors, and functions as a membrane-to-cytoskeleton linker that is involved in assembly of apical microvilli in parietal cells. It participates in the regulation of acid secretion. Example from human: database code EZRI_HUMAN, 585 amino acids (69.19 kDa).

Ff f symbol for femto+ (SI prefix denoting 10- 15 times). I symbol for 1 frequency (alternative to p). 2 activity coefficient referenced to Raoult's law. 3 fugacity (alternative to p). 4 frictional coefficient. 5 furanose form (added after the symbol for a monosaccharide, e.g. Araffor arabinofuranose). 6 (in mathematics) function. F symbol for I a residue of the a-amino acid L-phenylalanine (alternative to Phe). 2 fluorine. 3 the fluoro group in an organic compound. 4 (in genetics) filial generation. 5 farad. 6 Fick unit. 7 abbr. for fertility; see F plasmid. 8 abbr. sometimes used (not recommended) to designate folate or folic acid or their reduced derivatives. F1, F2a1, F2a2, F2b, F2c, F3 older nomenclature for histones. F signifies fraction; in early work, the histones were extracted from the nuclei with sulfuric acid solutions, and separated according to their solubility. F4Z0 see coenzyme F4Z0 ' F430 see coenzyme F430 . OF symbol for degree Fahrenheit. See Fahrenheit temperature scale. F+ symbol for a donor bacterial cell containing an F plasmid; Fdenotes a recipient bacterial cell lacking an F plasmid. F symbol for 1 Faraday constant. 2 force (bold italic in vector equations). 3 fluence (alternative to H). FA abbr. for 1 fatty acid. 2 folic acid or folate (not recommended). 3 filtrable agent. Fab fragment a ~45 kDa protein fragment obtained (together with Fe fragment and Fc' fragment) by papain hydrolysis of an immunoglobulin molecule. It consists of one intact light chain linked by a disulfide bond to the N-terminal part of the contiguous heavy chain (the Fd fragment). Two Fab fragments are obtained from each IgG antibody molecule; each fragment contains one antigen-binding site. The term Fab is derived from ['fragment antigen-binding']. Compare F(ab)zfragment. See also Fv fragment. F(ab')z fragment a ~90 kDa protein fragment obtained (together with pFc' fragment) by pepsin hydrolysis of an immunoglobulin molecule. It consists of that part of the immunoglobulin molecule N-terminal to the site of pepsin attack and contains both Fab fragments held together by disulfide bonds in a short section of the Fc fragment (the hinge region). One F(ab'h fragment is obtained from each IgG antibody molecule; it contains two antigen-binding sites but not the site for complement fixation. Compare Fab fragment. FABP abbr. for fatty acid binding protein (e.g. albumin, etc.); four motifs are characteristic of this function. Fabry's disease an X-linked inborn error of human metabolism due to defective lysosomal a-o-galactosidase A activity. It is a sphingolipidosis or sphingolipid lysosomal storage disease. The enzyme defect leads to the progressive deposition in most visceral tissues of neutral glycosphingolipids with terminal aD-galactosyl residues, principally globotriaosylceramide, Gal(al-4)Gal(pl-4)G1c(pI-I)Cer. [After Johannes Fabry (1860-1930), German physician.] facilitated diffusion diffusion (def. 2) across a biological membrane through the participation of specific transporting agents (transporters) or carriers. The equilibrium distribution reached is the same as that achieved by simple diffusion but at anyone site facilitated diffusion is mediated by a transport protein that exhibits specificity for the transported species. The existence of the transporter mediates passage across the membrane of molecules to which it would otherwise be impermeable. Sometimes termed mediated transport to distinguish it from active transport. FACIT abbr. for fibril-associated collagens with interrupted triplex helices; a group of collagens (types IX, XII, and XIV)

composed of triple-helical regions interrupted by non-triplehelical regions of 8-42 amino acids. FACS abbr. for fluorescence-activated cell sorter. F-actln the form of actin found in filaments. factor 1 any component or cause that contributes to an effect or result; a term often used to denote an uncharacterized (or incompletely characterized) component of a biological system. 2 (in mathematics) any integer or polynomial that can be divided exactly into another integer or polynomial. factor I to factor XIII, factor Va, etc. names of the blood coagulation factors. factor B a component of complement. factor D a component of complement. factor F an alternative name for initiation factor. factor F430 a nickel-containing tetrapyrrole compound involved in the terminal reductive step of methanogenesis in methanogenic bacteria, in which methane is formed from methyl-coenzyme M (see coenzyme M). It exists both as the protein-bound and free forms. The free form has an absorption maximum at 430 nm, which shifts to 421 nm in the bound form.

factor G an alternative name for EF-G; see also elongation factor. factor H a component of complement. factor I a component of complement. factorial symbol: !; the product of all positive integers from I up to and including the integer in question, n; hence n! = n(n - I)(n - 2)(n - 3) ... 3 x 2 x 1. factor IF an alternative name for initiation factor. factor R an alternative name for release factor. factor S a tetrapeptide, of unknown structure, isolated from cerebrospinal fluid of goats, that slowly induces delta (slow wave) sleep in rats on infusion into the cerebral ventricles. factor T an alternative name for EF·T; see also elongation factor. facultative able to live under more than one set of environmental conditions. facultative aerobe see aerobe. facultative anaerobe see anaerobe. FAD abbr. for flavin-adenine dinucleotide. fade the waning of a response in the continued presence of an agonist. Compare desensitization. FADH z abbr. for flavin-adenine dinucleotide (reduced). F agent see sex factor. Fahrenheit temperature scale a temperature scale in which 32 OF is set equal to 273.15 K and 212 OF is set equal to 373.15 K. Thus I Fahrenheit degree = 5/9 x K, and Fahrenheit tem-

226

fall curve

fast reaction

=

perature (OF) 9/5 x (Celsius temperature) + 32. [After G. D. Fahrenheit (1686-1736), German scientist.] fall curve the curve describing the decrease in the colour intensity of a sample with time, obtained in a colorimetric analysis using an autoanalyser. falling-drop method a method for the accurate determination of relative densities of liquids in which a drop of the liquid is aIlowed to faIl to its equilibrium position in a column containing a defined density gradient of an immiscible liquid. It was formerly used for determination of the deuterium oxide content of samples of water. falling-mercury electrode an alternative term for droppingmercury electrode. falling-sphere viscometer an instrument for measuring the viscosity of a liquid from the time taken for a solid sphere to fall through a given distance in a column of the liquid compared with the time taken for it to faIl through the same distance in a liquid of known viscosity. Fallopian tube an oviduct of a mammal. familial 1 of or pertaining to a given family. 2 describing something transmitted between members of a family, especiaIly a familial character, condition, or disease. family 1 (in taxonomy) a taxonomic category of related organisms ranking below the order and above the genus. 2 (in chemistry and biochemistry) an imprecise term for a group of substances closely related structuraIly. See also superfamily. 3 (in molecular biology) see Appendix E. Fanconi syndrome an inherited human disorder characterized by glycosuria, amino aciduria, phosphaturia, and acidosis. It is due either to functional deficiency of the proximal renal tubules or to abnormalities in amino-acid metabolism. See also renal rickets. [After Guido Fanconi (1892-1979), Swiss pediatrician.] farad symbol: F; the SI derived unit of electric capacitance. A capacitor has a capacitance of one farad when a charge of one coulomb raises the potential between its plates to one volt: i.e. 1 F = I C V-l. [After Michael Faraday (1791-1867), British physicist.] faradaic current an electric current flowing through an electrode that corresponds to the electrolytic oxidation or reduction of one or more chemical species. Faraday constant symbol: F; a fundamental constant, defined as the quantity of electricity required to deposit one mole of a univalent ion from a solution of an electrolyte. It is the arithmetic product of the Avogadro constant, L (or N A), and the elementary charge, e; hence F Le (or F NAe) 9.6485309(29) x 104 C mol-I. Faraday effect the rotation of the plane of vibration of polarized light, or of other polarized electromagnetic radiation, when passing through an isotropic, transparent medium in a magnetic field that has a component in the direction of the radiation. Farber's disease or Farber's lipogranulomatosis an alternative name for ceramidase deficiency. farnesol the trivial name for any of four possible stereoisomers of 3,7,II-trimethyl-2,6,10-dodecatrien-l-ol; a sesquiterpene alcohol. The 2E,6E-isomer is found in many essential oils. The 2Z,6E-isomer is a minor constituent of some essential oils.

=

=

=

OH

2E,6E-isomer

famesyl the (2E,6£)-3, 7, II-trimethyl-2,6, lO-dodecatrien-l-yl group; the alkenyl group derived from the sesquiterpene alcohol faroesol. 2E,6E-Farnesyl diphosphate (= trans.trans-farne-

syl diphosphate) is an intermediate in carotenoid, sesquiterpene, squalene, and sterol biosynthesis and is also a substrate in the addition of the farnesyl group to proteins (see prenylation). farnesyltransfera88 EC 2.5.1.21; recommended name: farnesyldiphosphate farnesyltransferase; systematic name: farnesyldiphosphate:farnesyl-diphosphate farnesyltransferase; other name: presqualene-diphosphate synthase. An enzyme that catalyses the formation of presqualene diphosphate from two molecules of farnesyl diphosphate with release of pyrophosphate. It occurs in the pathway for the synthesis of squalene and derivatives (cholesterol, sesquiterpenes). In eukaryotes it is a monomeric microsomal enzyme. Example from yeast: database code ERG9_YEAST, 444 amino acids (51.61 kDa). farnesyltranstransferase EC 2.5.1.29; systematic name: trans,trans-farnesyl-diphosphate:isopentenyl-diphosphate farnesyltranstransferase; other name: geranylgeranyl-diphosphate synthase. An enzyme that catalyses the formation of geranylgeranyl diphosphate from trans,trans-farnesyl diphosphate and isopentenyl diphosphate with the release of pyrophosphate. It occurs in the pathway for sesquiterpene and cholesterol synthesis and forms the prenyl derivative geranylgeranyl diphosphate. In some fungi and plants this activity is part of a multifunctional protein that also has the activities of geranylgeranyl-diphosphate synthase (see dimethylallylt'BRstransferase) and geranylt'BRstransferase. Example from Neurospora crassa: database code GGPP_NEUCR, 428 amino acids (47.83 kDa). farnoquinone an alternative name for menaquinone-6; see menaquinone. Farr test a radioimmunoassay technique for measuring the absolute antigen-binding capacity of an antiserum. The antibody is allowed to react with radiolabelled antigen and the antigen-antibody complex is then precipitated by addition of saturated ammonium sulfate solution to a final concentration of 40% w/v. The antigen that has reacted can be determined in the precipitate. far ultraviolet see ultraviolet. fascicle or fibre tract a tight paraIlel bundle of nerve fibres that are either axons or dendrites. It is formed during the growth of nerves, and is mediated in part by ceIl adhesion molecules. 'asciclin any of the proteins of a related group that are involved in nerve fascicles (bundles). They include fasciclin I, a neuronal ceIl adhesion molecule; example (precursor) from Drosophila melanogaster: database code FASl_DROME, 652 amino acids (72.52 kDa); and fasciclin II, which is a neuronal recognition molecule related to NCAM (see adhesion molecules): database code FS2LDROME, 873 amino acids (96.82 kDa). fascin a protein involved in the formation of actin bundles and actin polymerization. Example from Strongylocentrotus purpuratus: database code SUSFASCIN, 496 amino acids (54.88 kDa). fast 1 (of a component of a mixture or specified substance) one that migrates further or furthest from the origin in chromatography or electrophoresis. 2 uninfluenced by a specified agent, e.g. by light, acid, etc. See also acid-fast bacilli. 3 to abstain from, or to be prevented from, taking nourishment for at least 24 hours (in the case of laboratory animals). In clinical chemistry, the requirement is often for an overnight fast, normally at least 10 hours. -fasted ad}.; -fasting n. FASTA or FASIN a computer program used for searching and analysing protein and nucleic acid sequences. fast component an unusual component of a mixture, e.g. a hemoglobin variant, that moves in a specified buffer system more rapidly in chromatography or electrophoresis than does the normal component. fast reaction any reaction, or step in a reaction sequence, that has a large rate constant and proceeds rapidly. In a reaction sequence, a fast reaction is not the rate-limiting step.

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fat fat 1 any triacylglycerol or mixture of triacylglycerols that is solid below 20°C; those that are liquid at such temperatures are usually referred to as oils. 2 an alternative name for lipid. 3 an alternative name for adipose tissue; see brown adipose tissue, white adipose tissue. fatal familial insomnia a rare inherited neurological disease, first described in 1986 among inhabitants of mountainous regions of Italy. It is characterized by intractable insomnia and other neurological abnormalities. It is one of three familial forms of human prion disease. Neuropathologically, there is neuronal loss with associated gliosis. It is associated with a pathogenic mutation of the prion gene at codon Asn l78 (shared with Creutzfeldt-Jakob disease, but for unknown reasons of different phenotype) linked to codon Met 129 , a site that exhibits MetlVal polylmorphism. fat body any of the fat-containing cellular structures that serve as energy reserves in amphibians, insects, and reptiles. fat cell or fat-cell or lipocyte or (in animals) adipocyte any living cell containing noticeable amounts of lipid, primarily as fat or oil. fat index the mass of diethylether-extractable fat per unit mass of nonfat material (on a dry-weight basis) in, e.g., a foodstuff or tissue. F1 -ATPase see W-transporting AlP synthase. fat-soluble vitamin any of a diverse group of vitamins that are soluble in organic solvents and relatively insoluble in water. The group includes vitamins A, D, E, and K. fat solvent any lipid solvent e.g. chloroform or diethylether, that will extract triacylglycerols from biological or other materials. fatty derived from or containing fat. fatty acid any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes. See also fatty-acid nomenclature, polyunsaturated fatty acid. fatty-acid activation the conversion of a fatty acid molecule to its fatty acyl-coenzyme A thioester, the first step in the reactions of beta oxidation. Fatty acyl-coenzyme A can be formed in a reaction catalysed by the acid-thiol ligases EC 6.2.1.1, 6.2.1.2, and 6.2.1.3, or by a CoA-transferase of sub-subclass EC 2.8.3. fatty-acid nomenclature a system of symbols for describing fatty acids. The basic symbolism comprises the number of carbon atoms in the molecule, followed by the number of double bonds; the two numbers are separated by a colon. Thus, 16:0 represents palmitic acid, 16:1 palmitoleic acid, etc. To avoid ambiguity, double bond positions in unsaturated fatty acids should be indicated; 18:3 (9,12,15) represents a-linolenic acid, 18:3 (9,11,13) represents eleostearic acid. These symbols may also include the EIZ configurational descriptors (see E/Z convention). Although not now recommended, a still used system numbers the first double bond from the carboxyl group using the Greek letter ,1. Thus, oleic acid is 18:1 ,19 or 18:1 Ll 9• This system persists in some enzyme names; e.g., the systematic name for Iinoleate isomerase (EC 5.2.1.5) is linoleate Ll12_ cis-Llll-trans-isomerase. See also fatty acid oxidation complex. Double bonds may also be designated from the end of the chain remote from the carboxyl group. If n is the total number of carbons, n-3 represents CH 3-CH r CH=CH-, etc. Since in many unsaturated fatty acids the double bonds are successively separated by methylene groups, only the position of the first double bond may be given. Thus linoleic acid [18:2 (9,12)] is also represented as 18:2 n-6. The Greek letter 00 has also been used in the same way; e.g. for linoleic acid, 18:2 00-6. However, it is not recommended that a double bond position, e.g. that of oleic acid, should be designated as 009. See also fish oil, linoleic family, linolenic family, oleic family, palmitoleic family. fatty-acid oxidation complex a bacterial multifunction pro-

fatty-acid thiokinase tein complex that catalyses the beta oxidation of fatty acids. The example from Escherichia coli comprises a and ~ subunits. The a subunit contains decenoyl-CoA .oil-isomerase, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxybutyrylCoA epimerase; database code FADB_ECOLI, 729 amino acids (79.50 kDa). The ~ subunit contains 3-ketoacyl-CoA thiolase; database code THIK_ECOLI, 387 amino acids (40.84 kDa). For a mammalian system see beta-oxidation system. fatty acid synthase complex a large, well-defined multienzyme complex found in eukaryotes. These enzyme complexes, which are cytoplasmic, catalyse a cyclic set of reactions whereby fatty acids are synthesized from one molecule of acetyl coenzyme A and successive molecules of malonyl coenzyme A. In Escherichia coli and most bacteria the activities are in separate proteins. In animals, the enzyme complex (EC 2.3.1.85) produces a long-chain fatty acid (typically palmitate), whereas in yeast the product is a long-chain-fatty-acylCoA. The synthase complex of yeast has a mass of 2300 kDa and appears in the electron microscope as an ellipsoid, 25 /-lm long and 21 /-lm in cross section. The yeast enzyme comprises a and ~ subunits. It is termed fatty-acyl-CoA synthase (EC 2.3.1.86), and catalyses the overall reaction: acetyl-CoA + n malonyl-CoA + 2n NADH + 2n NADPH = a 10ng-chain-acyl-CoA + n CoA + n CO 2 + 2n NAD+ + 2n NADP+; To synthesize palmitoyl-S-[acyl-carrier protein] requires seven repetitions of the following set of reactions, where X = -S-[acyl carrier protein]: (I) R-CHrCO-X + -OOC-CHrCO-X ~ R-CH 2-CO-CH r CO-X + CO 2 + H-X (2) R-CH r CO-CH 2-CO-X + NADPH ~ R-CH 2-CH(OH)-CH r CO-X + NADP+ (3) R-CH 2-CH(OH)-CH 2-CO-X ~ R-CH 2-CH=CH-CO-X + H 2 0 (4) R-CH 2-CH=CH-CO-X + NADH ~ R-CH 2-CH 2-CH 2-CO-X + NAD+ The hydroxacyl product of reaction (2) has the 3R configuration and the enoylacyl product of reaction (3) has E configuration. Before the assembly begins, acetyl and malonyl units are transferred from their CoA derivatives to acylcarrier protein (ACP) by the activities of two transferases, EC 2.3.1.8 and EC 2.3.1.9. Representative enzyme activities for the four reactions are named as follows: reaction (I), EC 2.3.1.41, 3-oxoacyl[ACPj synthase; reaction (2), EC 1.1.1.100, 3-oxoacyl-[ACP] reductase; reaction (3), EC 4.2.1.61, 3-hydroxypalmitoyl[ACP] dehydratase; reaction (4), EC 1.3.1.9, enoyl-[ACP] reductase (NADH). Similar enzymes with different chain length specificities may also be involved. For the first round, R = H, the two synthase substrates thus being acetyl-[ACP] and malonyl-[ACP]; the product is 3-oxobutanoyl-[ACP]. After seven repetitions of the four reactions, R = C 12 H 25 , and the product is palmitoyl[ACP]. The yeast a subunit catalyses reactions (I) and (2); database code FAS2_YEAST, 1894 amino acids (207.86 kDa). The yeast ~ subunit catalyses the two acyl transfer reactions and reactions (3) and (4); database code FASI_YEAST, 2051 amino acids (228.43 kDa). The mammalian complex is a dimer of identical subunits (260 kDa). Since the product is palmitic acid itself a further enzyme is present: EC 3.1.2.14 (oleoyl-[ACP] hydrolase). Each polypeptide chain is folded into three domains: domain I contains the acyltransferase activities and catalyses reaction (I); domain 2 catalyses reactions (2), (3), and (4); domain 3 catalyses the hydrolysis of palmitoyl-[ACP] to palmitate. In liver, reaction (4) is catalysed by EC 1.3.1.39, enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific). fatty-acid thiokinase an alternative name for 1 butyryl-CoA

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fatty-acyl-CoA dehydrogenase ligase (EC 6.2.1.2). 2 10ng-chain-fatty-acid-CoA ligase; see fatty-acyl-CoA ligase. fatty-acyl-CoA dehydrogenase any of the acyl-CoA dehydrogenase components of the beta-oxidation system. fatty-acyl-CoA desaturase see stearoyl-CoA desaturase. fatty-acyl-CoA ligase either of two enzymes involved in fatty-acid activation. (I) Long-chain-fatty-acid-CoA ligase (EC 6.2.1.3); other names: acyl-activating enzyme; acyl-CoA synthetase; fatty acid thiokinase (long-chain); lignoceroyl-CoA synthase. It catalyses a reaction between ATP, a long-chain carboxylic acid, and CoA to form an acyl-CoA and pyrophosphate. In mammals there are tissue isoforms. Example from rat liver: database code LCFA_RAT, 699 amino acids (78.09 kDa). (2) Medium-chain-fatty-acid-CoA ligase (EC 6.2.1.-); other name: medium-chain-fatty-acid-CoA synthase. It catalyses the same reaction as above but with medium-chain fatty acids. Example from Pseudomonas oleovorans: database code ALKK_PSEOL, 546 amino acids (59.19 kDa). fatty-acyl-CoA synthase 1 the multifunctional protein responsible for the synthesis of long-chain fatty acyl moieties in some eukaryotes, e.g. yeast. See fatty acid synthase complex. 2 an enzyme of the endoplasmic reticulum, EC 6.2.1.3, longchain-fatty-acid-CoA ligase, that carries out a reaction between ATP, CoA, and a long-chain fatty acid to form the corresponding fatty-acyl CoA, AMP, and pyrophosphate. fatty-acyl group any acyl group derived from a fatty acid. fatty alcohol an alternative term for long-chain alcohol. fatty degeneration or fatty infiltration the deterioration of a tissue due to the deposition of abnormally large amounts of fat, usually as globules, in its cells. fatty liver a pathological condition of liver tissue that has undergone fatty degeneration. It results from administration of various poisons, especially chlorinated hydrocarbons, or as a result of a dietary deficiency of choline or threonine. favism a disease of humans in which hemolysis is caused by eating fava beans (Vicia faba) or by certain drugs, e.g. sulfonamides, primaquine, and nitrofuran antibiotics. The basic defect is an inherited deficiency of glucose-6-phosphate dehydrogenase in the red blood cells; about 70 variants are known. See also glucose-&-phosphate dehydrogenase deficiency. FBP abbr. for fructose 1,6-bisphosphate. FCCP abbr. for carbonylcyanide p-trifluoromethoxyphenylhydrazone; an uncoupling agent. F cell a former name for PP cell. F,-CFo the E subunit of the H+-transporting AlP synthase complex in the chloroplasts of Chlamydomonas reinhardtii, in which the subunit arrangement is different from that in higher plants. Fc fragment a crystallizable protein fragment obtained (together with Fab fragment) by papain hydrolysis of an immunoglobulin molecule. That obtained from human IgG is a 50 kDa protein consisting of the C-terminal halves of two heavy chains linked by two disulfide bonds. The Fc fragment has no antigen-binding activity but carries sites for complement fixation. [Fc is from 'fragment-crystallizable'.J Compare Fc' fragment, Fd fragment. Fc' fragment a protein fragment obtained in small amounts by papain hydrolysis of an immunoglobulin molecule, in addition to Fab fragments and Fe fragment. That obtained from human IgG is a 24 kDa protein; it forms noncovalently bonded dimers consisting of the C-terminal moieties of two Fc fragments minus their C-terminal tridecapeptide segments. It normally occurs in small quantities in human urine. See also pFc' fragment. Fc receptor any of a number of proteins that bind the Fc region of immunoglobulins A, E or G, and facilitate their recognition and uptake, especially by phagocytic cells (see phagocyte). Several types have been described; all of the proteins involved have a single transmembrane helical region. Fcy receptor I (abbr.: FcyRI) or CD64, is a high affinity receptor for IgG, capable of binding monomeric antibody. It is a char-

feedback acteristic marker of mononuclear phagocytes, but may also be expressed on activated neutrophils; example: database code FCGO_HUMAN, 347 amino acids (42.6 kDa). FcyRIl or CD32 is a low affinity receptor for IgG present on monocytes, neutrophils, eosinophils, B cells and platelets. Crosslinking of the surface antibody and the receptor leads to downregulation of the B cell. Binding of immune complexes to this receptor leads to degranulation of platelets and release of inflammatory mediators; example: database code FCGA_HUMAN, 317 amino acids (34.99 kDa). Another low affinity IgG receptor, FcyRIlI or CDI6 is found on macrophages, polymorphs, eosinophils and NK cells. On large granular lymphocytes it is a transmembrane glycoprotein that can link the cells to antibody-sensitized target cells, while on macrophages and neutrophils it has a GPI anchor. Two types of IgE receptor are known: (I) a high affinity receptor, FCERI, found on basophils and mast cells, which on activation leads to the release of histamine and the manifestation of allergy. It is a tetramer of one a chain, one p chain and two disulfide-linked y chains, examples: a chain, database code FCEA_HUMAN, 257 amino acids (29.6 kDa); p chain, database code FCEB_HUMAN, 244 amino acids (26.53 kDa); y chain, database code FCEG_ HUMAN, 86 amino acids (9.67 kDa). (2) a low affinity receptor, FCERII, found on lymphocytes and monocytes and involved in IgE production and differentiation of B cells. An IgA receptor is found on myeloid cells; example: database code FCAR_HUMAN, 287 amino acids (32.26 kDa). FCS abbr. for fetal calf serum. Fd symbol for ferredoxin. Fd s40 symbol for a membrane-bound ferredoxin with a redox potential of -0.54 V. Fd s90 symbol for a membrane-bound ferredoxin with a redox potential of -0.59 V. FDA abbr. for Food and Drug Administration (of the USA). Fd fragment a protein fragment obtained by papain hydrolysis of an immunoglobulin molecule followed by reduction of the disulfide bonds. It consists of the part of the heavy chain N-terminal to the papain hydrolysis site. The N-terminal moiety is variable and forms part of the original antigen-combining site; the C-terminal moiety is constant. Compare Fe fragment. FDNB abbr. for fluorodinitrobenzene; Sanger's reagent. FDP abbr. for fructose 1,6-diphosphate (now named fructose 1,&bisphosphate). FdU abbr. for fluorodeoxyuridine (the symbol FdUrd is recommended). FdUrd symbol for (a residue of) the deoxyribonucleotide fluorodeoxyuridine (see flurouracil). Fe symbol for iron. FeIn) symbol for ferrous (divalent) iron. Fehn) symbol for ferric (trivalent) iron. FEBS abbr. for Federation of European Biochemical Societies. fecal fat fat in the feces; the output of fecal fat is normally below about 18 mmol 24 h- I in the adult human. Tests that measure the fat content of feces may assist in diagnosis of generalized malabsorption syndrome; an alternative method is the [14C]triolein breath-test. fed batch process a process during which one or more nutrients are supplied to a bioreactor, usually without removing biomass and products. See batch process. Federation of European Biochemical Societies abbr: FEBS; an international scientific organization founded in 1964 and now representing some 32 countries, including all those of mainland Europe plus Israel. FEBS is governed by a Council composed of one delegate from each of the adhering national biochemical societies plus the members of the Executive Committee. FEBS organizes an annual meeting, advanced courses, and supports fellowships and three annual prizes. It publishes two journals, FEBS Letters and European Journal of Biochemistry. feedback 1 any feature of a system, e.g. of a metabolic pathway or of an electronic circuit, whereby information about the

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feedback control output of the system is used to influence the input to that system. Such feedback may increase the input to the system - positive feedback - or reduce the input to the system - negative feedback. A cyclic system of components participating in feedback forms a feedback loop, and the system is known as a closed-loop system. Compare open-loop system. 2 that part of the output of an electronic, mechanical, or other system that is returned to the input, so modifying its characteristics. Compare feedlorward. -feed back vb. feedback control control of the activity of any system by a mechanism involving feedback. feedback inhibition or retroinhibition inhibition of the activity of an enzyme by the accumulation of a substance produced further along a metabolic pathway of which the enzyme is a constituent. Compare enzyme repression, feedback repression. feedback repression an inhibitory feedback system in which the accumulation of a substance produced in a metabolic pathway represses the synthesis of an enzyme that is required at an earlier stage of the pathway. Compare enzyme repression, feedback inhibition. feeder cell an irradiated cell that is capable of metabolizing but not of dividing. Such cells are sometimes added to cultures of unirradiated cells to help in the provision of nutrients. feeder layer a layer of feeder cells in a cell culture. feeder pathway any (minor) metabolic pathway that supplies metabolites to another (major) metabolic pathway. feedforward 1 any feature of a system, e.g. a metabolic pathway, whereby information about the input to the system is used to influence the output of the system. Compare feedback (def. 1).2 that part of the input of a system that influences the output of the system. Fehling's solution a test reagent for glucose and other reducing substances. It is prepared as two solutions: Fehling's solution A containing 0.278 M copper (1I) sulfate, and Fehling's solution B containing approximately 1.65 M potassium sodium tartrate and 4.3 M potassium hydroxide; equal volumes of each solution are mixed before a test. When boiled with a reducing substance a yellow or red precipitate of copper (I) oxide is formed. Compare Benedict's solution. [After Hermann Christian von Fehling (1812-85), German organic chemist.] feline of, pertaining to, or resembling cats. felix a protein designed for theoretical modelling studies and expressed from a synthetic gene in Escherichia coli. Database code NRL_IFLX, 79 amino acids (8.77 kDa), which also gives the predicted 3-D structure. [From four-helix bundle.] female symbol: ~; 1 of, pertaining to, or designating the sex that only produces gametes that can be fertilized by male gametes. 2 describing a flower that lacks stamens or has nonfunctional stamens. female sex hormones any of the estrogens (estradiol-17/J, estrone, and estriol) that are concerned with the normal growth and development of the mammalian female reproductive tract and, together with progesterone, control the estrous and reproductive cycles. FeMo-co abbr. for iron-molybdenum cofactor (of component 1 of nitrogenase). FeMo protein any iron-molybdenum-containing protein. FEMS abbr. for Federation of European Microbiological Societies. femto+ symbol: f; S1 prefix denoting 10-15 times. femtomolar (informal) describing a solution containing 10-15 mol dm 3 (of a specified solute). femtomole symbol: fmol; one 10 15th part of a mole (of a specified substance). F episome an alternative name for F plasmid. Fe protein any iron-containing protein. feral wild; having escaped from cultivation or domestication and reverted to the wild state. ferment 1 any agent or substance that causes fermentation. 2 a former name for enzyme. 3 an alternative name for fermenta-

ferrimyoglobin tion. 4 to undergo or to effect fennentation. -fermentable adj.; fermentability n. fermentation 1 (or ferment) the decomposition of chemical substances, brought about by ferments (def. 1), resulting in the production of simpler substances and, often, of energy; an instance of this, especially the anaerobic breakdown of glucose to lactate or ethanol. 2 (in biotechnology) the use of microorganisms or cultured cells to produce useful materials, such as antibiotics, beverages, enzymes, and some commodity chemicals. fermenter 1 or fermentor or biofermenter an apparatus or a vessel in which to conduct fermentation under more or less controlled conditions. 2 a person or other agent that causes or is able to cause fermentation. 3 a genus, species, or strain of microorganism that ferments (or does not ferment) glucose or a specified sugar; e.g. lactose fennenter, non-lactose fennenter. fermentor a variant spelling offermenter (def. 1). Fernandez-Moran particle another name for elementary particle (def. 2), attached to the cristae of the mitochondrion. ferralterin a soluble nonheme, iron-sulfur-containing chloroplast protein, mediating the light activation of chloroplast fructose 1,6-bisphosphatase. ferredoxin symbol: Fd; any simple, nonenzymic iron-sulfur protein that is characterized by having equal numbers of atoms of iron and labile sulfur (releasable as hydrogen sulfide by acidification). The iron and sulfur atoms are present in one or two clusters of two or four atoms of each. Ferredoxins are of M, 6000-24 000; many have a particularly low redox potential (Eo' = -0.2 V to -0.6 V). They act as electron carriers in a variety of oxidation-reduction systems and have been found in a wide range of microorganisms, in chloroplasts, and in mitochondria from adrenal cortex (see adrenodoxin) and heart muscle. Example: 2Fe-2S type from Spirulina platensis: database code NRL_3FXC, 98 amino acids (10.49 kDa); three conserved motifs; 3-D structure known. Compare rubredoxin. See also high-potential iron-sulfur protein, nitrogenase. ferredoxin-NADP+ reductase another name for NADPH:adrenodoxin oxidoreductase. ferredoxin-nitrite reductase see nitrite reductase. ferri+ comb. form denoting containing ferric iron. ferric of or containing trivalent iron, Fe3+ or Fe(m). ferrichrome any of a group of growth-promoting Fe(m) chelates formed by various genera of microfungi, e.g. species of Aspergillus, Neurospora, and Ustilago. They are homodetic cyclic hexapeptides made up of a tripeptide of glycine (or other small neutral amino acids) and a tripeptide of an N 4 _ acyl-N4-hydroxy-L-ornithine (e.g. the N4- acetyl compound). They are thus siderochromes of the hydroxamic-acid-derivative category. ferricytochrome any cytochrome in which the iron atom is in the ferric form. ferriheme or (esp. UK) ferrihaem any Fe(m)-porphyrin coordination complex. ferriheme chloride another name for hemin. ferriheme hydroxide another name for hematin. ferrihemochrome any hemochrome containing Fe(m). ferrihemoglobin or methemoglobin (abbr.: MetHb) an oxidation product of hemoglobin in which all its four iron atoms are in the ferric, Fe(m), state, the sixth coordination valencies of which are occupied, in the acid form, by water molecules, or, in the alkaline form, by hydroxide ions; these two forms have characteristic absorption spectra. Unlike hemoglobin, it cannot bind and transport dioxygen. The 3-D structure is known (Brookhaven file IHGB.PDB). Compare ferrimyoglobin. ferrimyoglobin or metmyoglobin (abbr.: MetMb) an oxidation product of myoglobin in which its iron atom is in the ferric, Fe(m), state, the sixth coordination valency of which is occupied, in the acid form, by a water molecule, or, in the alkaline form, by a hydroxide ion. Unlike myoglobin, it cannot bind and store dioxygen. The 3D structure is known (Brookhaven file 1MBC.PDB). Compare ferrihemoglobin.

230 ferrioxamine ferrioxamine see desferrioxamine. ferritin any of a group of electron-dense, major iron-storage proteins that are widely distributed in animal and plant tissues; the iron is stored in a soluble, readily available form. Ferritins consist of a hollow protein shell; the functional molecule, called apoferritin, comprises 24 chains and is roughly spherical, with an external diameter of 12.4-13 nm and an internal diameter of 7-8 nm. The central cavity is able to accommodate a core of up to 4500 Fe(m) atoms, mainly as ferric hydroxide-phosphate, (FeO(OH))g(FeO·P0 4 H 2). There are two types of ferritin subunits: L (light) and H (heavy); the major chain can be L or H, depending on species and tissue type. In clinical chemistry, low plasma ferritin is an indication of a decrease in the body's iron stores; a concentration of less than 12lig L- l indicates a complete absence of stored iron. Examples from human: H chain, database code FRIH_HUMAN, 182 amino acids (21.07 kDa) (3D structure known: database code NRL_IFHA); L chain, database code FRIL_HUMAN, 174 amino acids (19.87 kDa). ferritin-labelling the use of ferritin as an electron-dense label by covalently linking ferritin molecules with the aim of making their position in microscopic specimens apparent by electron microscopy. ferro+ comb. form denoting containing ferrous iron. ferrochelatase EC 4.99.1.1; systematic name: protoheme ferro-lyase; other names: protoheme ferro-lyase; heme synthetase; an enzyme of the pathway for heme biosynthesis. It catalyses the formation of protoheme from protoporphyrin and Fe2+ with release of 2 H+. Hereditary ferrochelatase deficiency occurs in humans and leads to porphyria with accumulation of protopyroxin IX. In bacteria the enzyme is part of siroheme synthase. Example (precursor) from human: database code HEMZ_HUMAN. ferrocytochrome any cytochrome in which the iron atom is in the Fe(n) state. ferroheme or (esp. Brit.) ferrohaem 1 heme. 2 any Fe(n)-porphyrin coordination complex. ferrohemochrome any hemochrome containing Fe(Il). ferromagnetism the property displayed by certain substances, typically metallic iron, that have a high magnetic susceptibility and that show increasing magnetization with increasing applied magnetic field strength. Some ferromagnetic materials retain their magnetization in the absence of an applied magnetic field, i.e. they become permanent magnets. Ferromagnetism is due to alignment, temporary or permanent, of the spins of the unpaired electrons in domains in the material. -ferromagnetic ad). Compare diamagnetism, paramagnetism. ferroprotoporphyrin see heme. ferrous of or containing divalent iron, Fe 2+ or Fe(n). ferroxamine see desferrioxamine. ferroxidase see ceruloplasmin. fertile 1 capable of producing offspring; capable of producing gametes. 2 capable of undergoing growth and development, e.g. fertile seeds or fertile eggs. fertility the state of being fertile. fertility factor an alternative name for Fplasmid. fertility vitamin a former name for vitamin E. fertilization or fertilisation 1 the fusion of two gametes of opposite sex to form a zygote. 2 the act or process of fertilizing. fertilize or fertilise 1 to provide a female gamete with a male gamete to effect fertilization. 2 to supply soil or water with mineral and/or organic nutrients to assist the growth of plants. fertilizer or fertiliser 1 any substance or mixture of substances that is added to soil or water to assist the growth of plants. 2 any object or organism, e.g. an insect, that fertilizes an animal or plant. fertilizin a mucopolysaccharide from the jelly-coat of the eggs of some species that plays a part in sperm recognition and attracts sperms of the same species. ferulic acid 4-hydroxy-3-methoxycinnamic acid; 3-(4-hy-

FGR droxy-3-methoxyphenyl)-2-propenoic acid; an aromatic acid widely distributed in plants. It is a component of suberin. FES/FPS a family of genes encoding nonreceptor tyrosine kinases; v-fps is an oncogene of Fujinami-PRCII sarcoma, while v-fes is a cognate gene of feline sarcoma virus. FES/FPS proteins contain an SH2 domain (see SH domain) adjacent to the kinase domain. Overexpression of c-fes transforms fibroblasts. Example (human): database code KFES_HUMAN, 822 amino acids (93.47 kDa). Fe-S protein abbr. for iron-sulfur protein. fet+ a variant form offeto+ (before a vowel). fetal calf serum abbr.: FCS; a serum prepared from the blood of a fetal calf, widely used in tissue culture media. fetal hemoglobin an alternative name for hemoglobin F (see hemoglobin) . fetal-lung maturity test a test for maturity of the fetal lung based on its content of dipalmitoylphosphatidylcholine (dipalmitoyllecithin). Dipalmitoyllecithin appears in lung surfactant in embryonic life only when the lung reaches maturity. Its concentration in amniotic fluid reflects its production in the lung and can be measured to determine lung maturity as a prenatal test to aid the decision when to induce labour. Formerly, the lecithin/sphingomyelin ratio was measured. feto+ or (before a vowel) fet+ comb. form denoting fetus. fetomodulin see l3-thromboglobulin. a-fetoprotein abbr.: afp or AFP; a protein formed in fetal liver and found in amniotic fluid. In humans, increased levels in the amniotic fluid between the 14th and 17th weeks of gestation reliably predict most cases of anencephaly and spina bifida cystica, and afp determination is performed as an antenatal screening test for such defects. Increased serum levels may be found in adults with hepatoma and teratoma; afp is a valuable marker for liver tumours, blood levels being elevated in about 70% of cases. The normal level in adult human plasma is CHOH groups, as in the acyclic form of v- or L-gulose. See monosaccharida. L-gulonolactone oxidase EC 1.1.3.8; other name: L-gulono-ylactone oxidase; a flavoprotein enzyme that catalyses the oxidation by dioxygen of L-gulono-I,4-lactone to L-xylohexulonolactone (I) and HzO z. I isomerizes spontaneously to L-ascorbate. The flavin is FAD. The enzyme is essential for the formation of ascorbate, and a deficiency of the enzyme, as in humans, results in dependency on a dietary supply of ascorbate (see ascorbic acid). Example from rat: GGLO_RAT, 439 amino acids (50.42 kDa). gulose symbol: Gul; the trivial name for the aldohexose gulohexose; a stereoisomer of glucose in which the configurations at both C-3 and C-4 are inverted. There are two enantiomers. (Illustrated opposite.) guluronic acid symbol: GuIA; the uronic acid resulting from the oxidation of the hydroxymethylene group at C-6 of gulose to a carboxyl group. L-Guluronic acid is a component of alginic acid.

Guthrie test

~oo OH OH gulose (p-o-pyranose form)

gum any of numerous water-soluble or water-dispersible heteroglycans, frequently containing uronic acids, that are produced as exudates from certain plants, especially trees, following physical injury. Gums are tacky, slimy substances that harden when dry. See also gum arabic, gum ghatti. gum arabic a gum exuded from trees of the genus Acacia. Structurally it is a heteroglycan containing D-galactose, L-arabinose, L-rhamnose, and D-glucuronic acid. It is used in industry, e.g. in the manufacture of thickening agents, emulsifiers, inks, and pills. It is also used in glues and pastes. gum ghatti a gum from the tree Anogeissus latifolia. It has a complex structure and contains as major components Dmannose, v-galactose, and L-arabinose, the latter in both furanose and pyranose arrangement. Small amounts of D-XYlose and D-glucuronic acid are also present. Gunn rat any member of a mutant strain of Wistar rats with hereditary hyperbilirubinemia. The defect affects the rate of glucuronidation of a number of substrates, but not equally. [After C. H. Gunn.) Giintelberg-MiUler charging process a method of calculating the electrical energy of an ion. According to the process, only the ion under consideration is supposed to receive a charge; the surrounding ions are assumed to be already charged, and the only change that they undergo during the process is a gradual redistribution as the central ion receives its charge. Guo symbol for a residue of the ribonucleoside guanosine (alternative to G). GuoP symbol for guanosine phosphate. Gu02'P symbol for guanosine 2'-phosphate; see guanosine phosphate. Guo-2'.3'-P symbol for guanosine 2',3'-phosphate; see guanosine phosphate. Gu03'P symbol for guanosine 3'-phosphate; see guanosine phosphate. Guo-3'.5'-P symbol for guanosine 3',5'-phosphate. Gu05'P symbol for guanosine 5'-phosphate. Guo5'PP symbol for guanosine diphosphate (alternative to ppG). GuoPPlCHzlP symbol for guanosine 5'-[~,y-methylene) triphosphate (alternative to p[CHz)ppG). GuoPPMan symbol for guanosinediphosphomannose. GuoPPlNHlP symbol for guanosine 5'-[f3,y-imido]triphosphate (alternative to p[NH)ppG). Gu05'PPP symbol for guanosine 5'-triphosphate (alternative to pppG). Gu05'PPPlSl symbol for guanosine 5'-y-thiotriphosphate. Guo5'PPlSl symbol for guanosine 5'-P-thiodiphosphate. gustducin a taste-cell-specific G-protein u subunit closely related to the transducins and comprising 354 amino acids. gut a term variously used to describe the whole of the alimentary canal or only the intestine, i.e. the part from the stomach to the anus. gut glucagon (sometimes) an alternative term for enteroglucagon. gut hormone a general. inaccurate, but widely used term for all the various regulatory peptides of the gut. They are neither confined to the gut, nor are they exclusively hormones. Guthrie test a microbiological test in which a strain of Bacillus

gutta-percha

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subtilis that requires phenylalanine for growth is used to test for excessive levels of plasma phenylalanine in conditions such as phenylketonuria. [After R. Guthrie (1916- ).] gutta-percha a trans-l A-polyisoprene derived by coagulation of the latex of various Malayan trees of the genus Palaquium. It has a lower molecular mass than rubber and is thermoplastic. GUU a codon in mRNA for L-valine. g-value a factor expressing the size of the magnetic moment of a paramagnetic chemical species. It specifies the position at

gyromagnetic ratio which the absorption in electron spin resonance of the paramagnetic species occurs. See electron spin resonance spectroscopy. Gy symbolfor gray. gynaminic acid formerly. a name for a constituent of human milk, now known to be identical with sialic acid. gynogamone see gamone. gyrase see type II DNA topoisomerase. gyromagnetic ratio or magnetogyric ratio symbol: y; the ratio of the magnetic moment, fl., of a given atomic particle to its angular momentum, L; i.e. / = fl.1L. See also proton magnetogyric ratio.

Hh h symbol for 1 hecto+ (SI prefix denoting 102 times). 2 hour (supersedes hr.). h symbol for 1 Planck constant. 2 Hill coefficient (alternative to nH)' 3 height. h+ or (not recommended) H+ prefix to abbreviations for peptide hormone (names) denoting human, i.e. of (or as if of) human origin; e.g. hGH (for human growth hormone). H symbol for 1 hydrogen; see also protium, deuterium, tritium. 2 a residue of the a-amino acid histidine (alternative to His). 3 a residue of an incompletely specified base in a nucleic-acid sequence that may be adenine, cytosine, or either thymine (in DNA) or uracil (in RNA). 4 henry. 5 histone. 6 histamine (see histamine receptor). H+ see h+. H1 a DNA-binding protein from Escherichia coli belonging to the H-NS family of proteins. H7 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine; an inhibitor of protein kinase C (Ki = 6.0 11M), protein kinase A (Kj = 3.0 11M), and cyclic GMP-dependent protein kinase (Kj = 5.8 IlM).

Hz symbol for 1 dihydrogen. 2 the prefix dihydro+ in a trivial chemical name, e.g. H 2folate for dihydrofolate. H4 symbol for the prefix tetrahydro+ in a trivial chemical name, e.g. H 4folate for tetrahydrofolate. H symbolfor 1 fluence (alternative to F). 2 enthalpy. 3 magnetic field strength (light italic in nonvector equations; bold italic in vector equations). -H conformational descriptor designating the half-chair conformation of a six-membered ring form of a monosaccharide or monosaccharide derivative. Locants of ring atoms that lie on the side of the structure's reference plane from which the numbering appears clockwise are indicated by left superscripts and those that lie on the other side of the reference plane by right subscripts; e.g. methyl 2,3-anhydro-5-thio-P-L-lyxopyranoside- 5H s. See also conformation. H- or (sometimes) H (in chemical nomenclature) symbol for indicated hydrogen (at the position specified by a prefixed locant). Haber, Fritz (1868-1934), German chemist; Nobel Laureate in Chemistry (1919) 'for the synthesis of ammonia from its elements'. Haber-Weiss reaction the iron-catalysed reaction of a superoxide anion with hydrogen peroxide to form oxygen, a hydroxyl radical, and a hydroxyl ion. It is thought to proceed as follows: 02- + Fe3+ -t O 2 + Fe2+ H 20 2 + Fe2+ -t OH' + OH- + Fe 3+ [After F. Haber and Joseph Weiss.] HAc abbr. for acetic acid. HACBP see calreticulin. haem a variant spellings (esp. Brit.) of heme.

haema+ or (before a vowel) haem+ variant spellings (esp. Brit.) ofhema+. haemadin an anticoagulant peptide from the Indian leech, Haemadipsa sylvestris. It is a slow tight-binding inhibitor of thrombin, but does not inhibit trypsin, chymotrypsin, factor Xa, or plasmin. It comprises 57 amino acids. haemato+ or (before a vowel) haemat+ variant spellings of (esp. Brit.) of hemato+. haemo+ a variant spelling (esp. Brit.) ofhemo+. haemoglobin a variant spelling (esp. Brit.) of hemoglobin. Hageman factor an alternative name for factor XII; see blood coagulation. hairpin any part of a linear molecular structure, e.g. of a polynucleotide strand or a prostaglandin, in which two adjacent segments of the molecule are folded back one on the other and held in that conformation by secondary molecular forces such as hydrogen bonds or van der Waals interactions. Hairpin DNA (or foldback DNA or loopback DNA) contains inverted repeats; when denatured it renatures extremely rapidly by concentration-independent intrachain base-pairing between complementary sequences of the inverted repeat. Similar structures occur in certain large RNA molecules. The hairpin conformation of a prostaglandin molecule is thought to be necessary for expression of its hormonal activity; in this conformation the a and K chains of each molecule are extended, parallel to one another, at van der Waals contact distance for their full lengths. See also ribozyme, beta bend. Haldane coefficient the difference, per bound dioxygen molecule, in the number of hydrons bound by oxy- and deoxyhemoglobin, at constant pH. [After John Scott Haldane (1860-1936), British physiologist.] Haldane effect the observation that oxygenated blood absorbs less carbon dioxide than deoxygenated blood. It is the reciprocal of the Bohr effect. Haldane gas-analysis apparatus an apparatus once used for the estimation of the carbon dioxide and dioxygen contents of a gas sample. Haldane relation a relation for reversible enzyme reactions. In the single-substrate, essentially reversible reaction: k

k

k

E+ s..,1. ES ~ EP~ E+ P k_[ k- 2 L 3 the overall equilibrium constant, K = Cp/Cs = kjk2k3Ik_jk_2k_3' where C s and Cp are the concentrations of substrate, S, and product, P, respectively. It can further be shown that K = VsKmp/VpKmS' where V s and Vp are the maximum velocities of the reactions S -t P in the absence of P and of P -t S in the absence of S, and Kms and K mp are the respective Michaelis constants for these reactions. [After John Burdon Sanderson Haldane (1892-1964), British biochemist, physiologist, and geneticist] half-boat conformation either of the conformations of a nonplanar monounsaturated six-membered ring compound when the two ring atoms not directly bound to the doubly bonded atoms lie on the same side of the plane containing the other four (adjacent) atoms. half-cell one half of an electric cell, consisting of one reversible electrode inserted into a solution. Electrical connection between this solution and that in another half-cell is required to complete the electric circuit. half-chair conformation 1 either of the conformations of a nonplanar monounsaturated six-membered ring compound when the two ring atoms not directly bound to the doubly bonded atoms lie on opposite sides of the plane containing the

288

half-cystine other four (adjacent) atoms. 2 any conformation of the sixmembered ring form of a monosaccharide or monosaccharide derivative when four adjacent ring atoms are coplanar and the other two lie on opposite sides of the plane. The conformational descriptor -H may be added to the name of such compounds. half-cystine or hemicystine symbol: ds or cis; the group formally derived by removal of a hydrogen atom from the thiol group on the side chain in cysteine (or a cysteine residue), or by homolysis of the dithio linkage in cystine (or a cystine residue). It is used in describing or depicting the content or the linear sequence of amino-acid residues in a polypeptide when it contains more than two apparent cysteine residues and the positions of any dithio linkages between them are not known, or when only a coded sequence is being considered. half-cystyl or hemicystyl the acyl group, 'S-CHz-CH(NH2)CO-, derived from the half-cystine group. Compare cysteinyl. half-ester any monoester of a dibasic acid. half-life 1 symbol: t,;, or T,;,; the time for one half of the atoms of an amount of radionuclide to undergo radioactive decay. 2 a similar measure of the stability (i.e. rate of decay) of an excited atom or molecule, a radical, an unstable elementary particle, etc. 3 the time for one half of the amount of an administered substance to be metabolized or excreted. If the substance is radioactive, the time required for one half of the dose to be eliminated biochemically or physiologically is termed the biological half-life and that required for one half to disappear by radioactive decay as well as by the elimination is the effective half-life. 4 or (sometimes) half-time symbol: t'I,; the time required for the concentration of a reactant in a chemical reaction to reach a value that is the arithmetic mean of its initial and final (equilibrium) values. 5 the time for one half of the number of cells in a tissue or organ to be replaced by new cells. half-of-the-sites reactivity or half-site reactivity a phenomenon shown by many enzymes that exhibit negative cooperativity, in which the maximal stoichiometric yield of either an enzyme-substrate intermediate or a product in a single turnover amounts to only half the number of apparently equivalent active sites. This may be caused by the binding of substrate to one site of a dimeric enzyme, e.g., inducing a conformational change in the enzyme so as to abolish completely the binding affinity of the other site. half-reaction either of the two coupled chemical changes that together constitute an oxidation-reduction reaction. In one half-reaction there is a gain of electrons and in the other halfreaction a corresponding loss of electrons. half-site reactivity an alternative name for half-of-the-sites reactivity. half-thickness the thickness of a piece of a specified material that will reduce the intensity of a beam of transmitted electromagnetic radiation to one half that of the incident beam. half-time an alternative name for half-life (def. 4) for a firstorder process. half-time of exchange the time taken for one half of the exchangeable atoms (or molecules) to be exchanged in a reaction involving such an exchange. half-wave potential the electrical potential at the mid-point of the current-voltage curve in polarography. halide or halogenide 1 an anion of any halogen. 2 a salt of any halogen acid (halogen hydride). 3 any compound containing halogen atoms in organic linkage. hallucinogen any drug or other substance that causes hallucinations. -hallucinogenic adj. halo+ or (sometimes before a vowel) hal+ comb. form 1 relating to or containing a halogen. 2 relating to the sea or salt. halochromism the phenomenon or property of the formation of strongly coloured compounds on the addition of strong acids or certain metallic salts to colourless or faintly coloured substances. halofantrine 1,3-dichloro-a-[2-(dibutylamino)-ethyl]-6-

handedness (trifluoromethyl)-9-phenanthrenemethanol; a derivative of 9-phenanthrenemethanol that is effective against chloroquineresistant malarial infections.

halogen any of the monovalent chemical elements of group 17 of the IUPAC periodic table: fluorine, chlorine, bromine, iodine, and astatine. halogenate to treat or react (a substance) with a halogen; to introduce one or more halo groups into an organic compound. -halogenation n. halogenide an alternative name for halide. haloperidol 4-[4-(4-chlorophenyl)-4-hydroxy-I-piperidinyl]-I(4-fluorophenyl)-I-butanone; one of the butyrophenone group of neuroleptic drugs.

FY')~CI ~N o

~ OH

I

halophile 1 an organism that grows in or tolerates saline conditions, especially concentrations of sodium chloride equal to or greater than that in sea water. 2 describing such an organism. -halophilic adj. halorhodopsin an energy-transducing pigment identified in membranes of Halobacterium halobium. It is similar to, but distinct from bacteriorhodopsin and is associated with a lightdriven pump for sodium ions. halothane the trivial name for 2-bromo-2-chloro-I,I,I-trifluoroethane, a widely used, volatile, lipid-soluble general inhalational anesthetic agent.

hamamelose 2-C-(hydroxymethyl)-D-ribose; a substance found principally in tannin of witch hazel (Hamamelis virginiana). Hamburger shift an alternative name for chloride shift. Hamiltonian operator symbol: H; a function used to express the total energy of a system in joules: H = T + V, where Tis the kinetic energy operator and V the potential energy operator. For a particle of mass m and momentum p, H = p 2/2m + V. [After William Rowan Hamilton (1805-65), Irish astronomer and mathematician.] hammerhead see ribozyme. handedness a form of terminology (based on the human left and right hands) for describing objects and compounds that

289

handle are mirror images of each other and hence nonsuperimposable. A pair of enantiomers display molecular handedness. See chirality. handle a colloquial term for any chemical group attached to a specified substance with the purpose of making it more easily identified, more reactive, or more easily operated upon, or one that may serve in targeting or specific binding. The attachment of a handle may be brought about chemically or metabolically. handle technique a technique used to separate excess alkylating agents from products in peptide synthesis. For instance, the C terminus of a growing peptide chain can be protected with a basic function, e.g. by forming a 4-picolyl ester of the carboxyl group, thereby allowing separation of the products on cation-exchange resin columns or by extraction into aqueous acidic solutions. Hanes plot a graphical method for treating enzyme kinetic data using the following form of the Michaelis equation (see Michaelis kinetics): slv = KmlV + slV where s is the substrate concentration, v is the velocity of the reaction, and V is the limiting rate. If slv is plotted against s, the slope of the resulting straight line is l/V, the intercept on the slv axis is KmlV, and the intercept on the s axis is -Km. [After Charles Samuel Hanes (1903-90), British biochemist.] Hanks' balanced sah solution abbr.: HBSS; a balanced salt solution used in tissue culture to provide a suitable ionic and osmotic environment for cell growth and development. It contains, per 100 mL of distilled water, 0.8 g NaCl, 0.04 g KCI, 0.01855 g CaCI 2'IH 20, 0.02 g MgS0 4'7H 20, 0.006 g KH 2P0 4, 0.00475 g Na2HP04, 0.0350 g NaHC0 3 , 0.1 g glucose, and 0.0017 g sodium Phenol Red. The pH is 7.0-7.2. Hansch equation an equation relating the differences in the partitions of variously substituted compounds between an organic and an aqueous phase to the hydrophobicity constant, n, of the substituent. If Po is the ratio of the solubility of the parent compound in an organic phase to that in the aqueous phase, and P is the corresponding ratio for the substituted compound, then: n = 10g(PIPo). HansGnula see methylotrophic yeasts. H antigen see blood-group substance. haploid describing a cell, an organism or a nucleus of a cell having a single genome or a single set of homologous chromosomes; i.e. containing half the diploid number; having a ploidy of one. -haploidy n. haplotype a set of genes located on a single chromosome; the term is used also to denote the characteristics dependent on those genes. In outbred populations the maternal and paternal chromosomes usually differ, so an individual has two haplotypes, one derived from each parent. 'happiness hormone' a jocular name for any endorphin or enkephalin, so-named because of the supposed ability of such substances to promote a sense of well-being. hapt+ a variant form of hapto+ (before a vowel). hapten any, usually small, substance that can combine specifically with antibody but that is not immunogenic unless bound to a carrier (def. 8). Most haptens carry only one or two antigenic determinants. -haptenic adj. hapten-inhibition test a serological test for characterizing an antigenic determinant. It involves the use of haptens of known structure to block the combining site of a particular antibody. hapten-sandwich labelling a variant of the sandwich technique for amplification of an antigen-antibody reaction. In this modification, the primary antibody, specific for the antigen of interest, is combined with a number of residues of a hapten, e.g. p-azobenzene arsonate. The secondary (labelled or marked) antibody is a specific anti-hapten antibody; on reaction of secondary antibody molecules with a molecule of primary antibody, the hapten residues become sandwiched between the large molecules of antibody. By the use of different

Harden haptens and two or more non-cross-reactive anti-hapten antibodies bearing distinguishable markers, two or more antigens on the same or different cells may simultaneously be labelled. hapticity symbol: 1/; the attribute of a ligand entity or group that combines with a central (usually metal) atom to form a coordination entity in which the central atom is bonded to two or more contiguous atoms of the ligand rather than to a specific atom. Such a coordination entity is frequently (but not exclusively) a pi adduct. See also hapto. hapto or (less commonly) eta (in chemical nomenclature) the name by which to read the symbol 1/- (Greek eta), when prefixed to the name of the ligand group in a coordination entity (with added locants if appropriate) to indicate hapticity. hapto+ or (before a vowel) hapt+ comb. form indicating ability to bind or combine. haptocorrin a blood cobalamin-binding glycoprotein that may prevent uptake of bacterial cobalamin analogues. Example from Sus scrofa (fragment): database code HAPC_PIG, 416 amino acids (46.91 kDa). haptoglobin abbr.: Hp; any U2 globulin of blood plasma that can combine with free oxyhemoglobin to form a stable, ~300 kDa, complex. Such combinations occur when hemoglobin is liberated in the blood, and the complexes so formed, which have weak peroxidase activity and cannot be filtered by the kidney, are rapidly removed and degraded in the tissues. Three human haptoglobin phenotypes are known, designated Hp 1-1, Hp 2-2, and Hp 2-1, each of which contains two pairs of nonidentical polypeptide chains, U and P, joined by disulfide bonds. There are two kinds of u chain, Ul of 84 amino-acid residues (9 kDa) and U2 of 143 residues (17 kDa), and a single kind of P chain, of 244 residues (in human). The U2 chain, found solely in human haptoglobin, is identical in sequence to that of residues 1-71 or 1-72 of an Ut chain linked to residues 11 or 12 to 84. The basic subunit structure of Hp 1-1 is (uIPb that of Hp 2-2, (u2Pb and that of Hp 2-1, (U2P)(UIP), However, the U2 chain has an odd number of half-cystine residues, as a consequence of which larger oligomers of Hp 2-2 and Hp 2-1 may arise by formation of disulfide bonds with a2 chains of other molecules or of (U2P) half-molecules. Example (precursor) from human: database code HPTI_HUMAN, 347 amino acids (38.45 kDa). haptomer any substance (such as a lectin or the B fragment of diphtheria toxin) that can interact with the cell membrane and that binds or can be bound to an effectomer (such as gelonin or the A fragment of diphtheria toxin), thereby allowing the effectomer to exert its toxic action on intact cells. -haptomeric adj. haptophore a term introduced by Ehrlich to denote the specific chemical group in a toxin (i.e. antigen) molecule that attaches it to an antitoxin (i.e. antibody) molecule. Unlike the toxophore, it is not destroyed on conversion of the toxin to a toxoid. H+(aq) symbol for the hydrated hydrogen ion, the normal state of the hydrogen ion in aqueous solutions, consisting of a hydron surrounded by a shell of water molecules held by ion-dipole interaction. Compare oxonium (def. I). hard (in radiation physics) describing corpuscular or electromagnetic ionizing radiation (especially beta particles or X- or gamma-radiation) having relatively high energy, hence high ionizing power and long-range or high penetrating power. Hard X- or gamma-radiation has short wavelengths. Compare sott(def. I). Harden, (Sir) Arthur (1865-1940), British chemist and biochemist distinguished for his discoveries (with W. J. Young) that fermentation of sugar by yeast juice involved a heat-stable and separable fraction (later named cozymase by H. von Euler), required the presence of phosphate, and (also with R. Robison) resulted in the intermediate formation of two hexose phosphates (see Harden-Young ester, Robison ester); Nobel Laureate in Chemistry (1929), the prize being shared with H. von Euler 'for their investigations on the fermentation of sugar and fermentative enzymes'.

290

Hardltn-Young ester

Haworth representation

Harden-Young ester a former name for D-fructose 1,6-bisphosphate (before its chemical ~tructure had been elucidated). [After A. Harden and William John Young (1878-1942), British biochemists.) Hardy-Weinberg law a mathematical statement about the relation between gene frequencies and genotype frequencies within a population. If the genotypes are AA, Aa, and aa, and p is the frequency of allele A in the population, and q the frequency of allele a, so that p + q == I, then the relative proportions of the three genotypes in the population, AA:Aa:aa, is given by p2:2pq:q2. [After Godfrey Harold Hardy (1877-1947), British mathematician, and Wilhelm Weinberg (1862-1937), German physician.) harmaline 4,9-dihydro-7-methoxy-I-methyl-3H-pyrido[3,4b)indole; dihydroharmine: a cardioactive alkaloid from Syrian rue, Peganum harmala that also has hallucinogenic properties. See also harmidll. H

CH s

C~~

harmine }-methoxy-I-methyl-9H-pyrido[3,4-b)indole; a fJ-carboline alkaloid found hi, e.g., Peganum harmala (Syrian rue). It inhibits monoamirie oxidase and is a central nervous system stimulant. See also harmaline.

H~RT abbr. for,hybrid-arrested translation. Hartley filter funnel a development of the Biichner funnel comprising thre~. pieces, the reservoir, a perforated plate to support the filter disk, and a conical piece to collect the filtrate. [After (Sir) Percival Hartley (1881-1957), British bacteriologist.) Hartline, Haldan Keffer. (1903-83), US neurophysiologist; Nobel Laureate in Physiology or Medicine (1967) jointly with R. Granit an~ G. Wald 'for their discoveries concerning the primary physiological and chemical visual processes in the eye'. Hartnup disease a rare, llutosomal recessively inherited condition of humans in which there is a specific hyperaminoaciduria and indoluria, due to a diminished capacity for renal reabsorption of a group of monoamino-monocarboxylic acids, especially tryptophlln. There may lllso be an impaired transport of the same group of amino acids across the gut wall. The aminoaciduria is often associated with a pellagralike .skin rash, due to inefficient tryptophan utilization and metabolism. The pellagra may often be resolved by oral nicotinic acid. The primary defect remains unknown. [After E. Hartnup, the first patient with the condition to be described.) hashish a resinous extract obtained from the dried flower tops of the hemp plant (Cannabis sativa). The term may sometimes be used for various other extracts. See cannabis. Hassel, Odd (1897-1981), Norwegian physical chemist; Nobel Laureate in Chemistry (1969), the prize being shared with D. H. R. Barton 'for their contributions to the development of the concept of conformation and its application in chemistry'. HAT abbr. for hypoxanthine-aminopterin-thymidine (medium); a selective medium used in tissue culture. It is of particular use in the production of hybridomas. The medium was originally devised to select against cells deficient in hypoxanthine-gua-

nine phosphoribosyltransferase (HGPRT' cells). Amethopterin blocks de novo synthesis of purines and HGPRT cells are unable to utilize the salvage pathway, and hence are killed. hatching enzyme see envelysin. Hatch-Slack pathway or C 4 cycle or C 4 pathway a metabolic pathway for carbon-dioxide translocation occurring in C4 plants. In the mesophyII cells phosphoenolpyruvate carboxylase catalyses the condensation of CO 2 with phosphoenolpyruvate to form oxaloacetate; this is then reduced to malate by lightgenerated NADPH. The malate passes into the bundle-sheath cells where it is oxidatively decarboxylated by the malic enzyme to pyruvate and CO 2 ; the pyruvate returns to the mesophyll cells and is reconverted to phosphoenolpyruvate by ATP and pyruvate dikinase; the CO 2 remains in the bundle-sheath cells where it enters the reductive pentose phosphate cycle. The overall effect of the pathway is to carry CO 2 from the mesophyll cells, which are in contact with air, to the bundle-sheath cells, which are the major sites of photosynthesis. Haworth, (Sir) Walter Norman (1883-1950), British organic chemist noted for his structural studies on monosaccharides (see also Haworth representation) and polysaccharides and for producing the first chemical synthesis of ascorbic acid, vitamin C; Nobel Laureate in Chemistry (1937) 'for his investigations on carbohydrates and vitamin C' [prize shared with P. Karrer). Haworth representation a diagrammatic way of unambiguously representing the structural formulae of the cyclic forms of monosaccharides to show on a plane surface the relative configurational arrangements of the atoms and groups in space. Pyranoses are represented by a hexagon (five carbons and one oxygen) and furanoses by a pentagon (four carbons and one oxygen). A Haworth representation is derived from a Fischer projection as follows. The monosaccharide in question is depicted with the carbon-chain horizontal and in the plane of the paper, the potential carbonyl group being to the right. The oxygen bridge is then depicted as being formed behind the plane of the paper. The heterocyclic ring is therefore located in a plane approximately perpendicular to the plane of the paper and the groups attached to the carbon atoms of that ring are above and below the ring. The edge of the ring nearer the viewer is indicated by thickened lines. For clarity, the carbon atoms of the ring and their attached hydrogen atoms are not shown. Groups that, in the Fischer projection, appear to the right of the vertical chain then appear in the Haworth representation below the plane of the ring. However, at the asymmetric carbon atom involved via oxygen in ring formation

a-D

a-L

(e.g. C-5 in glucopyranose, C-4 in glucofuranose), a rotation about the bond to the preceding carbon atom must be envisaged in order to bring that oxygen atom into the correct orientation to link to the carbon atom of the carbonyl group. Thus, if the hydroxyl group that is engaged in ring formation lies to the right in the Fischer projection, the group that lies below it must point upwards in the Haworth representation, whereas if it lies to the left, it must point down in the Haworth representation. In representing the a and fJ anomers in the Haworth convention, it should be noted that for the a anomer, the anorneric hydroxyl points in the opposite direction to the R group (see structure); for o-sugars, the R group points upwards, so the a-hydroxyl must point down; conversely, if the R group points down (as in a-L-glucose), the a anomeric hydroxyl must point upwards. The above rules only obtain if the

291

Hb ring is numbered clockwise from the anomeric carbon, as is frequently the case, and it is important to appreciate that Haworth representations, unlike Fischer projections, cannot be rotated in the plane of the paper but must be reorientated in space. Hb abbr. and symbol for hemoglobin; hence, e.g., HbO z symbolizes oxyhemoglobin, and HbCO symbolizes carbonmonoxyhemoglobin. Hb A abbr. for adult hemoglobin. H band an alternative name for H zone (see sarcomere). HBD (in clinical chemistry) abbr. for a-hydroxybutyrate dehydrogenase, the LD 1 isoenzyme of lactate dehydrogenase, or 'heart-specific' lactate dehydrogenase, which is assayed using 2-hydroxybutanoate as substrate, a substance that does not occur naturally. Hb F abbr. for fetal hemoglobin. Hb S abbr. for sickle-cell hemoglobin; see sickle cell. HBSS abbr. for Hanks' balanced salt solution. hCG or HCG abbr. for human choriogonadotropin (see choriogonadotropin). H chain see heavy chain. HCO symbol for the formyl group (alternative to For). HCR abbr. for host-cell reactivation. Hey symbol for a residue of the a-amino acid L-homocysteine. HDEL a four-residue motif, His-Asp-Glu-Leu, of similar function to the KDEL motif. HDH abbr. for histidinol dehydrogenase. HDL abbr. for high-density lipoprotein. HDP abbr. for helix-destabilizing protein. He symbolfor helium. head 1 the foremost or uppermost part of the body of an animal; in vertebrates it comprises the skull containing the mouth, brain, and the organs of hearing, sight, smell, and taste. 2 the part of a molecular structure that bears a specific functional group or that is polar, reactive, bulky, or in some other characteristic way differs from the remainder of the molecule. 3 a common name for a centrifuge rotor. headgroup of a polar lipid, that part of the molecule that expresses its polar character. For a phospholipid, this comprises the phosphate group together with any polar entity attached to it. For a glycolipid, it comprises the carbohydrate moiety. headspace analysis a technique used in the identification of microorganisms involving gas-chromatographic analysis of the vapour in the headspace above the specimen or culture. heat symbol: q or Q; the energy possessed by a system in the form of kinetic energy of atomic or molecular translation, rotation, or vibration. It is measured in joules or calories. Heat energy can be transferred from points of higher temperature to points of lower temperature by conduction, convection, or radiation. When the temperature of a system changes, its enthalpy (heat content) changes by an amount equal to the product of its mass, specific heat capacity, and its change in temperature. heat capacity symbol: C; the amount of heat required to raise the temperature of a body or a system by I kelvin; it is usually measured in joules per kelvin. The heat capacity at constant pressure, Cpo is given by: Cp = (aHlanp J K-l and the heat capacity at constant volume, C v• is given by: Cv = (aU/anv J K- 1 where H is the enthalpy, U the internal energy, and T the thermodynamic temperature. heat content another name for enthalpy. heat-labile describing molecules that decompose at elevated temperatures or that lose biological activity when heated to a moderate temperature, e.g. 50 ·C. heat of activation the difference in heat content between a transition state and the state of its reactants. heat of combustion the amount of heat evolved when a given amount, usually one mole, of a substance is completely burnt in dioxygen. heat of evaporation an alternative name for heat of vaporization. heat of formation the amount of heat absorbed or evolved when one mole of a substance is formed from its elements.

heavy-chain switch heat of fusion or heat of melting the amount of heat absorbed or evolved when a specified quantity of substance, usually one mole, is converted from the solid to the liquid state at a specified pressure and a specified temperature. If the pressure is I atm the temperature is the melting point of the substance. heat of neutralization the amount of heat absorbed or evolved when one mole of an acid or base is completely neutralized. heat of reaction the amount of heat absorbed or evolved in the course of a (bio)chemical reaction, usually expressed per mole of reacting substances. heat of solution the amount of heat absorbed or evolved when one mole of a substance is dissolved in a large volume of specified solvent. heat of vaporization or beat of evaporation the amount of heat absorbed or evolved when a specified amount of substance, usually I mole, is converted from the liquid to the vapour state at a specified pressure and a specified temperature. If the pressure is I atm the temperature is the boiling point. heat-shock protein abbr.: hsp; any of a group of specific proteins that are synthesized by both prokaryotic and eukaryotic cells, e.g. bacteria, yeasts, and Drosophila, after they have been exposed to a temperature that is higher than normal. Other stresses, such as free-radical damage, have a similar effect. Many members of the hsp family are not induced but are normally present in all cells. Human cells in culture also produce heat-shock proteins but the induction of heat-shock proteins has not been clearly demonstrated in the human body. The heat-shock proteins are classified, according to their size, in three classes, Hsp60, Hsp70, and Hsp90. They are characterized by their role as molecular chaperones. A major chaperone in the lumen of the endoplasmic reticulum is binding protein, a member of the Hsp70 class. These proteins are highly conserved in structure so that the proteins from Escherichia coli and human are 50% identical in primary structure. The Hsp70 proteins possess ATPase and peptide binding domains. The other members of the Hsp70 class are Grp75 in mitochondria and DnaK in bacterial cytosol. In the Hsp60 class is GroEL in bacterial cytosol (see grofL). Example, hsp71: database code HS71_HUMAN, 641 amino acids (69.97 kDa). heat-shock regulatory element or heat-shock response element abbr.: HSE; a base sequence in prokaryotic and eukaryotic genomes responsible for regulating gene expression in response to heat-shock and related stress situations. heat-shock response element see HSE. heat-stable describing something that retains its (bio)chemical activity when heated to a moderate temperature, e.g. 50 ·C. heavy (in physics) of more than the usual mass. Compare light (def. 2). heavy atom or heavy isotope or heavy nuclide an isotopic form of an atom that contains more than the common number of neutrons and is thus of greater relative atomic mass than the most abundant or most commonly observed isotope. heavy carbon see carbon-13. heavy chain or H chain the heavier of the two types of polypeptide chain found in immunoglobulin molecules. Each heavy chain is linked, usually by disulfide bonds, to a light chain and to another, identical heavy chain. Heavy chains differ in relative molecular mass according to the type of immunoglobulin: in humans the M r is ~50 000 in IgG and ~70 000 in IgM. Each heavy chain consists of an Fe fragment and an Fd fragment. Heavy chains carry the antigenic determinants that differentiate the various immunoglobulin classes. heavy-chain disease a rare disease of humans in which there are tumours of lymphoid tissue associated with the presence of free immunoglobulin fragments in plasma and urine. heavy-chain switch or H-chain switch the change in the expression of the immunoglobulin heavy chain (H chain) gene system as manifested by the predominance of IgM (11 chain class) in the primary immune response and by the predominance of IgG (1 chain class) in the secondary immune response.

292 heavy hydrogen heavy hydrogen an alternative name for deuterium. heavy meromyosin abbr.: H-meromyosin or HMM; a 350 kDa fragment produced when myosin is subjected to tryptic digestion. It contains part of the helical, rod-shaped tail and both the attached globular heads of the original myosin molecule. Heavy meromyosin retains both the ATPase and the actin-binding activity of myosin. heavy nitrogen the stable nuclide I~N (nitrogen-IS); relative abundance in natural nitrogen 0.37 atom percent. It is used as a tracer in studies of nitrogen metabolism. heavy oxygen the stable nuclide \~O (oxygen-18), usually accompanied by the stable nuclide l~O (oxygen-I 7); relative abundances in natural oxygen: I~O, 0.20 atom percent; I'SO, 0.037 atom percent. \~O is used as a tracer in studies of reaction mechanisms and of oxygen metabolism. heavy strand or H strand 1 any polynucleotide chain labelled with a heavy isotope, e.g. nitrogen-IS. 2 any naturally occurring chain in a polynucleotide duplex that is heavier or has a greater density than the complementary strand. heavy water deuterium oxide; symbol: 2H 20 or D 20; water in which the hydrogen atoms in all of the molecules have been replaced by deuterium; or water in which the hydrogen is appreciably enriched in deuterium. The M r of pure 2H 20 is 20.028. Heavy water is prepared from natural water by exchange techniques or by fractional distillation or electrolysis. It is used as a tracer in metabolic studies, in investigation of reaction mechanisms, and as a solvent in resonance spectroscopy. hect+ see hecto+ (def. 2). hecto+ 1 symbol: h; an SI prefix denoting 102 times. 2 or (before a vowel) hect+ denoting 100 or 100 times. hedgehog protein a transmembrane protein involved in segment polarity and cell-to-cell signalling during embryogenesis and metamorphosis in Drosophila melanogaster. Database code (precursor): HH_DROME, 471 amino acids (52.03 kDa). See also sonic hedgehog protein. HEDTA abbr. for N-(2-hydroxyethyl)ethylenediamine triacetate, or its trisodium salt, or for its partially or fully protonated forms. It is a chelating agent, especially for ferric ions in the pH range 7.0-10.0.

HEETP abbr. for height equivalent to an effective theoretical plate. Heidelberger, Michael (1888-1991), US pathologist described as the father of modern immunology. The recipient of numerous awards, he continued to carry out research almost to the end of his life at age 103. height equivalent to an effective theoretical plate abbr. : HEETP; symbol: H; (in chromatography) the column length divided by the effective theoretical plate number. height equivalent to a theoretical plate or plate height abbr.: HETP; symbol: h; (in chromatography) the column length divided by the theoretical plate number. Heisenberg, Werner Karl (1901-76), German theoretical physicist renowned for his work on quantum theory and atomic structure and for advancing (in 1927) the theory known later as the Heisenberg uncertainty principle; Nobel Laureate in Physics (1932) 'for the creation of quantum mechanics', the application of which has, inter alia, led to the discovery of the allotropic forms of hydrogen'. Heisenberg uncertainty principle the principle that the simultaneous precise determination of the velocity (or any

helper peak-1 related property, e.g. momentum or energy) of a material particle and its position is impossible; the smaller the particle the greater the degree of uncertainty. [After Werner Karl Heisenberg (1901-76), German physicist; Nobel Laureate in Physics (1932).] HeLa cell an established tissue culture strain of human epidermoid carcinoma cells containing 70-80 chromosomes per cell (compared with 46 in normal cells). It is much used for biochemical work. HeLa cells have been in continuous culture since 8 February 19SI, and were derived from tissue removed from a patient named Henrietta Lacks. helical cross a name sometimes given to the X-shaped pattern of X-ray scattering from a continuous helical molecule. helicase a name sometimes given to the protein (repA) that promotes the ATP-dependent unwinding of the parental DNA duplex during DNA replication. See also DNA helicase, RNA helicase. helicorubin a b-type cytochrome that occurs in the hepatopancreas of the snail Helix pomatia and related species. helix (pl. helices) 1 a coiled or spiral structure, e.g. the thread of a bolt or a coil (tubular) spring. See also alpha helix, beta helix, gamma helix. 2 the curve traced on the surface of a cylinder or cone by a point crossing its right sections at a constant angle. 3 a space curve with turns of constant angle to the base and constant distance from the axis. -helical adj.; helicity n. helix breaker any amino-acid residue that, whenever it occurs in a polypeptide chain, interrupts the a-helical structure; e.g. proline, hydroxyproline, and, sometimes, other residues. helix-destabilizing protein abbr.: HDP; any of a group of proteins that bind tightly and preferentially to single-stranded DNA. They have, theoretically, the following properties: (I) they lower the melting temperature, T m , for thermally induced helix-to-coil transition; (2) they lower the optimum temperature for duplex renaturation; (3) they sterically hinder base pairing and the degradation of single strands by nucleases; (4) they induce a conformation for the single-stranded DNA that is optimal for its function in some processes, e.g. as a template in replication; and (S) they interact with other proteins (enzymes) to potentiate some process involving single-stranded DNA and these proteins. helix former any amino-acid residue that, whenever it is present in a polypeptide chain, tends to promote an a-helical structure. Compare helix breaker. helix-loop-helix abbr.: HLH; an alternative term for helix-turnhelix. helix-to-coil transition the transition of a macromolecule (polypeptide or polynucleotide) from an ordered to a disordered structure; it is equivalent to denaturation. Helix-to-coil transitions are usually detected by monitoring a change in some physical property of the macromolecule such as intrinsic viscosity, optical absorbance, or sedimentation coefficient. See also melting temperature. helix-turn-helix (abbr.: HTH) or helix-loop-helix (abbr.: HLH) a protein structural feature consisting of two helices separated by a short beta turn. It is found in several DNA-binding regulatory proteins; there are two sequence motifs. helix winding number see supercoil. helodermin see exendin. helospectin I see exendin. helper cell abbr.: T H cell; a T lymphocyte, carrying the surface markers CD4 and CDS in the human (L3T4 and Lyl in the mouse), that acts as an inducer of the effector cells for both humoral and cell-mediated immunity. Helper cells recognize and bind to antigen in combination with class II major histocompatibility complex molecules on the surface of antigen-presenting cells, and generate lymphokines that stimulate effector cytotoxic cells and B cells. Other cells of the helper phenotype, e.g. CD4+ cells, are known as T-suppressor cells and are responsible for suppression, exerting negative feedback control on the helper cells. helper peak-1 abbr.: HP-I; aformer name for interleukin 1.

293

heme

helper virus helper virus any virus that supplies one or more of the functions that a defective virus is unable to perform. When a cell is infected with both a defective virus and a helper virus, the former is able to replicate, a property that can be exploited in various molecular biological techniques. hem+ or (esp. Brit.) haem+ a variant form of hemo+ (before a vowel). hema+ or (esp. Brit.) haema+ a variant form of hemo+. hemagglutination or (esp. Brit.) haemagglutination the agglutination of red blood cells. hemagglutinin or (esp. Brit.) haemagglutinin 1 any IIgglutinin of red blood cells. 2 any non antibody substance, e.g. a lectin or a surface component of some virus particles, that can agglutinate red blood cells. 3 a viral envelope glycoprotein responsible for the attachment of virus to cell receptors and the initiation of infection. Example from influenza A virus (strain A/Aichi/2/68) (precursor): database code HEMA_IAAIC, 566 amino acids (63.34 kDa); 3-D structure known (much ~ structure). hemat+ or (esp. Brit.) haemat+ a variant form of hemato+ (before a vowel). hematin or (esp. Brit.) haematin 1 or ferriheme hydroxide the trivial name for ferriprotoporphyrin hydroxide (formerly called ferriprotoporphyrin IX hydroxide); hydroxo(protoporphyrinato)iron(m); hydroxoiron(m) protoporphyrinate. Compare heme (def. I), hemin (def. 1).2 the generic name for any hydroxo(porphyrinato )iron(m) coordination complex.

the trivial name for 2,7,12, 18-tetramethyl-3,8-bis(l-hydroxyethyl)porphyrin-13, 17-dipropionic acid; the porphyrin formed from heme (def. I) or a heme-containing protein on treatment with hydrogen bromide in glacial acetic acid.

COOH

COOH

hematoside or ( esp. Brit.) haematoside a ganglioside, NeuAc(a2-3)Gal(pl-4)GIc(pl-I)Cer, found in red blood cells. hematoxylin or (esp. Brit.) haematoxylin 7,lIb-dihydrobenz[b]indeno[l,2-djpyran-3,4,6a,9,IO(6H)-pentol; a dye isolated from the heartwood of logwood, Haematoxylon campechianum L. Colourless or yellowish, it turns red on exposure to light, and is used as a stain in microscopy.

OH

COOH

COOH

hemato+ or (before a vowel) hemat+ comb. form denoting blood. Also (esp. Brit.): haemato+, haemat+. See also hemo+. hematocrit or (esp. Brit.) haematocrit 1 or packed red cell volume the proportion of the volume of a sample of blood that is represented by the red blood cells. 2 an apparatus, essentially a graduated centrifuge tube, used to determine the proportion of the volume of a sample of blood that is represented by the red blood cells. hematocrit technique or (esp. Brit.) haematocrit technique a method for the rapid isolation of mitochondria or other particles, in which they are separated from the medium by centrifugation through a layer of silicone fluid. The latter is immiscible with water, and of a density intermediate between that of the particles to be separated and that of the medium. A high-density aqueous 'fixative' beneath the silicone layer can be used to stabilize labile compounds in the mitochondria or other particles. Compare hemlltocrit (def. 2). hematology or (esp. Brit.) haematology the branch of medicine concerned with diseases of the blood or of the bloodforming tissues. hematolysis or (esp. Brit.) haematolysis an alternative name for hemolysis. hematopoiesis or (esp. Brit.) haematopoiesis an alternative name for hemopoiesis. hematoporphyrin or (esp. Brit.) haematoporphyrin or (formerly) hematoporphyrin IX or (esp. Brit.) haematoporphyrin IX

hematuria or (esp. Brit.) haematuria the presence of red blood cells in the urine. It can be due to lesions in the urinary tract, but also to glomerular disease of the kidney. heme or (esp. Brit.) haem 1 or ferroheme or ferrohaem or protoheme the trivial name for ferroprotoporphyrin (formerly called ferroprotoporphyrin IX); 2,7,12, 18-tetramethyl-3,8-divinylporphyrin-13,17-dipropionic acid iron(n) coordination complex. It occurs free and as the prosthetic group of a number of

COOH

COOH

heme (def. 1)

hemoproteins, e.g. hemoglobins, erythrocruorins, myoglobins, some peroxidases, catalases, and cytochromes b. Compare

heme-heme interaction hematin (def. 1), hemin (def. 1). 2 the generic name for any iron-porphyrin coordination complex irrespective of the valence state of the iron atom (which may be specified). The name of an individual heme is derived from that of the corresponding porphyrin; e.g. cytoheme (from cytoporphyrin) and ferroprotoheme (from protoporphyrin). For biosynthesis, see tetrapyrrole. heme-heme interaction or (esp. Brit.) haem-haem interaction the cooperative interaction between the various heme binding sites for dioxygen molecules that occurs when dioxygen binds with hemoglobin; as oxygenation proceeds, the combination of additional dioxygen molecules is made easier. heme pocket or (esp. Brit.) haem pocket a hydrophobic crevice in the tertiary structure of myoglobin, or of a subunit of hemoglobin, into which the heme group fits. The nonpolar vinyl side chains of the heme are buried in the interior of the pocket, while the hydrophilic propionate side-chains project out of the pocket towards the surface of the molecule. heme protein or (esp. Brit.) haem protein an alternative name for hemoprotein. hemerythrin or (esp. Brit.) haemerythrin an oxygen carrier found in a few groups of invertebrates, e.g. sipunculid worms, certain molluscs, and crustaceans. It is a nonheme iron-containing protein, the subunits of which each contain about 113 amino-acid residues. Each monomer has an active site containing two atoms of Fe(n), 0.34 nm apart, between which a dioxygen molecule is thought to fit. The molecule is a homooctamer. Example from Themiste dyscritum: database code HEMT_THEDY, 113 amino acids (13.30 kDa); 3-D structure known. heme synthetase see ferrochelatase. heme-thiolate protein or (esp. Brit.) haem-thiolate protein see P450. hemi+ prefix denoting half, or affecting one half. Compare semi+. hemiacetal see acetal. hemicellulose any or all of the cell-wall polysaccharides that are extractable from wood or other plant material with aqueous alkali (in which cellulose itself is insoluble). Hemicelluloses are chiefly xylans, but other homoglycans or heteroglycans containing hexose and/or pentose residues, uronic acid-containing xylans, and other pectic substances may also be present. hemicystine an alternative name for half-cystine. hemicystyl an alternative name for half-cystyl. hemidesmosome a specialized cell junction between an epithelial cell and its underlying basal lamina. These resemble desmosomes morphologically but are chemically and functionally distinct. Between the cell membrane and the underlying connective tissue is a specialized mat of extracellular matrix sometimes known as the linker. The transmembrane linker proteins belong to the integrin family of extracellular matrix receptors rather than the cadherin family of cell-cell adhesion proteins found in desmosomes. hemidiaphragm a muscle preparation widely used for metabolic studies in vitro, consisting of either of the two excised and separated left and right halves of the diaphragm, usually from a rat. hemiketal see acetal. Hemimetabola or Exopterygota one of the two divisions of the subclass Pterygota, comprising those insects, e.g. cockroaches, locusts, and grasshoppers, in which the juvenile forms resemble the adults, except for their lack of fully developed wings. Such insects undergo incomplete metamorphosis. Compare Holometabola. hemin or (esp. Brit.) haemin 1 or ferriheme chloride or protohemin the trivial name for ferriprotoporphyrin chloride (formerly called ferriprotoporphyrin IX chloride); chloro(protoporphyrinato)iron(m); chloroiron(m) protoporphyrinate. Compare heme (def. I), hematin (def. 1).2 the generic name for any chloro(porphyrinato)iron(m) coordination complex. hemiport a model of translocation of solutes across mem-

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hemoglobin branes, based on the possibility that there is interaction through the membrane between superficially disposed protein subunits. These subunits are envisaged as being embedded within the bimolecular lipid layer, anchored to the aqueous phase, and perhaps mobile in the plane of each face of the membrane. The subunits bind the solute in question and, when associated with the symmetrical protein at the opposite face of the membrane, transfer the solute across the membrane. hemithioacetal see acetal. hemithioketal see acetal. hemizygous describing an organism in which a gene is present only once in a genotype, as a gene in a haploid cell or organism, a sex-linked gene in the heterogametic sex, or a gene in a segment of chromosome in a diploid cell or organism where its partner segment has been deleted. -hemizygosity n. hemo+ or hema+ or (before a vowel) hem+ comb. form denoting blood. Also (esp. Brit.): haemo+, haema+, haem+. See also hemato+. hemochromatosis or (e~p. Brit.) haemochromatosis a disease of humans characterized by an abnormal, widespread, massive accumulation of tissue iron associated with characteristic pathological changes of tissue structure and function. Primary hemochromotosis is a specific genetically determined disease in which hemochromatosis occurs as a result of increased absorption of iron from a normal diet. Secondary hemochromatosis results from an increased intake and accumulation of iron secondary to other causes. Compare hemosiderosis. hemochrome or (esp. Brit.) haemochrome any iron-porphyrin coordination complex with one or more strong-field axial ligands (e.g. pyridine). hemochromogen or (esp. Brit.) haemochromogen any compound of heme with a nitrogenous base such as a protein (whether native or denatured) or pyridine, typically with two absorption bands in the green part of the visible spectrum. See also chromogen. hemocuprein or (esp. Brit.) haemocuprein an alternative name for superoxide dismutase. hemocyanin or (esp. Brit.) haemocyanin a blue, copper-containing oxygen carrier present in many molluscs and arthropods. It is a nonheme protein that binds one dioxygen molecule for two Cu(I) atoms; the dioxygen molecule is thought to form a bridge between the two copper atoms. The oxygenated compound is very bright blue with an intensity of light absorption 5-10 times that of other known copper complexes. Example from the lobster Panulirus interruptus: hexamer of a number of different chains, of which A, B (88% identity between these two), and C have been identified: chain A, database code HCYA_PANIN, 657 amino acids (75.61 kDa); this contains two copper-binding sites (His ligands); two CuA motifs; two other motifs form an oxygen-binding domain; one CuB motif. hemocyte or (esp. Brit.) haemocyte any blood cell, especially of an invertebrate animal. hemocytometer or (esp. Brit.) haemocytometer an apparatus for counting the number of cells in a known volume of blood. It consists of a slide with a chamber of known depth; the base of the chamber is ruled with a graticule over which the cells can be enumerated under a microscope. hemodialysis or (esp. Brit.) haemodialysis the process of separating low-molecular-mass solutes from blood by dialysis through a semipermeable membrane, as in an artificial kidney machine. hemoglobin or (esp. Brit.) haemoglobin symbol: Hb; any of a group of red, iron-containing, oxygen-carrying pigments of the blood of vertebrates and some invertebrates; hemoglobin also occurs in the root nodules of leguminous plants. All vertebrate hemoglobins consist of two pairs of associated globin polypeptide chains, each polypeptide chain carrying a heme prosthetic group bound noncovalently, the iron atom of which is in the ferrous state and forms a coordination complex with the pyrrole nitrogens. All normal human hemoglobins contain one pair of 15.7 kDa a chains, of 141 amino-acid residues, and

hemoglobin A'e

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a pair of varying 16.5 kDa polypeptide chains, of 146 aminoacid residues and of similar amino-acid sequences. In adult human blood, 98% of the total hemoglobin is Hb A (or Hb AI), containing a pair of ~ chains, i.e. it has the composition U2~2, and 2% is Hb A b containing a pair of /) chains, Le. U2/)2' In fetal blood, from about 10 weeks to 30 weeks of gestation, >90% of the hemoglobin is Hb F, containing a pair of y chains, i.e. a2Y2' In embryonic blood, the second pair of chains are c chains, i.e. the structure is a2C2' Each of the four heme groups in a hemoglobin molecule is able to combine reversibly with one dioxygen molecule; the oxygen-saturation curve of hemoglobin is sigmoidal, showing that there is positive cooperativity between the subunits. The hemoglobin molecule has a two-fold axis of symmetry, each half containing one u chain and one non-a chain; the overall shape of the molecule is globular with the heme groups buried in pockets in the polypeptide chains. There are eight helical regions, called A to G. The histidine at position F8 (i.e. the eighth residue in helix F) is the fifth ligand of the heme Fe(n). Upon oxygenation, dioxygen becomes the sixth ligand of Fe(lI) and is also hydrogen bonded to HisE7 with an accompanying conformational change. In the absence of the correct bonding with the globin side chains, Fe(n) autooxidizes to Fe(m) and can no longer bind dioxygen. Examples: human and chimpanzee a chain, database code HBA_HUMAN, 141 amino acids (15.11 kDa); among a chain variants are Luxembourg, Ann Arbor, and Hirosaki; ~ chain, database code HBB_HUMAN, 146 amino acids (15.85 kDa). Among the hemoglobinopathies associated with ~-chain variants is sickle-cell anemia. In those invertebrates that have hemoglobin (not hemocyanin) there is a polymeric hemoglobin. Example from earthworm, 12 subunits arranged in a hexagonal bilayer structure of 3.8 MDa; each one-twelfth subunit is composed primarily of disulfide-linked trimers (chains A, B, and C) and monomers (chain D); D chain, database code GLBI_ LUTME, 142 amino acids (16.11 kDa). See also hemoglobin A'e' hemoglobin A'e or (esp. Brit.) haemoglobin Ale abbr.: Hb Ale; the most abundant of the glycated hemoglobins, which are present in normal adult hemoglobin as minor components (together they represent 3-5% of the total hemoglobin of the erythrocyte). Hb Ale is formed from Hb Al subsequent to biosynthesis by glycosylation of one of the two ~ chains, by a nonenzymic mechanism involving formation of an N-substituted aldimine (Schiffs base) between the amino group of the peptide chain and the aldehyde group of glucose, followed by an Amadori rearrangement to the corresponding N-substituted ketoimine (aminodeoxyfructose derivative) (see also Maillard reaction). In inadequately controlled diabetes mellitus the steady-state concentration of Hb Ale in serum is 2-3 times higher than normal, possibly reflecting an abnormally high mean blood glucose concentration during the preceding few months. Other glycosylated hemoglobins change very little in concentration in diabetes; thus measurement of serum levels of Hb Ale is considered to be useful in assessing the degree of control of the condition. hemoglobinopathy or (esp. Brit.) haemoglobinopathy any of many types of genetic disorder involving globin, the protein moiety of hemoglobin. These are divided into thalassemia syndromes, caused by defective synthesis of the component polypeptides of globin, and conditions that arise from mutations leading to amino-acid substitutions in the polypeptide chains. Of the latter there are over 400 known variants, including the classically important sickle cell hemoglobin. Many changes lead to increased oxygen affinity, e.g. Hb Rainier (~­ 145, Tyr -7 Cys), while in a few instances decreased oxygen affinity occurs, e.g. Hb Kansas (~-102, Asn -7 Thr). In some cases the substitution leads to an unstable hemoglobin molecule, as in Hb Hammersmith (~-42, Phe -7 Ser) where the important heme contact of the phenylalanine is lost, leading to the formation of ferrihemoglobin, or in Hb Bristol (~-67, Val-7 Asp) where replacement of the nonpolar valine by aspartic acid causes distortion of the E helix.

hemosiderin hemolin or (esp. Brit.) haemolin an insect hemolymph protein that is of the immunoglobulin superfamily. It is induced by bacteria. It contains four internal immunoglobulin-type repeats. Example (precursor) from the moth Hyalophora cecropia: 413 amino acids (45.78 kDa). hemolymph or (esp. Brit.) haemolymph a fluid occurring in the secondary body cavity (coelom) of some invertebrates, considered as functionally equivalent to the blood and lymph of higher animals. hemolysate or (esp. Brit.) haemolysate a preparation obtained by lysis of erythrocytes. hemolysin or (esp. Brit.) haemolysin 1 any substance, e.g. an antibody, that causes hemolysis. 2 any bacterial exotoxin that ruptures blood-cell membranes. Examples are the products of chromosomal genes of certain hemolytic Escherichia coli strains that cause predominantly non gastrointestinal (e.g. urinary tract) infections. There are four genes: hlyA encodes hemolysin (Ca 2+ -binding toxin): database code HLYI_ECOLl, 1023 amino acids (109.75 kDa); hlyB encodes an ABC transporter for HlyA export: database code HLY2_ECOLl, 707 amino acids (79.77 kDa); hlyC encodes a protein involved in hemolysin export: database code HL Y3_ECOLl, 170 amino acids (19.70 kDa); hlyD encodes a transmembrane protein component of the HlyA export system: database code HLY4_ECOLl, 478 amino acids (54.53 kDa). hemolysis or (esp. Brit.) haemolysis the lysis of red blood cells, either in vivo or in vitro. -hemolyse or haemolyse vb. hemolytic or (esp. Brit.) haemolytic 1 of, or pertaining to hemolysis. 2 an agent or condition that causes hemolysis. hemopexin or (esp. Brit.) haemopexin a 57 kDa ~I-glycopro­ tein of human blood serum with one high-affinity binding site for heme (def. I). The heme complex can be reduced with dithionite to give a three-band absorption spectrum characteristic of ferrohemochrome. Hemopexin may be necessary for heme to be taken up and degraded in the liver. hemophilia or (esp. Brit.) haemophilia any of various hereditary disorders in which there is a deficiency or defect in certain of the blood coagulation factors resulting in prolonged bleeding following injury. Classical hemophilia, or hemophilia A, is a condition in which the blood has a prolonged clotting time due to an abnormally slow conversion of prothrombin to thrombin. It is caused by a functional deficiency of antihemophilic factor (factor VIII), inherited as an X-linked recessive trait. Other deficiencies in the blood coagulation system, e.g. Christmas disease, or hemophilia B, due to a deficiency of factor IX, produce similar clinical pictures. hemopoiesis or hematopoiesis the process of blood formation, especially the formation of blood cells, occurring mainly in bone marrow. Also (esp. Brit.): haemopoiesis, haematopoiesis. -hemopoietic, hematopoietic or haemopoietic, haematopoietic adj. hemoprotein or heme protein any protein to which an iron-porphyrin compound is linked in a stoichiometric manner. Hemoproteins include hemoglobins, myoglobins, cytochromes, catalase, and some peroxidases. Also (esp. Brit.): haemoprotein, haem protein. hemorphin or (esp. Brit.) haemorphin any of a group of hemoglobin-derived peptides with affinity for opioid receptors. hemorrhage or (esp. Brit.) haemorrhage bleeding; the escape of blood from a ruptured blood vessel, either externally or internally. -hemorrhagic or (esp. Brit.) haemorrhagic adj. hemorrhagic toxin C and D see atrolysin C. hemosiderin or (esp. Brit.) haemosiderin an insoluble, granular, ill-defined complex formed by the denaturation of ferritin with associated loss of apoferritin and micellar aggregation; about one third of its mass is iron. Hemosiderin occurs in liver, spleen, and red bone marrow, its amount increasing with increased iron content of the body. It is responsible for the histochemical staining of tissue by the Prussian Blue reaction, a deep-blue ferric ferrocyanide (Fe IlI [Fe II (CN)6D. The distribution of stored iron is shifted from ferritin to hemosiderin in

hemosiderosis

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direct correlation with ascorbic acid deficiency. See iron overload. hemosiderosis or (esp. Brit.) haemosiderosis an abnormal increase in tissue iron content due to some defect in the control of iron turnover in the body or to increased iron ingestion. It is not associated with pathological changes in tissue structure and function. Compare hemochromatosis. hemostasis or (esp. Brit.) haemostasis 1 the stopping of bleeding or the arrest of the circulation to an organ or part. 2 the stagnation of blood in an organ or part. hemostat or (esp. Brit.) haemostat a device or a chemical agent that stops or retards bleeding. hemostatic or (esp. Brit.) haemostatic 1 of, relating to, or functioning to cause hemostasis (def. 1).2 a drug or other agent that retards or stops bleeding. Hench. Philip Showalter (1896-1965), US physician notable for his demonstration (with E. C. Kendall) that rheumatoid arthritis could be treated with an adrenal hormone (later known as cortisone); Nobel Laureate in Physiology or Medicine (1950) jointly with E. C. Kendall and T. Reichstein 'for their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects'. Henderson-Hasselbalch equation an equation relating pH to the composition of buffer solutions: pH = pKA + log([conjugate base]/[acid]), where pKA is the common logarithm of the acid dissociation constant of the buffer acid. The following approximation is often used: pH = pKA + log([salt]/[acid]). [After Lawrence Joseph Henderson (l878~1942), US physician and biochemist, and Karl A. Hasselbalch (1874- ), Danish biochemist, who together formulated the equation in 1910.] henna a preparation obtained from the dried and powdered leaves of Lawsonia alba, L. inermis, or L. spinosa, widely used for dyeing hair and fingernails. The active ingredient is lawsone. henry (pl. henrys or henries) symbol: H; the SI derived unit of inductance, equal to the inductance of a closed circuit with a magnetic flux of I weber per ampere of current, H = Wb A-I s = m 2 kg s-2 A-2 [After Joseph Henry (1797-1878), US physicist.] Henry's function a function used in the theoretical treatment of the electrophoretic mobility of macromolecules that is dependent on the radius of the macromolecule, r, and its reciprocal ion-atmosphere radius, K (derived from Debye-Hiickel theory). It varies between 1.0 and 1.5 as Kr goes from zero to infinity. Henry's law the principle that the concentration of a gas in solution, at constant temperature, is directly proportional to the partial pressure of the gas in the vapour phase in equilibrium with that solution. It holds with high precision for gases of low solubility at pressures below approximately 10 5 Pa. It may be expressed by: CG = kpG' where CG is the molar concentration of the gas in solution, PG is the partial pressure of the gas in the gas phase, and k is a proportionality constant. [After William Henry (1774-1836), British chemist.] heparan any polysaccharide derived by desulfation of heparan sulfate or heparin. heparan sulfate any member of a group of glycosaminoglycans that have repeat units consisting of alternating al~4­ linked hexuronic acid and glucosamine residues, the former being a mixture of sulfated and nonsulfated D-glucuronic and L-iduronic acids, and the latter being either sulfated or acetylated on its amino group as well as sulfated on one of its hydroxyl groups. They usually occur attached to protein to form proteoglycans, the mode of attachment being through a xylose residue as in chondroitin sulfates. Heparan sulfate accumulates in a number of the mucopolysaccharidoses, e.g. Hunter syndrome, Hurler syndrome, and Sanfilippo syndrome. See mucopolysaccharidosis. See also heparin.

hepatocyte growth factor heparan sulfate proteoglycan core protein abbr.: HSPG core protein; any of a group of modular heparan sulfate proteoglycan proteins with three heparan sulfate chains. Also known as perlecans, they have domains with homology to the low-density lipoprotein receptor, epidermal growth factor, laminin, and neural cell adhesion molecule, and have 15 immunoglobulin-like domains. Examples from Mus musculus: database code S18252, 3707 amino acids (397.85 kDa), and database code PGBM_MOUSE, 2481 amino acids (270.81 kDa). heparin any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average M r (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating al~4-linked D-galactose and Nacetyl-D-glucosamine-6-sulfate residues. Heparins are secreted into the bloodstream by the mast cells of liver, lung, and other tissues; they act as inhibitors of blood clotting by activating antithrombin III. heparinize or heparinise to treat with a preparation of heparin, usually as its sodium or lithium salt, in order to prevent clotting, either in vivo or in vitro, of blood or blood plasma. -heparinization or heparinisation n. hepat+ a variant form of hepato+ (before a vowel). hepatectomy surgical removal of the liver. In partial hepatectomy, only some of the lobes of the liver are removed; this causes the remaining lobes to regenerate so that the liver in toto regains its former weight. -hepatectomize or heparectomise vb. hepatic of, or pertaining to, the liver. hepatitis any inflammatory disease of the liver. In humans the most common cause is infection with a virus or an amoeba. The three most common forms of viral infectious hepatitis are designated A, B, and C. Hepatitis A is caused by a singlestranded RNA picornavirus, for which there is now a killed virus vaccine, the virus having been grown in tissue culture. Hepatitis B is caused by a double-stranded DNA virus of the Hepadnaviridae family. The causative agent is a spherical virion with a diameter of 42 nm, often referred to as the Dane particle. This virus is especially virulent and its presence is associated with the development of primary liver tumours ~ the incidence of these is particularly high in China. The antigens may be in the form of 22 nm diameter, spherical particles designated HBsAg; principal components include gp27, which is a glycosylated form of p24, and a 42 kDa protein, database code VMSA_HPBVA, 389 amino acids (42.73 kDa). HBsAg is produced in recombinant yeast, the 22 nm particles being similar to those found in the plasma of infected individuals. These provide a very effective vaccine. Hepatitis C, formerly called 'non-A non-B', is caused by a single-stranded RNA virus, for which there is as yet no vaccine. Another form, hepatitis D, can be controlled by the vaccine to hepatitis B, and there are probably three other types: E, F, and G, of which G has recently been characterized. hepato+ or (before a vowel) hepat+ comb. form denoting of or pertaining to the liver. hepatocarcinogen any carcinogen that acts specifically or primarily on liver. hepatocellular of, or pertaining to hepatocytes. hepatocyte or (formerly) parenchymal liver cell. the major (but not the only) cell type of the liver. They are arranged in folded sheets facing blood-filled spaces called sinusoids. Hepatocytes are responsible for the synthesis, degradation, and storage of a wide range of substances. They are the site of synthesis of all the plasma proteins, except for antibody, and are the site of storage of glycogen. hepatocyte growth factor abbr.: HGF; other name: scatter factor; a cytokine produced by platelets, fibroblasts, macrophages, endothelial cells, and smooth muscle cells that is a po-

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hepatocyte growth factor receptor tent mitogen for hepatocytes, epithelial cells, keratinocytes, melanocytes, and hematopoietic precursor cells. It is a glycoprotein, with four kringle domains and no known protease activity. The molecule is a disulfide-linked dimer of a (463 amino acids) and ~ (234 amino acids) subunits, which are derived from a common precursor. Example from human: database code HGF_HUMAN, 728 amino acids (83.04 kDa). hepatocyte growth factor receptor a type I membrane protein that binds hepatocyte growth factor and mediates its intracellular action by a protein tyrosine kinase (EC 2.7.1.112) activity on its intracellular domain. It is encoded by the MET protooncogene, and comprises a dimer of two subunits, a and ~. Example (precursor) from human: database code KMET_ HUMAN, 1390 amino acids (155.35 kDa). See also tpr-met. hepatoflavin or bepatoflavine a former name for riboflavin. hepatolenticular degeneration an alternative name for Wilson's disease. hepatoma any carcinoma derived from liver cells. hepatopancreas a digestive gland, found in many invertebrates, that performs functions similar to those of the liver and the pancreas in vertebrates. hepatosis any noninflammatory disease of the liver. hepatotoxin any toxin that acts specifically or primarily on the liver. Hepes or HEPES abbr. for (and trivial name of) 4-(2-hydroxyethyl)-I-piperazine-ethanesulfonic acid; a Good buffer substance, pK. (20°C) = 7.55.

hepoxilin abbr.: Hx; any of various epoxyhydroxy metabolites of 12-hydroperoxyeicosatetraenoate, e.g. 13-hydroxy-14,15epoxyeicosatetraenoate. A number of sites of formation have been reported, activities including modulation of neurotransmission in brain and release of insulin in pancreatic islets. hepoxilin-epoxide hydrolase EC 3.3.2.7; an enzyme that converts (52,9 E, 142)-(8';, II R, 128)-11, 12-epoxy-8-hydroxyeicosa-5,9,14-trienoate hepoxilin A 3 to the trioxilin, (52,9E, 142)-(8.;,1 1.;,128)-8, II, 12-trihydroxyeicosa-5,9, 14trienoate (trioxilin A 3). Hepps or HEPPS or EPPS abbr. for (and trivial name of) 4-(2hydroxyethyl)-I-piperazinepropanesulfonic acid; a Good buffer substance, pKa (20°C) = 8.0.

Heppso or HEPPSO abbr. for (and trivial name of) 4-(2-hydroxyethyl)-I-piperazine-(2-hydroxypropanesulfonic acid); a Good buffer substance, pKa (25°C) = 7.8.

hepsin EC 3.4.21.-; a serine protease, similar to other trypsinlike enzymes, that is a type II membrane protein. It is required for growth and maintenance of cell morphology in many tissues. Example from human: database code HEPS_HUMAN, 417 amino acids (44.96 kDa). hepta+ or (before a vowel) hept+ comb. form denoting seven.

herring heptanoate 1 the anion, CHr[CH2]~-COO, derived from heptanoic acid (formerly enanthic acid). 2 any salt or ester of heptanoic acid. heptanoyl symbol: Hpo; the univalent acyl group, CH r [CH 2Js -CO-, derived from heptanoic acid. heptitol any alditol having a chain of seven carbon atoms in the molecule. heptose any aldose having a chain of seven carbon atoms in the molecule. heptulose any ketose having a chain of seven carbon atoms in the molecule. heptyl symbol: Hp; the alkyl group, CH r [CH 2]s-CHr, derived from heptane. heptyl glucoside n-heptyl P-D-glucopyranoside; a nonionic detergent, CMC 79 mM. hepty' thioglucoside n-heptyl I-thio-P-D-glucopyranoside; a nonionic detergent; the CMC, 30 mM, remains unchanged between I and 20°C. HER2 see neu. herbicide any chemical substance that destroys plants or inhibits their growth, especially one used to control weeds. hereditary of, pertaining to, or caused by heredity; inherited. hereditary disease any pathological condition that is caused by the presence in the organism of an abnormal gene. hereditary fructose-bisphosphatase deficiency an inherited autosomal recessive condition in humans characterized by less than 20% of normal activity of fructose-bisphosphatase (EC 3.1.3.11). It is characterized in infants by episodic spells ofhyperventilation, apnoea, hypoglycemia, ketosis, and lactic acidosis. Surviving infants appear to become normal, but gluconeogenesis in their livers is severely impaired, and when glycogen stores are depleted, amino acids, lactate, and ketones accumulate. Subjects are not sensitive to fructose intake. Compare hereditary fructose intolerance. hereditary fructose intolerance a condition in humans, inherited as an autosomal recessive character, in which there is a deficiency of the aldolase-B isoenzyme of fructose-bisphosphate aldolase (EC 4.1.2.13) (there is less than 15% normal activity with fructose I-phosphate as substrate but activity is less depressed with fructose 1,6-bisphosphate as substrate) while the levels of aldolases A and C are normal (see aldolase (def. 2)). The condition is characterized by severe hypoglycemia and vomiting shortly after fructose intake. In this condition prolonged fructose ingestion in infants leads to poor feeding, vomiting, hepatomegaly, jaundice, hemorrhage, proximalrenal-tubule syndrome, and death. The hypoglycemia ensuing after fructose ingestion is caused by fructose I-phosphate inhibition of glycogenolysis at the phosphorylase level and of gluconeogenesis at the mutant aldolase level. Compare hereditary fructose-bisphophatase deficiency. heredity 1 the transmission from one generation to another of genetic factors that determine the characteristics of an organism. 2 all of the inherited factors in an organism or all the characteristics determined by them. heregulin abbr.: HRG; one of several glycoproteins that bind to the transmembrane tyrosine kinase ErbB2 pl85 and stimulate its activity. They are secreted by human breast cancer cells in culture. Example heregulin-a precursor from human: database code A43273, 640 amino acids (70.29 kDa). hermone an alternative term for hormone (suggested by E. Schiifer in 1913 as better expressing the concept of chemical messengers) . heroin see diacetylmorphine, morphine. herpes virus any of a family (Herpesviridae) of enveloped, icosahedral, double-stranded DNA viruses, many of which infect animals. The family includes human herpesviruses types I and 2, Epstein-Barr virus, zoster (varicella) virus, pseudorabies virus, cytomegalovirus, Lucke virus, and Marek's disease virus. herring any marine fish of the family Clupeidae, the flesh of

Hershey

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which is comparatively rich in oils with a high content of longchain n-3 fatty acids; typical composition (range of major fatty acids, expressed as % of total fatty acids): 16:0, 12-18%; 16:I(n-7),6-8%; 18:I(n-9), 11-25%; 20:I(n-9), 7-19%; 20:5(n3), 11-15%; 22:6(n-3), 5-8%. Hershey, Alfred Day (1908-97), US geneticist; Nobel Laureate in Physiology or Medicine (1969) jointly with M. Delbriick and S. E. Luria 'for their discoveries concerning the replication mechanism and the genetic structure of viruses'. Hershey-Chase experiment a seminal experiment, reported in 1952, in which it was demonstrated that when an Escherichia coli cell is infected with T2 bacteriophage, the phage DNA is injected into the cell whereas the phage coat protein remains on the outside of the infected bacterial cell. This was shown by demonstrating that most of the 35S-labelled phage protein could be removed from the surface of the bacterial cells by application of a shearing force without removing the 32P-Iabelled nucleic acid and without interfering with the course of productive infection. The phage nucleic acid could be shown to have moved into the bacterial cell. It was therefore concluded that only the phage DNA was required for infection, indicating that DNA must be the hereditary material. This confirmed earlier experiments in 1944 by Avery and colleagues (see transforming principle), but was somewhat more readily accepted when Watson and Crick deduced the structure of DNA. [After A. D. Hershey and Martha Chase (1927- ).] Hershey circle a circular duplex DNA structure in which each strand contains one interruption and in which the interruptions are not opposite each other. It is formed by some linear, double-stranded DNA molecules (e.g. from Escherichia coli phage A) containing short, complementary single strands (cohesive ends) at each end when these cohesive ends base-pair with each other. Hers's disease an alternative name for type VI glycogen disease. hertz symbol: Hz; the SI derived unit of frequency of a periodic phenomenon, equal to 1 cycle per second; i.e. 1 Hz = 1 S-I. [After Heinrich Hertz (1857-94), German physicist.] Hertz, Gustav (1887-1975), German physicist; Nobel Laureate in Physics (1926) jointly with J. Franck 'for their discovery of the laws governing the impact of an electron upon an atom'. Hess's law of constant heat summation the statement that the enthalpy change in a chemical reaction is the same whether the reaction takes place in one stage or in more than one stage. [After Germain Henri Hess (1802-50), Genevese-born Russian chemist; known in Russia as German Ivanovich Gess.] HETE abbr. for hydroxyeicosatetraenoate; see also dihydroxyeicosatetraenoate. hetero+ comb. form 1 other, different, unusual. Compare allo+ (def. 1), homo+ (def. 1), iso+ (def. 1), xeno+ (def. 1).2 for, from, or directed towards a different species. Compare allo+ (def. 2), homo+ (def. 2), iso+ (def. 2), xeno+ (def. 2). 3 containing atoms, groups, linkages, residues, or subunits of different kinds. 4 being or pertaining to an atom other than the predominant or significant one, especially of a nitrogen, oxygen, or sulfur atom in a ring containing mainly carbon atoms. Compare homo+ (def. 4). heteroantibody any antibody (including any autoantibody) that is able to react with an antigen derived from another species. Compare isoantibody. heteroantigen any antigen derived from one species that is able to stimulate an immune response in another species. Compare isoantigen. heteroatom any atom in the chain or ring of an organic compound that is not a carbon atom. -heteroatomic adj. heteroblfunctional describing any reagent that carries two differing reactive groups. Compare homobifunctional. heterocaryon a variant spelling of heterokaryon. heterochromatic 1 relating to or possessing more than one colour; relating to light or other electromagnetic radiation of more than one frequency. Compare monochromatic. 2 of, relating to, or possessing heterochromatin.

heterogeneous nuclear RNA heterochromatin a condensed form of chromatin, occurring in the nucleus at interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is replicated at a later stage in the cell-division cycle than euchromatin. 'Satellite' DNA is associated with heterochromatin, and the sex chromosomes of animals, especially the Y chromosome, contain large regions of heterochromatin. Compare euchromatin. heteroconjugation the association between a base and the conjugate acid of a different base through a hydrogen bond. See conjugate acid-base pair. Compare homoconjugation. heterocycle any compound or molecular structure that is heterocyclic (def. I); a heterocyclic (def. 2). heterocyclic 1 describing any cyclic molecular structure containing atoms of at least two different elements in the ring or rings; describing any compound having such a structure. Compare carbocyclic (def. 1), homocyclic (def. 1). 2 or heterocycle any such compound. heterocyst any of the clear cells that occur at intervals on the filaments of certain cyanobacteria. They are thought to be important sites of nitrogen fixation. heterodetic describing a cyclic peptide in which the ring consists of amino-acid residues only, but the linkages forming the ring are not solely eupeptide bonds; one (or, ifnonproximate, more than one) is an isopeptide, disulfide, ester, or other bond. Compare homodetic. heterodimer any molecular structure in which two nonidentical subunits are associated. Compare dimer, homodimer. heteroduplex 1 any double-stranded DNA in which the two strands do not have completely complementary base sequences. In a mutational heteroduplex a mutational event has occurred in one of the polynucleotide chains; such a molecule does not produce uniform progeny on replication. A recombinational heteroduplex is a double-stranded DNA molecule that gives rise to one parental and one recombinant molecule of DNA in the reproductive cycle that immediately follows its production. Heteroduplex DNA may also arise from annealing DNA single strands in vitro. 2 a DNA-RNA hybrid. Compare homoduplex. heteroduplex mapping the physical mapping of the base sequence homology of two DNA molecules. It is accomplished after the in vitro formation of a hybrid double-stranded molecule, in which one polynucleotide strand is from one of the DNA molecules and the complementary polynucleotide strand is from the other. Unpaired single-stranded regions are located and measured by electron microscopy. heterogametic describing the sex whose cell nuclei contain a pair of dissimilar sex chromosomes. The heterogametic sex is usually male in mammals but is female in the Lepidoptera, birds, reptiles, some amphibians and fishes, and a few plants. Compare homogametic. heterogeneous 1 differing in kind, as in a heterogeneous population. 2 describing a group of molecules that is not uniform with respect to size, charge, structure, or other property. 3 describing a system consisting of two or more phases. Compare heterogenous. -heterogeneity n. heterogeneous catalysis any catalytic system in which the catalyst constitutes a different phase from that of the reactants. Compare homogeneous catalysis. heterogeneous immunoassay any form of immunoassay that involves physical separation, at some stage of the procedure, of antibody-bound antigen from remaining free antigen. It includes radioimmunoassay. Compare homogeneous immunoassay. heterogeneous nuclear ribonucleoprotein abbr.: hnRNP; particulate complexes of heterogeneous nuclear RNA (hnRNA) with proteins, which are cell-specific and themselves heterogeneous. The protein component may playa role in the processing of the hnRNA to mRNA. heterogeneous nuclear RNA abbr.: hnRNA or HnRNA or H-RNA; a heterogeneous mixture of RNA molecules of high M, with a rapid turnover rate that occurs in cell nuclei during protein synthesis. It is the form of RNA synthesized in eu-

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heterogenesis karyotes by RNA polymerase II, i.e. that which is translated into protein. It represents the transcription products of both the exons and the introns of a gene or genes and is processed to form mRNA by the removal of the non translated portions (corresponding to the introns in the DNA). So-named because heterogeneity in size was one of the first characteristics used to distinguish it from other forms of nuclear RNA. heterogenesis the production of offspring having different characteristics in successive generations; e.g. the alternation between generations that produce gametes and those that reproduce through agametes or by parthenogenesis. heterogenetic describing chromosome pairing during meiosis when the pairing partners are derived from different original ancestors. Compare homogenetic. heterogenic } describing a population or a gamete containing more than one allele of a particular gene. 2 describing two genetic elements that are not known to have a common ancestry. 3 an alternative word for heterogenous. Compare homogenic. heterogenize or xenogenize to introduce a foreign, especially a more potent, antigen into a cell surface in order to enhance the response by T lymphocytes to other cell-surface antigens. heterogenization n. heterogenous or heterogenic not originating within the organism in question; of foreign origin. Compare heterogeneous. heteroglycan or heteropolysaccharide any polysaccharide (i.e. glycan) that contains residues of two or more kinds of monosaccharide (i.e. glycose) molecule. Compare homoglycan. heterograft or heterologous graft an alternative name for xenograft. Compare homograft. heteroimmune describing a pair of bacteriophages in which each is sensitive to its own repressor but not to that of the other. heterokaryon or heterocaryon any cell with more than one nucleus, in which the nuclei are not all of the same genetic constitution, or a tissue composed of such cells. Compare homokaryon. -heterokaryotic or heterocaryotic adj. heterokaryosis or heterocaryosis the association of genetically different nuclei in a common cytoplasm. heterolactic fermentation a type of fermentation of glucose in which the products include lactate, acetate and/or ethanol, and carbon dioxide. A key enzyme in the pathway is phosphoketolase, which cleaves xylulose 5-phosphate (produced by the pentose phosphate pathway) to D-glyceraldehyde 3-phosphate and acetyl phosphate, the former being then converted to lactate while the latter can form acetate and/or ethanol. Organisms that ferment in this manner include Leuconostoc spp. and some species of Lactobacillus; some produce D(~)-Iactate while others produce DL-Iactate. Compare homolactic fermentation. heterolipid a former name for any complex lipid. heterologous } consisting of different elements or of like elements in different proportions. 2 or heterospecific derived from another species, e.g. heterologous serum or tissue. Compare homologous, isologous. heterologous association describing any association between two protomers in which the domain of bonding is made up of two different binding sets. Compare isologous. heterologous desensitization see desensitization. heterologous graft or heterograft an alternative name for xenograft. heterolysin any antibody or other hemolysin formed in response to the introduction of erythrocytes from another species into the bloodstream of an animal. Compare autolysin, homolysin. heterolysis} (in chemistry) the cleavage of a bond in such a manner that both bonding electrons remain within one of the two fragments between which the bond is broken; e.g. A-B ~ A + + B-. Compare homolysis. 2 (in biochemistry) the lysis of cells or tissues by the action of exogenous agents, e.g. enzymes, detergents, or Iysins. Compare autolysis. -heterolytic ad). hetel"olysosome any early secondary lysosome concerned with the digestion of exogenous material (i.e. heterophegy). See heterophagosome. h.t.l'omorphic or heteromorphous } differing from the nor-

heterotypic mal form, e.g. in size, shape, or function. 2 describing the members of any pair of homologous chromosomes that differ from each other in size or shape. 3 (especially of insects) having differing forms at different stages of the life cycle. 4 an alternative term for polymorphic. Compare isomorphic. -heteromorphism or heteromorphy n. heterooligomer any oligomer made up of two or more kinds of constitutional repeating unit. -heterooligomeric ad). heterophagosome any phagosome containing material exogenous to the cell. Fusion with a lysosome leads to the formation of a heterolysosome. Compare autophagosome. heterophagy the process by which cells digest exogenous material that they have taken up. Compare autophagy. -heterophagic ad). heterophilic binding (of adhesion molecules) binding of an adhesion molecule in one cell to a non-identical adhesion molecule in an adjacent cell. Compare homophilic binding. heteroplasmy the presence of more than one type of mitochondrial DNA in a cell. A mutant mitochondrial DNA may be present in varying amounts so that phenotypic variation between cells is possible. heteroploid describing a cell that contains any number of chromosomes except the haploid or diploid number. The term includes all aneuploid or polyploid numbers of chromosomes. heteropolymer any polymer made up of two or more kinds of constitutional repeating unit. Proteins are typical heteropolymers. -heteropolymeric ad}. heteropolysaccharide an alternative term for heteroglycan. heteroside a former name for any glycoside containing a noncarbohydrate moiety (aglycon). heterospecific having specificity for or derived from a different species; heterologous (def. 2). heterotetramer any molecular structure that can be dissociated into four (or two pairs of) nonidentical monomers. -heterotetrameric adj. heterotope any of two or more chemical elements having atoms of different atomic number and occupying different places in the periodic table. The term includes isobar (def. I). Compare isotope. heterotopia or heterotopy the displacement, or unusual position, of a cell, organ, tissue graft, etc. heterotopic } (in chemistry) of, relating to, or being a heterotope or heterotopes. Compare isotopic. 2 (in biology and medicine) or heterotopous displaced or in an unusual anatomical position. heterotopic transplant any tissue graft that is transplanted from its normal position to another in the same organism. Compare orthotopic transplant. heterotopous a variant form of heterotopic (def. 2). heterotopy a variant form of heterotopia. heterotrimer any molecular structure that is dissociable into three nonidentical monomers. -heterotrimeric ad). heterotroph or heterotrophe or organotroph any organism whose nutritional requirements are not satisfied solely by simple inorganic substances and for which a supply of organic carbon is required for the synthesis of cellular constituents. Heterotrophs may be subdivided into chemoheterotrophs (or chemoorganotrophs) and photoheterotrophs (or photoorganotrophs) according, respectively, to whether they are chemotrophs or phototrophs. Compare autotroph. -heterotrophic ad).; heterotrophy n. heterotropic } describing an allosteric effect in which interaction occurs between nonidentical ligands; the effect may be either cooperative or antagonistic. The term is applied also to such an interaction, to an allosteric enzyme for which different substances act as the substrate and the effector, to the regulation of such an allosteric system, etc. Compare homotropic. 2 describing a chromosome that does not pair with another at meiosis, especially a sex chromosome in the heterogametic sex. heterotypic pertaining to, or being the first, reductive division in meiosis. Compare homeotypic.

heterozygosis heterozygosis 1 the union of genetically different gametes to form a heterozygote. 2 or heterozygosity the state or condition of being a heterozygote. Compare homozygosis. heterozygosity an alternative term for heterozygosis (def. 2). heterozygote any cell or organism having two different genes (alleles) at one or more corresponding loci on homologous chromosomes. With respect to such loci a heterozygote will produce two different types of gametes. Compare homozygote. heterozygous or heterozygotic of, pertaining to, or being a heterozygote; hybrid. HETP abbr. for height equivalent to a theoretical plate. heuristic describing any method for solving mathematical or other problems for which no algorithm (or closed method) exists. It involves narrowing down the field of search for a solution by inductive reasoning from past experience of similar problems. Compare stochastic. HEV abbr. for high-walled endothelium of the post-capillary venules. hevein an N-acetyl-D-glucosamine and N-acetyl-D-neuraminic acid binding lectin; it is present in the latex of the rubber tree, Hevea brasiliensis and has 56% homology with wheat germ agglutinin. Example (precursor) from H. brasiliensis: database code HEMO_HYACE, 413 amino acids (45.78 kDa). Hevesy, Gyiirgy (Karoly) (1885-1966), also styled, inter alia, as Georg (Karl) von Hevesy or George (Charles) von Hevesy or George (Charles) Hevesy or George (Charles) de Hevesy Hungarian-born Swedish radiochemist, analytical chemist, and biochemist who (with F. A. Paneth in 1913) was the first to recognize the possibility of using natural radioactive elements as indicators and is remembered for his subsequent pioneering researches employing natural and artificial radioisotopes as indicators or tracers in chemical and biological systems and also for the discovery of hafnium; Nobel Laureate in Chemistry (1943) 'for his work on the use of isotopes as tracers in the study of chemical processes'. hexa+ or (before a vowel) hex+ comb. form denoting six, sixfold, six times. hexabrachion a six-armed structure, characteristic of the tenascin molecule. Regions of the protein radiate outwards like spokes of a wheel. [From L. brachium arm.J hexadecadienoic acid any straight-chain fatty acid having sixteen carbon atoms and two double bonds per molecule. (allZ)-Hexadeca-6,9-dienoic acid is found in small amounts in some animal lipids. hexadecanoic acid the systematic name for palmitic acid; see palmitate. hexadecenoic acid any straight-chain fatty acid having sixteen carbon atoms and one double bond per molecule. The most common are the 9Z-isomer (palmitoleic acid; see palmitoleate) and the liZ-isomer, but the 3E-, 6E-, 6Z-, 9E-, and 10Z-isomers are also variously found in animals or plants; the 9E-isomer (Le. palmitelaidic acid) is a pheromone. hexaethyleneglycol mono-n-decyl ether a nonionic detergent; see CxE,. hexaethyleneglycol mono-n-dodecyl ether a nonionic detergent; see CxE,. hexagonal phase (of phospholipids) a phase in which the polar headgroups are orientated towards the interior of a phospholipid aggregate, with the fatty acyl carbon chains pointing outwards; a form of inverted micelle. It can occur in lipid bilayers, especially at higher temperatures. Certain phospholipids, such as phosphatidylethanolamine, have a greater tendency to adopt this phase than, e.g., phosphatidylcholine. A hexagonal phase with the polar headgroups oriented towards the exterior of the micelle can also exist. See also liquidcrystalline phase, phase transition. hexamer 1 any oligomer consisting of six monomers. 2 the group of six capsomeres in an icosahedral virus capsid. hexanoate or caproate 1 the anion, CHr[CH2J4-COO, derived from hexanoic acid. 2 any salt or ester of hexanoic acid. hexanolamino-PAF 1- O-hexadecyl-2- O-acetyl-sn-glycero-3-

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hexosaminidase phospho-(N,N,N-trimethyl)-hexanolamine; a substance that inhibits the effects induced by platelet activating factor, including platelet aggregation, secretion, and inositol phospholipid turnover; superoxide ion and H 20 2 release from macrophages; hepatic glycogenolysis; and vasoconstriction. hexanoyl or (formerly) caproyl symbol: Hxo; the univalent acyl group, CH3-[CH2J4-CO-, derived from hexanoic acid. See caproyl (def. 2). hexaric acid an aldaric acid formally derived from a hexose by oxidation at both C-l and C-6. hexitol any alditol having a chain of six carbon atoms in the molecule. hexokinase EC 2.7.1.1; systematic name: ATP:D-hexose 6phosphotransferase; other name (used for hexokinase IV): glucokinase; the phosphotransferase enzyme that catalyses the phosphorylation by ATP of D-hexose to form D-hexose 6phosphate and ADP. In vertebrates there are four major isoenzymes, designated hexokinase types I, II, III, and IV, also called hexokinases A-D. All of these types are relatively nonspecific with respect to sugar, and phosphorylate a number of hexoses such as glucose, fructose, and mannose. Thus the name glucokinase for type IV may mislead. Types I-III all have M, z 100 kDa and are sensitive to the product, glucose 6phosphate (abbr.: Glc-6-P). They differ from hexokinases found in yeast, which have M, z 50 kDa, and are not inhibited by Glc-6-P. Type III is inhibited by excess glucose. Type IV, despite being a monomer with only one active site, shows cooperativity with respect to glucose, and reaches physiologically significant activity at higher glucose concentrations than types I-III. In hepatocytes, at less than 5 mM glucose it is present as an inactive enzyme bound to a regulatory protein; a glucose concentration of 15 mM causes translocation and activation of the enzyme. Type II is the major isoenzyme of skeletal muscle and adipose tissue. There are strong sequence similarities between the different types. The mammalian enzymes could have evolved by duplication and fusion of an ancestral 50 kDa hexokinase. Examples: hexokinase IV from human mitochondrial outer membrane: database code HXKLHUMAN, 917 amino acids (102.39 kDa); the N-terminal and C-terminal halves of the sequence are similar; regulatory function of this monomeric allosteric enyme is associated with the N-terminal half; human brain hexokinase, type I: database code HXKLHUMAN, 917 amino acids (102.39 kDa); human liver glucokinase isozyme (hexokinase D): database code HXKH_HUMAN, 466 amino acids (52.08 kDa); yeast hexokinase (3-D structure with glucose): database code NRL_IHKG, 457 amino acids (38.89 kDa); also, from yeast: database code HXKG_YEAST, 500 amino acids (55.31 kDa). hexon a capsomere that is surrounded by six other capsomeres in an icosahedral virus capsid. hexonic acid any monocarboxylic acid (i.e. aldonic acid) formally derived from a hexose by oxidation at C-1. hexosamine any aminodeoxysugar with six carbon atoms. hexosaminidase EC 3.2.1.52; recommended name: fJ-N-acetylhexosaminidase; systematic name: ,B-N-acetyl-D-hexosaminide N-acetylhexosaminohydrolase; other name: fJ-hexosaminidase. An enzyme that catalyses the hydrolysis of terminal noureducing N-acetyl-D-hexosamine residues in N-acetyl-,B-D-hexosaminides. It is a lysosomal enzyme in mammals; there are two precursors (human): a, database code HEXA_HUMAN, 529 amino acids (60.62 kDa); and ~, database code HEXB_ HUMAN, 556 amino acids (63.04 kDa). The a chain, a glycoprotein, comprises amino acids 109-529 of its precursor; three glycoproteins (all similar to a) are derived from the ~ precursor: ~ (amino acids 122-556), ~-B (amino acids 122-311), and ~-A (amino acids 315-556). There are three forms of the enzyme: form A, responsible for degradation of GM 2 gangliosides, is a trimer composed of one a chain, one ~-A chain, and one ~-B chain; form B is a tetramer of two ~-A and two ~-B chains; form S is a homodimer of two a chains. Tay-Sachs dis-

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hexosan ease is due to defects of the a chain and Sandoff disease due to defects of the ~ chain. hexosan a former name for any of a class of polysaccharides that yield only hexoses on hydrolysis. hexose any aldose having a chain of six carbon atoms in the molecule. hexose diphosphate pathway an alternative name for Embden-Meyerhof pathway. hexose monophosphate pathway or hexose monophosphate shunt an alternative name for pentose phosphate pathway. hexose phosphate transport protein an integral membrane transport protein responsible for sugar phosphate uptake in bacteria. Example from Escherichia coli: database code UHPT_ECOLI, 463 amino acids (50.55 kDa). hexose-1-phosphate uridylyltransferase see UDPglucose-hexose-1-phosphate uridylyltransferase. hexulose any ketose having a chain of six carbon atoms in the molecule. hexuronic acid 1 any monocarboxylic acid (i.e. uronic acid) formally derived from a hexose by oxidation at C-6. 2 a historical name originally used for ascorbic acid. hexyl symbol: Hx; the alkyl group, CH 3-[CH 2l 4-CH n derived from hexane. hexyl glucoside hexyl p-D-glucopyranoside; a mild nonionic detergent, CMC 250 mM. Heyrovsky. Jaroslav (1890-1967), Czech physical chemist; Nobel Laureate in Chemistry (1959) 'for his discovery and development of the polarographic methods of analysis'. Hf symbol for hafnium. HFBA abbr. for heptafluorobutyric acid; a reagent used in automatic peptide sequence analysis. It renders the action of cyanogen bromide specific to the cleavage of tryptophanyl peptide bonds. HFCS abbr. for high fructose corn syrup. Hfr abbr. for high-frequency recombinant. HFT abbr. for high-frequency transduction. Hg symbol for mercury. HGF 1 abbr. for hepatocyte growth factor. 2 abbr. for hyperglycemic-glycogenolytic factor; see glucagon. HGF receptor see hepatocyte growth factor receptor. HGG abbr. for human gamma-globulin. hGH or HGH abbr. for human growth hormone (i.e. human somatotropin). HGPRT abbr. for hypoxanthine/guanine phosphoribosyltransferase; an enzyme that is important for the metabolic activation of purines, e.g. 6-mercaptopurine. Its deficiency is the cause of Lesch-Nyhan syndrome. HHT abbr. for hydroxyheptadecatrienoic acid. 5-HIAA abbr. for 5-hydroxyindoleacetic acid. hidden (immunological) determinant or cryptodeterminant any antigenic determinant so positioned that it is cryptic, i.e. normally not accessible for recognition by lymphocytes or antibody, but that becomes accessible after some stereochemical change occurs, e.g. by breakage, decomposition, or denaturation of the antigen. See also cryptotope. hide the skin of an animal, especially the tough, thick skin of larger mammals. Powdered, dried hide is used in assays of some proteinases. high-density lipoprotein abbr.: HDL; one of the classes of lipoproteins found in blood plasma in many animals (data normally relate to humans). They are also known as a lipoproteins, from having the highest electrophoretic mobility of the lipoproteins. HDL particles are the smallest of the blood lipoproteins: diameter 7.5~10 nm; solvent density for isolation 1.063~1.21 g mL-l; hydrated density 1.21 g mL- 1 • Their approximate composition (% by weight) is 6% unesterified cholesterol, 13% esterified cholesterol, 28% phospholipid, 3% triacylglycerol, 50% protein. Their apolipoprotein composition (% by weight total apolipoprotein) is 67% A-I, 22% A-II, 5-11% C-I + C-II + CollI, 1-2% E-II + E-III + E-IV, trace of D. They are synthesized in liver as precursor molecules, which

high-pressure liquid chromatography undergo modification in plasma to the mature molecules, especially as a result of the action of lecithin-cholesterol acyltransJerase. They appear to function in reverse transport of cholesterol from tissues to liver. See also apolipoprotein for individual apolipoproteins. high-energy bond symbol: -; a term formerly sometimes used by biochemists for a chemical bond whose hydrolysis is accompanied by an unusually large (>20 kJ mol I) negative standard free energy change. Although long used, the term has been recognized as incorrect and misleading, since it suggests that such a bond actually contains an unusually large amount of energy and fails to take into account the various factors that contribute to the large negative free energy change. high-energy compound a term formerly sometimes applied by biochemists to any compound containing one or more socalled high-energy bonds, e.g. ATP, phosphoenolpyruvate, acetyl-coenzyme A, etc. high-frequency recombinant any bacterial strain that has a high frequency of recombination because the F plasmid has become incorporated into the bacterial chromosome. See also Hfr. high-frequency transduction abbr.: HFT; any transduction in which the transducing phage(s) constitute a large proportion of the total phage population. high-fructose corn syrup abbr.: HFCS; a mixture of fructose and glucose used as a sweetener in soft drinks, etc.; it is sometimes called high fructose syrup or, especially in Europe, isoglucose. The breakdown of corn starch to glucose (plus oligosaccharides) is followed by the action of glucose isomerase yielding a mixture consisting mainly of fructose and glucose. The product thus manifests the greater sweetness of fructose compared with glucose. The content is typically 42% fructose, 51 % glucose, 5% maltose, and 2% other oligosaccharides. highly conserved see conserved. highly repetitive DNA a form of DNA that consists of short tandemly repeated sequences. It is found outside coding regions, and its role is unknown. Such DNA forms a significant proportion of most mammalian genomes. high mobility group proteins abbr.: HMO proteins; small nuclear proteins that bind to nucleosomal DNA and probably maintain genes in a transcribable conformation. The name derives from their behaviour on electrophoresis. Example, HMO 14 from human: database code HOI7_HUMAN, 89 amino acids (9.25 kDa). high-performance capillary electrophoresis electrophoresis through a long coiled capillary column that gives very high resolution of e.g. peptides. See also capillary electrophoresis. high-performance liquid affinity chromatography abbr. : HPLAC; a technique that combines the use of bioaffinity supports and high-pressure liquid chromatography. high-performance liquid chromatography abbr.: HPLC; an alternative name for high-prassure liquid chromatography. high-potential iron-sulfur protein abbr.: Hipip or HiPIP or HiPiP; a type of ferredoxin, originally found in the photosynthetic bacterium Chromatium vinosum, that has a very much higher redox potential (Eo' '" 0.3 V) and different magnetic properties compared with other ferredoxins. The term has been used increasingly, but inappropriately, for other ferredoxins that, like the Chromatium protein, are able to form a higher than usual oxidation level but do not have high redox potentials. high-pressure liquid chromatography or high-performance liquid chromatography abbr.: HPLC; a technique of column chromatography that is rapid and provides high resolution. It can be used with the various modes of liquid chromatography, the liquid being forced at high pressure, normally up to 420 kg cm- 2 (6000 psi)~ through the column (which is usually of stainless steel) and tnence through a detector into a fraction collector. Because of the ability to use high pressures, the particles of the support materials used for the stationary phase can be of very small diameter (3~ 10 !tm), which greatly improves resolution.

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high-speed supernatant

histamine receptor

high-speed supernatant a jargon term for the supernatant resulting from high-speed centrifugation (~100 000 g). high-spin complex any of the complex transition-metal ions having a maximal number of unpaired electrons in the d- or fshell. This state occurs when pairing energy is higher than the crystal field splitting energy. Compare low-spin complex. high-voltage electron microscope a type of electron microscope that employs accelerating voltages of I Mev, ten times that of previous instruments, enabling images of thick sections and even intact cells to be produced without significant loss of resolution. high-voltage electrophoresis abbr.: HVE; a technique of paper or thin-layer electrophoresis that results in better and more rapid separations (10-60 min) than the standard technique, which suffers from minimal diffusion of low-Mr components. The high-voltage technique employs currents of up to 500 mA and potential gradients of up to 200 V cm- I . The high field strength requires cooling of the support and adequate protection devices to be incorporated into the apparatus. Hildebrand solubility parameter symbol: 15; a measure of what is commonly called the polarity of a solvent; nonpolar solvents have low 15 values while polar solvents have large values. In liquid-liquid chromatography the Hildebrand parameter indicates the relative position of a solvent in an eluotropic series. The parameter is the sum of a number of factors: 15 = J d + 15 0 + J a + J h , where J d is a measure of interactions due to dispersion forces, 15 0 is a measure of interactions due to dipole interactions, Ja is a measure of the ability of the solvent to interact as a hydrogen acceptor, and J h is a measure of its interactions as a hydrogen donor. [After Joel Henry Hildebrand (1881-1983), US chemist.] Hill 1 (Sir) Archibald Vivian Hill (1886-1977), British physiologist and biophysicist; Nobel Laureate in Physiology or Medicine (1922) 'for his discovery relating to the production of heat in the muscle' [prize shared with O. F. Meyerhof]. 2 Robert ('Robin') Hill (1899-1991), British plant biochemist noted for his studies of the mechanism of photosynthesis. Hill coefficient or Hill constant symbol: h or nH; see Hill equation and Hill plot. Hill equation 1 an equation, y = K[x]hl(1 + K[x]h), used to express the binding of a ligand to a (macro)molecule. It may be rearranged to give: log[yl(l - y)] = -logK + hlog[x], where y, the fractional saturation, is the fraction of the total number of binding sites occupied by ligand, [x] is the free (unbound) ligand concentration, K is a constant, and h is the Hill coefficient. 2 (in pharmacology) an equation derived from the above relating the effect of a drug to its concentration. For an effect, E, produced when an agent, A, is applied at a concentration [A], then the relationship between E and [A] may often be described empirically by the equation

EIEmax = [Ajh/([A]soh + [Ay'),

where E max is the maximal value of E and [Also is the concentration that produces an effect that is 50% of E max . [After A. V. HilL] Hill-Langmuir equation (in pharmacology) a variation of the Langmuir absorption isotherm; for a ligand, L, binding to a receptor, R, according to the equilibrium

against log[x], where y is the fractional saturation with ligand and [x] is the free (unbound) ligand concentration. The slope at anyone point, h, is the Hill coefficient at that value of y. The values of h along the plot, which usually do not exceed the number of binding sites on each molecule and which tend to unity as y tends to 0 or I, give an indication of the nature and degree of cooperativity (interaction) between the various binding sites on the molecule. [After A. V. HilL] Hill reaction the phenomenon in which isolated chloroplasts evolve dioxygen when illuminated in the presence of a suitable electron acceptor, e.g. ferricyanide or ferrioxalate, with a concomitant reduction of the electron acceptor. [After R. HilL] Hill reagent any electron acceptor that functions in a Hill reaction, e.g. ferrioxalate or ferricyanide. hinge region 1 a flexible, proline-rich region of an immunoglobulin molecule, adjacent to the two disulfide bonds linking the two heavy chains together. It probably acts as a hinge on which the Fab fragments can rotate allowing the immunoglobulin molecule to take up a V-shape when it reacts with antigen. The hinge region is near the sites of action of papain and pepsin. 2 the region in the helical, rod-shaped part of a myosin molecule that is susceptible to cleavage by trypsin to give light meromyosin and heavy meromyosin. 3 a region in any protein about which rigid body motions occur. Hipip or HiPIP or HiPiP abhr. for high-potential iron-sulfur protein. hippocalcin a neuron-specific Ca 2 +-binding protein with EFhands, similar to recoverin. It is expressed exclusively in the pyramidal layer of the hippocampus. Example from human: database code HIPP_HUMAN, 192 amino acids (22.30 kDa). hirudin a dried extract obtained from leeches and possessing anticoagulant activity. The name is also applied to the purified active component, a 65-amino-acid polypeptide with three disulfide bridges; this has highly specific antithrombin properties, inactivating thrombin by blocking substrate-binding groups. Example from the leech Hirudo medicinalis: database code ITHLHIRME, 65 amino acids (6.97 kDa). hirudisin a recombinant hirudin variant engineered to inhibit a-thrombin and exhibit disintegrin activity. Hirudisins have antiplatelet aggregation activity. Replacement of the hirudin sequence Ser-Asp-Gly-Glu (residues 32-35) by Arg-Gly-AspSer (RGDS) yields hirudisin, or by Lys-Gly-Asp-Ser yields hirudisin-1. The integrin-binding RGD motif of hirudisin is implicated in its antiplatelet action. hirulog any synthetic peptide based on hirudin and designed as an inhibitor of the thrombin catalytic site, and exhibiting specificity for the anion-binding site of thrombin. hirustasin an antistasin-like serine proteinase inhibitor isolated from the medicinal leech, Hirudo medicinalis. His symbol/or a residue of the a-amino acid L-histidine (alternative to H). hist+ a variant form ofhisto+ (before a vowel). histaminase see amine oxidase (copper-containing). histamine 2-(4-imidazolyl)ethylamine; a compound formed by the decarboxylation of L-histidine and present in many mammalian tissues, with especially high concentrations in lung, skin, and intestine; it is stored in the granules of tissue mast cells and circulating basophil cells. Histamine is a potent vasodilator; it also increases capillary permeability, causes contraction of smooth muscle, plays a role in the regulation of gastric secretion, and acts as a mediator in allergic and anaphylactic conditions.

KL

L+R ..... LR, PLR = [L]/(KL +[L]), where PLR is the fraction (proportion) of binding sites occupied by a ligand at equilibrium and K L is the dissociation equilibrium constant. Hill plot a plot of the Hill equation in the form 10g[yI(1 - y)]

histamine receptor any of the receptors in mammalian tissues that interact specifically with histamine. Histamine receptors

303

histohematin

histidase may be divided into three categories. HI receptors mediate the stimulating effects of histamine on smooth muscle in the gut and bronchi and most of the depressor effects on blood pressure. They are antagonized (blocked) by such classical antihistamines as pyrilamine (mepyramine) and promethazine. The HI receptor has seven transmembrane domains coupled to the phosphatidylinositol-Ca 2+ second messenger system. Example: database code HHIR_HUMAN, 487 amino acids (55.78 kDa). H2 receptors mediate the stimulation of gastric acid secretion, the increase in the contraction frequency of cardiac muscle, the increase in cyclic AMP stores in basophil and mast cells, the inhibition of release of histamine by mast cells, and the remaining depressor effects on blood pressure. They are antagonized by, e.g., cimetidine. In humans the H2 receptor has seven transmembrane domains, positively coupled to adenyl ate cyclase. Example: database code HH2R_HUMAN, 359 amino acids (40.1 kDa). H3 receptors have a receptor site characterized pharmacologically by radioligand binding; second messenger coupling and structure are unknown. They are associated with presynaptic nerve terminals and attenuate the release of neurotransmitters, e.g. histamine, acetylcholine, and norepinephrine. They are antagonized and blocked, e.g., by thioperamide and c1obenpropit. histidase an alternative name for histidine ammonia-lyase. histidinal a-amino-p-4-imidazolepropionaldehyde; 2-amino-3(IH-imidazol-4-yl)propanal; (C3H3N2)CHrCH(NH2)-CHO; the a-amino-aldehyde analogue of histidine. It is the immediate biosynthetic precursor of histidine. histidinase an alternative name for histidine ammonia-lyase. histidinate 1 histidine anion; the anion, (C3H3N2)CHrCH(NH2)-COO-, derived from histidine. 2 any salt of histidine anion. 3 any ester of histidine. histidine the trivial name for P-4-imidazolylalanine; a-aminop-imidazole-4-propionic acid; 2-amino-3-(lH-imidazol-4yl)propanoic acid; (C3H3N2)CHrCH(NH2)-COOH; a chiral a-amino acid. L-Histidine (symbol: H or His), (S)-2-amino-3(IH-imidazol-4-yl)propanoic acid, is a coded amino acid found in peptide linkage in proteins; codon: CAC or CAU . It is also a component of the isopeptide carnosine. In mammals it is an essential dietary amino acid and is glucogenic. D-Histidine (symbol: D-His or DHis), (R)-2-amino-3-(lHimidazol-4-yl)propanoic acid, is not known to occur naturally. N-I and N-3 of the imidazole ring are designated rand 11: respectively. 1t

U

NH NA't

H°~ ')C'~)NH ' '-/ ~ lr

°

L-histidine histidine ammonia-lyase EC 4.3.1.3; systematic name: L-histidine ammonia-lyase; other names: histidase; histidine adeaminase; histidinase. An ammonia-lyase (deaminase) enzyme that catalyses the deamination of L-histidine to urocanate. It is widely distributed in animals, plants, and microorganisms; in plants it is present in glyoxysomes. The activity of this enzyme is defective in histidinemia. histidine (base) a histidine residue in which the imidazole group is unprotonated. histidine decarboxylase abbr.: HDC; EC 4.1.1.22; systematic name: L-histidine carboxy-lyase. A pyridoxal phosphate enzyme that catalyses the decarboxylation of L-histidine to histamine. It is similar to dopa and glutamate decarboxylases. Example from human (homodimer): database code DCHS_ HUMAN, 662 amino acids (74.10 kDa). histidinemia or (esp. Brit.) histidinaemia a rare, hereditary,

human metabolic disorder in which abnormally high levels of histidine are found in the blood and urine. It is due to a defect in the activity of histidine ammonia-lyase. histidine tail a sequence of (usually) about six histidine residues that is deliberately introduced at the C terminus of certain recombinant proteins. The purpose is to allow purification of the recombinant product by a type of affinity chromatography using a nickel chelating resin. Only the histidinetailed proteins are retained by the column and these may then be eluted using a buffer containing imidazole. histidinium 1 a term normally used to mean histidinium( I +); the (imidazolinium) monocation of histidine. In theory, the term denotes any ion or mixture of ions formed from histidine and having a net charge of + I, although the species (C 3H 4 N 2+)CH r CH(NH 3+)-COO- generally predominates in practice. 2 the systematic name for histidinium(2+); the dication of histidine. histidino 1 N 2-histidino; the alkylamino group, (C 3H 3N 2)CH r CH(COOH)-NH-, derived from histidine by loss of a hydrogen atom from its a-amino group. 2 either of the two possible groups, N"-histidino or NT-histidino, HOOC-CH(NH2)-CHr(C3H2N2h derived from histidine by loss of a hydrogen atom from its position on one or other of the nitrogen atoms of the imidazole ring. histidinol 4-(2-amino-3-hydroxypropyl)imidazole; 2-amino-3(I H-imidazol-4-yl)propanol; (C3H3N2)CHrCH(NH2)-CH20H; the a-amino-alcohol analogue of histidine. It is an intermediate, together with its phosphate ester, in the biosynthesis of histidine, and a powerful reversible inhibitor of protein synthesis. histidinol dehydrogenase abbr.: HDH; EC I. I. 1.23; L-histidinol:NAD+ oxidoreductase. An enzyme that catalyses the oxidation of two molecules of NAD+ of L-histidinol to L-histidine with reduction of the NAD+ to NADH. Example from the his operon of Salmonella typhimurium: database code HISX_SALTY, 434 amino acids (45.85 kDa); the protein is a dimer and bifunctional as it also has an aldehyde dehydrogenase site, histidinol; being an intermediate. See also Salmonella mutagenicity test. histidyl the acyl group, (C3H3N2)-CHrCH(NH2)-CO-, derived from histidine. histo+ or (before a vowel) hist+ comb. form denoting tissue. histochemistry the chemistry of the tissues, as studied with a combination of the methods of chemistry and histology. histocompatibility the extent to which an organism will tolerate a graft of a foreign tissue. -histocompatible ad). histocompatibility antigen any of the genetically determined isoantigens present on the surface of many animal cells that determine the immune reactions to tissue grafts. If tissue is grafted onto a recipient of the same species that does not carry the same histocompatibility antigens as the graft material, an immune response may be provoked in the recipient leading to graft rejection. See also HLA histocompatibility system, major histocompatibility complex. histocompatibility gene any gene determining the formation of a histocompatibility antigen. See HLA histocompatibility system, major histocompatibility complex. histoelectrofocusing a technique in which an unfixed frozen section of tissue, 25-40 flm thick, is applied to a support gel and then subjected to electrofocusing. The proteins and enzymes present in the tissue move into the gel and may be revealed by staining or zymographic techniques. histogram a diagram representing a frequency distribution. It consists of a number of contiguous rectangles whose widths are proportional to the class interval under consideration and whose heights are proportional to the frequency associated with each class. histohematin or (esp. Brit.) histohaematin a term originally used (1884) by Charles Alexander MacMunn (1852-1911) for the pigments now known as cytochromes. It included myohematin.

304

histone

Hodgkin

histone any of a group of evolutionarily highly conserved basic proteins, of molecular mass 11-21 kDa, that constitute about half the mass of the chromosomes of all eukaryotic cells, except spermatozoa. They comprise single polypeptide chains with a (lysine plus arginine) content of about 25%, and are concerned in the packing of DNA in chromatin. The principal his tones may be classified into five types as shown in the table. Type HI

H2A H2B H3 H4

Other names FI,la F2a2,Ilbl F2b,Ilb2 F3,III F2al,IV

Lys/Arg ratio

Mr

Location

20.0 1.25 2.25 0.72 0.79

21000 14500 13 800 IS 300 11 300

linker core core core core

The octomer (H2A,H2B,H3,H4h forms the nucleosome core. Examples from yeast: H2A.2, database code H2A2_YEAST, 131 amino acids (13.84 kDa); H2B.I, database code H2BI_ YEAST, 130 amino acids (14.10 kDa); H3, database code H3_YEAST, 135 amino acids (15.21 kDa); H4, database code H4_YEAST, 102 amino acids (11.22 kDa). HI is associated with nucleosomes, especially the linking DNA; example HIA (human): database code HIA_HUMAN, 222 amino acids (22.15 kDa). See also H-NS. hitchhiking 1 a jargon term for the sequence of events in which a genetic element (or transposon) inserts into an active secondary site on a replicon which is then transferred to a recipient, the transposon then coming immediately to occupy its normal primary site in the DNA of the recipient organism. 2 the spread of a neutral allele through a population due to its linkage with a beneficial allele that is subject to selection. Hitchings. George Herbert (1905-98), US biochemist and pharmacologist distinguished for his introduction, largely in collaboration with his colleague G. B. Elion, of a range of widely used synthetic drugs designed as antimetabolites, including the antifolate bactericidal agent co-trimoxazole, the immunosuppressants mercaptopurine and its derivative azathioprine, and the xanthine-oxidase inhibitor allopurinol; Nobel Laureate in Physiology or Medicine (1988) jointly with J. W. Black and G. B. Elion 'for their discoveries of important principles for drug treatment'. HIV abbr. for human immunodeficiency virus; a retrovirus, the causative agent of AIDS. Two such viruses are known: HlV-I, found worldwide, and HlV-2, which is much less common, being found mainly in West Africa. In terms of the gene structure of the viral envelope sequences (see HIV protein) HlV-1 and HlV-2, although both members of the Lentivirus family of retroviruses, are not closely related. HlV-2 is closely related to a simian immunodeficiency virus (SIV) common in sooty mangabeys and probably originated there. HlV-I, which probably originated from a non-human primate in Africa, is closely related to SIV from chimpanzees. However, since the rate of SIV infection in chimpanzees is very low, it is not clear that they represent the natural host of these viruses. HlV is subclassified into eight alphabetical subtypes or clades, plus one orphan clade. The reverse transcriptase enzyme of HlV is highly error-prone, leading to a high mutation rate. Thus these viruses evolve very quickly even within single patients, and drug-resistant mutations appear rapidly. For HlV-l to enter its target cells, it must not only bind to the cell-surface protein CD4 but also to one or more chemokine receptors. One of these, named CCR5, is effective in the early stages of infection. Patients with defective CCR5 cannot be infected with HIV-1. During the later stages of infection, another chemokine receptor, CXCR4 (former name: fusin) dominates. HIV-1 protease an aspartyl protease that is a homodimer of two subunits each containing 99 amino acids, with cysteines at positions 67 and 95. Its proteolytic function is essential for the life cycle of human immunodeficiency virus (HIV) and is, therefore, a target for the design of inhibitors as therapeutic drugs, several examples of which are in use.

HIV protein any of the proteins encoded by the human immunodeficiency virus (HlV). The HlV-1 genome (9.5 kb) is transcribed to give 12 different mRNAs generated by alternative splicing. The proteins are conventionally named for the gene andlor their size (kDa) with the convention that p = protein and gp = glycoprotein. The primary translation products are: Gag precursor (p53); Pol precursor; Env precursor (gpI60); Nef (p27; negative regulator); Vif (p23); Tat (pI4; regulatory protein); Rev (p 19; regulatory protein); Vpr (p 18); and Vpu (pIS). The Gag precursor is cleaved to myristoylated Gag protein (pI7), structural protein (p24), and pIS; piS is the precursor for RNA-binding protein (p7) and proline-rich protein (p9). The Pol precursor is cleaved to protease (plO), reverse transcriptase (pSI), and endonuclease (p32). The Env precursor is cleaved to extracellular protein (gpI20) and transmembrane protein (gp41). Protease, reverse transcriptase, and endonuclease are synthesized as part of a polyprotein: database code POL_HVIBR, lOIS amino acids (115.03 kDa). See also retrovirus. HLA abbr. for human leukocyte-associated antigen. See also histocompatibility antigen, major histocompatibility complex. HLA histocompatibility system a family of histocompatibility antigens encoded by the complex of genetic loci known as the major histocompatibility complex (MHC). It is the major histocompatibility system in humans, equivalent to the H-2 histocompatibility system in mice. The MHC genes control the presence of HLA isoantigens on cell surfaces. These antigens are of primary importance in tissue grafting since HLAincompatible grafts are more likely to be rejected than incompatible grafts of other isoantigen groups. HLH abbr. for helix-loop-helix (see helix-turn-helix). hly genes see hemolysin. HMC abbr. for 5-hydroxymethylcytosine. H-meromyosin abbr. for heavy meromyosin. hMG or HMG abbr. for human menopausal gonadotropin (i.e. human urogonadotropin). HMG 1 abbr. for 2-hydroxy-2-methylglutaryl. 2 abbr. for high mobility group of nuclear proteins. 3 see hMG. HMG-CoA abbr. for hydroxymethylglutaryl-CoA. HMG-CoA lyase abbr. for hydroxymethylglutaryl-CoA lyase. HMG-CoA reductase abbr. for hydroxymethylglutaryl-CoA reductase. HMG-CoA synthase abbr. for hydroxymethylglutaryl-CoA synthase. HMM abbr. for heavy meromyosin. HMMA abbr. for hydroxymethoxymandelate. HMP abbr. for hexose monophosphate. HMP pathway or HMP shunt abbr. for hexose monophosphate pathway (shunt) (i.e. pentose phosphate pathway). HNPCC a human gene that may normally function in the repair of regions of mismatch of DNA. It is named from hereditary nonpolyposis colorectal cancer, a condition associated with mutations in this gene. hnRNA or HnRNA abbr. for heterogeneous nuclear RNA (alternatives to H-RNA). hnRNP abbr. for heterogeneous nuclear ribonucleoprotein. hnRNP particles abbr. for heterogeneous nuclear ribonucleoprotein particles; particles in the nucleus containing hnRNA bound to protein. H-NS bacterial proteins of several families that are basic DNAbinding proteins, possibly the prokaryotic counterparts of histones in eukaryotic chromatin. Their role remains unclear. They have the ability to bind to curved DNA and may have a role in transcriptional regulation. The N-terminal tetrapeptide, consensus Ser-Glu-Xaa-Leu, is characteristic. Example from Escherichia coli: protein HI, dimer, database code HNS_ ECOLI, 136 amino acids (15.39 kDa). The name derives from an isolation procedure extracting them from the 30S ribosomal native subunit. Ho symbol for holmium. Hodgkin 1 (Sir) Alan Lloyd (1914-98) British physiologist

305

Hoechst 33258 renowned for his researches on nerve-impulse conduction; Nobel Laureate in Physiology or Medicine (1963) jointly with J. C. Eccles and A. F. Huxley 'for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cells membrane'. 2 Dorothy (Mary) Crowfoot-Hodgkin nee Crowfoot, (1910-94), British chemist and crystallographer renowned for her elucidation by X-ray crystallography of the molecular structures of benzylpenicillin (formerly termed penicillin G) and cyanocobalamin (a version of vitamin Bn) and in particular of the complete three-dimensional structure of crystalline zinc insulin (announced in 1969, having - as D. M. Crowfootfirst observed its diffraction pattern in 1934); Nobel Laureate in Chemistry (1964) 'for her determination by X-ray techniques of the structures of important biochemical substances', e.g. penicillin, vitamin B 12 , and insulin. Hoechst 33258 see bisbenzimide. Hoechst 33342 see bisbenzimide. Hoff see van't Hoff. Hofmeister series or lyotropic series an arrangement of either the simple anions or the simple cations (or of the salts of such ions) in order of their ability to remove lyophilic substances from colloidal solutions. Each series is an index of, inter alia, the relative abilities of the ions to salt-out proteins from solution. The order for anions is: citrate 3- > tartrate 2- > acetate- > NO) > CI04 - > CNS-, and that for cations is: Mg2+ > Ca 2+ > Sr 2+ > BaH> Li+ > Na+ > K+ > Rb+ > Cs+. [After Franz Hofmeister (1850-1922).] Hofstee plot see Eadie-Hofstee plot. Hogness box an alternative name for TATA box. hol+ a variant form of (before a vowel) holo+. holandric inherited solely in the male line. Compare hologynic. holdback agent or holdback carrier any nonradioactive substance that is added to a sample to prevent either coprecipitation or adsorption of some soluble radioactive substance. hold-up volume symbol: V M ; (in chromatography) the volume of eluent required to elute a component whose concentration in the stationary phase is negligible relative to that in the mobile phase. In gas chromatography, the volume of carrier gas (eluent) is specified at the same temperature and pressure as the total retention volume. hole (in physics) the absence of an electron in a normally filled valency structure of a crystalline semiconductor that behaves as a carrier of charge and is mathematically equivalent to a positron. Holley, Robert William (1922-93), US biochemist and molecular biologist noted for his establishment of the structure of alanine transfer RNA, this being the first occasion on which the sequence of a nucleic acid had been determined; Nobel Laureate jointly with H. G. Khorana and M. W. Nirenberg (1968) for their 'interpretation of the genetic code and its function in protein synthesis'. Holliday junction or Holliday structure one of the junctions between four strands of DNA that are important intermediates in genetic recombination. They are part of the mechanism for crossing over during the long prophase of meiotic cell division T, when four strands of DNA are aligned. The process involves breaking the DNA double helix in a maternal chromatid and in a homologous paternal chromatid and then exchanging fragments between the two non-sister chromatids in a reciprocal fashion. At this point, in each four strands, a paternal strand links across to a maternal strand, forming the junction known by the name of its proposer. [After Robin Holliday (1932- ), British biologist.] hollow-cathode discharge lamp a radiation source used in atomic absorption spectrophotometry to produce a spectrum of radiation specific to the element being assayed. A sample of the element in question is held in a metal cup-shaped cathode, which, together with a tungsten anode, is enclosed in a glass or quartz envelope filled with argon at low pressure. A high voltage is used to produce an arc spectrum of the element.

homeotic gene hollow-fibre technique a technique in which bundles of semipermeable, hollow fibres with pores of controlled dimensions that function as molecular sieves are used for concentrating, desalting, dialysing, and fractionating macromolecules in solution. Compare capillary filtration. holo+ or (before a vowel) hol+ comb. form whole, entire, complete; wholly, entirely, completely. holocellulose the complex mixture of polysaccharides remaining after the removal of lignin from tree-wood by treatment with sodium chlorite solution. It consists of a mixture of cellulose and hemicellulose. holocrine 1 describing a type of secretion that involves disintegration of the entire secretory cell to release the secretory products. 2 describing a gland made up of such cells. Compare apocrine, eccrine, merocrine. holoenzyme a catalytically active complex comprising the protein part of an enzyme (apoenzyme) combined with the appropriate cofactor or cofactors. hologram 1 the pattern produced when light, or other electromagnetic radiation, that has been reflected, diffracted, or transmitted by an object placed in a coherent beam, interferes with a reference beam related in phase to the first beam. 2 a photograph of such a pattern. holograph 1 to make a hologram (def. 1,2).2 any book or other document handwritten by its author. holography the process of making and using holograms (def. 1, 2). -holographic adj. hologynic inherited solely in the female line. Compare holandric. Holometabola or Endopterygota one of the two divisions of the subclass Pterygota, comprising those insects, e.g. butterflies, moths, flies, and beetles, in which the juvenile forms (larvae) are very different from the adults. Such insects undergo complete metamorphosis during a resting stage (pupa). Compare Hemimetahola. holoprotein the functional form of a protein containing a protein part (apoprotein) together with any appropriate ligand or ligands. holorepressor a functional repressor protein consisting of an aporepressor plus corepressor complex. homeo+ or homoeo+ or homoio+ comb. form denoting like or similar. homeobox a short (180 bp) conserved DNA sequence that encodes a DNA-binding motif famous for its presence in genes that are involved in orchestrating the development of a wide range of organisms. See also homeotic gene. homeodomain the DNA-binding motif of 60 amino acids encoded by a homeobox. homeomorphism or homoeomorphism (in chemistry) the property shown by certain substances of having the same crystal form but different compositions. -homeomorphic, homeomorphous, or homoeomorphic, homoeomorphous adj. homeostasis or homoeostasis the maintenance of a relatively constant internal environment in the bodies of higher animals by means of a series of interacting physiological and biochemical processes. -homeostatic or homoeostatic adj. homeotic gene or homeodomain-encoding gene or homeoboxencoding gene or Box gene; any of the genes that are allelic for mutations resulting in the conversion of one body part into another. Homeotic genes were first discovered in Drosophila; a mutation in such a gene could, e.g., result in a leg replacing an antenna. While Drosophila has only two Box clusters, in nematodes there is one, and in vertebrates four clusters of 9 to 11 genes each located on a separate chromosome and spanning more than 100 kb. The vertebrate Hox genes are expressed in specific patterns and at particular stages in embryogenesis. They are activated by retinoic acid and sonic hedgehog protein. In the limb these are active in concert with fihroblast growth factor. The degree of homology of the Hox genes in different species is remarkably high. The structure of some homeodomains has been determined, as has their interaction with DNA.

306

homeothermic

homogeneously staining region

homeothermic the usual US spelling of homoiothermic. homeotypic pertaining to, or being the second, reductive division in meiosis. Compare heterotypic. homo+ comb. form 1 the same, similar, alike. Compare allo+ (def. 1); hetero+(def. 1); iso+(def. I); xeno+(def. 1).2 from, or directed towards, the same species. Compare allo+ (def. 2); hetero+ (def. 2); Iso+ (def. 2); xeno+ (def. 2). 3 containing atoms, groups, linkages, residues, or subunits of the same kind. Compare hetero+ (def. 3). 4 denoting the next higher homologue of a specified chemical compound, especially one whose molecules contain, in a hydrocarbon chain or ring, one more methylene, -CH r , than those of of the parent compound, e.g. homocysteine, homoserirte, homo-Sa-pregnane. Compare nor+ (def. 2). Homo a genus of primates that includes modern man (Homo sapiens) and a number of more primitive, fossil species. homoarginine (sometimes) a trivial name for N6-amidino lysine. homobifunctional describing a chemical reagent that carries two identical reactive groups. Compare heterobifunctional. homocarnosine (sometimes) a trivial name for N a -(4aminobutyryl)histidine. homochromatic a less common term for monochromatic (def. I). homochromatography a chromatographic technique for the separation of labelled oligonucleotides, in which a mixture of unlabelled oligonucleotides is used to displace the labelled components according to differences in size. homocitrate 2-hydroxybutane-I,2,4-tricarboxylate; the (R) enantiomer)s a component of the amlnoadipic pathway and is formed by t1omocitrate s~nthase.

HOYX0° "" OH """ OH o eOOH homocitrate synthase EC 4.1.3.21; systematic name: 2-hydroxybutane-l,2,4-tricarboxylate 2-oxoglutarate-lyase (CoAacetylating). An enzyme that catalyses the formation of homocitrate from 2-oxoglutarate and acetyl-CoA and H 20. See also aminoadipic pathway. homoconjugation the association between a base and its conjugate acid through a hydrogen bond. See conjugate acid-base pair. Compare heteroconjugation. homocyclic 1 describing any cyclic molecular structure containing atoms of a single element in the ring or rings; describing any compound having such a structure. The term is preferred to its synonym isocyclic; it includes carbocyclic (def. 1). Compare heterocyclic (def. I). 2 any such compound. homocysteine symbol: Hcy; a-amino-y-mercaptobutyric acid; 2-amino-4-mercaptobutanoic acid; an important intermediate in the metabolic reactions of its S-methyl derivative, methionine. Its concentration in human serum is raised after stroke.

L-homocysteine homocysteine methyltransferase one of several enzymes, e.g. the two alternative forms of enzyme synthesizing methionine: (1) 5-methyltetrahydrofolate~homocysteine S-methyltransferase. (EC 2.1.1.13); other name: tetrahydropteroylglutamate methyltransferase; it catalyses a reaction between

5-methyltetrahydrofolate and L-homocysteine to forin tetrahydrofolate and L-methionine; cobalamin is a cofactor. Example, metH gene product in Escherichia coli: database code METH_ECOLl, 1226 amino acids (135.81 kDa). (2) 5-methyltetrahydropteroyltrigllitamate-homocysteine S-methyltransferase (EC 2.1.1.14); other name: tetrahydropteroyltriglutamate methylttansferase; it catalyses a reaction between 5methyltetrahydropteroyltri-L-glutamate and L-homocysteine to form tetrahydropteroyltri-L-glutamate and L-methionine. Example, metE gene product in E. coli: database code METE_ ECOLl, 752 amino acids (84.91 kDa). homocystine 2,2'-diamino-4,4'-dithiobis(butanoic acid); the disulfide oxidation product of homocysteine. homocystinemia or (esp. Brit.) homocystinaemia inherited biochemical abnormality of humans, characterized by an abnormally high concentration of homocystine in the blood; this may be accompanied by a corresponding elevation 6f homocystine in the urine (homocystinuria); alternatively, homocystinuria may be the chief presenting sign. Either condition may be due to either: (1) a deficiency of cystathionine p-synthase (EC 4.2.1.22) activity (the deficiency preventing the co~· densation of homocysteine with serine to form cystathionine); or (2) a deficiency of the 5-methyltetrahydrofolate-depend~nt pathway for the remethylatlon of homocysteirte to methiohlne. homodetic describing a cyclic peptide in which the ring consists solely of amino-acid residues in eupeptide linkage. Compare heterodetic. homodimer any macromolecular structure in which two identical subunits (monomers or protomers).a~e noncovalehtly associated. See also dimer. Compare heterodimer. homoduplex hybrid DNA involving two strands that are complementary. Compare heteroduplex. homoeo+ a variant form ofhomeo+. homogametic describing the sex whose cell nuclei contain a pair of similar sex chromosomes. The homogametic sex is usually female, but is male in the Lepidoptera, birds, some amphibians and fishes, and a few plants. Compare heierogametic. homogenate any disrupted tissue preparation in which cell disrupti()n is maximal while the destruction of intracellular organelles is kept to the minimum. homogeneic an alternative term for allogeneic. Compare heterogeneic. homogeneous 1 being uniform ip kind, as in a homogeneous population. 2 (describing a group of molecules) uniform in structure or composition. 3 (describing a system), consisting of only a single chemical phase. Compare heterogeneous, homogenOdS. -homogeneity n. . . homogeneous catalysis any catalytic action or process in which the catalyst is uniformly distributed in the same chemical phase as the reactants. Compare heterogeneous catalysis. homogeneous enzyme immunoassay or enzyme~multiplied immunoassay technique (abbr.: EMIT) a technique of homogeneous immunoassay in which an enzyme is covalently coupled to the substance to be assayed. The enzymic activity of the complex is inhibited by an antiserum specific for the substance and this inhibition is relieved by the presence of free molecules of the substance to be assayed. The enzyme acts as a molecular amplifier. homogeneous immunoassay any immunoassay that does not involve physical separation of antibody-bound antigen from antigen molecules that remain free. Labels that may be attached to the antigen include: enzymes, cofactors, prosthetic groups or substrates of enzymes, chemiluminescent or fluorescent molecules, stable free radicals. Compare heterogeneous immunoassay. homogeneously staining region a region in a chromosome that stains homogeneously, rather than with the banding pattern normally seen. The region contains massively amplified numbers of copies of a small segment of the genome. The amplified DNA may often consist of multidrug resistance gene DNA (see MDR).

307

homogenesis homogenesis the production of offspring having the same characteristics in successive generations. Compare heterogenesis. homogenetic describing chromosome pairing during meiosis when the pairing partners are derived from one of the original ancestors. Compare heterogenetic. homogenic or congenic 1 describing a gamete that contains only one allele of a particular gene. 2 describing two genetic elements that are descended from a common ancestor by a known sequence of steps. 3 an alternative word for homogeneous. Compare heterogenic. homogenize or homogenise prod uce a homogenate. -homogenization or bomogenisation n. homogenizer or homogeniser any apparatus for producing a homogenate. homogenous 1 of, pertaining to, or exhibiting homogeny. 2 an alternative word for homogeneous. homogentisate or (formerly) alcapton 2,5-dihydroxyphenyJacetate; an intermediate in the catabolism of tyrosine and in the biosynthesis of plastoquinone and tocopherol. It is excreted in abnormally large quantities in the urine in alcaptonuria. See also homogentisate 1.2-dioxygenase. homogentisate 1,2-dioxygenase EC 1.13.11.5; systematic name: homogentisate:oxygen I,2-oxidoreductase (decyclizing); other names: homogentisicase; homogentisate oxygenase; homogentisic acid oxidase. An enzyme that catalyses the oxidation by dioxygen of homogentisate to 4-maleylacetoacetate: iron(lI) is a cofactor. In the catabolism of L-tyrosine, homogentisate is formed from 4-hydroxyphenylpyruvate; maleylacetoacetate is converted to fumarylacetoacetate, which is split to fumarate and acetoacetate. homogeny (in biology) similarity in the structure of organisms or parts of organisms because of common ancestry. homoglycan or homopolysaccharide any polysaccharide (i.e. glycan) that contains residues of only one kind of monosaccharide (i.e. glycose) molecule. Compare heteroglycan. homograft an old term for allograft. Compare heterograft. homoio+ a variant form ofhomeo+. homoiosmotic describing organisms with a constant internal osmotic pressure. Compare poikilosmotic. homoiothermic or homoiothermal or (esp. US) homeothermic or homeotbermal describing an organism (poikilotherm) that sustains a relatively constant body temperature, usually higher than that of its surroundings. Compare poikilothermic. -homoiothermy or (esp. US) homeothermy n. homokaryon or homocaryon any cell with more than one nucleus, and in which the nuclei are all of the same genetic constitution; a tissue composed of such cells. Compare heterokaryon. -homokaryotic or homocaryotic adj. homokaryosis or homocaryosis the condition of having a homokaryon or homokaryons. Compare heterokaryosis. homolactic fermentation a type of fermentation of glucose to lactate via the Embden-Meyerhof pathway. Compare heterolactic fermentation. homolog (sometimes) the US spelling of homologue. homologous 1 having a related or similar position, structure, etc.; corresponding; exhibiting homology. 2 (in chemistry) describing compounds that form a series with successive constant differences in composition. 3 (in biology) of common ancestry; especially of organs and tissues that have a similar anatomical position and structure in different species by virtue of their common evolutionary origin, even though their functions may have come to differ; e.g. the wing of a bird and the forelimb of a reptile. Compare analogous. 4 (in genetics) describing chromosomes that pair during meiosis, each member of a homologous pair being a duplicate of one of the chromosomes contributed at syngamy by the mother or the father. S (in biochemistry) a (of sequences of residues in encoded macromolecules) having the same or similar residues at corresponding positions (see also conserved). With respect to proteins the term is used to imply a common evolutionary origin. Specifically this requires evidence based on gene structure and

hornothallic not merely a similarity of protein structure. b (of proteins from different species) having identical or similar functions. Compare heterologous. -homology n. homologous antibody the antibody elicited by a specified antigen. homologous antigen the antigen that has elicited a specified antibody. homologous desensitization see desensitization. homologue or (sometimes) US homolog 1 (something) exhibiting homology. 2 (in chemistry) any member of a homologous (def. 2) series of compounds. 3 (in biology) anyone of a series of homologous (def. 3) organs or structures. 4 (in genetics) a either members of a pair of homologous (def. 4) chromosomes. b either one of two genes in corresponding loci in homologous chromosomes. homology domain any of the regions in an immunoglobulin involved in forming the immunoglobulin fold. homolysis (in chemistry) the cleavage of a covalent bond in such a manner that each of the fragments between which the bond is broken retains one of the bonding electrons; e.g. A-B ~ A· + B·. -homolytic adj. homooligomer any oligomer made up of only one kind of constitutional repeating unit. -homooligomeric adj. homophilic binding (of adhesion molecules) binding of an adhesion molecule in one cell to an identical molecule in an adjacent cell. Compare heterophilic binding. homopolymer any polymer made up of only one kind of constitutional repeating unit. For example, cellulose contains only glucose as the monomeric unit. -homopolymeric adj. homopolymer tailing a jargon term for a procedure useful in joining two types of duplex DNA molecules to form mixed dimeric circular DNA. In this procedure, homopolymer sequences of one type, e.g. poly(dA), are added to the 3'-ends of one of the populations of DNA molecules, while complementary homopolymer sequences, e.g. poly(dT), are added to the 3'-ends of the other population of DNA molecules. The two types of molecules are then annealed to form mixed dime ric circles. homopolysaccharide an alternative name for homoglycan. homoserine symbol: Hse; a-amino-y-hydroxybutyric acid; an intermediate in the biosynthesis of cystathionine, threonine, and methionine. It also occurs in bacterial peptidoglycans and, as its O-guanidino derivative, in canavanine. The term normally implies the L enantiomer. homoserine deaminase see cystathionine y-Iyase. homoserine dehydratase see cystathionine y-Iyase. homoserine dehydrogenase EC 1.1.1.3; systematic name: Lhomoserine:NAD(P)+ oxidoreductase; an enzyme of the pathways for the biosynthesis of methionine and threonine. It catalyses the formation of L-homoserine and NAD(Pt from L-aspartate 4-semialdehyde and NAD(P)H. Example, a homotetrameric bifunctional enzyme from Escherichia coli: database code AKIH_ECOLI, 820 amino acids (89.02 kDa). Amino acids 1-249 form the aspartokinase I domain, amino acids 250-470 form a large 'interface', and 471-820 form homoserine dehydrogenase; regulation is by L-Thr. Another example is from Corynebacterium glutamicum and Brevibacterium lac tofermentum: database code DHOM_CORGL, 445 amino acids (46.39 kDa). See also aspartokinase/homoserine dehydrogenase. homoserine lactone symbol: Hsl; a-amino-y-butyrolactone; a substance formed by the cleavage of methionine-containing peptides by cyanogen bromide. homosterism or homostery the phenomenon in which a second molecule of normal substrate, or a structurally similar compound, combines at the catalytic site of an enzyme leading to a modification in the reaction of the bound intermediate. Compare allosterism. -homosteric adj. homostery an alternative term for homosterism. homothallic describing species, e.g. of certain fungi and algae, in which a sexual spore can result from the fusion of nuclei that are genetically distinct (i.e. not necessarily homozygous), but are derived from the same thallus; thus the species is self-fertile.

homothallic switching endonuclease homothallic switching endonuclease a sequence-specific endonuclease, with a site on yeast chromosome III, that is involved in mating-type switching. It is a zinc finger protein. Database code HO_YEAST, 586 amino acids (66.06 kDa). homotherm an alternative wordfor homoiotherm. homotope any residue that can take the place of another residue in a particular position in a polymer; e.g. the serine and glycine residues at position 9 of the A chain of bovine and ovine insulin, respectively, are homo topes. homotransplant 1 an alternative term for homograft. 2 to effect such a transplant. homotropic describing an allosteric effect in which interaction occurs between identical ligands; the effect appears to be always cooperative. The term is applied also to such an interaction in the case of an allosteric enzyme for which the same substance acts as both the substrate and the allosteric effector, etc. Compare heterotropic (def. 1). homovanillic acid 4-hydroxy-3-methoxyphenylacetic acid; a metabolite of catecholamine metabolism, found in human urine. It is the principal urinary metabolite of dopa and dopamine. It is used as a reagent in the f1uorometric determination of glucose oxidase and other oxidases.

rC~

308

host-controlled modification hopanoids pentacyclic sterol-like molecules based on the hopane nucleus. They are found in bacteria, some plants and lichens, and in sediments and crude oils, and are said to be the most abundant organic molecules in the biosphere (estimated total biomass 1011 to 10 12 tonnes), thus outranking cellulose. Hopkins, (Sir) Frederick Gowland (1861-1947), British biochemist renowned for his discoveries of essential amino acids and accessory food factors (later termed vitamins), for his isolation of glutathione and tryptophan, and for playing an important part in establishing biochemistry as an independent discipline; Nobel Laureate in Physiology or Medicine (1929) 'for his discovery of the growth-stimulating vitamins' [prize shared with Christiaan Eijkman]. Hopkins-Cole reaction a colour reaction for free or combined tryptophan, in which a violet colour is produced when a solution containing tryptophan is treated with glyoxylic acid (present in impure glacial acetic acid) and subsequently layered onto a solution of pure, concentrated sulfuric acid. [After F. G. Hopkins and Sydney William Cole (1877-1951).] HOQNO or HQNO abbr. for 2-n-heptyl-4-hydroxyquinoline Noxide; an inhibitor of the mitochondrial respiratory chain at cytochrome be} and of photosynthetic electron flow immediately before cytochrome b 559 LP. OH

~OCH3 OH

homozygosis 1 the union of gametes identical for one or more pairs of genes to form a homozygote. 2 or homozygosity the state or condition of being a homozygote. Compare heterozygosis. homozygosity an alternative term for homozygosis (def. 2). homozygote any cell or organism having identical genes (alleles) at one or more corresponding loci on homologous chromosomes. With respect to such loci, a homozygote will produce two identical gametes. Compare heterozygote. homozygotic or homozygous adj. Hoogsteen base pair a nucleic-acid base pair that differs from the Watson-Crick base pair. In the Hoogsteen adeninethymine base pair the 6-NH 2 and N-7 of the adenine are hydrogen bonded respectively to the 4-0 and H-l of the thymine. The Hoogsteen guanine-cytosine pair requires that N-l of the cytosine is protonated. In this base pair the 6-0 and N-7 of the guanine are hydrogen bonded respectively to the 4NH 2 and the protonated N-I of cytosine. In Watson-Crick base pairs the glycosidic bond of both nucleotides has the anti conformation, but in the Hoogsteen pairs the glycosidic bond of the purine nucleotide has the syn conformation. Hoogsteen base pairs are particularly important in the structure of DNA triple helices, where the third strand forms Hoogsteen pairs to bases in the DNA duplex. [After Karst Hoogsteen (1923- ), Dutch-American biochemist, who first described it.] hopane the pentacyclic triterpene hydrocarbon parent of hopanone and derivatives found in plant resins. See also hopanoids.

hordein a type of glutelin found in barley. hormone any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which it has a specific regulatory action; an endocrine (def. 2). The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects. Compare autacoid, hermone. See also secretin. -hormonal ad). hormone cascade see cascade sequence. hormone-sensitive lipase any enzyme of the sub-subclass EC 3.1.1 that, when activated in adipose tissue, catalyses the mobilization of fatty acids into the circulation. Such enzymes are activated by cyclic AMP-dependent phosphorylation under the influence of catecholamines, and are inactivated by insulin-dependent dephosphorylation. Example from human: database code LIPS_HUMAN, 786 amino acids (85.38 kDa). hormonotoxin any conjugate of a peptide hormone and a peptide toxin, e.g. ovine luteinizing hormone-gelonin. host 1 any organism in which another organism, especially a parasite or symbiont, spends part or all of its life cycle and from which it obtains nourishment and/or protection. 2 any organism that harbours a pathogenic or nonpathogenic infectious agent. 3 the recipient of a transplanted tissue or organ graft. 4 a cell or organism that contains recombinant DNA. host cell any cell whose metabolism is used for the growth and reproduction of a virus. host-cell reactivation abbr.: HCR; the restoration of activity in a UV-damaged DNA bacteriophage by the excision-repair mechanisms of the host cell in which it multiplies. host-controlled modification or host-controlled variation or host-induced modification or host-induced variation any nonheritable change in the properties of a DNA bacteriophage re-

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host-controlled modification suiting from the phage DNA assuming the DNA modification pattern characteristic of the host bacterium. It is usually recognized by restriction in the efficiency of plating of the newly modified phage on its former host strain. Similar phenomena have been described for viruses infecting eukaryotic cells. host-induced modification or host-induced variation see host-controlled modification. host range the spectrum of host organisms that can be in-

fected by a specified infectious agent or parasite. host-vector system a compatible combination of host and vector (def. 3) that allows propagation of DNA. hot (in physics) an informal term describing a substance or material that contains a radio nuclide, especially if carrier-free or

at a dangerously high activity or specific activity. Compare cold. hot laboratory or hot lab an informal term for a laboratory re-

served and equipped for the manipulation of radioactive substances or materials of (dangerously) high activity. hot room 1 a room (or laboratory) maintained at a constant, higher-than-ambient temperature. 2 an informal term for a room (or laboratory) that is specially equipped to deal with high levels of radioactivity. hot spot any site at which mutations are observed with an unusually high frequency. Such sites have a highly enhanced, inherent susceptibility to mutation that cannot be ascribed to the type of base pair involved, the way in which it is altered, or the resulting change in any protein encoded by the DNA molecule. hour symbol: h or hr; a non-SI unit of time equal to 3600 s. housekeeping genes see constitutive genes. Houssay, Bernardo Alberto (1887-1971), Argentinian physiologist and endocrinologist noted for his researches on diabetes and on the internal secretions of the adrenal, anterior pituitary, and thyroid glands; Nobel Laureate in Physiology or Medicine (1947) 'for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar' [prize shared with C. F. and G. T. Cori]. Houssay animal a pancreatectomized animal which has also undergone hypophysectomy. The latter ameliorates the diabetic state that results from pancreatectomy by abolishing the secretion of somatropin. [After B. A. Houssay.) Hox gene see homeotic gene. Hp 1 symbol for the heptyl group, CHdCH 2ls-CH r . 2 abbr. for haptoglobin. HP-1 abbr. for helper peak-l (now called interleukin 1). HPCE abbr. for high performance capillary electrophoresis. HpETE abbr. for hydroperoxyeicosatetraenoate. hPL or HPL abbr. for human placental lactogen. HPLAC abbr. for high-performance liquid affinity chromatography. HPLC abbr. for high-pressure liquid chromatography or highperformance liquid chromatography. Hpo symbol for the heptanoyl group, CHdCH 2ls-CO-. HpODE abbr. for hydroperoxyoctadecadienoate. HPR abbr. for H protein; a low-M p heat-stable, cytoplasmic phosphocarrier protein found in some bacterial species and concerned in the phosphoenolpyruvate (PEP)-hexose transferase system for the transport of hexoses across the cell membrane. The phosphate of PEP is transferred transiently to HPR. Example from Escherichia coli (identical sequence for Salmonella typhimurium): database code PTHP_ECOLI, 85 amino acids (9.11 kDa). See enzyme I, enzyme II. H+ pump see hydrogen ion pump. HQNO see HDQND. hr abbr. for hour (now superseded by h). H1, H2, H3 receptors see histamine receptor. H-RNA abbr. for heterogeneous nuclear RNA (alternative to hnRNA or HnRNA). HRT abbr. for hybrid-released translation. HSA abbr. for human serum albumin. Hse symbol for a residue of the a-amino acid L-homoserine.

HSE abbr. jar heat-shock regulatory element or heat-shock re-

sponse element. 5-HT IF , 5-HT 2A , 5-HT 2B , 5-HT 2C ' 5-HT J , 5-HT 4 , 5HT sA , 5-HT sB , 5-HT6 , and 5-HT? The members of the 5-HT I family all have seven transmembrane domains and are negatively coupled to adenyl ate cyclase through G-proteins, but the 5-HT IA receptor also increases K+ conductance; example, 5-HT IA from rat: database code 5HIA_RAT, 422 amino acids (46.43 kDa). 5-HT IC is now classified as a 5-HT2 receptor. 5HT 2A , 5-HT 2B , and 5-HT 2C have seven transmembrane domains and activate the phosphatidylinositol cycle; example, 5-HT 2C from rat: database code 5H2C_RAT, 460 amino acids (51.92 kDa). 5-HT J opens a CI channel; 5-HT4 has four transmembrane domains and is positively coupled to adenylate cyclase; 5-HT 5 has seven transmembrane domains but the main effector is unknown; example, 5-HTSA from rat: database code 5H5A_RAT, 357 amino acids (40.67 kDa). 5-HT6 and 5-HT? are both of the seven-transmembrane-helix type and are positively coupled to adenylate cyclase. 5-hydroxytryptophan a nonprotein amino acid found in plants; it is formed in legumes by hydroxylation of tryptophan. It is also formed in animals. See also serotonin. hydroxyurea NH 2CONHOH; an analogue of urea with antineoplastic activity, possibly through inhibition of DNA synthesis. hygro+ comb. form denoting moisture, especialIy that due to water. hygrometer any instrument for measuring the relative humidity of a gas. hygromycin B an aminoglycoside antibiotic from Streptomyces hygroscopicus; the inclusion of genes conferring resistance to hygromycin B in certain fungal recombinant DNA vectors allows selection of recombinants when these are plated out on medium containing this antibiotic. hygroscopic (of a substance) tending to absorb water from the surrounding atmosphere. Compare deliquescent. Hyl or (formerly) Hylys symbol for a residue of any of the hydroxy derivatives of the a-amino acid L-Iysine, especially 5-hydroxY-L-lysine. See hydroxylysine. SHyl symbol for a residue of the a-amino acid 5-hydroxyL-Iysine (preferred alternative to Lys(5-0H) or Hyl). See hydroxylysine. Hylysformer symbol for a residue of (5-)hydroxY-L-lysine (5Hyl or Hyl now recommended). hyoscine or scopolamine an alkaloid found, e.g., in Datura stramonium (thorn apple) and related to atropine in its structure and effects; it is a tertiary ammonium compound noted for its actions as a muscarinic receptor antagonist. It has found use as a sedative and preanesthetic and for prevention of motion sickness.

hydroxyprolinemia or hyperhydroxyprolinemia a metabolic disorder of humans characterized by high levels of free 4-hydroxyproline in the blood plasma and urine. It is probably due to a deficiency in the activity of so-called hydroxyproline oxidase, i.e. the enzyme 4-oxoproline reductase (EC 1.1.1.104). 1S-hydroxyprostaglandin dehydrogenase (NAD+) EC 1.1.1.141; an enzyme involved in the inactivation of prostaglandins E2, F 2a , and Bj, by oxidizing the 15-hydroxyl group to a keto group. It catalyses a reaction between (52, 13E)-( 15S)-lla, 15-dihydroxy-9-oxoprost-5, 13-dienoate and NAD+ to form (52, 13E)-lla-hydroxy-9, 15-dioxoprost5,13-dienoate (l5-keto PGE 2) and NADH. Example from human: database code PGDH_HUMAN, 266 amino acids (28.94 kDa). 5-hydroxytryptamine abbr.: 5-HT; an alternative name for serotonin. S-hydroxytryptamine receptor any of several membrane

hyoscyamine 3a-tropanyl S-(-)-tropate; an anticholinergic material obtained from Atropa belladonna and other plants. It undergoes partial racemization on isolation; this process is completed by alkali treatment, and the racemic mixture is known as atropine. (Illustrated on p. 318.) hyp+ a variant form of hypo+ (before a vowel).

droxyproline, HO-(C 4 H 6NH)-COOH, both of which are chiral cyclic N-alkylated a-amino acids. Each constitutional isomer possesses two chiral centres; each can therefore exist as an enantiomeric (D and L) pair of each of two (cis and trans) diastereoisomers, making eight possible isomeric structures for hydroxyproline in all. Both trans-3-hydroxy-L-proline (symbol: 3Hyp or Pro(3-0H», (2S,3S)-3-hydroxypyrrolidine2-carboxylic acid, and trans-4-hydroxY-L-proline (symbol: 4Hyp or Pro(4-0H», (2S,4R)-4-hydroxypyrrolidine-2-carboxylie acid, are noncoded amino acids found in peptide linkage in proteins. In collagen nearly 50'10 of the proline residues are hydroxylated to 4Hyp and a small proportion to 3Hyp; hydroxyproline residues are also found in elastin, enamel of the teeth, in the CIa moiety of the C I component of complement, and in extensin. In collagen formation, enzymic hydroxylation of proline residues occurs while the growing peptide chains are still attached to ribosomes. Residues of both the cis-(2S,3R)-, and the trans-(2S,3S)-isomers of 3-hydroxy-L-proline, one of each per molecule, occur in the peptide antibiotic telomycin. One residue per molecule of cis-4-hydroxy-L-proline, the (2S,4S)-isomer, occurs in every member of the amatoxin group of toxic fungal octapeptides. None of the D series of isomers is known to occur naturally.

.pH

O-COOH N H

trans-(2S,3Sl-3-hydroxY-l-proline

trans-(2S,4R)-4-hydroxy-L-proline

HO

Q-COOH H

318 Hyp

hyperimmunization

(-)-hyoscyamine Hyp 1 or (formerly) Hypro symbol for a residue of either the 3hydroxy or the 4-hydroxy derivative of the a-amino (strictly, a-imino) acid L-proline, usually 4-hydroxy-L-proline. See hydroxyproline. See also 3Hyp, 4Hyp. 2 symbol for a residue of the purine base hypoxanthine. 3Hyp symbol for a residue of the a-amino acid 3-hydroxyL-proline (preferred alternative to Pro(3-0H) or Hyp). See hydroxyproline. 4Hyp symbol for a residue of the a-amino acid 4-hydroxyL-proline (preferred alternative to Pro(4-0H) or Hyp). See hydroxyproline. hypelcin A a 20-residue peptide of microbial origin containing 10 a-arninoisobutyric acid residues. The N terminus is acylated and the C terminus amidated with leucinol. It modifies the permeability of phospholipid bilayers. hyper+ prefix indicating over, beyond, excessive, or in excess; above the normal range. Compare hypo+, normo+. hyperaldosteronism an elevated level of aldosterone in the blood. In primary aldosteronism, there is overproduction of aldosterone due to a lesion of the adrenal(s), e.g. an adrenal tumour as in Conn's syndrome. In secondary aldosteronism the overproduction is caused by excessive levels of stimulatory hormones, especially increased renin secretion. hyperammonemia or (esp. Brit.) hyperammonaemia the presence of excess ammonia in the blood (the normal range is 10-47 /lmol L -1). It occurs in a number of conditions including inherited disorders of the urea cycle, organic acidemias, liver disease, and severe systemic illness. See also ornithine-urea cycle. hyperbaric of, relating to, or operating at higher than normal pressures. hyperbilirubinemia or (esp. Brit.) hyperbilirubinaemia the presence of higher than normal concentrations of bilirubin in the blood; it may involve unconjugated or conjugated bilirubin. It occurs in liver disease or biliary obstruction, and is characteristic of neonatal hemolytic jaundice, where the bilirubin is mainly unconjugated. -hyperbilirubinemic or hyperbilirubinaemic adj. hyperbola one of the conic sections; a plane curve in which the focal distance of any point bears to its distance from the directrix a constant ratio greater than unity. It has two foci and two asymptotes. Compare rectangular hyperbola. -hyperbolic ad). hyperbolic function anyone of a group of functions of an angle, analogous to the trigonometric functions, expressed as a relationship between the distances of a point on a hyperbola to the origin and to the coordinate axes. The group includes sinh (hyperbolic sine), defined as sinh x = (eX - e- X )/2; cosh (hyperbolic cosine), defined as cosh x = (eX + e- X)f2; and tanh (hyperbolic tangent), defined as tanh x = (sinh x)/(cosh x). The corresponding reciprocal functions are cosech (hyperbolic cosecant), sech (hyperbolic secant), and coth (hyperbolic cotangent), respectively. hyperbolic kinetics curve a description sometimes used of the vIIS) plot obtained for enzymes exhibiting Michaelis-Menten kinetics. The axes of the plot are not those of the rectangular hyperbola that results, but are rotated 45° (and displaced) from the true axes of the hyperbola.

hypercalcemia or (esp. Brit.) hypercalcaemia the presence of higher than normal concentrations of calcium in the blood. Clinical features include tiredness, muscle weakness, anorexia, weight loss, cardiac arrhythmia, and hypertension. It arises from a multiplicity of causes including malignancy, primary hyperparathyroidism, hyperthyroidism, acute adrenal insufficiency, familial hypocalciuric hypercalcemia, vitamin D or A overdose, or sarcoidosis. -hypercalcemic or hyperca\caemic adj. hypercapnia or hypercarbia the presence of greater than normal amounts of carbon dioxide in a vertebrate or in its blood. Compare hypocapnia. -hypercapnic or hypercarbic ad). hyperchlorhydria the presence of greater than normal amounts of hydrochloric acid in the gastric juice. hyperchlorhydric ad). hypercholesterolemia or (esp. Brit.) hypercholesterolaemia the presence of higher than normal concentrations of cholesterol in the blood. See also hyperlipidemia -hypercholesterolemic or hypercholesterolaemic ad). hyperchromatic 1 of, relating to, or exhibiting hyperchromatism. 2 an alternative wordfor hyperchromic (def. 1). hyperchromatism the condition or property (of a cell or cell organelle) of staining more intensely than normal; the presence of a greater than normal amount of chromatin. hyperchromic 1 or hyperchromatic more highly coloured than normal; intensely coloured. 2 of, pertaining to, exhibiting, or resulting from hyperchromism. 3 (of a substance) displaying a hyperchromic effect. 4 describing erythrocytes that contain, or appear to contain, more hemoglobin than normal. hyperchromic eHect the large increase in absorption of ultraviolet light, usually measured at 260 nm, shown by a solution of any natural or synthetic polynucleotide with a hydrogenbonded structure when it is denatured or degraded. The effect is due to alterations in the electronic interactions between the initially stacked and hydrogen-bonded bases. hyperchromicity a measure of the increase in absorption of electromagnetic radiation at a specific wavelength, usually that of the absorption maximum, due to hyperchromism, or to the hyperchromic effect. It is equal to the reciprocal of the hypochromicity minus unity. hyperchromism the increased absorption of electromagnetic radiation exhibited by an ordered structure above that predicted on the basis of its constitution. hyperfine splitting the splitting of a spectral line into multiplets of closely spaced lines. In electron spin resonance spectra hyperfine splitting is due to the interaction of unpaired electrons with neighbouring nuclei and can be used to determine the structure of a free radical or to identify the ligands of a paramagnetic ion and to measure the degree of covalent binding that exists between them. In nuclear magnetic resonance spectra hyperfine splitting, sometimes called spin-spin splitting, is due to the interaction of the nuclear magnetic moment with those of neighbouring nuclei and can be used to assign particular nuclear resonances and to determine molecular conformations. hyperfine structure the presence in a spectrum of multiplets of closely spaced lines resulting from hyperfine splitting. hyperglycemia or (esp. Brit.) hyperglycaemia an abnormally high blood glucose concentration, especially in relation to the fasting value. See also glycemia. -hyperglycemic or hyperglycaemic ad). hyperglycemic factor or hyperglycemic-glycogenolytic factor a former name for glucagon. hyperhydroxyprolinemia see hydroxyprolinemia. hyperimmune describing the state of an animal in which very high concentrations of specific antibody are present in the serum, brought about by hyperimmunization. hyperimmunization or hyperimmunisation any method of immunization designed to stimulate the production in the animal immunized of very large quantities of specific antibody. It typically involves the repeated administration of immunogen, often in increasing amounts.

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hyperkalemia hyperkalemia or (esp. Brit.) hyperkalaemia the presence in the blood of an abnormally high concentration of potassium. There are many causes including excessive K+ intake (infusion, transfusion), increased transcellular movement (tissue damage, systemic acidosis), and decreased K+ loss (renal failure, mineralocorticoid deficiency). -hyperkalemic or hyperkalaemic adj. hyperlactatemia or (esp. Brit.) hyperlactataemia a clinical condition characterized by a persistent raised blood lactate concentration, usually below 5 mmol L-I, and not accompanied by a lowered blood pH. The normal range is between 0.5 and 2.2 mmol L-I. Compare lactic acidosis. -hyperlactatemic or hyperlactataemic adj. hyperlipidemia or hyperlipemia or (esp. Brit.) hyperlipidaemia or hyperlipaemia the presence in the blood of an abnormally high concentration of fats (or lipids). Hyperlipidemias have been classified into various types according to which lipoprotein class is found to be elevated in the blood. The Fredrickson classification scheme designates: type I, elevated chylomicrons; type n, elevated low-density lipoprotein; type nl, elevated intermediate-density lipoprotein; type IV, elevated very-low-density lipoprotein; type V, elevated chylomicrons and very-low-density lipoprotein. A simpler distinction, of use in treatment, is between elevated cholesterol levels (type n, hypercholesterolemia) and elevated triacylglycerollevels (types I, nl-V, hypertriglyceridemia, an older term still often used). Hyperlipidemia may be secondary to other conditions; several drugs cause or exacerbate hyperlipidemia, including thiazides, beta blockers lacking intrinsic sympathomimetic activity, and corticosteroids. Estrogens may lower hypercholesterolemia, but may cause or exacerbate hypertriglyceridemia; hypothyroidism is commonly associated with hypercholesterolemia; high alcohol intake causes hypertriglyceridemia, but modest alcohol intake may have a beneficial effect on cholesterol status, as it tends to increase high-density lipoprotein concentration. -hyperlipidemic, hyperlipemic or hyperlipidaemic, hyperJipaemic adj. hypermodified base any extensively modified nucleic-acid base occurring adjacent to the 3' end of the anticodon in many tRNA molecules. Examples are N6-(2-isopentenyl)adenosine (symbol: iA) and N6-(threonylcarbamoyl)adenosine (symbol: tA). Hypermodified bases are thought to be important for proper binding of tRNA molecules to ribosomes. hypernatremia or (esp. Brit.) hypernatraemia the presence in the blood of an abnormally high concentration of sodium. It may be associated with conditions in which body water is depleted. -hypernatremic or hypernatraemic adj. hyperoxa'uria the presence of oxalate in the urine in abnormally high amounts. Primary hyperoxaluria is a rare inherited metabolic disorder of which there are two types: one results in increased oxalate synthesis, the other in increased oxalate excretion by the kidney. More usually, hyperoxaluria results from increased absorption of oxalate from the intestine. It is associated with the formation of renal calculi. hyperoxia the presence of greater than normal amounts of dioxygen in a vertebrate or in its blood. Compare hypoxia. hyperoxic adj. hyperparathyroidism the increased production of parathyroid hormone. It may be primary, as a result of a tumour of the parathyroid gland, or secondary, as a result of a disturbance in calcium metabolism. hyperphosphatemia or (esp. Brit.) hyperphosphataemia an excessive level of phosphate in the blood. It occurs most commonly in renal insufficiency, but may also accompany hypoparathyroidism, vitamin D intoxication, or excessive administration of phosphate. -hyperphosphatemic or hyperphosphataemic adj. hyperplasia the increase in size of a tissue or organ resulting from an increase in the total number of cells present. The part thus affected retains its normal form. Compare hypertrophy. hyperplastic adj.

hypocalcemia hyperpro'actlnemia or (esp. Brit.) hyperprolactinaemia the presence in the blood of abnormally high levels of prolactin, due to excessive secretion of the hormone. The most common example of pituitary hyperfunction, it results from pituitary adenoma, and also from treatment with dopamine receptor blockers. It can be treated with dopamine agonists, e.g. bromocriptine. -hyperprolactinemic or hyperprolactinaemic adj. hypersecretion excessive secretion by any endocrine or exocrine gland. hypersensitive having an abnormally great sensitivity, especially to an allergen, drug, or other agonist. hypersensitivity 1 the state or condition of being hypersensitive. 2 (in immunology) an immune response that occurs in an exaggerated or inappropriate form. Such responses may result from agents including pollen or drugs, or from genuine pathogens. Also of importance are the different kinds of tissue damage seen in autoimmune diseases. In general terms the reactions may be classified into four types, although they do not occur in isolation from each other: type I, immediate hypersensitivity; type n, antibody-mediated hypersensitivity; type IlJ, immune complex-mediated hypersensitivity; and type IV, delayed hypersensitivity. hypersharpening the formation of a 'sharper' boundary in sedimentation and moving boundary electrophoresis experiments than would be expected as a result of diffusion-broadening, because molecules in the trailing portion of the boundary tend to move at a greater velocity per unit field than molecules on the leading edge or in the plateau region. hypertension the state or condition of having a higher than normal arterial blood pressure. -hypertensive adj. hyperthyroidism or thyrotoxicosis a clinical state resulting from excessive secretion of thyroid hormones. The most common cause is Graves' disease; other causes include goitre and solitary toxic adenoma. The clinical manifestations include nervousness, irritability, fatigue, and heat intolerance; exophthalmia is present in some cases. Most symptoms derive from exaggeration of normal responses to thyroid hormones. See also thyroxine. -hyperthyroid adj. hypertonic 1 (0/ a solution) having a higher osmotic pressure than that of some given solution, especially that of the fluid in or surrounding a given type of cell or a body fluid. 2 (0/ a muscle) showing or characterized by excessive tone or tension. Compare hvpotonic. -hypertonicity n. hypertriglyceridemia or (esp. Brit.) hypertriglyceridaemia see hyperlipidaemia. hypertrophy the increase in the size of a tissue or organ resulting from an increase in the size of the cells present. Compare hyperplasia. -hypertrophic adj. hyperuricemia or (esp. Brit.) hyperuricaemia the presence of abnormally high amounts of uric acid in the blood. This may be due to increased purine synthesis arising from a metabolic disorder, inherited or otherwise, or it may be due to reduced excretion - this may result from renal disease, the effect of drugs (e.g. salicylates) on the kidney, or the presence of organic acids (e.g. lactate) that competitively inhibit urate excretion. Hyperuricemia is associated with gout. hypervariable regions regions in an immunoglobulin molecule where the amino-acid residues show a high degree of variation between one molecule and another. There are three hypervariable regions, two in the Vregion and one in the 0 region. hypo a common name for sodium thiosulfate, especially when used in photographic processing. hypo+ or (be/ore a vowel) hyp+ prefix denoting under, beneath, below, less than, or in deficit; below the normal range. Compare hyper., normo•. hypoalphalipoproteinemia see hypolipoproteillemia. hypobaric of, relating to, or operating at pressures lower than normal. hypobetalipoproteinemia see hypolipoproteinemia. hypocalcemia or (esp. Brit.) hypocalcaemia the presence of a lower than normal concentration of calcium in the blood. It

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hypocapnia may be associated with disorders of vitamin 0 metabolism, hypoparathyroidism, magnesium deficiency, or pancreatitis. Clinical features include behavioural disturbances, stupor, numbness, paresthesia, muscle cramps or spasms, and convulsions. -hypocalcemic or hypocalcaemic ad). hypocapnia or hypocarbia the presence of less than the normal amount of carbon dioxide in a vertebrate or in its blood. Compare hypercapnia. -hypocapnic or hypocarbic ad). hypochlorhydria the presence of less than the normal amount of hydrochloric acid in the gastric juice. -hypochlorhydric ad). hypocholesterolemia or (esp. Brit.) hypocholesterolaemia the presence of a lower than normal concentration of cholesterol in the blood. -hypocholesterolemic or hypocholesterolaemic adj. hypochromatic 1 of, relating to, or exhibiting hypochromatism. 2 an alternative word for hypochromic (def. I). hypochromatism the condition or property (of a cell or cell organelle) of staining less intensely than normal; the presence of an abnormally low amount of chromatin. hypochromic 1 or hypochromatic less highly coloured than normal; weakly coloured. 2 of, pertaining to, exhibiting, or resulting from hypochromism. 3 (of a substance) displaying a hypochromic effect. 4 describing erythrocytes that contain, or appear to contain, less hemoglobin than normal. hypochromic effect the observed decrease in absorption of certain frequencies of electromagnetic radiation by solutions of some macromolecules when the structure of the molecules becomes more ordered. hypochromicity a measure of the decrease in absorption of electromagnetic radiation at a specific wavelength, usually that of the absorption maximum, due to hypochromism. hypochromism the decreased absorption of electromagnetic radiation exhibited by an ordered structure below that predicted on the basis of its constitution. hypoglycemia or (esp. Brit.) hypoglycaemia the presence of an abnormally low blood glucose concentration, especially in relation to the fasting value. See also glycemia. -hypoglycemic or hypoglycaemic ad). hypoglycin or hypoglycine A 'p-(methylenecyclopropyl)alanine; 2-amino-3-(methylenecyclopropane)propanoic acid. A nonprotein a-amino acid identified as the hypoglycemic and toxic principle of the unripe fruit of the ackee (Blighia sapida), where it is present both in the fleshy aril and in the seeds. In the latter it occurs also as the N-L-glutamyl derivative, hypoglycin B. Certain other fruits also contain hypoglycin. It is degraded in animals to methylenecyclopropylacetate, either free or conjugated to glycine or coenzyme A. Methylenecyclopropylacetyl-CoA is a potent and specific inhibitor of the oxidation of short-chain acyl-CoAs, particularly of butyryl-CoA. In hypoglycin poisoning butyryl-CoA undergoes hydrolysis to yield free butyrate, which accumulates in the blood to abnormal concentrations. See also Jamaican vomiting sickness. Hyp(3-0H) symbol for a residue of the a-amino acid 3-hydroxyL-proline (alternative to 3Hyp or Hyp). See hydroxyproline. Hyp(4-0H) symbol for a residue of the a-amino acid 4-hydroxyL-proline (alternative to 4Hyp or Hyp). See hydroxyproline. hypokalemia or (esp. Brit.) hypokalaemia the presence in the blood of an abnormally low concentration of potassium. It may result from alkalosis, insulin administration, primary or secondary aldosteronism, or administration of drugs that are aldosterone antagonists. -hypokalemic or hypokalaemic ad). hypolipoproteinemia the partial or total absence of any lipoprotein, or the presence of a defective lipoprotein, in the plasma. Several types of this condition are recognized. Hypobetalipoproteinemia is arbitrarily defined as a low density lipoprotein (I.DI.) cholesterol level below the fifth percentile for a given sex- and age-matched population. Such patients also have low triacylglycerol levels. In this condition, LDL cholesterol is always detectable, in contrast to homozygous abetalipoproteinemia, in which it is entirely absent. Hypobetalipoproteinemia appears to be due to a low rate of synthesis of

hypotonic LDL from very-low-density lipoprotein. Abetalipoproteinemia is a rare autosomal recessive disorder. It probably results from an abnormality in the synthesis or secretion of apo B, and it is accompanied by fat malabsorption, as chylomicron formation requires apo B. In the homozygote, levels of triacylglycerols, cholesterol, and phospholipids are extremely low. Heterozygotes may present with hypobetalipoproteinemia. Hypoalphalipoproteinemia is in some cases familial, and may result from defective apo A-I. In another disorder, known as fish-eye disease (due to severe corneal opacity) the structure of apo A-I is normal, but high-density lipoprotein (HOI.) levels are only 10% of normal. In analphalipoproteinemia, or Tangier disease, HOI. is virtually absent. hyponatremia or (e~p. Brit.) hyponatraemia the presence in the blood of an abnormally low concentration of sodium. It can occur as a result of incorrect administration of fluid intravenously or in parenteral feeding, after administration of diuretics, in congestive heart failure, or in protein imbalance. -hyponatremic or hyponatraemic ad). hypoparathyroidism underactivity of the parathyroid glands. hypophase the lower layer of a two-phase system. Compare epiphase. -hypophasic adj. hypophosphatemia or (esp. Brit.) hypophosphataemia the presence of an abnormally low level of phosphate in the blood. It occurs in vitamin D deficiency, primary hyperparathyroidism, incorrect parenteral nutrition, and during recovery from diabetic ketoacidosis. hypophysectomy surgical removal of the pituitary gland (i.e. hypophysis). -hypophysectomize or hypophysectomise vb. hypophysiotropic factor or hypophysiotropic hormone an alternative name for hypothalamic (regulatoryl factor. hypophysis or hypophysis cerebri an alternative name for pituitary gland. See also adenohypophysis, neurohypophysis. -hypophyseal or hypophysial ad). hypopituitarism total or (more often) partial loss of pituitary function, usually due to destructive lesions of the pituitary. hypoplasia underdevelopment or defective formation of an organ or tissue. -hypoplastic ad). hypoprothrombinemia or (esp. Brit.) hypoprothrombinaemia the presence of abnormally low (inadequate) levels of plasma prothrombin (factor II). It is commonly linked with vitamin K deficiency. hyposecretion lesser than normal secretion by any endocrine or exocrine gland. hypotension the state or condition of having a lower than normal arterial blood pressure. -hypotensive ad). hypothalamic (regulatory) factor or hypothalamic hormone or hypophysiotropic factor or hypophysiotropic hormone any peptidic substance that is synthesized in the mammalian hypothalamus and released into the hypophyseal-portal circulation in response to neural and/or chemical stimuli, and that regulates the secretion (and perhaps also the synthesis) of a specific polypeptide hormone by the anterior lobe of the pituitary gland (i.e. adenohypophysis). These specific factors may be either releasing or release-inhibiting factors (or hormones); their recommended names are now formed by replacing the word-ending 'tropin' (or '-in' in prolactin) in the name of the corresponding pituitary hormone by the word-ending '-liberin' (for a releasing factor) or '-statin' (for a release-inhibiting factor). hypothalamus (pl. hypothalami) the region of the vertebrate brain lying below the thalamus and around the floor of the third ventricle, just posterior to the attachment of the cerebral hemispheres. It lies just above the pituitary gland, to which it supplies various hypothalamic (regulatoryl factors. -hypothalamic ad). hypothyroidism deficient secretion by the thyroid gland, for whatever reason. In infants it leads to cretinism; in adults the consequences include low metabolic rate, lethargy, menstrual disorders, and in extreme cases myxedema. -hypothyroid ad). hypotonic 1 (of a solution) having a lower osmotic pressure

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H zone

hypovolemia than that of some given solution, particularly the fluid in or surrounding a given type of cell or a body fluid. 2 (of a muscle) showing or characterized by diminished tone or tension. Compare hypertonic. -hypotonicity n. hypovolemia or (esp. Brit.) hypovolaemia a reduction in the volume of circulating blood. It may be due to hemorrhage or to redistribution of fluid from the plasma to the extravascular tissues and spaces. hypox abbr. for hypophysectomized. See hypophysectomy. hypoxanthine symbol: Hyp; purin-6(lH)-one; 6-hydroxy purine; an intermediate in the degradation of adenylate. Its ribonucleoside is known as inosine and its ribonucleotide as inosinate. Compare xanthine. See also hypoxanthine phosphoribo-

Hypro (formerly) symbolfor a residue of (4- )hydroxy-L-proline

(4Hyp or Hyp now recommended). hypsochromic describing the shift of an absorption band in the direction of shorter wavelengths. Compare bathochromic. hypusine NE-[4-amino-2-hydroxybutyl]lysine; an amino acid

uniquely formed by post-translational modification of one of the lysyl residues of eukaryotic translation initiation factor 5A (eIF-5A). It is formed by deoxyhypusine synthase, an enzyme that transfers the butylamine portion of spermidine to the eNH z group of a specific lysine of the eIF-5A precursor, followed by addition of the hydroxyl group by deoxyhypusine hydroxylase.

syltransferase. hypoxanthine-guanine phosphoribosyltransferase abbr.: HGPRT; see hypoxanthine phosphoribosyltransferase. hypoxanthine phosphoribosyltransferase EC 2.4.2.8; sys-

tematic name: IMP: pyrophosphate phospho-D-ribosyltransferase; other names: hypoxanthine-guanine phosphoribosyltransferase (abbr.: HGPRT); IMP pyrophosphorylase. An enzyme that catalyses a reaction between 5-phospho-a-D-ribose I-diphosphate and either hypoxanthine or guanine to form IMP or GMP respectively, with release of pyrophosphate. It is an enzyme of the purine salvage pathway, and a deficiency is associated with Lesch-Nyhan syndrome and gout. Example from human: database code HPRT_HUMAN, 217 amino acids (24.45 kDa); many mutations leading to deficiency diseases have been identified. hypoxia the presence of less than normal amounts of dioxygen in a vertebrate or in its blood. Compare hyperoxia. -hypoxic adj.

hysteresis the delay between the effect on a system and the

cause producing the effect. -hysteretic ad). hysteretic enzyme any enzyme that responds slowly (in terms

of some kinetic characteristic) to a rapid change in ligand (either substrate or modifier) concentration. Such slow changes, defined in terms of their rates relative to the overall catalytic reaction, result in a lag in the response of the enzyme to changes in the ligand level. Hz symbol for hertz. H zone see sarcomere.

Ii i symbol for 1 iso (def. 3); (as a prefix or superscript in symbols and abbreviations for iso compounds or groups; e.g. isopropyl can be symbolized as iPr or Pri). 2 the chemical group 2isopentenyl; 3,3-dimethylallyl (as a prefix to a single-letter symbol for a nucleoside residue to designate substitution of the base, as in iA). 3 the square root of -1. ; symbol for 1 electric current (alternative to 1).2 van't Hoff factor. I symbol for 1 iodine. 2 an iodo group in an organic compound. 3 a residue of the a-amino acid L-isoleucine (alternative to lie). 4 a residue of the ribonucleoside inosine (alternative to Ino). I symbol for 1 electric current (preferred alternative to i). 2 intensity; the subscripts e (for energetic), p (for photon), or v (for visible) may be added to distinguish between radiant intensity, photon intensity, and luminous intensity, respectively. 3 ionic strength; the subscripts c or m may be added to indicate whether it is expressed based on concentration or molality respectively. 4 the inductive effect of a particular chemical group in an organic compound. iA symbolfor N6-(2-isopentenyl)adenosine, a hypermodified base. IAA abbr. for indole-3-acetic acid or indoleacetate. IAN abbr. for indoleacetonitrile. lAP abbr. for islet-activating protein; see pertussis toxin. iatrogenic describing a condition or disease induced unintentionally by a physician through his or her diagnosis, manner, or therapy. -iatrogenicity n. I-band abbr. for isotropic band. The I-bands of striated muscle contain the thin filaments and correspond to the light bands. The name derives from the fact that they are isotropic in polarized light. See also sarcomere. IBMX abbr. for isobutylmethylxanthine. ibuprofen 2-(4-isobutylphenyl)propionic acid; a nonsteroidal anti-inflammatory agent of the substituted propionic acid type; others of this type are flurbiprofen, ketoprofen, and naproxen. They inhibit the cyclooxygenase activity of prostaglandin-endoperoxide synthase, reversibly over short time intervals, followed by time-dependent irreversible inactivation, due probably to conformational rather than covalent changes. The racemic mixture is present in many over-the-counter drugs, but the (S)-enantiomer is the active form. Proprietary names include: Advil; Brufen; Motrin.

C~~

H3C~ ~ (5)-ibuprofen

ic or i.e. abbr. for intracutaneous or intracutaneously. IC abbr. for internal conversion. IC 50 1 the median inhibitory concentration (in mol L-') of an antagonist, i.e. the concentration that reduces a specified response to 50% of its former value; compare EC50 • 2 the median inhibitory concentration (in mol L-l) of an agent (agonist or antagonist), i.e. the concentration that causes a 50% reduction in the specific binding of a radioligand. ICAM abbr. for intercellular adhesion molecule; any of several type I membrane glycoproteins of the immunoglobulin superfamily. They act as ligands for leukocyte adhesion to target cells, in conjunction with LFA-1; in fact LFA-I-ICAM links mediate adhesion between many cell types. There are three subclasses. ICAM-l (or CD54), of molecular mass 90-115

kDa, are expressed on Band T cells, endothelial, epithelial, and dendritic cells, fibroblasts, keratinocytes, and chondrocytes. They are inducible in 12-24 hours by cytokines such as gamma interferon, interleukin-Ip, and tumour necrosis factor(l. Example (human, precursors): ICAM-I major group rhinovirus receptor: database code ICALHUMAN, 532 amino acids (57.76 kDa). ICAM-2 (or CDI02), of molecular mass 55-65 kDa, are constitutively expressed on endothelial cells, some lymphocytes, monocytes, and dendritic cells. Example (human): database code ICA2_HUMAN, 275 amino acids (30.62 kDa). ICAM-3 (or CD50), of molecular mass 116-140 kDa, are constitutively expressed on monocytes, granulocytes, and lymphocytes; upon physiological stimulation they become rapidly and transiently phosphorylated on serine residues. Example (human): database code ICA3_HUMAN, 547 amino acids (59.32 kDa). ICD (in clinical chemistry) abbr. for isocitrate dehydrogenase (EC 1.1.1.41). ice the solid form of water that can exist at temperatures below the triple point of water (273.16 K at 101325 Pa). iceberg a metaphor used to describe an interpretation of the anomalous entropies of solution of noble gases and other nonpolar substances in water, suggesting that water tends to organize itself into quasi-solid supramolecular structures around the molecules of such substances. In the case of alkyl compounds, this tendency increases markedly with the length of the alkyl chain. ICE-like protease any of a family of endopeptidases that structurally resemble interleukin-1f3 convertase (ICE). They are involved in apoptosis, being implicated in the proteolysis that causes cell death. I cell 1 or CCK cell any of a group of cells, widely distributed in the duodenal and jejunal mucosa, that produce cholecystokinin. So named because their histological features are intermediate between those of S cells and L cells. 2 abbr. for inclusion cell. See also I-cell disease. I-cell disease or inclusion-cell disease or mucolipidosis II an autosomal recessive disease in which most of the lysosomes in the connective tissue (fibroblasts) contain large inclusions of glycoaminoglycans and glycolipids as a result of the absence of several lysosomal hydrolases. These enzymes, which are synthesized in the endoplasmic reticulum, are secreted into the extracellular medium rather than being directed to the lysosomes. This is due to the absence of a mannose 6-phosphate marker on the carbohydrate moieties of these hydrolases because of a deficiency in an enzyme required for mannose phosphorylation. The failure of the phosphorylation in the cis Golgi network means that the enzymes are not segregated by the mannose 6-phosphate receptors into the appropriate transport vesicles in the trans Golgi network. The patients have an abnormally high level of lysosomal enzymes in their sera and body fluids. A milder form of I-cell disease is Hurler's polydystrophy (Hurler syndrome). ice point the temperature at which ice melts. It is taken as the temperature (273.15 K) at which ice and water are in equilibrium at standard pressure (101 325 Pa). It was used as a reference temperature on the Celsius scale, but the kelvin is based instead on the temperature at the triple point of water (273.16 K). ICF abbr. for intracellular fluid. ichthyotocin an alternative name for isotocin. icosa+ or (before a vowel) icos+ comb. form recommended for denoting twenty or twenty times. Also (formerly): eicosa+, eicos+. (Note: the eicos(a)+ variant is still always used for the C 20 fatty acids and skeletally related compounds, e.g. the eicosanoids.) icosadeltahedron (pl. icosadeltahedra) any solid geometrical

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icosahedral symmetry figure obtained by dividing the triangular faces of an icosahedron into smaller triangles. If divided into more than four smaller triangles, the original faces will not be flat, in which case the 12 pentameric vertices will be supplemented by hexameric vertices. -icosadeltahedral adj. icosahedral symmetry a form of cubic symmetry, being the crystallographic symmetry displayed by an icosahedron and by the capsid of some types of virus. icosahedron (pl. icosahedra) any solid geometrical figure having 20 triangular faces, 30 edges, and 12 pentameric vertices. A regular icosahedron has faces that are congruent plane equilateral triangles; there is twofold rotational symmetry about an axis through the midpoint of each edge, threefold rotational symmetry about an axis through the centre of each face, and fivefold rotational symmetry about an axis through each vertex. -icosahedral adj. ieosanoate or (formerly) eicosanoate the systematic name for arachidate. ieosanoid the recommended name for eicosanoid, but not generally used. ICRO abbr. for International Cell Research Organization. ICSH abbr. for interstitial cell-stimulating hormone (Le. luteinizing hormone). ICSU abbr. for International Council of Scientific Unions. icterus (in pathology) an alternative name for jaundice. icterogenic causing jaundice. id or i.d. abbr. for 1 intradermal, or intradermally (alternative to ID). 2 inside diameter. 10 1 (in clinical chemistry) abbr. for iditol dehydrogenase (EC 1.1.1.14).2 abbr. for intradermal, or intradermally (alternative to id). 10ao or ID50 abbr. for median infectious dose. idaric acid the aldaric acid derived from idose. 100M abbr. for insulin-dependent diabetes mellitus (see diabetes mellitus). +ide suffix (in chemical nomenclature) denoting a laetide. It replaces the terminal '+ic acid' of the trivial name of the parent hydroxy acid, and a multiplying prefix indicates the number of molecules of hydroxy acid involved; e.g. dilactide (formed from two molecules of lactic acid). ideal describing any object, process, or system that is perfect, or that behaves exactly in accordance with some simple law or theory. See also ideal gas, ideal solution. -ideality n. ideal gas any gas whose behaviour is accurately described by the gas laws. ideal solution any solution in which, for each component, d,ui = RT dlnxi, where ,ui is the chemical potential of the ith component and Xi is its mole fraction, R is the universal gas constant, and T is the thermodynamic temperature. Integration of the above equation gives: Pi = ,ut + RT Inx;, where ,uio is the standard chemical potential of the ith component. idio+ comb. form denoting 1 peculiar, distinct, one's own, separate. 2 self-produced, arising within. idiogram or karyogram a diagrammatic representation of the karyotype of a cell, based on measurement of the chromosomes in several or in many cells. idiom (in immunology) the group of idiotypes to which the apitopes carried by components of one individual animal belong. idiopathic 1 (in pathology) describing a disease arising by itself, not consequent upon, or symptomatic of, another disease; of the nature of a primary morbid state; essential. 2 of the nature of a particular affection or susceptibility. -idiopathy n. idiopathic pentosuria see pentosuria (def. 1). idiotope 1 the group of epitopes carried by components of one individual animal. 2 as originally defined by Jerne, an individ-

iduronic acid ual determinant (i.e. site) on an antibody molecule; together, the idiotopes constitute the idiotype. idiotype 1 an antigenic specificity, particularly of antibodies directed against a single antigen. 2 any class or group of related antigenic characteristics or idiotopes; an epitype that is characteristic of a particular animal. -idiotypic adj. iditol the hexitol derived formally by reduction of the aldehyde group of idose. L-Iditol is a rare natural product accompanying sorbitol in the fermented juice of berries of mountain ash (Sorbus aucuparia). 10L abbr. for intermediate-density lipoprotein. iONA abbr. for intercalary DNA. IDNPAP abbr. for isethionyl-3-(N-2,4-dinitrophenyl)amino propioimidate; a reagent useful in the isolation of plasma membranes. It reacts with, but does not penetrate, the membranes and leaves the net charge on the proteins unaltered. ido- prefix (in chemical nomenclature) indicating a particular configuration of a set of four (usually) contiguous >CHOH groups, as in the acyclic form of D- or L-idose. See monosaccharide. Ido symbol for a residue (or sometimes a molecule) of the aldohexose idose. IdoA symbol for a residue of iduronic acid. idose symbol: Ido; ido-hexose; an aldohexose whose D- and Lenantiomers are epimeric at C-2, C-3, and C-4 with D- and Lglucose, respectively.

H;c~~H ~ OH

pOD-idose idoxuridine 5-iodo-2'-deoxyuridine; a pyrimidine analogue, metabolized to the triphosphate, that inhibits DNA replication by substituting for thymidine in viral and mammalian DNA incorporation. It is used as an antiviral agent.

lOP abbr. for 1 the ribonucleotide inosine (5'-)diphosphate. 2 isopentenyl diphosphate (formerly called ,.j3-isopentenyl pyrophosphate). IOU abbr. for 5-iodo-2'-deoxyuridine (see idoxuridine). IdUrd symbol for 5-iodo-2'-deoxyuridine (see idoxuridine) (preferred to IDU, IUdR, or IUDR). iduronate 1 the anion of iduronic acid. 2 any salt or ester of iduronic acid. iduronate-2-sulfataae EC 3.1.6.13; other name: chondroitinsulfatase; an enzyme that hydrolyses the 2-sulfate groups of the L-iduronate 2-sulfate units of dermatan sulfate, heparan sulfate, and heparin. Example (precursor) from human: database code IDS_HUMAN, 550 amino acids (61.80 kDa). iduronic acid symbol: IdoA; the uronic acid formally derived

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L-iduronidase from idose by oxidation to a carboxyl group of the hydroxymethylene group at position 6. In nature a-linked L-iduronicacid residues, sulfated at position 2, occur in terminal positions in derma tan sulfate and heparan sulfate; these iduronic-acid residues are formed by epimerization of the configuration at C-5 of D-glucuronic-acid residues in these heteropolysaccharides. L-iduronidase EC 3.2.1.76; an enzyme that hydrolyses a-Liduronosidic linkages in desulfated dermatan. Example (precursor) from human: database code IDUA_HUMAN, 653 amino acids (72.58 kDa). iduronosyl the glycosyl group formed by removal of the anomeric hydroxyl group from iduronic acid or iduronate. IE abbr. for immunoelectrophoresis (alternative to IEP). IEC abbr. for ion-exchange cellulose. lED abbr. for individual effective dose. IED so denotes the median of the IEDs within a group of subjects. IEF abbr. for isoelectric focusing. IEP abbr. for 1 immunoelectrophoresis (alternative to IE). 2 or i.e.p. isoelectric point (pI preferred). IF abbr. for initiation factor. Suffixed numerals are added to designate individual factors, e.g. IF-l, IF-2, IF-2a, IF-3. Eukaryotic initiation factors are generally denoted by the prefix 'e', e.g. eIF-2, eIF-3. IF-' an Escherichia coli initiation factor. IF-2 an Escherichia coli initiation factor. IF-3 an Escherichia coli initiation factor. IFCC abbr. for International Federation of Clinical Chemistry. IFN abbr. for interferon. Suffixed Greek letters are added to differentiate the main classes, e.g. IFN-u, IFN-~, IFN-y. Ig symbol for immunoglobulin. IgA symbol for immunoglobulin A. IgA protease another name for IgA-specific serine endopeptidase. IgA-specific serine endopeptidase EC 3.4.21.72; other name: IgA protease; an enzyme that catalyses the cleavage of immunoglobulin A molecules at certain Pro-I-Xaa bonds in the hinge region. No small molecule substrates are known. It is an excreted bacterial serine proteinase. A signal peptide guides the enzyme precursor to the periplasmic space, and the C-terminal helper domain associates with the outer membrane to form a pore for excretion of the protease domain. The helper domain is then released by autoproteolysis. Example from Neisseria gonorrhoeae: database code IGA_NEIGO, 1532 amino acids (168.79 kDa). IG cell the intestinal gastrin cell, a small, granulated, gastrinproducing cell occurring in the human upper small intestine. IG cells react both with gastrin-specific antisera and with antisera recognizing the C-terminal pentapeptide sequence common to gastrin and cholecystokinin (CCK). IG cells are smaller than, and ultrastructurally different from, CCK-producing I cells, gastrin-producing G cells of the gastric pylorus, and TG cells. IgD symbolfor immunoglobulin D. IgE symbol for immunoglobulin E. igensin a neutral cytosolic serine proteinease, activated by sodium dodecyl sulfate and found in a number of mammalian tissues. IGF abbr. for insulin-like growth factor. IGFBP abbr. for insulin-like growth factor binding protein. IgG symbol for immunoglobulin G. Suffixed numerals are added to designate individual subclasses, e.g. IgG I, IgG2, IgG3,IgG4. Ig-like domain see immunoglobulin fold. IgM symbol for immunoglobulin M. ~IG·M' see connective tissue growth factor. ~IG-M2 see connective tissue growth factor. ignose the name first proposed for ascorbic acid by A. SzentGyorgyi, before he knew its structure. See also godnose, . IGT abbr. for impaired glucose tolerance. Ii system a blood group system in which the antigenic determinant is an oligosaccharide structure. It is structurally related to

imidazolium the ABH system (see ABH antigens), anti-I and anti-i antibodies being inhibited by ABH and Lewis glycoproteins. Anti-I and anti-i are the major cold autoantibodies; the anti-I factors occur in the transient anemia accompanying viral or Mycoplasma pneumoniae infections; the i-specific antibodies are characteristic of the so-called chronic cold agglutinin disease, accompanying chronic lymphoproliferative diseases of the nonHodgkin type. The structures of the determinants are: i determinant, GlcNAc(pl-3)Gal(pl-4)GlcNAcpl-R; I determinant, Gal(pl-4)[Gal(pl-4)GlcNAc(PI-6)]GlcNAc(pl-3)Gal(pl-4)Glc NAcpI-R. ikaros a protein that binds and activates the enhancer of a gene CD3-o involved in T-lymphocyte specification and maturation. Similar to hunchback, it is a zinc-finger protein. Example from mouse: database code IKAR_MOUSE, 431 amino acids (48.13 kDa). IL abbr. for interleukin. Various distinct interleukins are distinguished by suffixed numerals, e.g. IL-l, IL-2, IL-3, etc. ILA abbr. for insulin-like activity. lie symbol for a residue of the a-amino acid L-isoleucine (alternative to I). ileum the lower part of the small intestine, extending from the jejunum to the large intestine. -ileal ad). illegitimate transcription transcription at a low level of a normally tissue-specific transcribing gene in nonspecific cells. 1M or Lm. abbr. for intramuscular, or intramuscularly. imidate 1 any salt or ester of an imidic acid. 2 to convert an oxo diacid into its corresponding imide. -imidation n. imidazole or (formerly) glyoxaline or iminazole 1,3-diazole; 1,3-diaza-2,3-cyclopentadiene; a weak base, pKa z6.95. The numbering and tautomerism of the imidazole ring are described at histidine.

C3 N

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imidazole 4-acetate a product of histamine metabolism; it results from the action of monoamine oxidase on histamine to form imidazole 4-acetaldehyde, which is then oxidized by an NAD+-dependent aldehyde dehydrogenase to imidazole 4-acetate. See also histidine. imidazoline receptor any of a class of mitochondrial or plasma membrane binding sites for compounds from the generic groups imidazoles, imidazolines, imidazolidines, guanidines, and oxazolines, and having a putative endogenous ligand, agmatine. They occur throughout the brain, where they are possibly associated with glial cells, and in peripheral tissues. Two subtypes (at least) have been characterized pharmacologically: II receptors, which have high affinity for p-aminoclonidine and are localized in plasma membranes, and 12 receptors, which have high affinity for idazoxan and are localized in mitochondrial membranes. The latter are known alternatively as non adrenergic imidazoline binding sites (NAIBSs). Photoaffinity labelling to at least three proteins occurs: two, of M r 55 000 and 61 000, are found in rat liver and differ in their binding affinity for the guanidium, amiloride; a third, of M r 61 000, is found in PC-12 cells and has high affinity for amiloride but low affinity for idazoxan. These proteins may represent different 12 receptors. Subtypes of 12 receptors are also suggested pharmacologically. The function of imidazoline receptors is not yet known, but many of the effects of imidazoline compounds, formerly attributed to their binding to U2 receptors (e.g. hypotension) are now attributed to NAIBSs. imidazolium 1 the cation formed by addition of a proton (hydron) to a molecule of imidazole. 2 the cationic chemical group formed by addition of a proton (hydron) to an imidazolvl group.

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immunoadsorbent

imidazolyl imidazolyl the chemical group derived formally by removal of one hydrogen atom from imidazole. The position from which the hydrogen atom has been removed may be indicated, e.g. 2imidazolyl. The imidazolyl group is present in histidine and its derivatives. imide any secondary organic amide (i.e. any diacyl derivative of ammonia or a primary amine), especially any that is a cyclic compound in which both of the acyl groups (which may be the same or different) are derived formally or actually from a diacid. (Note: Noncyclic symmetrical secondary organic amides are generically termed diacylamines.) +imide suffix (in chemical nomenclature) designating any organic compound that is an imide. The nitrogen atom may be substituted with a named alkyl or other group. An example is succinimide:

succinimide

imidic acid any derivative of a carboxylic acid in which the carbonyl oxygen atom of the carboxyl group has been replaced by an imino (def. I) or alkylimino group; i.e. any containing the -C(=NR)-OH group. Distinguish from imino acid. imido+ comb. form designating any inorganic oxo acid (including the anions, salts, and esters) in which =0 has been replaced by =NH or =NR (where R is a named substituent), or any derived di-, trio, etc. acid in which a bridging oxygen atom, -0-, has similarly been replaced by -NH- or -NR-; e. g., adenosine 5' -LB. y-imidoltriphosphate. Imigran see sumatriptan. iminazole a former name for imidazole. imine 1 any organic compound having the general structure R 2C=NR where R may be any organyl group or H. See also aldimine, azomethine, ketimine, Schiff base. 2 an obsolete term for azacycloalkane. iminium the bivalent quaternary nitrogen-containing cationic group =+NR 2 attached to carbon in a chemical compound, where the R groups may each be hydrogen or any organyl group. imino the bivalent group =NH attached to carbon in a chemical compound. imino+ comb. form denoting the presence in a chemical compound of one or more imino groups; the number of imino groups in the molecule may be specified, e.g. diimino+. imino acid any carboxylic acid in which an imino substituent replaces two hydrogen atoms. In biochemistry the term is commonly applied also to certain cyclic alkyl amino (especially a-alkylamino) derivatives of aliphatic carboxylic acids, e.g. proline, although such compounds are now preferably classed as azacycloalkane carboxylic acids. Compare imidic acid. iminodipeptidase see Pro-X dipeptidase. imipenem a carbapenem p-lactam antibiotic that is a semisynthetic derivative of thienamycin produced by Streptomyces cattleya. Its broad-spectrum antibiotic actions resemble those of penicillins, i.e. inhibition of bacterial peptidoglycan synthesis.

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immediate gene or immediate-early gene see early gene. immediate hypersensitivity or type I hypersensitivity a type of hypersensitivity responsible for asthma, hayfever, and some types of eczema. It occurs within minutes of exposure to antigen and is dependent on the activation of mast cells and the release of mediators of acute inflammation. The mast cells bind immunoglobulin E (IgE) via their surface Fc receptors and when antigen cross-links the IgE, the mast cel1s degranulate releasing vasoactive amines that mediate the symptoms. immobilize or immobilise to render any agent, whether a micro- or macrosolute, a particle, or an intact cel1, nondispersible in an aqueous medium with retention of its specific ligating, antigenic, catalytic, or other properties. Immobilization may be achieved by, e.g., encapsulation, entrapment in a smal1-pore gel, adsorption on, or covalent linkage to, an insoluble supporting material (matrix), or through formation of aggregates by cross-linkage. immobilized enzyme see solid-phase technique. immortalization or immortalisation the transformation of a cel1 population with a finite life span to one possessing an infinite life span. It is a characteristic of cancer cel1s, and is of practical importance in, e.g., the creation of monoclonal antibodies. Immortalization of eukaryotic cells may be effected experimentally by infection with certain viruses, or by fusion of the cell with a neoplastic cell to form a hybridoma. -immortalize or immortalise vb. immune 1 relating to or possessing immunity. 2 regarding or describing an animal that has been immunized. 3 an alternative word for immunological. immune adherence the complement-dependent adherence of antibody-antigen complexes, or of antibody-coated bacteria (or other particles), to primate erythrocytes, causing the agglutination of the latter. immune clearance an alternative term for immune elimination. immune complex an alternative term for antigen-antibody complex. immune complex-mediated hypersensitivity or type III hypersensitivity a type of hypersensitivity caused by the deposition of antigen-antibody complexes in tissue and blood vessels. The complexes activate complement and attract polymorphs and macrophages to the site. immune cytolysis the complement-dependent lysis of cel1s by antibody molecules. When the cells concerned are erythrocytes the process is termed immune hemolysis. immune elimination or immune clearance the accelerated, exponential removal of antigen from an immune animal as a result of complexing with antibody molecules. immune globulin (sometimes) an alternative name for immunoglobulin. immune hemolysis see immune cytolysis. immune response the total immunological reaction of an animal to an immunogenic stimulus. It includes antibody formation, the development of hypersensitivity, and immunological tolerance. immune serum an alternative term for antiserum. immunity freedom and protection from 'infection'. Two forms of immunity can be recognized: (I) innate, meaning non-specific anti-microbial systems (e.g. phagocytosis) that are innate in that they are not intrinsically affected by prior contact with the infectious agent; and (2) the state of an animal that has an enhanced ability, above the nonimmune state, to respond to some (specific) antigen in which the antigen is bound and rendered inactive or eliminated from the body. See also active immunity, passive immunity. immunization or immunisation any procedure carried out on an animal, e.g. the administration of antigen or antibody, that leads to an increased reactivity of the animal's immune system towards an antigen or antigens. -immunize or immunise vb. immuno+ comb. form indicating immune or immunity. immunoadsorbent any insoluble preparation of an antigen

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immunoadsorption (or antibody) suitable for use in immunoadsorption. See also immunosorbent. immunoadsorption the use of an insoluble antigen (or antibody) to remove specifically unwanted antibodies (or antigens) from a mixture so as to make the antibody (or antigen) more specific. Compare adsorption (def. 2). See also immunosorption. immunoaffinity chromatography a type of affinity chromatography in which one of the two components of an antigen-antibody system is coupled to an insoluble matrix and used for the separation and purification of the other component. immunoaffinity column a chromatographic column used in immunoaffinity chromatography. immunoassay 1 any of a group of techniques for the measurement of specific biochemical substances, commonly at low concentrations and in complex mixtures such as biological fluids, that depend upon the specificity and high affinity shown by suitably prepared and selected antibodies for their complementary antigens. A substance to be measured must, of necessity, be antigenic - either an immunogenic macromolecule or a haptenic small molecule. To each sample a known, limited amount of specific antibody is added and the fraction of the antigen combining with it, often expressed as the bound:free ratio, is estimated, using as indicator a form of the antigen labelled with a radioisotope (radioimmunoassay), fluorescent molecule (fluoroimmunoassay), stable free radical (spin immunoassay), enzyme (enzyme immunoassay), or other readily distinguishable label. The amount of the antigen in the sample is found by comparison with standards containing known amounts. See also heterogeneous immunoassay, homogeneous immunoassay, saturation analysis. 2 an alternative name for radioimmunoassay. 3 to carry out or to estimate (something) by an immunoassay (def. I, 2). immunobiology the branch of biology dealing with the activities of the cells of the immune system and their relationship to each other and to their environment. -immunobiological adj. immunochemical 1 of or relating to immunochemistry. 2 any specific immunological reagent that consists of or incorporates an antigen or an antibody, especially one of commerce. immunochemistry the branch of biochemistry dealing with the chemical nature of antigens, antibodies, and their interactions, and with the chemical methods and concepts as applied to immunology. immunochromatogram the pattern of precipitation bands formed in immunochromatography. immunochromatography any of various techniques for separating and identifying soluble antigens. In one method, analogous to immunoelectrophoresis, the antigens are first fractionated through a thin-layer chromatogram, e.g. of Sephadex; the fractions are then diffused against a trough containing a solution of antibodies (antiserum). In another method a small drop of antigen-antiserum mixture is applied to filter paper, or resin-impregnated paper, and the chromatogram developed with buffer; any antigen-antibody complex remains at the point of application and can be detected with a protein stain, while the other proteins are washed away from the origin. immunocompetent cell an immunologically competent cell. immunocyte any immunologically competent cell. immunocytochemistry cytochemistry using appropriately labelled antibody preparations to detect specific cellular components. -immunocytochemical adj. immunodeficiency any condition in which there is a deficiency in the production of humoral and/or cell-mediated immunity. -immunodeficient adj. immunodeterminant an alternative name for antigenic determinant. immunodiagnosis the diagnosis of disease by immunological methods. immunodiagnostic 1 of or relating to immunodiagnosis. 2 any specific immunological reagent used in diagnosis.

immunogenetics immunodiffusion any of various analytical methods by which components of soluble antigen or antibody mixtures may be distinguished. Essentially, the antigens and antibodies are allowed to diffuse towards each other in a translucent gel, wherein they react to gives lines or bands of precipitation in characteristic positions. Such methods include: double immunodiffusion, electroimmunodiffusion, immunochromatography, immunoelectrophoresis, immunorheophoresis, and single radial immunodiffusion. -immunodiffuse vb. immunodominance the attribute of a part of an epitope that contributes a disproportionately great portion of the binding energy; e.g. the immunodominance shown by a monosaccharide residue in determining the antigenic specificity of a polysaccharide. -immunodominant adj. immunoelectrofocusing or immunoisoelectric focusing a technique that is analogous to immunoelectrophoresis but with the preliminary fractionation of one of the reactants being effected by electrofocusing instead of electrophoresis. immunoelectron microscopy a form of electron microscopy in which structures are stained with specific antibodies labelled with an electron-dense material. immunoelectropherogram (sometimes) the record of an immunoelectrophoresis experiment, either the electrophoretic support itself or a tracing derived therefrom. immunoelectrophoresis abbr.: IE or IEP; a technique for separating and identifying soluble antigens. It consists of zone electrophoresis, in a reasonably transparent gel, in one direction followed by immunodiffusion against a solution of antibodies (antiserum) placed in a trough parallel to the direction of electrophoresis. In suitable conditions each antigen shows up as an arc of precipitation in a characteristic position. -immunoelectrophoretic, immunoelectrophoretical adj. immunoenzymatic of or pertaining to the particular techniques used in immunoenzymology. immunoenzymology the subspeciality of immunochemistry in which the activity of enzymes coupled to antigens or antibodies is utilized as a molecular amplifier of antigen-antibody reactions. immunofixation or immunofixation electrophoresis a variant of immunoelectrophoresis, or immunoelectrofocusing, in which proteins of a single immunological species are anchored to the support by treatment with monospecific antibodies, allowing the other proteins to be washed out of the support. It is useful in the identification of proteins in complex mixtures or of minor proteins obscured in electrophoretic patterns. immunofluorescence or immunofluorescence microscopy a technique in which an antigen or antibody is made fluorescent by conjugation to a fluorescent dye and then allowed to react with the complementary antibody or antigen in a tissue section or smear. The location of the antigen or antibody can then be determined by observing the fluorescence by microscopy under ultraviolet light. -immunofluorescent adj. immunogelfiltration a variant of radial single immunodiffusion in which antigen is first fractionated according to its molecular size by permeation, in a buffer solution, into a thin layer of an appropriate cross-linked dextran gel. The dextran layer is then covered with a layer of agarose gel containing antibody. Rings or spots of antigen-antibody precipitate develop in the agarose gel over the complementary antigens. immunogen t any substance that, when introduced into the body, elicits humoral or cell-mediated immunity, but not immunological tolerance. 2 any substance that is able to stimulate an immune response, as distinct from substances (antigens) that can combine with antibody. 3 any substance that is able to stimulate protective immunity against a pathogen, as distinct from an immune response that is of no intrinsic value to the animal immunized. -immunogenic adj. immunogenetics (functioning as sing.) the branch of biology that combines immunology and genetics. It includes the use of immunological methods and knowledge in the study of genet-

327

immunogenicity ics, and the use of genetics in the study of immunological phenomena and substances. -immunogenetic adj. immunogenicity an alternative term for antigenicity. immunoglobulin symbol: Ig; any member of a group of proteins occurring in higher animals as major components of the immune system. They are produced by cells of the lymphocyte series, and virtually all possess specific antibody activity. Each immunoglobulin molecule essentially comprises four polypeptide chains, two identical heavy chains and two identical light chains, linked together by disulfide bonds; all contain in addition differing amounts of attached oligosaccharide. There are five classes, IgA, IgD, IgE, IgG, and IgM. The primary structures of the heavy chains differ among the various classes, being designated a, 0, E, y, and J.I, respectively for the classes listed above, and there are two types of light chain, K and A. IgA and IgM molecules contain multiples of the four-chain unit. The homology units form a characteristic motif, the immunoglobulin fold. See also immunoglobulin A, immunoglobulin D, immunoglobulin E, immunoglobulin G, immunoglobulin M. immunoglobulin A symbol: IgA; an immunoglobulin found in human plasma, where its role is uncertain. It occurs mostly as a 170 kDa monomer of the basic four-chain immunoglobulin structure or, as a 400 kDa dimer, together with an extra 15 kDa polypeptide, the J chain, linked to secretory piece. It is the major immunoglobulin of seromucous secretions, in which it is concerned in the defence of external body surfaces against attack by microorganisms. It has the structure (a212)nJ, where a is the heavy chain, I is the light chain (K or A), J is the J chain, and n is 1 or 2. Example, at C region: database code ALCLHUMAN, 353 amino acids (37.61 kDa). See also IgAspecific serine endopeptidase. immunoglobulin D symbol: IgD; a 185 kDa immunoglobulin that is very susceptible to proteolytic degradation and has a very short half-life in plasma. It is found in large amounts on the surface of B lymphocytes together with immunoglobulin M; it is probable that these two immunoglobulins function as mutually interacting antigen receptors and playa part in the control of lymphocyte activation and suppression. It has the structure 0212 where 0 is the heavy chain and 1 is a light chain (K or A). Example, heavy chain (C region): database code DTC_HUMAN, 383 amino acids (42.08 kDa). immunoglobulin E symbol: IgE; a 200 kDa immunoglobulin of high carbohydrate content, normally found in very low concentrations in plasma, although its concentration there is elevated in a number of allergic conditions. IgE is synthesized mainly in lymphoid tissue of gut and respiratory tract. It binds strongly to mast cells and contact with antigen leads to degranulation of the mast cells and release of inflammatory mediators. It has the structure £212 where E is a heavy chain and I is a light chain (K or A). Example, heavy chain C region: database code EPC_HUMAN, 428 amino acids (46.97 kDa). immunoglobulin fold a series of ~ strands, arranged as two anti parallel ~ sheets packed tightly against each other, that is highly characteristic of immunoglobulin structure. In the constant region, the two ~ sheets are formed from four and three ~ strands respectively. In the variable region there are nine ~ strands (five and four) rather than seven. This type of structure is found in many other proteins, especially cell surface receptors, and is often referred to as an Ig-like domain. immunoglobulin G symbol: IgG; the principal immunoglobulin of human plasma and other internal body fluids. It is a 150 kDa protein and is the major immunoglobulin synthesized during the period of secondary response to an antigen. In the tissue fluids it neutralizes bacterial toxins and binds to microorganisms thereby enhancing their phagocytosis. Complexes of IgG with microorganisms activate complement by the classical pathway. IgG binds to macrophages and polymorphonuclear lymphocytes and can cross the placenta. It has the structure Y212 where Yis a heavy chain and I is a light chain (K or A). There are subclasses of IgG depending on different types of y chain. Example, IgG y-l C region: database code

immunometry GCl_HUMAN, 330 amino acids (36.06 kDa); 3-D structure known. immunoglobulin M symbol: IgM; a 900 kDa immunoglobulin consisting of a star-shaped polymer of five basic four-chain structures, each heavy chain bearing an extra constant domain. Polymerization is dependent on the presence of J chain, which may act to stabilize the sulfhydryl groups in the constant portion of the heavy chains during IgM synthesis. IgM is produced early in the immune response and is mainly found intravascularly. Because of its high antigen-combining valency it is very effective in binding microorganisms and mediating complement-dependent cytolysis. It has the structure (J.l212)5J where J.I is a heavy chain, I is a light chain (K or A), and J is a J chain. Virgin B lymphocytes have an altered sequence at the C terminus of J.I and the switch is effected by alternative splicing. Example, the protein from heavy chain disease, which has no C and CHI regions due to deletion: database code MUCB_ HUMAN, 391 amino acids (43.00 kDa). immunoglobulin superfamily a superfamily of proteins that have similarities of sequence and structure to immunoglobulins. The superfamily has been divided into three sets, based on immunoglobulin domains: one with variable-like domains, the V set, and two with different variants of the constant-like domains, the Cl and C2 sets. immunogram (sometimes) the pattern of bands or lines of precipitation formed in a gel by immunodiffusion. immunohistochemistry a form of histochemistry in which appropriately labelled antibody preparations are used to detect specific structures in tissues. -immunohistochemical ad). immunoliposome a liposome bearing a chemically coupled monoclonal antibody. immunolocalization or immunolocalisation the use of appropriately labelled antibody (or antigen) preparations to detect the position of specific structures or components that contain or are the complementary antigens (or antibodies). immunological or (esp. US) immunologic of, concerned with, or pertaining to immunity or immunology. -immunologically adv. immunologically competent (of cells, tissues, etc.) qualified for and capable of giving an immune response. immunological paralysis an alternative name for acquired tolerance. immunological rejection the destruction, by a specific immune reaction, of foreign cells or tissues transplanted or inoculated into a recipient animal from a donor animal. immunological response any specific response to an antigen. It includes cell-mediated immunity, humoral immunity, and immunological tolerance. immunological surveillance the postulated monitoring of the cells of large, long-lived animals by their immunological systems so that aberrant cells arising from somatic mutations, and so containing new antigens, are destroyed. immunological tolerance a type of immunological response in which there develops a specific nonreactivity of the lymphoid tissues towards a given antigen, one that in other circumstances is able to induce cell-mediated or humoral immunity. Immunological tolerance may follow contact with the antigen in fetal or early postnatal life or the administration of the antigen to adults (acquired tolerance). The reaction towards other, unrelated antigens is unaffected. immunology the study of immunity and related phenomena. The science of immunology grew out of the study of resistance to infectious disease, and now encompasses the study of antigens, antibodies, and their interactions both in vivo and in Vitro, and the cellular phenomena of recognition of, and responsiveness to, foreign substances. Related disciplines include immunobiologyand immunochemistry. immunometry the measurement of amounts of substances by the use of specific antigen-antibody reactions. -immunometric adj.; immunometrically adv.

immunomodulation

328

immunomodulation the alteration of an immune response by an agent other than the antigen. immunomodulator any agent that alters the extent of the immune response to an antigen, by altering the antigenicity of the antigen or by altering in a nonspecific manner the specific reactivity or the nonspecific effector mechanisms of the host. Immunomodulators include adjuvants, immunostimulants, and immunosuppressants. immunoosmophoresis an alternative term for counter(immunolelectrophoresis. immunophenotyping the typing of cells with immunological markers such as monoclonal antibodies. immunophilin any member of a family of receptors that includes the major FK506 binding protein FKBP and cyclophilin. These two proteins are unrelated in amino-acid sequence, but both possess peptidyl-prolyl isomerase activity which is blocked by immunosuppressants that block signal-transduction pathways leading to T-cell activation such as FK506 and rapamycin, which block FKBP, or cyclosporin A, which blocks cyclophilin. Example, the rapamycin-selective 25 kDa human immunophilin: database code FKB2_HUMAN, 224 amino acids (25.15 kDa). immunoprecipitate 1 the precipitate formed in an antigenantibody reaction. 2 to precipitate (something) by reaction with a specific antibody or antigen. -immunoprecipitation n. immunoradiometric assay abbr.: IRMA; an alternative method to radioimmunoassay for the measurement of very small amounts of nonradioactive material. An excess amount of a specific antibody labelled with a radioactive isotope is added to the sample containing the substance to be assayed. After equilibration, unreacted antibody is removed and the amount of radioactive material remaining is measured. immunoreactive capable of reacting with a specific antibody. The term is used especially of substances that react with an antibody directed against a particular peptide hormone (or part of such a hormone) but that do not necessarily exhibit the expected physiological or pharmacological activity. -immunoreactivity n. immunosorbent any sorbent used in, or useful for, immunosorption. See also immunoadsorbent. immunosorption the use of antigens (or antibodies) immobilized on a solid matrix to remove specifically the complementary antibodies (or antigens) from a mixture and their subsequent elution from the solid phase. It is used in, and is useful for, purification of antibodies (or antigens). See also immunoadsorption. immunostimulant any agent that nonspecifically enhances the immunologically specific reactivity of an animal to an antigen and also the animal's nonspecific effector mechanisms. -immunostimulatory adj. immunosuppressant or (sometimes) immunosuppressive any agent that causes immunosuppression. immunosuppressed describing an organism that is incapable of showing an immune response to an antigen. immunosuppression the suppression of immune responses to antigens. This can be achieved by various means, including physical (e.g. X-irradiation), chemical (e.g. antimetabolic drugs), or biological (e.g. antilymphocyte serum). After transplant surgery azathioprine is commonly used. This drug has a preferential effect on T-cell-mediated reactions. It is degraded in the body first to mercatopurine and is then converted to the active agent, the ribotide, which inhibits nucleic-acid synthesis. Methotrexate, cyclophosphamide, cyclosporin A, and FK506 are also highly effective immunosuppressants, the latter two being used extensively. Infection by HIV-I eventually leads to a reduction in the population of helper T-cells and macrophages. This immunosuppression of the system is associated with occurrence of Kaposi's sarcoma and allows infection by agents such as Pneumocystis carini, cytomegalovirus, and tuberculosis. Compare immunodeficiency. See also suppressor cell.

impurity immunosuppressive 1 able to cause immunosuppression. 2 an alternative term for immunosuppressant. immunosympathectomy the destruction of some or all of the neurons of the sympathetic nervous system by injections into a newborn animal of an antiserum to the appropriate nerve growth factor. immunotoxin any of a class of therapeutic drugs consisting of a monoclonal antibody linked to a toxic protein (e.g. ricin, diphtheria toxin). IMP ahbr. for 1 inosine monophosphate; i.e. inosine phosphate. 2 ion-moderated partition. impaired glucose tolerance abbr.: IGT; the term recommended to denote a clinical state or condition of humans that is intermediate between the normal one and the overtly diabetic. Characteristically, in a standard oral glucose-tolerance test in non-pregnant adults, the glucose concentration in capillary whole blood or venous plasma taken at 2 hours is in the range 8~ II mmol L-I (1.4-2.0 g L-I); the corresponding values for venous whole blood are 7-10 mmol L- 1 (1.2-1.8 g L-I). In addition, the fasting plasma glucose must be below 8 mmol L- 1, and plasma glucose during the test must be greater than II mmol L-I at 30, 60, and 90 min. IMP cyclohydrolase EC 3.5.4.10; other names: IMP synthetase; inosinicase; an enzyme of the pathway for de novo purine biosynthesis that cyclizes 5-formamido-I-(5'-phosphoribosyl)imidazole-4-carboxamide to IMP with elimination of H 20. For an example, see phosphoribosylaminoimidazolecarboxamide formyltransferase. IMP dehydrogenase EC 1.1.1.205; other name: inosine-5'monophosphate dehydrogenase; an enzyme that catalyses the conversion of inosine 5'-phosphate, NAD+, and H 20 to xanthosine 5'-phosphate and NADH. The reaction involves the introduction of an oxo group at the purine C-2. Xanthosine 5'phosphate is then converted to guanosine 5'-phosphate by GMP synthase (glutamine hydrolysing). Examples from human, in which there are two isoenzymes: database code IMPI HUMAN, 514 amino acids (55.39 kDa); database code IMP2_ HUMAN, 514 amino acids (55.74 kDa). impedance symhol: Z; the quality determining the amplitude of the current flowing in a circuit for a given applied alternating electric potential. It depends upon the electric resistance, self-inductance, and capacitance of the circuit. impeller 1 the vaned, rotating disk of a centrifugal pump. 2 any device incorporating an impeller (def. I). impermeable (of a substance or structure) not permitting the passage through it of a fluid or of a particular solute in a fluid; not permeable. -impermeability n. impermeant (of a fluid or a solute in a fluid) incapable of passing through a particular substance or structure. imprinting (in genetics) the differential degree to which the effects of maternally and paternally derived DNA are exerted. For example, the onset of Huntington's disease is earlier if the defective allele is inherited from the father rather than the mother. impulse 1 (in physics) a vector quantity equal to the integral of the force, F, acting on a body with respect to the time, t, over which the force acts: fFdt. If the force is constant the expression reduces to the product Ft. It also equals the total change of momentum of the body induced by the applied force. 2 (in physics) an electrical surge of unidirectional polarity. 3 (in physiology) or nerve impulse an all-or-none signal propagated along the axons of neurons by which information is transmitted rapidly and precisely through the nervous system. It consists of a sequence of changes in ionic permeability of the neuronal membrane that gives rise to ionic currents and associated changes in transmembrane electrical potential. impure not pure, lacking purity; (of a substance or material) containing contaminants. impurity 1 the state or quality of being impure. 2 any or all of the admixed components in an impure substance or material.

impurity quenching

329

impurity quenching chemical quenching due to an impurity (def. 2).

In symbol for indium. inappropriate secretion a clinical syndrome in which the secretion of a specified hormone, commonly antidiuretic hormone, is abnormally high relative to the state of the normal regulatory mechanisms. It is so termed because it results from an unknown or unmistakably abnormal cause and serves no recognizable homeostatic function. inborn error of metabolism any of the genetically determined biochemical variations occurring in humans. They are highly specific and represent many diverse metabolic phenomena, resulting in very varied effects on the viability of the individual. inbred strain or inbred line a group of organisms obtained by repeated inbreeding over several successive generations, e.g. by self-pollination in plants or by repeated brother x sister matings in animals. Eventually, all individuals will possess identical sets of autosomes, and all the chromosome pairs will become homozygous. inclusion (in cytology) 1 any discrete body or particle within a cell, especially a passive product of cell activity such as a starch or volutin granule. 2 an alternative (less common) name for inclusion body. inclusion body or inclusion 1 any discrete assembly of virions and/or viral particles that may be visualized in virus-infected cells, either in the nucleus or in the cytoplasm. 2 (in bacteriology) anyone of a number of bodies found within bacterial cells, e.g. storage granules, gas vacuoles, carboxysomes. inclusion cell abbr.: I cell; a type of cell that is seen in tissues from patients with mucolipidosis II (I-cell disease) and that contains inclusions consisting of very large lysosomes whose contents are heterogeneous, comprising mucopolysaccharide, whorls of membrane, and other material. inclusion-cell disease or mucolipidosis II see I-cell disease. inclusion complex or inclusion compound any chemical complex in which one component (the host molecule) forms a crystal lattice containing tunnel- or channel-shaped spaces in which molecular entities of a second species (the guest molecule) are located. There is no bonding between the host and the guest molecules. incompatibility 1 a criterion for classifying bacterial plasmids; two plasmids of the same incompatibility group cannot coexist in one host cell. The molecular basis is that the incompatible plasmids share sites during plasmid segregation (def. 3). 2 the state of being incompatible. incompatibility group a group to which plasmids are said to belong if they cannot coexist in the same bacterial host over several generations without selection. incompatible 1 (in immunology) having antigenic nonidentity between a donor and a recipient, e.g. in blood transfusion or tissue transplantation. 2 (in therapeutics) (of two drugs) incapable of being used together or combined; antagonistic. incomplete antibody 1 any antibody whose activity in an agglutination test can only be demonstrated indirectly, e.g. by an antiglobulin test. 2 (sometimes) a univalent antibody fragment produced enzymically, e.g. a Fab fragment. incomplete Freund's adjuvant see Freund's adjuvant. incorporation 1 the act or process of including (something) as a part of a whole. 2 (in biochemistry) the inclusion of (isotopically labelled) metabolites, by covalent linkage, into biopolymers by living cells or cell-free preparations; often taken as an index of biosynthesis. -incorporate vb. incretin a putative insulinogenic principle secreted from the duodenum and jejunum in response to the presence of glucose. Its effects are now generally considered to be attributable to glucose-dependent insulinotropic peptide. incubate 1 to maintain at an appropriate temperature so as to favour growth, development, or continued survival (e.g. of cells); by extension, to maintain under specified conditions in a controlled or artificial environment (e.g. in studies of en-

indigo zymic or antigen-antibody reactions), especially at a particular ambient temperature (which may be above or below that of the environment). 2 a material or preparation that has been incubated. -incubation n. incubation mixture any reaction mixture that is maintained at a controlled temperature and/or in a controlled, artificial environment. incubation period 1 (in pathology) the time interval between the invasion of an organism by a pathogenic virus or microorganism and the overt manifestation of disease. 2 (in microbiology) the period of development of a culture of bacteria or other microorganisms. incubator any closable, heat-insulated cabinet that is maintained at a constant internal temperature (and, sometimes, humidity and/or atmosphere) and that is used for the growth or maintenance of cells, cultures, tissues, or organisms, or for the hatching of eggs. Inderal see propranolol. index of refraction see refractive index. Indian tobacco see lobelia. indican 1 metabolic indican indol-3-yl hydrogensulfate; 3-indoxylsulfuric acid; a so-called ethereal sulfate, formed in the gut by bacterial action on tryptophan and excreted in the urine, where its level may be taken as an index of intestinal stagnation. 2 plant indican indol-3-yl-jJ-D-glucopyranoside; indoxyl-jJ-D-glucoside; a substance isolated from Indigofera spp., members of the Leguminosae, and Polygonium tinctorium. The glucoside is hydrolysed during extraction by water or dilute acid, and the indoxyl is liberated spontaneously, oxidizing to the blue dye indigo. indicated hydrogen symbol: H- (or sometimes H) (with a prefixed locant); (in chemical nomenclature) an atom of hydrogen whose position in the molecular structure of an unsaturated cyclic organic compound or group requires to be explicitly stated in order to make the name of the compound or group specific to a particular structural isomer (or taut orner) if otherwise the name would apply equally to two or more isomers (or tautomers). The compound or group in question commonly consists of or is derived from a condensed ring system with the maximum number of non-cumulative double bonds, although the notation is applied also to certain monocyclic systems. The symbol (with its locant) ordinarily precedes the name or the relevant part of the name, e.g. IH-purin-6-amine or 6-amino-IH-purine (alternative semisystematic names for one of the tautomers of adenine); however, where the insertion of a substituent into a cyclic structure has necessitated the addition of a hydrogen atom at another position the symbol is placed in parentheses after the locant for the substituent, e.g. purin-6(lH)-one (a semisystematic name for one of the tautomers of hypoxanthine). indicator 1 any substance used in a chemical operation to indicate by a colour change the completion of a reaction or the attainment of a desired state. 2 any substance that by a characteristic colour change indicates the presence of another particular substance. 3 (in saturation analysis) the labelled substance whose distribution between the reactants of the system is used to determine the amount of analyte present. 4 an isotope, often a radioactive one, that is used as a tracer. indicator enzyme an alternative name for marker enzyme. indicator organism or indicator species any species of organism whose presence or population characteristics in a particular habitat are used to provide information about the nature of that habitat, especially regarding its degree of pollution. indicator yellow the original name for N-retinylidene opsin. It was so called because its colour changes between yellow and orange according to the pH of its aqueous solution. It spontaneously hydrolyses into opsin and (all-trans- )retinal. See rhodopsin. indigo a blue dye prepared from the same plants as plant indican. Its major blue component is indigotin.

330

indigotin

infective

indigotin [,12,2'-biindolineJ-3,3'-dione; the major blue component of indigo,

indirect antagonism a form of antagonism (def. 2) arising as a consequence of competition by the antagonist for the binding site of an intermediate that links receptor activation to the observed effect. INDO-, 1-[2-amino-5-(6-carboxyindol-2-yl)phenoxy-2-(2amino-5-methylphenoxy)ethane-N,N,N',N'-tetraacetic acid; a fluorescent calcium chelator, named from the indolyl moiety, that can be used as an indicator of Ca 2+ concentration; it has a large shift in fluorescence emission, from 480 to 400 nm, on binding Ca2+ , indole 2,3-benzopyrrole; a compound formed by the degradation of tryptophan.

~ ~NI H

indoleacetate abbr.: IAA; the anion of indole-3-acetic acid. Formed from L-tryptophan, it is a plant hormone, and the main auxin of higher plants. indoleacetonitrile abbr.: IAN; an auxin, second in abundance to indoleacetate. indole-3-glycerol-phosphate synthase see trp genes. indole test a test used for the identification of certain microorganisms, e.g. members of the Enterobacteriaceae. It determines the ability of the organism to produce indole from tryptophan. indolicidin a bactericidal and fungicidal 13-residue peptide amide from the cytoplasmic granules of bovine neutrophils. It contains five tryptophan residues, hence its name. Some therapeutic success has been achieved in animals against the fungus, Aspergillus fumigatus, using liposomally encapsulated indolicidin, indicating that neutrophil-derived antimicrobial peptides may have therapeutic value. indoluria the presence in (human) urine of compounds containing an indole ring. indomethacin I-(p-chlorobenzoyl)-5-methoxy-2-methylindole-3-acetic acid; an inhibitor of prostaglandin-endoperoxide synthase, It is useful as an anti-inflammatory drug.

COOH CH30m

I '

CH3

~o~ !lAc

I

INDOR abbr. for internuclear double resonance spectrometry. induced enzyme or inducible enzyme any enzyme that is synthesized in a cell only in very small amounts except when induced by the presence of its substrate or a closely related compound. Compare constitutive enzyme.

induced-fit theory a possible explanation, first proposed by D. E. Koshland, of enzyme specificity. It suggests that reaction between an enzyme and its substrate can occur only following a change in the enzyme's structure, induced by the substrate itself. It is proposed that: (I) a precise orientation of catalytic groups is required for enzyme action; (2) the substrate may cause an appreciable change in the three-dimensional relationship of the amino-acid residues at the active site; and (3) the changes in enzyme structure caused by a substrate will bring the catalytic groups into the proper orientation for reaction, whereas a nonsubstrate will not. It is similar to the zipper model of hormone-receptor interaction. Compare lock-and-key model, inducer any compound that causes cells to produce larger amounts of the particular enzymes involved in its uptake and/or metabolism (or in the uptake and/or metabolism of a structurally similar compound), than are found in cells when the inducer is absent. inducible capable of being induced. inducible enzyme an alternative name for induced enzyme. induction 1 see Jacob-Monad model. 2 (in physics) any physical effect brought about (i.e, induced) in an object by the action of a field without any direct physical contact with the inducer. It may be electrostatic, magnetic, or electromagnetic. See also induced enzyme. induction coil a device for producing a rapid succession of large pulses of induced emf in a secondary coil from an intermittent low emf in a primary coil. induction motor an electric motor in which an alternating current is supplied to the winding of the stator, arranged in such a manner as to produce in effect a rotating magnetic field. This in turn induces electric currents in the winding of the rotor, and interaction between these currents and the magnetic flux exerts a torque on the rotor. Induction motors are useful in situations where sparks caused by moving electric contacts are undesirable. inductive effect (in chemistry) symbol: I; an experimentally observable effect (on reaction rates, etc.) caused by the transmission of charge through a chain of atoms by electrostatic induction. It is symbolized by +I or -1, according to whether the group in question is left with a small positive or a small negative charge. +ine suffix designating 1 an organic compound that is either an amine (including any monoamino monocarboxylic acid other than tryptophan), or a nitrogen-containing heterocycle other than one containing four or five atoms in the ring. 2 a halogen. 3 any of a group of certain inorganic binary hydrogen compounds, namely arsine, bismuthine, phosphine, and stibine; also hydrazine. inert 1 having little or no ability to react chemically or physiologically. 2 having no inherent ability to move or resist being moved. -inertness n. inertia 1 (in physics) the tendency of an object to resist changes to its state of rest or uniform motion; by analogy extended to other physical qualities that resist change. 2 the state of being inert or inactive. -inertial adj. inertial mass see mass. infect 1 to cause infection in (an organism, wound, etc.), especially with pathogenic microorganisms. 2 to affect or become affected with a communicable disease, infection 1 the invasion of a cell or organism by other (especially pathogenic) organisms. 2 the act or process of infecting; the state of being infected. 3 any agent or process that infects. infectious 1 (of a disease) caused by pathogenic (micro)organisms. 2 causing or transmitting infection. 3 (of a disease) capable of being transmitted to another organism. -infectiously adv.; infectiousness n. infectious mononucleosis see Epstein-Barr virus. infectious viral nucleic acid a purified viral nucleic acid that, when it infects a host cell, causes the production of progeny viral particles. infective 1 capable of causing infection. 2 an alternative (less

331

infinite common) word for infectious. -infectively adv.; infectiveness or infectivity n. infinite having no limits in extent, magnitude, space, or time; immeasurably numerous or great. -infiniteness n.; infinitely adv. infinite dilution a hypothetical state (of a solution) in which the solute concentration is considered to be zero and the activity coefficient unity. infinitely thick (of a radioactive sample) having a thickness no less than infinite thickness for the particular radionuclide to be measured. infinitely thin (of a radioactive sample) having a thickness no greater than infinite thinness for the particular radionuclide to be measured. infinite thickness the thickness of a sample containing a particular radionuclide, especially a soft beta-emitter, beyond which, because of self-absorption, any increase results in no further increase in recordable disintegrations. Under these conditions the (radio)activity is proportional to the specific (radio)activity of the substance. infinite thinness the thickness of a sample containing a particular radionuclide at or below which self-absorption is negligible. Under these conditions the (radio)activity is proportional to the amount of the radionuclide present. inflammable very liable to catch fire and produce flame; flammable. inflammation the immediate defensive reaction of vertebrate tissue to infection or to injury by chemical or physical agents. The part affected is characterized by pain, heat, redness, swelling, and loss of function; there is local vasodilatation, extravasation of plasma into the intercellular spaces, and accumulation of white blood cells and other macrophages in the injured part. Plasma enzyme systems are important sources of inflammatory mediators. These include the complement, blood coagulation, fibrinolytic, and kinin systems. Also active are the mediators released by mast cells, basophils, and platelets, as well as the eicosanoids generated by many cells at inflammatory sites. -inflame vb. informatics the science concerned with the structure and properties of scientific information, its theory, history, methodology, and organization. Compare information science. -informatical adj.; informatician n. informatin see informofer. information 1 communicated or communicable factual knowledge; data; news. 2 genetic information. 3 (in computing) the results obtained by processing raw data according to programmed instructions. informational 1 of, pertaining to, giving, or carrying information. 2 (in biochemistry) describing any biological macromolecule that contains or transmits genetic information in the form of specific sequences of nucleotides or amino acids. information retrievaf the selective tracing and recovery of information stored in printed works, computers, etc. information science the science concerned with the procedures by which information, especially scientific or technical information, is stored, retrieved, and disseminated. Compare informatics. information theory the quantitative theory of the coding and transmission of signals and information. informofer a specific, 30S macroglobular particle consisting of the protein informatin. Informofers are present in the cell nucleus, tightly packed along molecules of heterogeneous nuclear RNA. informosome a cytoplasmic mRNA-carrying ribonucleoprotein particle of relatively low buoyant density. Informosomes are believed to function in the protection of mRNA from nuclease attack and in the transport of mRNA from the nucleus to the cytoplasm. infra+ prefix denoting below, beneath, coming after, within. Compare sub+, supra+, ultra+ (def. I).

initial velocity infradlan describing any biological activity that occurs, or varies cyclically, more often than once every 24 hours. Compare circadian, u/tradian. infranatant 1 lying below. 2 a solid or liquid lying below a supernatant liquid. Compare subnatant. infrared of, pertaining to, or being infrared radiation. infrared dichroism the dichroism of polarized infrared radiation. It is used in studies of polypeptide structure. infrared radiation abbr.: IR or i.r.; electromagnetic radiation of wavelengths in the range 730 nm to 1 mm (frequencies 300 GHz to 410 THz). This range lies between those of visible light and microwaves. infrared spectrophotometer any instrument for infrared spectrophotometry. infrared spectrophotometry the measurement of the absorption or emission of infrared radiation at particular wavelengths or frequencies. See infrared spectrum. infrared spectrum any absorption spectrum or emission spectrum of infrared radiation. It includes photons that are absorbed or emitted during vibrational and rotational transitions in a molecule. Infrared spectra are widely used in organic chemistry to identify particular groups of atoms by their characteristic vibrational frequencies. infuse 1 to introduce gradually, as of a solution into a vein or body cavity. 2 to make an infusion (def. 2). infusion 1 the process of infusing. 2 an extract, e.g. of meat or leaves, obtained by soaking in water. ingest to take material, e.g. food or liquid, into a cell or organism. -ingestible adj.; ingestion n.; ingestive adj. inhibin one of several polypeptides (another is activin of the transforming growth factor ~ family) that participate in differentiation and growth of diverse cell types. Inhibin and activin are glycoproteins, secreted by the gonads. Inhibin inhibits secretion of follicle-stimulating hormone by the pituitary. It is present in seminal plasma and follicular fluid. It has an M r of 31 000, and consists of two subunits crosslinked by disulfide bridges. There are two isoforms, A and B, with the same a subunit but different ~ subunits. Inhibin A is a dimer of a and ~A subunits, and inhibin B is a dimer of a and ~B subunits. Example of the a chain, from Mus musculus: database code IRA_MOUSE, 366 amino acids (39.54 kDa). The inhibin/activin precursor is a protein generated by alternative splicing of a gene for subunits for both activin and inhibin. Examples of ~ chains, inhibin ~A chain (precursor) from human (other name: erythroid differentiation protein; abbr.: EDF): database code IRBA_HUMAN, 426 amino acids (47.39 kDa); amino acids 311-426 are the inhibin ~A chain; inhibin ~B chain (precursor) from Bos taurus: database code IHBB_BOVIN, 408 amino acids (44.89 kDa). inhibit 1 to restrain or hinder. 2 to stop, prevent, or reduce the rate of (some process, e.g. the growth or functioning of an organism or part of an organism, or a chemical or enzymic reaction). inhibition constant symbol: Ki ; the equilibrium (dissociation) constant for the reaction: EI """" E + 1. It is given by K i = [E][I]/[EI], where E is the enzyme and I the inhibitor, the square brackets indicating concentrations. inhibition index an inverse measure of the potency of an antimetabolite. It is the ratio of the concentration of antimetabolite that is required to inhibit the biological effect of unit concentration of corresponding metabolite. inhibitor 1 any agent that inhibits. 2 (in biochemistry) any substance that inhibits an enzymic reaction. See also competitive inhibition, noncompetitive inhibition, uncompetitive inhibition. initial velocity or initial steady-state rate symbol: V o or v; the reaction velocity in the earliest stage of an enzyme-catalysed reaction. It is given by the tangent at the origin to the curve of reaction velocity as a function of time. In practice it is often measured over the period when the initial substrate concentration has diminished by C=O, joined to two carbon atoms. 2 the functional class name for any ketone (def. 1) that does not have a trivial name, e.g. ethyl methyl ketone. ketone body any of the three substances: (I) acetoacetate, formed enzymically from acetyl-CoA; (2) 0-3-hydroxybu-

tyrate (P-hydroxybutyrate), formed by liver mitochondrial 3hydroxybutyrate dehydrogenase (EC 1.1.1.30) from acetoacetate; or (3) acetone, formed by spontaneous decarboxylation of acetoacetate. Ketone bodies may accumulate in excessive amounts in the body in starvation, diabetes mellitus, or in other defects of carbohydrate metabolism. They are formed in the post-absorptive state and during more prolonged fasting, and can be used as an energy source as an alternative to glucose, sparing glucose and thus indirectly muscle protein, since the carbon source for glucose synthesis under such conditions derives from muscle amino acids. Biosynthesis involves the formation of hydroxymethylglutaryl-CoA, which is cleaved to acetoacetate and acetyl-Co A by hydroxymethylglutaryl-CoA lyase; it occurs largely in the liver, but to a small extent also in kidney. Utilization of ketone bodies in peripheral tissues involves conversion by 3-oxo-acid CoA-transferase of acetoacetate to acetoacetyl-CoA, which is then converted to two molecules of acetyl-CoA by acetyl-CoA C-acetyltransferase. Although not a ketone, 3-hydroxybutyrate is classed as a ketone body because it exists in an equilibrium with acetoacetate that depends on the redox state in the liver mitochondria. To determine the extent of ketone body formation, it is therefore necessary to include 3-hydroxybutyrate in the analysis. ketonemia or (esp. Brit.) ketonaemia an abnormally high concentration of ketone bodies in the blood. ketonic of, relating to, or having the properties of a ketone or a keto (def. I) group. ketonize or ketonise to convert into or become converted into a ketone. -ketonization or ketonisation n. ketonuria a condition in which there is an abnormally large excretion of ketone bodies in the urine. ketopentose any ketose having a chain of five carbon atoms in the molecule. Two enantiomeric pairs of such compounds are possible, these being the D and L isomers of ribulose and xylulose. ketoprofen 2-(3-benzoylpheny1)propionic acid; a nonsteroidal anti-inflammatory agent; it is one of the substituted propionic acids that inhibit prostaglandin-endoperoxide synthase (EC 1.14.99.1). See also ibuprofen.

(S)-ketoprofen ketopyranose any ketose in the pyranose form. ketose any monosaccharide in the acyclic form of which the actual or potential carbonyl group is nonterminal, i.e. ketonic. The systematic names and many of the trivial names of ketoses have the ending '+ulose'. The position of the (potential) carbonyl group is indicated by a prefixed locant (e.g. 3-ketose, 5nonulose), which may be omitted from the name of a 2-ketose when no ambiguity can arise. The term is frequently modified by an infix indicating the number of carbon atoms in a chain in the molecule; thus ketopentose, ketotetrose, etc. Compare aldose. ketosis any clinical condition in which there are abnormally high concentrations of ketone bodies in the tissues. The condition is usually accompanied by acidosis. See also ketogenesis. -ketotic adj. ketosteroid a former name for oxosteroid. keto sugar a common name for any ketose. ketotetrose either of two ketoses having a chain of four carbon atoms in the molecule, these being the enantiomeric pair Dand L-glycero-tetrulose. J3-ketothiolase see acetyl-eoA C-acyltransferase.

358

ketotriose ketotriose the single achiral ketose having a chain of three car-

bon atoms in the molecule and known as dihydroxyacetone, or glycerone. kex2 a structural gene for pre-pro-alpha mating type polypeptide in Saccharomyces cerevisiae. It gives rise to the designation Kex2 site, a cleavage site (Arg-J-Arg or Lys-j-Arg) for kexin in the processing of the mating polypeptide and several extracellular fungal proteins. kexin EC 3.4.21.61; other names: yeast Kex2 protease; proteinase YSCF; prohormone-processing endoprotease; pairedbasic endopeptidase. An enzyme that catalyses the cleavage of Lys-Arg-I-Xaa and Arg-Arg-I-Xaa bonds to process yeast afactor pheromone and killer toxin precursors. Example, kexin precursor from yeast: database code KEX2_YEAST, 814 amino acids (89.90kDa); the human enzyme with the same specificity (and EC number) is neuroendocrine convertase I precursor, database code NECI_HUMAN, 753 amino acids (84.03 kDa). See also furin, kex2, proopiomelanocortin. kg symbolfor kilogram. KHF abbr. for killer cell helper factor (i.e. interleukin 2). Khorana, Har Gobind (1922- ), Indian organic chemist and biochemist renowned, inter alia, for his chemical synthesis of coenzyme A, various codon-containing polyribonucleotides, and a double-stranded DNA segment containing the gene for the tyrosine tRNA of Escherichia coli and its (larger) precursor RNA; Nobel Laureate in Physiology or Medicine (1968) jointly with R. W. Holley and M. W. Nirenberg 'for their interpretation of the genetic code and its function in protein synthesis' . kicksorter a multichannel pulse-height analyser, especially one used to distinguish between radioisotopes by sorting them according to the energies (i.e. 'kicks') of their emitted radiations. kidney either of a pair of organs of vertebrates concerned with osmoregulation and the elimination of nitrogenous waste products. Kidneys of different species vary in structure according to the animal's mode of life, but their basic design and function is the same. Each kidney is enclosed in a capsule and is made up of an outer cortex and an inner medulla, and contains numerous nephrons and their associated blood supply. The nephrons filter constituents from the blood to form urine, which is discharged from the kidney via the ureter. kieselguhr an alternative name for diatomaceous earth. killed vaccine any suspension of killed (or otherwise inactivated) microorganisms or virus used as an antigen to produce immunity. killer cell any cell that is cytotoxic to in vitro cell cultures, e.g. killer T-lymphocytes and macrophages. Antibody-dependent cell-mediated cytotoxicity may be displayed by a number of cell types, e.g. by human monocytes or interferon-activated neutrophils, which can kill antibody-coated tumour cells, and by NK cells, which kill hybridoma cells through the NK cell FcyRII receptor. See also Kcell. killer-cell helper factor abbr.: KHF; an alternative name for interleukin 2. killer factor an RNA molecule responsible for the lethal property of killer strains of yeast. killer strain any strain of cells that is able to kill sensitive cells of the same species, e.g. some strains of yeast and Paramecium. See also kappa particle, killer factor. killer T-Iymphocyte any T lymphocyte that is able to kill target cells. Killer T-lymphocytes are produced in response to viral infection or an allogeneic tissue graft, and are specifically cytotoxic to host cells infected with virus or to grafted cells carrying the major histocompatibility antigens of the donor, respectively. kilo+ symbol: k; an SI prefix denoting 10 3 times. kilobase symbol: kb; a unit of length of a polynucleotide equal either to 1000 base residues in a single-stranded polynucleotide or to 1000 base pairs in a double-stranded polynucleotide.

kinetic proofreading kilocalorie or kilogram calorie or (esp. in nutrition) Calorie a non-SI unit of heat or energy equal to 10 3 caln. See calorie. kilodalton symbol: kDa; a unit of molecular mass equal to 10 3 daltons. kilogram symbol: kg; the SI base unit of mass, and also the

fundamental unit of mass in the metric system; it is equal to the mass of the international prototype of the kilogram. kilogram calorie an alternative name for kilocalorie. kinase any phosphotransferase enzyme that transfers a phos" phate group, usually from ATP. Kinases are divided into EC sub-subclasses according to the nature of the phosphate-accepting group: EC 2.7.1 - phosphotransferases with an alcohol group as acceptor; EC 2.7.2 - phosphotransferases with a carboxyl group as acceptor; EC 2.7.3 - phosphotransferases with a nitrogenous group as acceptor; EC 2.7.4 - phospho transferases with a phosphate group as acceptor. The name is also used for enzymes that transfer a phosphate group from other nucleoside triphosphates. Compare dikinase, pyrophosphokinase, thiokinase. +kinase suffix (in the trivial name of an enzyme) 1 designating a kinase or, by extension in certain instances, one that transfers some other inorganic oxo-acid group, e.g. sulfokinase. 2 designating an enzyme that activates a zymogen by proteolysis, e.g. enterokinase, streptokinase, thrombokinase. kinasing a jargon term for the act or process of labelling the 5'

end of a nucleic-acid molecule or fragment with phosphorus32 by reaction with adenosine 5'-[a- 32 Pjtriphosphate and the enzyme T4 polynucleotide kinase. This is a step in the chemical cleavage method for sequencing DNA and RNA. kinematic viscosity symbol: f/', the dynamic viscosity, 'l, of a fluid divided by its density, p, i.e. P = 'lIp. kinesin microtubular motor protein, composed of two heavy chains and several light chains, that uses the energy of ATP hydrolysis (ATPase activity in the head of the heavy chain) to move along micro tubules, mostly to the plus end but in some cases to the minus end (e.g. in Drosophila). Kinesins are involved in organelle transport, and in mitosis and meiosis. Example, kinesin heavy chain from human: database code KINH_HUMAN, 963 amino acids (109.56 kDa). See also dynein. kinetensin or neurotensin-related peptide (abbr.: NRP) the

nonapeptide I1e-Ala-Arg-Arg-His-Pro-Tyr-Phe-Leu; it has neurotensin-like immunoreactivity and is isolated from human, bovine, and canine plasma. kinetic 1 of or relating to the motions of material bodies and the forces and energies associated therewith; of or relating to motion. 2 of or relating to the rate(s) of change of physical or chemical systems. 3 of or relating to kinetics. kinetic energy symbol: E k or Tor K; the energy possessed by a material body by virtue of its motion, determined by the work necessary to bring it to rest. kinetic proofreading a suggested mechanism of twice using the same Michaelis kinetic ability of an enzyme system to distinguish between two substrates C and D. The essential features of the mechanism are contained in the following reaction scheme, shown for substrate C, but identical in form if substrate C is replaced by D.

C+E

k[

~

k_ 1

EC ----- ~ EC*

k3 ~

E + product

k 4 Jt k-4

E+ C*

~

ks

C

The second step is enzymically coupled to an energy source, typically the hydrolysis of a nucleoside triphosphate, and is strongly enough driven to be essentially irreversible. BC*, a high-energy intermediate, may either react to give free enzyme plus product or diffuse into the solution where it decomposes

359

Kjeldahl method

kinetics to free enzyme plus the nonproduct C*. which can further decompose to C. According to kinetic proofreading, the incorrect intermediate, ED*, diffuses into the solution and decomposes faster than it reacts to give the wrong product, Le. for ED* k] « L 4 , while for EC* k] > k 4. In this way, the better binding of C is used twice, once in the formation of EC and again in the binding of the intermediate EC*. If the discrimination in the formation of the initial complex is f, a second factor of f may theoretically be attained, giving a total discrimination off 2 • kinetics 1 the branch of chemistry concerned with studying rates of chemical reactions. 2 the branch of mechanics concerned with the effects of forces on the motions of material bodies. kinetin 6-furfurylaminopurine; N'-furfuryladenine; an artefactual compound formed by autoclaving DNA. It exhibits cytokinin activity in plants and was originally thought to be a naturally occurring substance. Compare Kinetin. Kinetin a proprietary name for hyaluronidase. Compare kinetin. kinetochore a specialized assembly of proteins that bind to the centromere and also attach to microtubules growing out from centrosomes during mitosis. They are involved in the separation of chromosomes into the daughter cells. They are composed of centromere-binding proteins. kinetochore microtubule see mitotic spindle, prometaphase. kinetoplast a DNA-rich organelle located within an expanded region of a mitochondrion lying close to the basal body in members of the order Kinetoplastida. The kinetoplast is self-replicating and divides before the nucleus in cell division. Kinetoplastida an order of protozoans whose members are characterized by the presence of a kinetoplast in the mitochondrion. It includes the genera Trypanosoma, Leishmania, and Crithidia. kinetosome an alternative name for basal body. King-Altman method a general method for obtaining steadystate expressions for enzymic mechanisms with n enzyme-containing intermediates EX! ... EX". First, a simple geometrical pattern describing the mechanism is drawn. Second, all possible patterns, consisting of (n - I) lines, that interconnect the possible enzyme forms are drawn; closed loops are forbidden. In general there will be m!/(n - I)!(m - n+ I)! patterns, where m is the number of interconversion steps. Third, n expressions for (d[EXd/dt[EtotD = 0 in terms of the rate constants are set out and solved by determinant methods, using the fact that

L" ([EXd/[Eto,D = I

j=1

where [E tot] is the total enzyme concentration. [After E. L. King and C. Altman, who described it in 1956.] kinin 1 or kinin-hormone any member of a varied group of linear polypeptides that constitute a class of so-called tissue or local hormones. Each is locally released from diffuse stores in the body, not having specialized glands of secretion, and is rapidly inactivated at the site of release. Among the most important are angiotensins, bradykinin, substance P, colostrokinin, urinary kinins, and secretin. 2 kinin-9 an alternative name (sometimes) for bradykinin. 3 kinin-lO an alternative name (sometimes) for kallidin (lysylbradykinin). See bradykinin. 4 an alternative name for cytokinin. kininase any enzyme concerned in the natural breakdown of a kinin (def. I). Included are kininase I (or lysine carboxypeptidase, EC 3.4.17.3), a carboxypeptidase circulating in plasma that inactivates bradykinin and possibly also kallidin, and kininase II (peptidyl-dipeptidase A, EC 3.4.15.1), also known as angiotensin-converting enzyme. kininogen any inactive precursor of a kinin (def. I). kininogenin an alternative name for kallikrein. kinked-helix model of duplex DNA a speculative model of the structure of double-stranded DNA in chromatin, proposed in 1975 by F. Crick and A. Klug to account for the high degree of folding of the DNA (to about one seventh of its length). In

this model, based on the B form of duplex DNA, all the base pairs of the double helix remain intact but a sharp turn, or kink, of 95-100° occurs every 20 base pairs along the duplex. At this point one base pair has become unstacked from an adjacent pair through change of the conformation of the deoxyfuranose ring of a nucleotide residue from one of its possible staggered conformations to another. It was suggested that a kink might render several base pairs more easily available for specific interaction with a protein, and that a similar type of folding might occur in double-stranded DNA in other situations, especially when closely associated with protein. kinomere an alternative term for centromere. Kirkwood-Riseman theory of hydrodynamic properties of complex structures a theory providing an approximate method for computing the friction of a structure made up of identical subunits. A linear or coiled polymer is approximated as a string of beads, each with identical hydrodynamic properties, while an oligomeric protein is modelled as a cluster of identical subunits each with identical hydrodynamic properties. Kirkwood theory of dielectric polarization of polar liquids an extension'ofthe Onsager theory in which the dielectric constant of the central molecule and its first shell of neighbours is considered to differ from its macroscopic value. [After John Gamble Kirkwood (1907-59).] Kirkwood theory of ion-dipole interactione a model in which the electrical contribution to the chemical potential of an ion having an arbitrary charge distribution is calculated with the aid of the Debye-Hiickel theory and in which the Born relation between the free energy of solvation of a spherical ion and the dielectric constant of the solvent is generalized to include ions of arbitrary charge distribution. Kirkwood-Westheimer theory of electrostatic effects on acid dissociation constants an extension and amplification of the Bjerrum theory of the influence of substituents on acid dissociation constants, the molecules and ions entering into ionization equilibria being treated as cavities of low dielectric constant. [After John Gamble Kirkwood (1907-59) and Frank Henry Westheimer (1912- ), US biochemist.] kirromycin or mocimycin an antibacterial antibiotic isolated from Streptomyces collin us and others. It specifically interacts with elongation factor EF-Tu (see EF- and prevents the release of EF-Tu from the bacterial ribosome after GTP hydrolysis. In the absence of ribosomes, the antibiotic induces an EF-Tudependent hydrolysis of GTP. kistrin a protein isolated from the venom of the Malayan pit viper, Agkistrodon rhodostoma. It contains the RGD sequence and binds to a platelet adhesion site. It is a potent platelet aggregation inhibitor and antagonist of a family of glycoproteins that mediate aggregation. For example, see disintegrin. KIT a family of genes encoding plasma membrane class III receptor tyrosine kinases. The viral gene, v-kit, is the oncogene of the Hardy-Zuckerman 4 strain of acutely transforming feline sarcoma virus. The product of the protooncogene c-kit has five immunoglobulin-like loops in the extracellular domain; the cytoplasmic region contains a tyrosine kinase domain with an insert region, and is myristoylated. Interaction with its ligand, steel factor (see stem cell factor), brings about dimerization, leading to enhanced autophosphorylation and binding of phosphatidylinositol 3-kinase and phospholipase Cy. Kit and its ligand are highly expressed in small-cell lung cancer and a significant proportion of testicular germ cell tumours. Example from human (precursor): database code KKIT_HUMAN, 976 amino acids (109.74 kDa). Kjeldahl. Johan Gustav Christoffer Thorsager (1849-1900), Danish brewing chemist; first director of the Carlsberg Laboratory, Copenhagen. Kjeldahl flask a small pear-shaped glass flask with a long neck, as used in the Kjeldahl method. Kjeldahl method a method for the determination of the total nitrogen in an organic compound or mixture of compounds.

n

360

Kleinschmidt technique The sample, in a Kjeldahl flask, is digested in hot, concentrated sulfuric acid in the presence of a catalyst, usually one containing mercury, copper, or selenium; the nitrogen in the sample is thereby converted to ammonium hydrogen sulfate. The ammonium formed may be estimated by neutralization and steam distillation of the resultant ammonia into a known amount of acid, the residual acid being determined by titration, or it may be estimated by nesslerization or with an ammonium electrode. Kleinschmidt technique a technique for preparing monolayers of DNA for electron microscopy in which the DNA molecules are bound to a film of denatured basic protein, e.g. cytochrome c, on the surface of an aqueous solution. The DNA molecules are consequently brought from a three-dimensional conformation to a two-dimensional one by adsorption to the protein layer. The DNA-protein complex is then transferred to a solid surface, e.g. an electron microscope grid or collodion film, dried, and contrasted with heavy metals by shadowing or staining. The tendency of ssDNA to fold back on itself with the formation of intramolecular base pairs can be overcome by using formamide (which denatures short basepaired regions) or by replacing cytoch~ome c with DNA-unwinding proteins, which have high affinity for ssDNA. The method may also be applied to RNA. [After Albrecht K. Kleinschmidt (19l6~ ), German microbiologist.] Klenow enzyme or Klenow fragment a name sometimes used for the larger (75 kDa) of the two fragments formed by the treatment of Escherichia coli DNA polymerase I with subtilisin in the presence of DNA. The Klenow enzyme retains the polymerase activity and the single-strand-specific 3'45' exonuclease activities but lacks the 5'43' exonuclease activity of DNA polymerase 1. It is useful in sequencing single-stranded DNA. [After Hans Klenow (1923~ ), Danish biochemist.] Klotz plot a name sometimes given to a plot of the reciprocal form of an equation describing ligand binding at multiple independent sites on, e.g., a macromolecule. It has the form: 1111 = (llnk)(II[A]) + lin, where 11 is the average number of ligand molecules bound per molecule of the macromolecule, n is the number of binding sites per macromolecule, [A] is the molar concentration of free ligand molecules, and k is the intrinsic association constant. If the equation correctly describes the equilibria involved, a plot of 1111 versus II[A] gives a straight line of slope (lInk) and with an intercept on the 1111 axis of lin and on the II[A] axis of -11k. [After Irving Myron Klotz (b. 1916), US biochemist.] Klug, (Sir) Aaron (1926- ), Lithuanian-born South African and subsequently British molecular biologist distinguished for his determination of the structure of transfer RNA and for his contributions to the understanding of the three-dimesional structure of complexes of proteins and nucleic acids, especially tobacco mosaic virus and the nucleosome, through his invention of the technique of image reconstruction; Nobel Laureate in Chemistry (1982) 'for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid~protein complexes'. KMEF group abbr. for keratin-myosin-epidermin-fibrinogen group; a group of proteins that have in common an a-type xray diffraction pattern. Some of these may show a ~-type pattern in some conditions. Silk fibroin, which normally occurs with a ~ structure, is often included in the KMEF group. knallgas bacteria or hydrogen bacteria any of a number of bacterial species that can obtain energy from the knallgas reaction i.e. the oxidation of dihydrogen to water by dioxygen. They include some Alcaligenes and Pseudomonas spp. and Paracoccus denitrificans. [From the German, Knallgas, an explosive mixture of hydrogen and oxygen.] knallgas reaction the energy-yielding direct oxidation of dihydrogen by dioxygen occurring in certain bacteria (see knallgas bacteria). The reaction is: 2 H 2 + 0 2 42 H 2 0 + energy.

Kossel knockout indicating an animal in which function of a gene has been deleted by genetic engineering techniques. Knoop's hypothesis the hypothesis that fatty acids are metabolically oxidized by the successive removal of two-carbon fragments as acetic acid. See also beta oxidation. [After Franz Knoop (1875-1946), German physiologist and biochemist.] Knop solution an aqueous solution containing the major inorganic constituents required for the growth of cells of higher plants, namely calcium nitrate, potassium nitrate, magnesium sulfate, potassium dihydrogen phosphate, and potassium chloride. [After J. A. 1. W. Knop (1817~1901), German chemist.] Knox plot (in high-performance liquid chromatography) a plot of relative separation efficiency versus flow rate, useful in determining the optimal conditions for a desired separation. [After John H. Knox.) Koch phenomenon a cell-mediated hypersensitivity reaction in which inflammation of guinea-pig skin, when injected with living or dead Mycobacterium tuberculosis, is very much greater in animals actively infected with the organism than in uninfected animals injected with dead organisms. [After (Heinrich Hermann) Robert Koch (l843~1910), German bacteriologist, who isolated the bacillus in 1882.] Kohler, Georges Jean Franz (1946-95), German immunologist famous for his discovery (with C. Milstein) of the technique of using cell fusion to generate a clonal cell population capable of producing unlimited quantities of a pure antibody; Nobel Laureate in Physiology or Medicine (1984) jointly with N. K. Jerne and C. Milstein 'for theories concerning the specificity in development and control of the immune system and the discovery of the principle for production of monoclonal antibodies'. kojibiose the disaccharide 2-0-a-D-glucopyranosyl-D-glucopyranose. kojic acid 5-hydroxy-2-(hydroxymethy1)-4H-pyran-4-one; a metabolite from Aspergillus oryzae and A. terreus. It can be obtained in large amounts and has some industrial application.

HO~

1l,,~oH o

Kok effect the sharp difference in. yield of photosynthesis above and below the compensation point. Below compensation, where respiration can supply intermediates at a greater rate than the rate of photosynthesis, the yield is about twice as great as above compensation, where CO 2 has presumably to be drawn into the process. [After Bessel Kok (l918~81) Dutchborn US plant physiologist.) Kornberg 1 Arthur Kornberg (1918- ), US biochemist distinguished especially for his discovery and purification of the enzyme DNA polymerase and its use to synthesize segments of DNA molecules and viral DNA; Nobel Laureate (1959) in Physiology or Medicine jointly with S. Ochoa 'for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxiribonucleic [sic) acid'. 2 Hans Leo Kornberg (1928- ) German-born British biochemist notable for his studies of intermediary metabolism in bacteria. Kornberg enzyme an alternative name for DNA polymerase 1. See DNA polymerase. [After A. Kornberg.] Korsakoff's psychosis see Wernicke--l90% a helical) and forms large ordered aggregates at low ionic strength. Light meromyosin has no ATPase activity and cannot bind actin. light path 1 the path followed by a beam of light when passing through an optical device or a particular part of one. 2 or path length the length of such a path. light pen an input/output device for use with a computer that, when pointed at a spot on a visual display unit, can sense whether or not the spot is illuminated; the output current from the light pen can then be used to control the operations of the computer. light reactions of photosynthesis or light phase of photosynthesis those reactions of photosynthesis in higher plants and algae in which light energy is used to generate NADPH and ATP. light repair an alternative name for photoreactivation. light-scattering a technique used for the determination of the relative molecular mass, M r , in solution of a macromolecule whose size is large relative to the wavelength of the light used.

limit dextrinosis The value of M r of the macromolecule can be calculated from the wavelength of the incident light, the angle and intensity of the scattered light, the refractive indices of the solvent and solute, and the concentration of the solute. See also Rayleigh scattering. light strand or L strand 1 a polynucleotide strand not labelled with heavy isotope. 2 the strand in a naturally occurring polynucleotide duplex that is of a lower density than its complementary strand. Compare heavy strand. light trapping 1 the process of capturing the energy of incident light in a photosynthetic pigment system. 2 the act or process of using focused light in a liquid medium so arranged as to trap phototactic organisms in a restricted part of that medium. Iignan any member of a class of phenylpropanoid dimers in which the phenylpropane units are linked tail-to-tail and thus having a 2,3-dibenzylbutane skeleton (compare neolignan). Until recently such compounds had been found only in higher plants, but certain types have now been identified in humans and other mammals as products of the action of gut flora on dietary lignans of plant origin. Guaiaretic acid is structurally one of the simplest; podophyllotoxin and more particularly its semisynthetic derivatives Etoposide and Teniposide have defined actions in clinical medicine, with anti tumour and possibly antiviral actions. See also lignin. lignify to make or become woody; to accumulate or deposit lignin in the cell walls (of plant tissues). -lignification n. lignin any random phenylpropanoid polymer formed in higher plants by the dehydrogenative radical polymerization of various 4-hydroxycinnamyl alcohols, in which the residues are joined in differing proportions and by several different linkages, some of which are nonhydrolysable. Lignin is of high molecular mass, is insoluble in water, and is found in the cell walls of vascular plants (especially of the supporting and conducting tissues), on which it confers strength, rigidity, and resistance to degradation. It is one of the most abundant biopolymers. See also Iignan. ligninase an enzyme that catalyses breakdown of lignin; strictly most lignin-degrading systems rely on peroxide formed from oxygenases to cleave carbon-carbon bonds. An example is diarylpropane peroxidase, EC 1.11.1.14; systematic name: diarylpropane:oxygen,hydrogen peroxide oxidoreductase (C-Cbond-cleaving); other name: ligninase 1. It is a hemoprotein enzyme that catalyses a reaction between 1,2-bis(3,4dimethoxyphenyl)propane-l,3-diol and H 20 2 to form 3,4dimethoxybenzaldehyde, 1-(3 ,4-dimethylphenyl)ethane-l ,2diol, and 4H 20. Example from Phanerochaete chrysosporium: database code LIG2_PHACH, 371 amino acids (39.33 kDa). lignocellulose a covalent adduct of lignin and cellulose, found in the walls of xylem cells in woody tissues of plants. -lignocellulosic adj., n. Iignocerate 1 the trivial name for tetracosanoate, CH3-[CH2hrCOO-, the anion derived from lignoceric acid (i.e. tetracosanoic acid), a saturated straight-chain higher fatty acid. 2 any mixture of lignoceric acid and its anion. 3 any salt or ester of lignoceric acid. lignoceroyl symbol: Lig; the trivial name for tetracosanoyl, CH 3-[CH 2ln-CO-, the acyl group derived from lignoceric acid (i.e. tetracosanoic acid). It occurs naturally as acylglycerols in peanut and rapeseed oils, and in certain sphingomyelins. lignoceroyl-CoA synthase see long-chain-fatty-acid-CoA ligase. limit (in mathematics) a value to which a function or the sum of a series approaches as an independent variable approaches a specified value or infinity. limit dextrin the highly branched core that remains after exhaustive treatment of amylopectin or glycogen with a- and/or ,B-amylases. It is formed because these enzymes cannot hydrolyse the (I ~6) glycosidic linkages present. limit dextrinase see a-dextrin endo-1,6-a-glucosidase, oligo-1,6glucosidase. limit dextrinosis an alternative name for type III glycogen disease.

377

limit digest

line immunoelectrophoresi!5

limit digest a digest in which no further degradation can occur under the particular conditions adopted. limiting current (in polarography) the maximal value of the current reached in circumstances when the steady-state current/potential characteristic has a positive slope. limiting rate symbol: V; the recommended name for the extrapolated rate of an enzyme-catalysed reaction when the enzyme is saturated with substrate(s). It is equal to the product of the stoichiometric concentration of active centres, [El o, and the catalytic constant, k o. It can be determined by a number of methods, including graphical methods such as the Lineweaver-Burk plot. Other names: maximum rate; maximal rate; maximum velocity; maximal velocity. limiting viscosity number the recommended name for intrinsic viscosity. Iimonene p-mentha-I,8-diene; a compound that occurs in many essential oils (e.g. oils of lemon, orange, and dill); both enantiomers and the racemic mixture (i.e. dipentene) occur naturally.

(RH+) form

L1MS abbr. for laboratory information management systems; normally, systems involving automatic electronic data capture and computerized manipulation of data. Lin symbol for the linoleoyl group, CH 3-[CH zh-[CH zCH=CHlr [CHzh-CO- (all-Z isomer). lin3 a gene in Caenorhabditis elegans that encodes an epidermal growth factor-like type I membrane protein. The protein has two versions (produced by alternative splicing), and is essential for vulval development. Database code LIN3_CAEEL, 438 amino acids (48.87 kDa). See also let23. lin 14 a gene involved in embryonic development in Caenorhabditis elegans that codes for a nuclear protein. Regulatory sequences in the 3' untranslated region generate a temporal switch during development. There are three forms of the product: A, database code B40581, 537 amino acids (59.09 kDa); BI, database code A40581, 539 amino acids (59.28 kDa); B2, database code C40581, 515 amino acids (56.65 kDa). Iinalool 3,7-dimethyl-I,6-octadien-3-01; a compound that occurs in linaloe oil and other essential oils; both enantiomers occur naturally. It is used in perfumery. lincomycin an antibiotic produced by Streptomyces lincolnensis. It consists of an amide formed between a substituted pyrrolidine-2-carboxylic acid and methyl I-thio-a-lincosamine. Lincomycin is active mainly against Gram-positive bacteria; it inhibits protein synthesis by interacting with the 50S ribosomal subunit, inhibiting the early steps of peptide bond formation prior to the formation of polysomes.

Iincosamides generic name for a group of antibiotics structurally related to lincomycin. Iincosamine 6-amino-6,8-dideoxY-D-erythro-D-galacto-octose; the carbohydrate component of lincomycin.

CH 3 I HQ-C-H I

H~~O~

~-VH OH

line I (in spectroscopy) a very narrow band of frequencies of electromagnetic radiation that is noticeably more intense or less intense than adjacent parts of the spectrum; the image of such a line in a spectrogram. 2 (in biology) several generations of a family. See also cell line, lineage. -lineal or linear adj. LINE abbr. for long interspersed nucleotide element (or sequence or repeat); part of the moderately repetitive DNA of mammalian genomes. Any highly repeated DNA sequence interspersed in a mammalian genome and characteristically several kilobases in length. LINEs are retroposons resulting from the action of RNA polymerase II (see RNA polymerase). Mammalian genomes may contain up to 50 000 copies of particular LINEs. They are regarded as processed pseudogenes. The function of LINEs is unknown. Compare SINE. See also Alu sequence. lineage lineal descent, especially from a common ancestor. linear accelerator a device for producing high-energy particles, in which charged particles are accelerated in a straight line along a long evacuated tube by potential differences applied to a series of circular electrodes along the tube. linear chain a chain of atoms in a molecule, or a chain of residues in a macromolecule, that is neither branched nor covalently closed. linear correlation any relationship between two variables such that a graphical plot of one variable against the other is a straight line. linear density gradient a gradient of linearly and continuously increasing density. linear dichroism the dichroism (def. I) occurring when linearly polarized light is absorbed by a sample containing partially or completely oriented anisotropic molecules. linear equation any equation containing any number of variables that is of the first degree, i.e. one in which the variables are all raised to the power of one. linear growth the growth of a culture such that the number of cells (or the cell mass) increases in direct proportion to the duration of growth. linearity the condition of being in a straight line. linearize or linearise I to make linear, i.e. into a straight line. 2 to convert a branched or cyclic form of a (macro)molecule to a linear form, i.e. one with only two ends. -linearization or !inearisation n. linearly polarized or plane-polarized describing light (or other electromagnetic radiation) in which the electric vectors of the vibrations all lie in a given plane containing the light beam. See polarized light. linear velocity the distance moved in a straight line in unit time. line formula a two-dimensional representation of a molecular entity in which atomic symbols are joined by lines representing single bonds, without any indication or implication of stereochemistry. line immunoelectrophoresis a one-dimensional single electroimmunodiffusion technique, useful for the qualitative and

line spectrum

378

quantitative comparison of the antibody spectra of different polyvalent antisera. Samples of antigens to be compared are moulded into adjoining rectangular sample gels along one edge of a gel containing a mixture of the corresponding antibodies, into which the antigens are forced at right angles by electrophoresis. Precipitation lines form parallel to the origin at a distance of antigen migration proportional to the antigen/antibody ratio. Precipitation lines from the samples against the same antibody are continuous and can be directly compared. line spectrum any spectrum consisting of discrete spectral lines. Lineweaver-Burk plot a method of plotting enzyme kinetic data. The Michaelis equation is rearranged to give: 1/v = Km/V[S] + 1/V, where K m is the Michaelis constant, [S] the concentration of the substrate S, v the (initial) rate of reaction at a given value of [S], and V the limiting rate of reaction at infinite [S]. If the Michaelis equation holds for the system, a plot of 1/v against 1/[S] gives a straight line of slope Km/V, with intercepts on the 1/v axis at 1/Vand on the 1/[S] axis at -1/Km. See Michaelis kinetics. [After Hans Lineweaver and Dean Burk.] Iinewidth the width of a spectral line, usually taken as the distance, in terms of wavelength, frequency, or magnetic flux difference, between the two points of half-peak intensity (half-maximum height). link (in chemistry) an informal term for bond (def. 1). See also linkage (def. 2). linkage 1 (in genetics) an association of two or more nonallelic genes so that they do not show independent assortment; i.e. they tend to be transmitted together usually due to physical association on the same chromosome. 2 (in chemistry) an informal term for bond (def. 1). See also link. linkage disequilibrium the preferential association of linked genes/DNA markers in a population; i.e. the tendency for some alleles at a locus to be associated with certain alleles at another locus on the same chromosome with frequencies greater than would be expected by chance alone. linkage group any group of genes whose members show a marked tendency to segregate as a unit. See also genophore. linkage map a map of a chromosome showing in linear order the relative positions of the known genes on that chromosome. linked genes genes that exhibit linkage (def. I). linker 1 any small synthetic single-chain oligodeoxynucleotide that is six or more residues long and has a self-complementary base sequence. When self-annealed it forms a stable duplex with blunt ends and containing a restriction site. Such linkers are useful for gene splicing. 2 see cross-link. linker DNA see chromatin, nucleosome linking number symbol: L; a topological property of closed circular duplex DNA, defined as the number of turns one strand makes about the other. It must be an integer, and is positive if the turns are right-handed and negative if they are left-handed. It can change only when one or both strands are nicked. It comprises the sum of the writhing number (W) and the twist number (T), so that a change (,iL) in the linking number (L) is equal to,iW + ,iT. Iinoleate 1 the trivial name for (all-Z)-octadeca-9,12-dienoate, CHdCHzh-[CHz-CH=CHh-[CHzh-COO-, (all-Z isomer) the anion derived from linoleic acid, (all-Z)-octadeca-9,12dienoic acid, a diunsaturated straight-chain higher fatty acid essential in the diet of mammals. It occurs naturally as acylglycerols in many vegetable oils and in the lipids of many animal tissues. 2 any mixture of free linoleic acid and its anion. 3 any salt or ester of linoleic acid. See also linoleic family. linoleate synthase see phosphatidylcholine desaturase. linoleic family (of polyunsaturated fatty acids) a series of polyenoic acids occurring in mammals, in which the hydrocarbon chain terminates with the alkenyl grouping, CH3-[CH2]4-CH=CH- (as in linoleic acid; see linoleate) and

Iinoleoyl

that are synthesized from linoleic acid by chain elongation and/or further desaturation (but which in mammals cannot be synthesized from the corresponding saturated acids or from (9,12,15)-linolenic, oleic, or palmitoleic acids - the latter represent three other series of polyenoic acids). The linoleic family is also known as the w6, or n-6, family because of the position of the double bond nearest the terminal methyl group. The series includes (6,9,12)-linolenic acid, eicosa11,14-dienoic acid, eicosa-5, II, 14-trienoic acid, eicosa8,11,14-trienoic acid, and arachidonic acid. Iinolenate 1 or (9,12,15)-linolenate or (formerly) a-linolenate the alternative trivial names for (all-Z)-octadeca-9, 12, 15trienoate; CHdCH 2-CH=CHh-[CH zh-COO- (all-Z isomer); the anion derived from (9,12, 15)-linolenic acid, (all-Z)octadeca-9, 12, 15-trienoic acid, a triunsaturated straight-chain higher fatty acid synthesized by plants (notably found in linseed oil) but essential in the diet of mammals (see linolenic family). The name equally refers to any mixture of (all-Z)octadeca-9,12,15-trienoic acid and its anion, or any salt or ester of this acid. 2 (6,9,12)-linolenate or (formerly) y-linolenate the trivial name for (all-Z)-octadeca-6,9,12-trienoate; CHdCH zb-[CH 2-CH=CHh-[CH 2]cCOO- (all-Z isomer), the anion derived from (6,9,12)-linolenic acid (all-Z)-octadeca6,9,12-trienoic acid, a triunsaturated straight-chain higher fatty acid belonging to the linoleic family. It occurs naturally as acylglycerols in certain plant-seed oils, especially that of the evening primrose (Oenothera spp.), and also in small amounts in the lipids of many animal tissues, especially human breast milk. It is the biosynthetic precursor of arachidonate and the prostaglandins. The name refers equally to any mixture of (allZ)-octadeca-6,9,12-trienoic acid and its anion or any salt or ester of the acid. linolenic family (of polyunsaturated fatty acids) a series of polyenoic acids occurring in mammals, in which the hydrocarbon chain terminates with the alkenyl grouping CH 3-CH 2CH=CH- (as in (9,12,15)-linolenic acid; see Iinolenate). The linolenic family is also known as the w3 or n-3 family because of the position of the terminal double bond three carbon atoms from the methyl end. The longer-chain members of the family can be synthesized in mammals only from dietary (9, 12, 15)-linolenic acid by chain elongation and/or further desaturation (but not from the corresponding saturated acids or from linoleic, oleic, or palmitoleic acids - the latter represent the other three series of polyenoic acids). If animals are deprived of a source of these fatty acids in the diet, certain tissues, such as the eye, retain existing stores of these fatty acids tenaciously, even in offspring of such animals when the restricted diet is continued for more than one generation. Under these conditions, long-chain acids of the linoleic family, e.g. (4,7,IO,13,16,)-docosapentaenoic (C22:5 n-6) acid, are synthesized in appreciable amounts and presumably partially support the function supplied by long-chain w3 acids, though the nature of this is unknown. The series includes eicosapentaenoic (C20:5 w3) and docosahexaenoic (C22:6 w3) acids, which are found in high concentration in fish oils; these w3 acids may have value in protecting against heart disease, a role that, if real, would be unrelated to their function as essential fatty acids, since the amount considered necessary for this purpose greatly exceed those needed to fulfil their role as essential fatty acids. linolenoyl 1 or (9,12,15)-linolenoyl or (formerly) a-linolenoyl symbol: aLnn or (sometimes) Lnn; the alternative trivial names for (all-Z)-octadeca-9, 12, 15-trienoyl; CH3-[CHz-CH=CHh[CH 2h-CO- (all-Z isomer); the acyl group derived from (allZ)-octadeca-9, 12, 15-trienoic acid. 2 (6,9,12)-linolenoyl or (formerly) y-linolenoyl symbol: yLnn; the trivial names for (allZ)-octadeca-6,9,12-trienoyl; CH r [CH 2h-[CH z-CH=CHh[CHZ]4-CO- (all-Z isomer); the acyl group derived from (all-Z)-octadeca-6,9, 12-trienoic acid. See Iinolenate. Iinoleoyl symbol: Lin; the trivial name for (all-Z)-octadeca9,12-dienoyl; CHdCHzh-[CHz-CH=CHh-[CH2h-CO- (all-Z isomer); the acyl group derived from linoleic acid. See linoleate.

379 Iiothyronine Iiothyronine a pharmaceutical name for L-3,5,3'triiodothyronine. Iip+ a variant form oj'lipo+ (before a vowel). lipaemia a variant spelling (esp. Brit.) of lipemia. lipase 1 (in enzyme nomenclature) a general term for any acylglycerol carboxylic ester hydrolase, of EC sub-subclass 3.1.1. The term may be incorporated in the enzyme name as the suffix '+lipase'. 2 abbr. (in clinical chemistry): LPS; an alternative name for triacylglycerol lipase. See also hormone-sensitive lipase, lipoprotein lipase, pancreatic lipase. lipemia or lipidemia the condition when there is a greater than normal content of lipid in the blood, e.g. after a fatty meal or in certain pathological states. Also (esp. Brit.) lipaemia, lipidaemia. lipid or (formerly) lipide or lipoid or lipin(e) 1 any member of a large and diverse group of oils, fats, and fatlike substances that occur in living organisms and that characteristically are soluble in lipid solvents but only sparingly soluble in aqueous solvents. Lipids constitute one of the four major classes of compounds found in living tissues (the others being carbohydrates, proteins, and nucleic acids) and they include: (I) fatty acids; (2) neutral fats (i.e. triacylglycerols), other fattyacid esters, and soaps; (3) long-chain (or fatty) alcohols and waxes; (4) sphingoids and other long-chain bases; (5) glycolipids, phospholipids, and sphingolipids; and (6) carotenes, polyprenols, sterols (and related compounds), terpenes, and other isoprenoids. See individual entries for details. 2 any oily, fatty, or fatlike material that occurs in living organisms. 3 of, concerned with, for, or relating to lipid (def. 2); consisting of or containing lipid (def. 1,2); lipoid (def. I) or lipoidal. -lipidic adj. lipid A the glycolipid moiety of bacterial lipopolysaccharide. Iipidaemia a variant spelling (esp. Brit.) of lipidemia; see lipemia. lipid bilayer any layer, two molecules thick, of amphipathic lipid molecules. If it is surrounded by a polar environment, the polar parts of the lipid molecules are oriented outwards towards the environment and the nonpolar parts inwards into the interior of the bilayer. The two layers of lipid are referred to as leaflets, e.g. the inner and outer leaflets of the bilayer. See also black lipid membrane. lipide a variant spelling of lipid. Iipidemia an alternative term for lipemia. lipidosis or lipoidosis (pl. lipidoses or lipoidoses) any clinical disorder, also called lipid storage disease, that results in the excessive deposition within specific tissues of particular types of lipids. Many lipidoses are inherited disorders of galactosphingolipid metabolism. lipid-soluble a vague term applied to various classes of nonpolar substances, e.g. sterols, certain vitamins, carotenoids, and polyprenoids, that are commonly present in small amounts in association with the major lipid. lipid solvent any relatively nonpolar solvent that can be used to extract lipids from tissues or other materials. lipid storage disease an alternative term for lipidosis. Iipin or lipine a former term for lipid (def. I), especially one containing nitrogen andlor phosphorus. Lipmann, Fritz Albert (1899-1986), German-born US biochemist; Nobel Laureate in Physiology or Medicine (1953) 'for his discovery of co-enzyme A and its importance for intermediary metabolism' [prize shared with H. A. Krebs]. Iipo+ or (before a vowel) lip+ comb. form denoting lipid, lipidcontaining, or lipid-like. Iipoamide or (sometimes) lipoyllysine a Iipoyl group when in amide linkage to the e-amino group of a specific lysine residue in dihydrolipoamide acetyltransferase (EC 2.3.1.12) and dihydrolipoamide succinyl transferase (EC 2.3.1.61), which form, respectively, parts of the pyruvate dehydrogenase complex and the 2-oxoglutarate dehydrogenase complex. Iipoamide reductase (NADH) EC I. 8.1.4; recommended name: dihydrolipoamide dehydrogenase; other names: E3 com-

lipophilic ponent of a-ketoacid dehydrogenase complexes; lipoyl dehydrogenase; dihydrolipoyl dehydrogenase; diaphorase. An enzyme that catalyses the oxidation by NAD+ of dihydrolipoamide to form lipoamide and NADH. FAD is a coenzyme. It is typically a homodimer, occurring in the mitochondrial matrix (in eukaryotes), with a redox-active S-S bond similar to glutathione reductase. Example (precursor) from yeast (the first 21 amino acids form the mitochondrial transit peptide): database code DLDH_YEAST, 499 amino acids (53.95 kDa). Iipoate 1 1,2-dithiolane-3-pentanoate, the anion derived from lipoic acid (i.e. thioctic acid). 2 any salt or ester of lipoic acid. lipocaic a substance extractable from the pancreas that was said to be lipotropic in pancreatectomized animals. Iipocalin any of a large group of ligand-binding proteins, particularly one that binds hydrophobic ligands, e.g. biliverdin pheromone. The family includes retinol-binding protein, crmicroglobulin, insect bilin-binding proteins, and beta lactoglobulin. The name derives from the fact that the ligand is enclosed by the protein as a flower is enclosed by the calyx (i.e. the sepals). All members of the family have a similar ~­ barrel structure of eight barrels crossing in the centre; different ligand-binding properties are determined by loops on the periphery. See also Appendix E. lipochrome a former name for any of various lipid-soluble biological pigments. Iipocortin see annexin. Iipofection a lipid-mediated DNA-transfection technique that makes use of unilamellar liposomes that contain a cationic lipid and spontaneously react with DNA. lipofuscin any of various brownish lipid-soluble pigments that are deposited in animal cells, especially in senility. lipogenesis the formation of fat. The term is applied especially to the processes by which higher fatty acids are synthesized from nonlipid sources. -lipogenic adj. lipogenic amino acid any amino acid that can provide carbon atoms for the biosynthesis of higher fatty acids. lipoic acid or a-lipoic acid symbol: Lip(Sz); 1,2-dithiolane-3pentanoic acid; thioctic acid; the naturally occurring form is the (R)-( +)-enantiomer. Lipoic acid provides the reversibly reducible moiety, Iipoyl, of Iipoamide and is a growth factor for certain microorganisms. The reduced form is dihydrolipoic HS-CHz-CHz-CH(SH)-[CHz14-COOH (symbol: acid, Lip(SH}z); the redox potential of the system is -0.29 V at pH7. Lipoic acid is an essential component of the u-ketoacid dehydrogenase complexes. See pyruvate dehydrogenase complex and 2-oxoglutarate dehydrogenase complex.

lipoid 1 or lipoidal being or resembling an oil or a fat; oily, fatty. 2 aformer term for lipid (def. 1,2). lipolysis the breakdown of lipids, especially the (enzymic) hydrolysis of acylglycerols. -lipolytic adj. lipolytic hormone an alternative name for Iipotropin. Iipomodulin or annexin 1 a 40 kDa regulatory protein isolated from rabbit neutrophils that, in its nonphosphorylated form, is an inhibitor of phospholipase A z and that on phosphorylation by a cyclic-AMP-dependent protein kinase loses this inhibitory property. It has been suggested that lipomodulin thereby regulates the release of arachidonate from leukoytes, or other cells, that may occur in response to chemoattractants and other external stimuli. lipophilic tending to dissolve in, having a strong affinity for, or readily mixing with lipids or substances of low polarity. See also hydrophilic, lyophilic. -lipophilicity n.

lipophilin Iipophilin another name for myelinproteolipid. See myelin protein. Iipophorin any member of the major class of lipid-transporting proteins found in the hemolymph of insects. In locusts the apoprotein is synthesized in the fat body as an 85 kDa polypeptide. See also apolipophorin. Iipophosphoglycans see GPI anchor. lipopolysaccharide abbr.: LPS; any of a group of related, 10 kDa, structurally complex components of the outer leaflet of the outer membrane of Gram-negative bacteria. Lipopolysaccharide molecules consist of three covalently linked regions: lipid A, core oligosaccharide, and an 0 side chain. The innermost layer, lipid A, which is responsible for the toxicity of the lipopolysaccharide, consists of six fatty acyl chains (sometimes hydroxylated) linked in various ways to two glucosamine residues. The branched core oligosaccharide contains ten saccharide residues, several of them unusual, and has a structure that appears to be similar in closely related bacterial strains. The outermost 0 side chain, which is highly variable and determines the antigenic specificity of the organism, is made up of many (~50) repeating units of a branched tetrasaccharide containing further unusual sugar residues. lipopolysaccharide N-acetylglucosaminyltransferase EC 2.4.1.56; an enzyme of the lipopolysaccharide core biosynthetic pathway in enteric bacteria; it catalyses a reaction between UDP-N-acetyl-D-glucosamine and lipopolysaccharide to form UDP and N-acetyl-D-glucosaminyl1ipopolysaccharide. Example from Salmonella typhimurium: database code RFAK_ SALTY, 381 amino acids (43.10 kDa). There is little similarity between the given example and the corresponding enzyme in Escherichia coli. See also glycolipid. lipoprotein any conjugated, water-soluble protein in which the nonprotein moiety consists of a lipid or lipids. The lipid may be triacylglycerol, cholesterol, or phospholipid, or a combination of these. Compare proteolipid. Iipoprotein(a) one or two molecules of apolipoprotein(a) linked by a disulfide bridge to apolipoprotein B-IOO; it may be a physiological inhibitor of plasminogen activation. Levels in hum.an plasma (which range from undetectable to 100 mg dL-3) show correlation with the incidence of atherosclerosis. lipoprotein lipase EC 3.1.1.34; abbr.: LPL; other names: clearing factor lipase; diglyceride lipase; diacylglycerol lipase. An enzyme that catalyses the hydrolysis of triacylglycerol to diacylglycerol and fatty-acid anion. Its function, after uptake of dietary lipid, is to hydrolyse triacylglycerols in chylomicrons and very-low-density lipoproteins, to diacylglycerols and fatty-acid anions; the fatty acids are then taken into peripheral tissues for futher metabolism; it wil1 also hydrolyse diacylglycerols. It acts in the presence of apolipoprotein CoIl on the luminal surface of vascular endothelium. It is a GPI-anchor dimer, and is released by heparin, etc. Example (precursor) human: database code LIPL_HUMAN, 475 amino acids (53.10 kDa). lipoprotein signal peptidase see premurein-Ieader peptidase. Iiposome 1 a natural lipid globule suspended in the cytoplasm of some cel1s. 2 any smal1, roughly spherical, artificial vesicle consisting of a continuous bilayer or multi bilayer of complex lipids enclosing some of the suspending medium. Liposomes are formed by al10wing complex lipids to 'swel1' in aqueous solution sometimes with the aid of sonication. They are used experimental1y as models of biological membranes and therapeutical1y for entrapment of drugs, enzymes, or other agents with a view to their more effective delivery to target cells. Original1y, such a structure was termed a cellule (when bilayered), smectic mesophase, spherule, or spherulite. See also liquid crystal. Iipotaurine the 7,13-dihydroxy-2-trans-octadecenoyl amide of taurine. It is found in the lipid fraction of Tetrahymena thermophila. Iipoteichoic acid any of a group of teichoic acids that contain lipid, are present in the membranes of al1 species of Gram-positive bacteria so far examined, and, unlike wall teichoic acids, are extractable with hot water or phenol.

380

Iipoxygenase

lipotropic or lipotrophic tending to prevent the accumulation of, or to remove, abnormal amounts of lipid (in a tissue or organ, e.g. adipose tissue, liver). lipotropic agent or lipotropic substance any substance capable of preventing or correcting fatty infiltration of the liver caused by choline deficiency. lipotropic hormone or lipotrophic hormone a former name for Iipotropin. Iipotropin or lipotropic hormone (abbr.: LPH) either of two polypeptides, p- and y-lipotropin, that can be isolated from the anterior and intermediary lobes of mammalian pituitary glands and are characterized by their ability to elicit lipolysis in adipose tissue. p-Lipotropin corresponds in sequence to the 91 C-terminal amino-acid residues of proopiomelanocortin, and y-lipotropin corresponds to the 58 N-terminal residues of Plipotropin. In fact, they are of no greater lipotropic potency than corticotropin and a-melanotropin, and whether they have any intrinsic physiological function is still uncertain. Both P- and y-lipotropins are found in normal human blood. Other names: lipolytic hormone; adipokinetic hormone; former names: lipotrophin; lipotrophic hormone. lipotropism the state or quality of being lipotropic. Iipovitellin a ~135 kDa phospholipoprotein that, together with phosvitin, constitutes the bulk of the yolk proteins of the eggs of oviparous vertebrates. These two proteins are synthesized and secreted by the liver as a single large molecule, vitellogenin, which is taken up by the ovary and split into the two components. lipoxin abbr.: LX; any of a group of eicosanoids containing a conjugated tetraene structure and having three hydroxyl groups. They are generated by the action of Iipoxygenase enzymes on polyunsaturated fatty acids (arachidonate and eicosapentaenoate). The major lipoxins, A4 and B4 , are derived from arachidonate; lipoxin A 4 (LXA 4 ) is (7 E,9E, liZ, 13E)(5S,6R, 15S)-5,6, 15-trihydroxy-eicosa-7,9, II, 13-tetraen-I-oate; lipoxin B4 (LXB 4) is (6E,8Z,IOE,12E)-(5S,14R,15S)-5,14,15trihydroxy-eicosa-6,8, I0, 12-tetraen-I-oate. LXA4 has been found to cause contraction of guinea-pig lung strips, but not ileum; LXA 4 and LXB 4 cause dilatation of arterioles.

OH eOOH

OH Iipoxin A 4

OH lipoxin B.

Iipoxygenase 1 EC 1.13.11.12; systematic name: linoleate:oxygen 13-oxidoreductase; other names: lipoxidase; carotene oxidase. An enzyme that catalyses the oxidation by dioxygen of linoleate to (9Z,IIE)-(l3S)-13-hydroperoxyoctadeca-9, II-dienoate (abbr.: 13(S)-HpODE); iron is a cofactor. 2 any member of a group of dioxygenase enzymes that catalyse the oxidation of polyunsaturated fatty acids to a particular corresponding hydroperoxide. Such enzymes are

381

lipoyl widely distributed in plants and in animals from invertebrates to humans. They are found variously in leukocytes, mast cells, platelets, and lung, their positional specificities varying from tissue to tissue; notably a l2-lipoxygenase predominates in platelets, and a 5-lipoxygenase in neutrophils. They are important in the conversion of arachidonate to 5- and 12-hydroperoxyeicosatetraenoates (the 5-hydroperoxy compound being the biosynthetic precursor of the leukotrienes). Lipoxygenase activity has also been observed upon a variety of polyunsaturated fatty acids, indicating that such enzymes exist in a wide variety of forms. The configuration at the oxidized carbon is most often S, but R products are known, e.g. of sea urchin egg lipoxygenase. Of the three main lipoxygenase activities, the function of 12-lipoxygenase (ECI.13.11.31) remains to be clarified; 5-lipoxygenase (EC 1.13.11.34) is important in yielding precursors for leukotriene biosynthesis; 15-lipoxygenase (EC 1.13.11.33) yields precursors for the Iipoxins. All three, however, are involved in the synthesis of hydroperoxy- and dihydroxy-eicosatetraenoates. Compounds that inhibit both lipoxygenase and prostaglandin-endoperoxide synthase include curcumin, eicosatetraynoic acid, and phenidone (l-phenyl3-pyrazolidinone). Compounds that selectively inhibit lipoxygenases without inhibiting prostaglandin-endoperoxide synthase include eicosatriynoic acid and esculetin. See also dihydroxyeicosatetraenoate. hydroperoxyeicosatetraenoate, hydroperoxyoctadecadienoate, hydroxyeicosatetraenoate. Iipoyl the acyl group, 1,2-dithiolane-3-pentanoyl, derived from lipoic acid. It provides the reversibly reducible moiety of lipoamide. Iipoyllysine an alternative name for lipoamide. Lip(Sz) symbol for a residue of (the oxidized form of) lipoic acid. Lip(SH)z symbol for a residue of dihydrolipoic acid, the reduced form of lipoic acid. Iipstatin an irreversible inhibitor of several lipases, e.g. pancreatic, gastric, carboxyl ester, or bile-stimulated lipase of milk, isolated from Streptomyces toxytricini. It blocks fat absorption selectively. lipuria the presence of lipid or oily droplets in the urine. liquefy or liquify to become, or cause to become, liquid. -liquefaction or Iiquifaction n. liquid 1 a state of matter, intermediate between a solid and a gas, in which the molecules are relatively free to move with respect to each other but are restricted by intermolecular forces strong enough to prevent spontaneous expansion or significant compression. 2 any substance that is liquid at normal room temperature and pressure. 3 of, pertaining to, being, or behaving as a liquid. Compare fluid. liquid air a pale-blue liquid containing principally liquid nitrogen and liquid oxygen, b.p. -194.35 °C (78.80 K), obtained by compressing and cooling gaseous air. It is used as a refrigerant and in the preparation of nitrogen and oxygen. liquid chromatography abbr.: LC; any form of chromatography in which a liquid is used as the mobile phase. liquid crystal or mesomorphic state or mesophase any new phase, resembling both liquid and solid phases, that appears when certain pure liquids are cooled, or pure solids are heated. These new phases have a translucent or cloudy appearance. In liquids of asymmetric molecules the molecular axes are arranged at random. In liquid crystals, however, there is some alignment, which occurs in three main distinguishable modes (certain such mesomorphic substances displaying more than one). In nematic liquid crystals the long axes of the molecules are aligned parallel to each other but the molecules are not arranged in layers. These scatter light strongly and appear translucent. In cholesteric liquid crystals the molecular axes are aligned and the molecules are arranged in layers but the orientation of the axes changes in a regular way on going from one layer to the next. Because the distance between any two layers with the same molecular orientation is of the order of the wavelength of visible light such crystals display vivid iridescence. Smectic liquid crystals are formed by certain mol-

liquor ecu1es that have chemically dissimilar parts, e.g. polar and nonpolar; the chemically similar parts attract one another and the molecules form layers and align themselves in one direction. See also liquid-crystalline phase. liquid-crystal display abbr.: LCD; any display of characters or numbers in a calculator, clock, or other device, based on liquid crystal cells whose reflectivity is changed by application of an electric field liquid-crystalline phase any of several types of phase adopted by polar lipids at moderately elevated temperatures. Two major types exist, the lamellar and hexagonal phases. In the lamellar phase, also known as the La phase, the lipids form sheets of bilayers with the polar groups oriented outwards and the fatty-acyl moieties oriented into the hydrophobic core between the two bilayers. Such a phase is likely to include many such bilayers stacked on top of each other, with their polar groups apposed. In the hexagonal phase, the lipids form a spherical aggregate, in which the polar headgroups may be oriented either into the centre of the sphere, when this is known as the HI phase, or towards the surface of the sphere, the Hz phase. In liquid-crystalline phase, the lipid adopts a looser packing, with greater mobility of the fatty-acyl chains than in the crystalline state. At low temperatures, in the absence of water, lipids exist in a crystalline state. If the lipid is heated to a point that attains the transition temperature, a temperature characteristic of each pure compound, the lipid undergoes a transition to one of the liquid-crystalline phases. On further heating, it melts completely. Addition of water at low temperature to the crystalline state causes formation of a gel phase, with water layers between the apposed polar headgroups. This gel phase will, on heating to the transition temperature, undergo transition to a liquid-crystalline phase similar to those described above. liquid-gel chromatography a type of liquid chromatography in which the stationary phase is a gel. It includes gel-permeation chromatography and ion-exchange chromatography. liquid glucose an alternative name for corn syrup. liquid-junction potential the electric potential, not experimentally measurable, that arises across the boundary of two solutions of different compositions, e.g. between two halfcells. It is a complex function of the activities and transference numbers of the several ions in the transition layer. liquid-liquid chromatography abbr.: LLC; a type of liquid chromatography in which the stationary phase is a liquid supported on a solid. liquid medium any liquid culture medium. liquid nitrogen nitrogen in the liquid state. It has a b.p. of -195.79 °C (77 .36 K), and is useful as a cooling and freezing agent. liquid oxygen oxygen in the liquid state. It has a b.p. of -182.96 °C (90.19 K). liquid paraffin a colourless, odourless fraction of higher liquid hydrocarbons obtained from petroleum. Light liquid paraffin has a density of 0.83-0.86 g ML-l and heavy liquid paraffin has a density of 0.86-0.89 g ML-I. It is used for (hot) oil baths, and the purified material is used as a suspending medium in infrared spectroscopy. liquid-scintillation counting abbr.: LSC; a technique for counting particulate radiation. The (radioactive) sample is dissolved or suspended in, or placed in close approximation to, a solvent containing one or more substances that are fluorescent and emit a pulse of light (scintillation) when excited by an incident ionizing particle or photon. The light is detected by photomultipliers, in a liquid-scintillation counter. liquid-scintillation spectrometry liquid-scintillation counting of particulate radiation of one or more selected ranges of f'nergies. liquid-solid chromatography abbr.: LSC; a type of liquid chromatography in which the mobile phase is a liquid and the stationary phase a solid. liquor 1 (in pharmacy) a (usually aqueous) solution of a pure

382

liquorice

locus

substance. 2 a solution in a chemical manufacturing process. 3 the water used in brewing. liquorice or (esp. US) licorice or glycyrrhiza the dried roots and rhizome of Glycyrrhiza glabra. This preparation contains glycyrrhizin, the glucoside of glycyrrhetic acid; it resembles aldosterone and has effects similar to the mineralocorticoids. LISP a high-level computer language used for artificial intelligence. [Acronym from 'list processing'.] liter the US spelling of litre. lithiasis (in pathology) the presence of calculi (stones), e.g. in the biliary or urinary tracts. lithium symbol: Li; an element of group I of the IUPAC periodic table; atomic number 3; relative atomic mass 6.939. It is a soft, silvery white, alkali metal of such high reactivity that it must be stored in an inert atmosphere or under oil. It is not found free in nature, occurring in the minerals spodumene and lepidolite. Lithium carbonate, Li 2 C0 3 (commonly referred to as 'lithium') is used to control the symptoms of manic-depressive illness. Li+ inhibits inositol phosphate phosphatase, thereby inhibiting the recycling of inositol, and reducing its availability for phosphatidylinositol synthesis. lithogenesis (in pathology) the processes leading to formation of calculi (stones). -lithogenic adj. Iithotroph any member of either of two groups of organisms, chemoautotrophs (see chemotroph) and photolithotrophs, that use CO 2 as a carbon source. litre or (US) liter symbol: L or I; a non-SI unit of volume, now identical to the cubic decimetre; Le. I L I dm 3 10-3 m 3 . little gastrin see gastrin. liver one of the largest organs of the vertebrate body, situated in the abdominal cavity and formed as a diverticulum of the gut. It is highly vascular; venous blood carrying the products of digestion enters via the hepatic portal vein, while arterial blood enters via the hepatic artery. Blood leaves via the hepatic vein. The liver functions as a gland by secreting bile and is an important site of metabolism of carbohydrates, proteins, and fats; it stores carbohydrate as glycogen, is active in gluconeogenesis, and is important in the regulation of the blood glucose level. It is also an important site for the synthesis of urea and ketone bodies. The liver synthesizes fibrinogen, prothrombin, serum albumin, and other blood proteins and plays an important part in detoxication. The major cells in the liver are the hepatocytes. The liver also contains Kupffer cells of the reticuloendothelial system, cells derived from the bile duct cannuliculae, and fibroblasts, which are particularly important in the pathogenesis of liver cirrhosis. See also regeneration (def. 2). LLC abbr. for liquid-liquid chromatography. LLD factor abbr. for Lactobacillus lactis Dorner factor; a growth factor for this organism, identical to vitamin B12 . LLF or L-L factor abbr. for Laki-Lorand factor, i.e. factor XIII (see blood coagulation). 1m symbolfor lumen (def. I). L meromyosin abbr. for light meromyosin. LMM abbr. for light meromyosin. In symbol for natural, or Napierian, logarithm (alternative to loge)' aLnn or (sometimes) Lnn symbolfor the Iinolenoyl or (9,12,15)linolenoyl or (formerly) a-Iinolenoyl group; see Iinolenoyl (def.

=

=

1).

yLnn symbol for the (6,9, 12)-linolenoyl or (formerly) y-linolenoyl group; see Iinolenoyl (def. 2). InRNA abbr. for low-molecular-weight nuclear RNA (see small nuclear RNAs). load (in metabolic studies) the amount (of a specified substance) given in a metabolic test. loading test or load test a metabolic test in which the subject is given a dose of a specific substance and the concentration in blood and/or urine of the substance, or of some related metabolite, is determined as a function of time. Such a test is useful for determining the capacity of a particular metabolic pathway in the subject.

lobelia 1 any plant of the genus Lobelia. 2 or Indian tobacco the dried leaves, shoot tips, and seeds of Lobelia inflata, which contain the alkaloid lobeline. lobeline 2-[6-(8-hydroxyphenethyl)-I-methyl-2-piperidyl]acetophenone; an alkaloid derived from lobelia (def. 2) with actions on the central and peripheral nervous systems that resemble those of nicotine. It is responsible for some of the properties of herbal cigarettes.

(-)-Iobeline

Lobry de Bruyn-van Ekenstein transformation a nonenzymic transformation occurring in carbohydrates, usually in alkaline conditions, that includes epimerization of both aldoses and ketoses and aldose-ketose isomerization. [After Cornelius Adrian Lobry de Bruyn and W. Alberda van Ekenstein (1857-1937), who first described it in 1895.] localized melting the (reversible) destabilization of tertiary structure in a limited region of an ordered biopolymer through interaction with a specific agent, e.g. an enzyme. locant a prefix or infix used in organic chemical nomenclature to identify the position of a substituent in a parent structure or of an isotopic modification to a compound. Locants are commonly Arabic numerals, but Greek letters and italicized symbols of heteroatoms are also used. In isotopically modified compounds the italicized name of the function containing the modification may be used if it has no number, e.g. in [methyl14C]methionine. loci the plural of locus. lock-and-key model a model for the mechanism of an enzyme-substrate combination, of a hormone-receptor interaction, or of an antibody-antigen reaction. In this model, which is based on the analogy of the complementarity of a lock and its key, one reactant is envisaged binding to the other on a site to which it is structurally complementary. Locke's solution or Locke solution or Ringer-Locke solution anyone of several balanced salt solutions modified from Ringer's solution, initially for the perfusion of mammalian heart and other tissues in physiological experiments. Such solutions have usually contained (in grams per litre, approx.) NaCI (9.0-9.5), KCI (0.20-0.42), CaCI 2 (anhydrous, 0.20-0.24), NaHC0 3 (0.1-0.3), and glucose (1.0-2.5). [After Frank Spiller Locke (1871-1949), British physiologist, who devised them in 1894 and 1900.] lock-washer structure a putative intermediate structure formed during the assembly of subunits of the coat protein of tobacco mosaic virus into the helically organized structure of the fully formed virion. It is believed to arise after the primary subassembly, which is a two-layered disk with 17 subunits per layer, has self-aggregated into a cylinder; a dislocation in each disk then occurs so that it becomes a two-turn flattened protohelix, of similar shape to a lock washer of the sprung type. loco disease see locoweed. locoweed any of various plants belonging to the genera Astragalus or Oxytropis, found mainly in western USA. They contain L-2-amino-3-(methylseleno)propionic acid (methylselenocysteine), a nonprotein amino acid, and may cause poisoning (loco disease) when ingested by livestock. [From Spanish loco, mad.] locus (pl. loci) 1 (in genetics) the specific position, in all homologous chromosomes, of a particular gene or one of its alleles. 2 (in mathematics) the curve or line traced by a point moving so as to satisfy a particular set of conditions.

383

locus control region locus control region abbr.: LCR; a group of five regions upstream of the structural genes for the ~ chain of hemoglobin in human and mouse. These regions are essential for the expression of all the genes of the ~-Iike gene cluster. lod score abbr. for log of the odds score; a statistical test to determine whether a set of linkage data indicates linkage or not, the loglO of the odds favouring linkage. For genetic disorders that are not X-linked, a lod score of +3 (1000:1 odds of linkage) indicates linkage, whilst a score of -2 is odds of 100: I against linkage. Loewi, Otto (1873-1961), German-born VS physiologist; Nobel Laureate in Physiology or Medicine (1936) jointly with H. H. Dale 'for their discoveries relating to chemical transmission of nerve impulses'. log 1 symbol for logarithm. 2 abbr. for logarithmic. logarithm abbr. and symbol: log; the power to which a fixed number (the base) must be raised in order to produce a specified number; i.e. in the expression a = b", a is the specified number, b is the base, and n is the logarithm. In decadic (common) or Briggsian, logarithms the base is 10; the common logarithm of a is written as log lOa, or Ig a. In natural, or Napierian, logarithms the base is e (= 2.718 28 ... ); the natural logarithm of a is written as logea or In a. In binary logarithms the base is 2, and the binary logarithm of a is written as logza or Ib a. In converting between them, logea = 2.303 x 10glOa, and logza = 3.322 x 10glOa. logarithmic or logarithmical abbr.: log; 1 of, pertaining to, using, or containing logarithms of numbers or variables. 2 describing a relationship in which one variable is proportional to the logarithm of another. logarithmic growth a type of growth pattern shown by bacteria or other cells in which the number of cells, or the cell mass, increases logarithmically (exponentially) with time. The rate of increase at any time is proportional to the number of cells, or the cell mass, present. logarithmic phase abbr.: log phase; the phase of growth of bacterial or other cells during which they undergo logarithmic

growth. logarithmic plot abbr.: log plot; a graph in which one axis has a logarithmic (def. I) scale and the other a linear scale. logical operation an operation on binary numbers or statements used in computing and also in applications such as databases and library searches. There are three common binary operators (AND, OR, XOR) and one unary operator (NOT). log-log plot double logarithmic plot; a graph on which both variables are plotted logarithmically. Lohmann reaction a name sometimes given to the reversible reaction, catalysed by creatine kinase, in which ATP and creatine are formed from ADP and phosphocreatine. [After Karl Lohmann (1898-1978), German biochemist.] Lohmann's enzyme an alternative name for creatine kinase. lombricine the 2-guanidoethanol phosphoester of phosphoserine. In earthworms, the guanidine group can undergo phosphorylation to phospholombricine, which acts as a phosphagen. lomustine 1-(2-chloroethyl)-3-cyclohexyl-l-nitrosourea; a chloroethylnitrosourea derivative with actions resembling carmustine.

r l J.~CI ~N N I

NO

London forces see dispersion forces. lone pair or nonbonding electrons a pair of electrons of opposite spins occupying the same orbital in the valence shell of an atom.

loop of Henle long-acting thyroid stimulator abbr.: LATS; an IgG immunoglobulin found in the serum of a large proportion of thyrotoxic patients. It binds competitively with thyrotropin to thyrotropin receptors in thyroid plasma membrane, stimulates membrane adenylate cyclase, and causes longer-lasting stimulation of thyroid-hormone secretion than thyrotropin itself. long-chain describing an aliphatic compound of any type with a chain length greater than ten carbon atoms (i.e. C IO). long-chain alcohol or fatty alcohol any aliphatic compound with a chain length greater than C IO that possesses a terminal hydroxymethyl group. They are components of ether lipids, and esterified with long-chain fatty acids they form wax esters, often major components of plant cuticular waxes. long-chain-alcohol D-fatty-acyltransferase EC 2.3.1.75; other name: wax synthase; an enzyme that catalyses the formation of a long-chain fatty acyl ester, i.e. a wax, from acyl-CoA and a long-chain alcohol with release of CoA. long-chain base any aliphatic compound with a chain length greater than C 10 that possesses a terminal basic group. long-chain fatty acid any aliphatic compound with a chain length greater than C IO that possesses a terminal carboxyl group. 10ng-chain-fatty-acid-CoA ligase EC 6.2.1.3; other names: acyl-activating enzyme; acyl-CoA synthetase; fatty acid thiokinase (long-chain); lignoceroyl-CoA synthase; an enzyme that catalyses the reaction between ATP and a long-chain carboxylic acid and CoA to form an acyl-CoA with release of AMP and pyrophosphate. It activates free fatty acids formed, e.g., by phospholipase action for further metabolism. Examples from yeast: 10ng-chain-fatty-acid-CoA ligase I (Iongchain acyl-CoA synthetase I; fatty acid activator I): database code LCFLYEAST, 700 amino acids (77.78 kDa); longchain-fatty-acid-CoA ligase 2 (long-chain acyl-CoA synthetase 2; fatty acid activator 2): database code LCF2_ YEAST, 744 amino acids (83.34 kDa); long-chain-fattyacid-CoA ligase 3 (long-chain acyl-CoA synthetase 3; fatty acid activator 3): database code LCF3_YEAST, 694 amino acids (77.86 kDa). long-chain-3-hydroxyacyl-CoA dehydrogenase EC 1.1.1.211; other name: p-hydroxyacyl-CoA dehydrogenase; an enzyme of the beta-oxidation system that catalyses the oxidation by NAD+ of (S)-3-hydroxyacyl-CoA to 3-oxoacyl-CoA with the formation of NADH. See 3-hydroxyacyl·CoA dehydrogenase. longitudinal relaxation time an alternative name for spin-lattice relaxation time. long-patch repair see short-patch repair. long-range interaction describing an interaction between residues that are situated relatively far apart in a polypeptide or polynucleotide sequence. long terminal repeat abbr.: LTR; a double-stranded DNA sequence, generally several hundred base pairs long, that is repeated at the two ends of the DNA of retroviruses and retrotransposons. loop 1 the round or oval figure produced by a line, wire, thread, etc. that curves round to cross (or nearly cross) itself. 2 (in electronics) any closed electric or magnetic circuit through which a signal can circulate. 3 (in computing) any set of instructions in a program that is carried out repeatedly until some specified condition is satisfied. loopback DNA an alternative name for hairpin DNA; see hairpin. loop injector a device for introducing samples into a highpressure liquid chromatographic column without interruption of the solvent flow to the column. It consists of a loop of metal tubing of small volume, which is filled with the sample; this can then, by an appropriate valve, be flushed by eluent directly onto the column. loop of Henle or Henle's loop the V-shaped part of a nephron lying in the renal medulla. It comprises a thin descending tubule and an ascending tubule formed of both a thin and a

384

lophotoxin thick segment. It plays a role in the selective reabsorption of fluid and solutes. [After Friedrich Gustav Jakob Henle (1809-85), German anatomist and pathologist.] lophotoxin a cyclic diterpenoid, isolated from Pacific gorgonians (sea fans and whips) of the genus Lophogorgia, that irreversibly inactivates the nicotinic acetylcholine receptor on intact BC3H-I cells. Lorentz correction factor a correction factor for the effect of solvent polarizability on optical rotation by solutions of proteins or other macromolecules. It is given by: 3/(n 2 + 2), where n is the refractive index of the solvent. [After Hendrik Antoon Lorentz (1853-1928).] Lorentzian Iineshape function an equation for the lineshape of a nuclear magnetic resonance absorption signal: g(w) = T 2/[1 + (w - wo)2T22], where g(w) is a measure of the intensity of the resonance at a frequency w, Wo is the actual Larmor frequency of the resonating nucleus, and T 2 is the spin-spin relaxation time. loricrin the major protein of the cornified cell envelope of terminally differentiated epidermal keratinocytes. It is a substrate for transglutaminase, and exists as monomers cross-linked by disulfide and N-(y-glutamyl)lysine isodipeptide bonds. Example from human: database code LORe HUMAN, 316 amino acids (26.01 kDa). losartan 2-butyl-4-chloro-I-(p-(O-IH-tetrazol-5-ylphenyl)benzyl)imidazol-5-methanol; an antihyperactive drug that blocks the binding of angiotensin II (see angiotensin )to the AT I receptor. Affinity for this receptor is much greater than for the AT 2 receptor. It is oxidized by a cytochrome P450 to a carboxylicacid metabolite that is largely responsible for most of its angiotensin II antagonistic effects. Loschmidt constant symbol: N L ; the number of molecular entities in unit volume of an ideal gas at I atm and 273.15 K. It is equal to the Avogadro constant divided by the molar volume, and has the value 2.686 763 x 10 25 m- 3. [After Josef Loschmidt (1821-95), Austrian physicist.] Loschmidt number or Loschmidt's number the numerical value of the Loschmidt constant. lovastatin or mevinolin 6a-methylcompactin; a metabolite from some fungi (e.g. Monascus ruber, Aspergillus terreus) that is a potent inhibitor of hydroxymethylglutaryl-CoA reductase. It is useful clinically as an antihypercholesterolemic; it reduces plasma levels of total low-density-lipoprotein (LDL), and very-Iow-density-lipoprotein cholesterol, but it can increase high-density-lipoprotein cholesterol. Its effects result in the induction of up-regulation of LDL receptors on hepatocytes. Two proprietary names are: Mevacor; Mevinacor.

low-complexity region a region in the amino-acid sequence

of a protein in which a particular amino acid or a small number of different amino acids are enriched. See, for example, leucine zipper. low-density lipoprotein abbr.: LDL; one of the classes of

lipoproteins found in blood plasma in many animals (data normally relate to humans). LDLs are also known as ~ lipoproteins due to their electrophoretic mobility intermediate between high-density or a lipoprotein, and the origin. LDL

luciferase particles have diameter 19.6-22.7 nm, solvent density for isolation (g mL-l) 1.019-1.063, hydrated density (g mL-l) 1.034. Their approximate composition (% by weight) is 13% unesterified cholesterol, 39% esterified cholesterol, 17% phospholipid, II % triacylglycerol, 20% protein. Their apolipoprotein composition (% by weight total apolipoprotein) is 98% B-IOO with traces of different C and E apolipoproteins. They are synthesized in plasma from very-low-density lipoproteins and intermediate density lipoproteins through the action of lipoprotein lipase; they transport cholesterol to peripheral tissues. They have the highest content of cholesterol of any plasma lipoprotein, and have been linked to the incidence of coronary heart disease in epidemiological studies. See also apolipoprotein (for individual apolipoproteins), and LDL receptor. low-density-lipoprotein receptor see LDL receptor. low-energy compound a name sometimes applied improperly to certain compounds that undergo reaction leading to release or transfer of, e.g., phosphate, where the standard free energy change for the hydrolysis of the bond is CHOH groups, as in the acyclic forms of D- or L-Iyxose. See monosaccharide. Iyxose symbol: Lyx; a trivial name for the aldopentose, lyxopentose; the C-2 epimer of xylose, rare in nature.

~ OH 0

HO

OH

a-D-Iyxose (pyranose form)

Mm m symbol for 1 metre. 2 milli+ (SI prefix denoting 10-3 times). m+ prefix (in peptide hormone nomenclature) denoting mouse, murine; derived, or as if derived, from a mouse. m, symbol for relative electrophoretic mobility. m symbol for 1 mass; the various associated terms are distinguished by subscripts: me' symbol for electron rest mass; m o , symbol for neutron rest mass; m p, symbol for proton rest mass; mu , symbolfor atomic mass constant. 2 molality (alternative to b). 3 (bold italic) magnetic moment. 1ft- prefix (in chemical nomenclature) denoting meta-. Compare o-,p-.

M symbol for 1 mega+ (SI prefix denoting 106 times). 2 a residue of the a-amino acid L-methionine (alternative to Met). 3 a residue of an incompletely specified base in a nucleic-acid sequence that may be either adenine or cytosine. 4 mesomeric effect. 5 a metal (in chemical formulae). 6 molar (concentration), i.e. moles per litre (alternative to M or M; mol dm- 3 is recommended). 6 6-mercaptopurine ribonucleoside, 6-thioinosine. M symbol for molar (concentration), i.e. moles per litre (alternative to M or M; mol dm- 3 is the recommended form). az-M abbr. for az-macroglobulin. M symbol for 1 mass, especially molar mass; related terms are designated by subscripts: M ro, symbol for mass-average molar mass (see average molar mass); M o , symbol for number-average molar mass (see average molar mass); M o , symbol for mean relative residue mass; M r, symbol for relative molecular mass; M w ' symbol for weight-average molar mass; M z symbol for Z-average molar mass (see average molar mass). 2 molar (concentration), Le. moles per litre (alternative to M or M; no longer recommended; use mol dm- 3). 3 (or M v ) luminous exitance. 4 (or Me) radiant exitance. 5 (bold italic) magnetization. 6 (bold italic) moment of a force. MAA abbr. for macroaggregated (human serum) albumin. MAC abbr. for 1 membrane attack complex. MAC 1 is a cellsurface glycoprotein of monocytes, macro phages, and granulocytes that is implicated in adhesive interactions of these cells as well as in mediating the uptake of complement-coated particles. It probably recognizes the RGD peptide in complement component C3b. It is a heterodimer of aM and pz chains (see integrin). Examples: (human) MAC I aM (precursor): database code !TAM_HUMAN, 1153 amino acids (127.16 kDa); MAC I pz (precursor): database code !TB2_HUMAN, 769 amino acids (84.69 kDa). 2 mammalian artificial chromosome. MACIF abbr. for membrane attack complex inhibition factor. MAC-IP abbr. for MAC-inhibitory protein (i.e. CD59). mackerel any marine fish of the subfamily Scombroidei. These fish are of importance as food fish, and their flesh is rich in oils with a relatively high content of n-3 fatty acids; typical composition (major fatty acids, expressed as percentage of total fatty acids): 14:0,8%; 16:0, 16%; 18:0,2%; 16:1 (n-7) 8%; 18:1 (n-9), 8%; 18:1 (n-7), 4%; 18:4 (n-3), 2%; 20:1 (n-9), 11%; 20:5 (n-3), 8%; 22: I (n-II), 13%; 22:6 (n-3), 8%. Macleod. John James Richard (1876-1935), British physiologist and biochemist; Nobel Laureate in Physiology or Medicine (1923) jointly with F. G. Banting 'for the discovery of insulin'. maconha see cannabis. macro+ or (hefore a vowel) macr+ comb. form 1 denoting large, long, or great in size or duration; large-scale. 2 denoting larger than normal, overdeveloped. Compare micro+. macroaggregate any macromolecular aggregate large enough to be visible to the unassisted eye. macrocycle any macrocyclic compound. macrocyclic 1 (in chemistry) describing any compound containing a ring structure consisting of a large number (usually 15 or more) atoms. 2 (in biology) having a long life cycle. macrocytic anemia anemia in which the circulating erythro-

cytes are larger than normal. It is often due to deficiency of vitamin B 12 (cobalamin) or folic acid. macroglobulin any plasma globulin of >400 kDa. Macroglobulins include immunoglobulin M, az-macroglobulin, and many lipoproteins. az-macroglobulin abbr.: az-M; a glycoprotein found in vertebrate plasma that strongly inhibits proteinases of all classes. In humans it constitutes about one third of the azglobulins; in hypoalbuminemia its synthesis is enhanced, when it constitutes a major proportion of the increased az-globulin band on electrophoresis strips. Human az-M is a 726 kDa molecule comprising two pairs of disulfide-linked, identical 185 kDa subunits, which also contain heterodetic peptide rings containing reactive thiol ester linkages, each formed between the )i-carboxyl group of a glutamic residue and the thiol group of a cysteine residue in the same peptide chain. It can inhibit all four classes of proteinase by a mechanism involving a bait region. This contains specific sites, cleavage of which induces a conformational change that results in trapping of the proteinase: following cleavage in the bait region a thiol-ester bond is hydrolysed and mediates the covalent binding of the protein to the proteinase; subsequently e-amino groups of the proteinase react with the thiol-ester linkages in the inhibitor to form stable amide links. The entrapped proteinase is then able to act on substrates of low molar mass only. Example, subunit precursor from human: database code A2MG_ HUMAN, 1474 amino acids (163.09 kDa). macroglobulinemia or (esp. Brit.) macroglobulinaemia a condition in humans in which there is an increase in the concentration of macroglobulins, especially immunoglobulin M, in the blood. It is often associated with lymphocyte tumours. macro histone 2A abbr.: macro H2Aa; the counterpart of histone H2A that replaces this in certain nucleosomes, with an implied role in nucleosome positioning. Example from rat: database code H2AM_RAT, 367 amino acids (38.91 kDa). macroion an ion of a macromolecule, especially one that does not pass through a dialysis membrane. macrolide any of a large group of structurally related antibiotics produced by Streptomyces spp. They contain a large lactone ring (see +olide) with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar moieties. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins. They are active mainly against Gram-positive bacteria and they inhibit the early stages of protein synthesis. macroligand (sometimes) any macromolecular ligand. macrometabolite (sometimes) any metabolite present in a system in reasonably high concentration, especially as opposed to a trace metabolite, i.e. one present in extremely small concentrations. macromolecule any molecule composed of a very large number of atoms, operationally defined as any molecule of mass greater than about 10 kDa (and ranging up to IO z MDa or more) that is incapable of passing through the pores of dialysis tubing as generally used. The term includes nucleic acids and most polysaccharides and proteins. Compare micromolecule. -macromolecular adj. macronutrient any element that is required by living organisms in relatively large quantities for normal growth. Compare micronutrient. macrophage any cell of the mononuclear phagocyte system that is characterized by its ability to phagocytose foreign particulate and colloidal material. Macrophages occur in connective tissue, liver (Kupffer cells), lung, spleen, lymph nodes, and other tissues. They contain prominent Iysosomes, stain with vital dyes, and play an important part in nonspecific immune reactions.

macrophage-activating factor

392

macrophage-activating factor abbr.: MAF; see Iymphokine. macrophage-colony stimulating factor see colony stimulating factor. macrophage inflammatory protein abbr.: MIP; any of a number of cytokines produced by Band T cells, monocytes, mast cells, and fibroblasts. MIP la is a chemoattractant for monocytes, T cells, and eosinophils; it also inhibits hematopoietic stem cell production; example from Mus musculus: database code MIlA_MOUSE, 92 amino acids (10.34 kDa); residues 1-23 are the signal peptide. MIP I~ is a chemoattractant for monocytes and T cells and is an adhesion molecule, binding to ~I (VLA family) integrins; example from M. musculus: database code MIlB_MOUSE, 92 amino acids (10.17 kDa); residues 1-23 are the signal peptide. macrophage migration enhancement factor see Iymphokine. macrophage migration inhibitory factor abbr.: MIF; other name: delayed early response protein 6; a Iymphokine that is released by primed lymphocytes on incubation with the priming antigen. It inhibits the migration of macrophages out of macrophage-rich tissue such as spleen, and is probably a mediator of macrophage participation in inflammation. Example from human: database code MIF_HUMAN, 114 amino acids (12.30 kDa). macrophage system see mononuclear phagocyte system. macropipette (sometimes) a pipette of similar construction to a standard plunger-type micropipette but of capacity in the range 0.25-5 mL. macropore any pore (in a gel or porous solid) whose width is greater than about 50 nm. Compare mesopore, micropore. -macroporous adj. macroreticular describing a three-dimensional polymer with a very open structure, the cross links being widely spaced. macroscopic 1 of a size that is visible to the unaided eye. Compare microscopic (def. I). 2 concerned with large units. Compare microscopic (def. 2). 3 relating to the behaviour of atoms or molecules in bulk. Compare microscopic (def. 3). -macroscopically adv. macroscopic equilibrium constant any constant describing the overall equilibrium between two chemical entities that may be interconverted through two or more alternative intermediates. Compare microscopic equilibrium constant. macrosolute an operational term describing any solute of a size larger than will pass through a membrane of a specified pore size or permeability limit. macrotetrolide or macrotetralide any of a group of antibiotics characterized structurally by the presence of a 32-membered ring built up of four hydroxy-acid residues and containing four ether and four ester bonds; the group includes nonactin and related antibiotics. Some similar compounds have an open-chain structure, e.g. monensin and nigericin. macula adherens an alternative term for desmosome. MadCAM abbr. for mucosal addressin cell adhesion molecule; MadCAM I, M r 58-66 kDa, is a member of the immunoglobulin superfamily of adhesion molecules. It is constitutively expressed on endothelial cells of post-capillary venules. It mediates lymphocyte homing to mucosal lymphoid organs and lamina propria venules, and binds L-selectin and integrin a4~7' Example from Mus musculus: database code 533601, 405 amino acids (43.65 kDa). mad cow disease an informal name for bovine spongiform encephalopathy. madder the ground root of Rubia tinctoria, used as a plant dyestuff; the principal component is ruberythric acid. MAF abbr. for macrophage-activating factor; see Iymphokine. magainin any of several antibiotic peptides from Xenopus skin, whose pore-forming activity (see PFP) results in the permeabilization of bacterial membranes. They have a wide spectrum of action against bacteria, protozoa, and fungi. Magainin I has the sequence GIGKFLHSAGKFGKAFVGEIMKS;

magnetic immunoassay (Lys IO,Asn 22 )-magainin

magamm II is I. An analogue with greater antibiotic potency is (Ala 8• 13 •18)-magainin II amide. Compare dermaseptin. magic spot I see magic spot (compound), ppGpp. magic spot II see magic spot (compound), pppGpp. magic spot (compound) abbr.: MS; either of the guanosine polyphosphates produced when stringent strains of Escherichia coli are starved of an amino acid required for protein synthesis. MS I is guanosine 5'-diphosphate 2'-(or 3')-diphosphate (symbol: ppGpp); MS II is guanosine 5'-triphosphate 2'(or 3')-diphosphate (symbol: pppGpp). magnesium symbol: Mg; a metallic element - an alkaline earth metal - of group 2 of the IUPAC periodic table; atomic number 12; relative atomic mass 24.305. It occurs naturally only in the combined state and is a mixture of stable nuclides of mass 24, 25, and 26. Magnesium is one of the most abundant elements of the Earth's crust and an essential component of all living material. It forms a divalent cation, Mg2+, which is a component of chlorophyll, occurs in bone, and is an essential cofactor for many enzymes, including the majority of enzymes utilizing ATP. It is a major biological cation, the fourth most abundant cation in the human, much of it being in the skeleton; the range in normal human plasma is 0.8-1.2 mmol L-l. An excretion mechanism in the kidney is partly regulated by parathyroid Ijormone. See also magnesium-2B. magnesium-28 the artificial radioactive nuclide of magnesium, HMg, of half-life 21.2 h. It emits a moderate-energy beta particle (i.e. electron) (0.46 MeV max.) and gamma radiation of various energies (1.35, 0.95, 0.40, and 0031 MeV). magnesium porphyrin a general term for chlorophyll. magnet any body that can produce an appreciable magnetic field external to itself. Magnets may be either permanent or temporary. -magnetic adj. magnetic circular dichroism spectroscopy circular dichroism spectroscopy in the presence of a magnetic field. magnetic constant symbol: flo; an alternative name for permeability of vacuum. magnetic dipole moment symbol: m or fl (italic bold); a vector quantity indicating the strength of a magnet: the product of a magnet's dipole moment and the ambient magnetic flux density gives the torque on the magnet. The SI unit is the A m 2 (ampere square metre = joule per tesla (J T-l». magnetic field 1 a field of force existing in the neighbourhood of either a permanent magnet or a circuit carrying an electric current. Another magnet will experience a couple when placed in a magnetic field. 2 an alternative name for magnetic field strength. magnetic field strength or magnetic field or (formerly) magnetic intensity symbol: H (italic bold); a vector quantity, the magnetizing force at any point in a medium. It is measured by a couple that would act on a small magnet of unit moment placed at that point with its axis at right angles to the direction of the magnetic field. It is the magnetic flux density, B, divided by the permeability, fl; i.e. H Blfl. The SI derived unit H Am-I. magnetic flux symbol: Dyn > Met> Leu; for /): End = Leu = Met> Dyn; and for K: Dyn » End » Leu = Met. Morphine and its analogues are primarily Jl agonists, but also have activity on /) and K receptors. Effector pathways for all of these types are G-protein-mediated, Jl and /) depressing cyclic AMP levels and opening a G-protein-modulated K+ channel, K inhibiting a G-protein-modulated Ca 2 + channel. Some opioids also bind to other receptors known as cr, but morphine has a very low affinity for these receptors and naloxone does not block its action. opiomelanocortin or opiocortin a polypeptide, present in the intermediate lobe of the pituitary gland, that includes within it the entire sequences of the peptide hormones corticotropin, a and ~ melanocyte stimulating hormone, ~ and y lipotropin, and ~ endorphin. It is formed from proopiomelanocortin.

optical rotation opium the milky, air-dried exudate from incised, unripe seed capsules of the opium poppy, Papaver somniferum, and some other species. Opium contains approximately 20 alkaloids, the most significant of which are codeine, morphine, papaverine, and thebaine. OPLC abbr. for overpressure(d) layer chromatography. OPRTase see orotate phosphoribosyltransferase. opsin 1 any of a group of hydrophobic glycoproteins that occur in the visual pigments of vertebrates in equimolecular combination (as Schiffs bases) either with II-cis-retinal - in iodopsin and rhodopsin - or with 3,4-didehydro-ll-cis-retinal in cyanopsin and porphyropsin. These opsins are of ~35-40 kDa and consist of single-chain polypeptides glycosylated with two branched oligo saccharides. See also photopsin, scotopsin. 2 any of a group of proteins of ~25 kDa that occur in combination with retinal in the purple-membrane pigments present in some strains of Halobacterium halobium; e.g. bacterioopsin (in bacteriorhodopsin), halo opsin (in halorhodopsin), and slowopsin (in slow-cycling rhodopsin). opsonifya less common word for opsonize. opsonin any blood-serum protein that, when combined with microorganisms or other particulate material (e.g. foreign erythrocytes), increases the latter's susceptibility to phagocytosis. The two main classes are immunoglobulin G antibodies and the C3b and IC3b fragments formed from the C3 component of complement; other classes include fibronectin and the soluble mannose-binding protein of serum. An opsonin molecule acts by linking the surface of the particulate matter to a specific receptor on the surface of a phagocytic cell; commonly this receptor is either an Fc receptor (recognizing the Fc domain of an IgG immunoglobulin molecule) or a CR3 receptor (recognizing the IC3b fragment of complement). -opsonic adj. opsonize or opsonise or (less commonly) opsonify to render (microorganisms or other particulate material) more susceptible to phagocytosis by coating with opsonin. -opsonization or opsonisation or opsonification n. optic 1 or optical of or pertaining to the eye or the sense of sight; aiding vision. 2 a less common word for optical (def. 1,2). optical 1 or optic of, pertaining to, or involving light. 2 or optic of or pertaining to optics. 3 a less common word for optic (def. I). optical activity the ability (of chiral substances or their solutions, and chiral crystals) to rotate the plane of polarization of a transmitted beam of plane-polarized light. There is usually a correspondence between chirality of molecules and optical activity. See also chiroptical. optical antipode an older term for enantiomer. optical density a term (no longer recommended) for absorbance. optical isomer an older term for enantiomer. optical isomerism an older term for enantiomerism. optically active having or displaying optical activity; the term is often used interchangeably with chiral. optically inactive lacking optical activity (through being either achiral or racemic). optical purity the ratio (usually expressed as a percentage) of the specific optical rotation of a sample of an enantiomeric substance to the specific optical rotation of a pure single enantiomer of the substance. Compare enantiomeric purity. optical rotation or rotation 1 the phenomenon of rotation of the plane of polarization of plane-polarized light on its transmission by (solutions of) chiral substances, and by chiral crystals. By convention, optical rotation is designated as rightwards, or positive - and termed dextrorotation - when it is clockwise as seen by an observer looking towards the light source, and designated as leftwards, or negative - and termed levorotation - when it is anticlockwise. 2 or optical rotatory power the ability of (a solution of) a chiral substance to effect such rotation, an effect that is normally associated with optical activity. 3 symbol: a; any measure, expressed in angular degrees, of such ability under specified conditions; see molar optical rotation, specific optical rotation.

471

optical rotatory dispersion optical rotatory dispersion abbr.: ORD; the variation of optical rotation with the wavelength or frequency of the transmitted light. The shape of an optical rotatory dispersion spectrum of a solution of a macromolecule often gives useful information about the conformation of the solute. See also circular dichroism, Cotton effect. optical rotatory power an alternative term for optical rotation (def. 2). optical system any arrangement of diffraction gratings, lenses, mirrors, prisms, etc., frequently within a specific instrument and used for a specific purpose. optics 1 (functioning as sing.) the branch of physics concerned with the nature, properties, and behaviour of (visible) light and with the characteristics of optical devices, instruments, and systems. The term is extended to other kinds of electromagnetic or particulate radiation in so far as they have similar properties to light. 2 a collective term for an arrangement of optical components (in an instrument); the optical properties of such an arrangement. OPTLC abbr. for overpressured thin-layer chromatography. See overpressure(dllayer chromatography. oral of or pertaining to the mouth; adminstered by mouth. orbit 1 a closed circular or near-circular course taken by a moving body (often around something). 2 the depression in the skull that contains the eye. 3 to move in or as if in an orbit (def. I). See also orbital. orbital 1 any wave function, '¥, of an electron in a molecular entity. It is characterized by a particular energy value and a unique set of three quantum numbers; the counterpart in wave mechanical theory of an electron orbit in Niels Bohr's concept of atomic structure. Any particular orbital may be occupied either by one electron or by two electrons of opposed spins, or it may be unoccupied. The square of the value of '¥ at any point can be interpreted as the probability of the electron being located at that point, or as the average fractional charge density at that point. See also atomic orbital, molecular orbital, pi orbital, sigma orbital. 2 of, relating to, occupying, or moving in or as ifin an orbit (def. 1).3 belonging to the orbit (def. 2). orbital shaker a device designed to impart an orbital motion to flasks, tubes, etc. with the purpose of mixing their contents and facilitating the transfer of gases from the gaseous to the liquid phase. It is useful especially for growing cultures of cells. orcinol test or Bial's test a colorimetric test specific for aldopentoses. The sample is heated with strong acid to convert any aldopentose present to furfural (i.e. 2-furaldehyde), which is then reacted with orcinol (Le. 5-methyl-I,3-benzenediol) in the presence of ferric chloride to give a blue-green compound extractable into amyl alcohol. The test is used for the determination of RNA and the detection of pentosuria. [After Manfred Bial (1870-1908), German physician.] ORD abbr. for optical rotatory dispersion. Ord symbol for a residue of the ribonucleoside orotidine (alternative to 0). order 1 (in chemistry) sequence (of residues in a polymer). 2 order of reaction. 3 (in taxonomy) a category cO'nsisting of a number of similar families (sometimes only one family). One or more orders make up a class. 4 (in mathematics) the number of times a function must be differentiated to obtain a particular derivative. 5 (in mathematics) the number of columns or rows in a determinant or a square matrix. 6 order of magnitude. ordered mechanism or ordered pathway (for an enzymic reaction involving two substrates, A + B ~ C) a mechanism in which the enzyme, E, must necessarily first bind to one substrate, e.g. E + A ~ EA, and then to the second substrate, thus EA + B ~ EAB, this ternary complex then reacting to form the product, EAB ~ E + C. Compare random mechanism. order of magnitude 1 a tenfold range of magnitude extending from a particular value either upwards or downwards. 2 a magnitude expressed to the nearest power of ten. order of reaction symbol: n; the sum of the exponents of the concentration terms in the rate equation for an elementary

orient chemical reaction considered in one direction only. It may also be applied to certain composite reactions. order of reflection symbol: n; the integer, n, in the equation of Bragg's law. ordinate the vertical, or y, coordinate in a plane rectangular (Cartesian) coordinate system. Compare abscissa. ORF abbr. for open reading frame. organ any part of the body of a multicellular organism that is adapted and/or specialized for the performance of one or more vital functions. The term is sometimes extended to include organelles of unicellular organisms. organ culture a category of tissue culture, in which an organ, part of an organ, or an organ primordium, after removal from an animal or plant, is maintained in vitro in a nutrient medium with retention of its structure and/or function. organelle any discrete structure in a unicellular organism, or in an individual cell of a multicellular organism, that is adapted and/or specialized for the performance of one or more vital functions. organic 1 of, pertaining to, or derived from an organism or organisms. 2 of, pertaining to, or affecting an organ or organs. 3 of, relating to, or being a compound of carbon, whether or not of natural origin. 4 of any element contained in an organic compound. 5 any organic compound. organic chemistry the branch of chemistry concerned with the compounds of carbon in covalent linkage, whether natural or artefactual, including most compounds of biological origin but excluding some simple carbon compounds, e.g. oxides, sulfides, and cyanides. See also organic compound. organic compound any compound containing carbon in covalent linkage; various simple carbon compounds, especially carbon dioxide, carbonic acid, and salts and ions of carbonic acid, are usually excluded. organiser a variant spelling of organizer. organism any unicellular or multicellular prokaryote or eukaryote, usually extended to include various noncellular nucleic-acid-containing infective agents such as viruses. organizer or organiser (in embryology) any part of an embryo that, through substances produced by it, stimulates the morphological development and differentiation of other parts. organo+ comb. form denoting organic (def. I, 2, 3). organogenesis the formation and development of organs in an organism. -organogenetic adj. organoleptic affecting, involving, or making use of the sense organs, especially those of smell and taste. organomercurial 1 or organomercury of, pertaining to, or being an organic compound containing mercury, especially one in which a mercury atom is linked directly to one or more carbon atoms. 2 or organomercury compound any such compound. organometallic 1 or organometal of, pertaining to, or being a metal-containing organic compound, especially one in which a metal atom is linked directly to one or more carbon atoms. 2 or organometal compound any such compound. organophosphate 1 any organic compound containing a phosphoric (including fluorophosphoric, thiophosphoric, etc.) residue in amide, anhydride, ester, or thioester linkage. 2 any of a number of organophosphorus compounds originally developed as nerve gases, but formerly used as agricultural insecticides and as anthelmintics, the best known being diisopropylphosphofluoridate. These compounds inhibit serine proteases (including acetylcholinesterase, crucial for nerve transmission) by blocking an essential serine residue. See also aminoethylbenzenesulfonylfluoride, diisopropyl f1uorophosphonate, phenylmethylsulfonyl fluoride. organotroph an alternative term for heterotroph(e). organotrophic 1 heterotrophic; see heterotroph(e). 2 of, pertaining to, or influencing the formation or nourishment of bodily organs. organyl any organic substituent group, regardless of functional type, that has a single free valence at a carbon atom; e.g. ethyl, CH 3CH r ; glycyl, H 2 NCH 2C(=0)-; ribosyl, C 5H 9 0 4 -.

472

origin

orotidine-5'-phosphate decarboxylase

origin (in mathematics) the point of intersection of a set of (usually two or three) coordinate axes; the point whose coordinates are all zero. -original adj. O-ring a toroidal ring, usually of circular cross-section, made of neoprene or similar material and useful as a fluid- or gastight seal between particular parts of a device while permitting relative movement between them. Orn symbol for a residue of the a-amino acid L-ornithine. ornaline an alternative name for nopalinic acid. ornithine symbol: Orn; a,J-diaminovaleric acid; 2,5-diaminopentanoic acid; an amino acid only rarely found in proteins. LOrnithine is an intermediate in the biosynthesis of arginine (see ornithine-urea cycle) and, in plants, of pyrrolidine and tropane alkaloids; it was first found as its dibenzoyl conjugate, ornithuric acid. D-ornithine is a component of bacitracin A. ornithine acetyltransferase see glutamate N-acetyltransferase. ornithine carbamoyltransferase abbr. (in clinical chemistry): OCT; EC 2.1.3.3; systematic name: carbamoyl-phosphate:L-ornithine carbamoyltransferase; other names: ornithine transcarbamylase; citrulline phosphorylase. An enzyme of the ornithine-urea cycle that catalyses a reaction between carbamoyl phosphate and L-ornithine to form L-citrulline and orthophosphate. It is deficient in congenital hyperammonemia. Example, product of argl gene in Escherichia coli: database code ECARGI, 334 amino acids (36.93 kDa). ornithine decarboxylase EC 4.1.1.17; systematic name: L-ornithine carboxy-lyase; an enzyme that catalyses the decarboxylation of L-ornithine to putrescine and CO 2; pyridoxal-phosphate is a coenzyme. It is the first enzyme of polyamine biosynthesis; its activity increases in the cell in response to many agonists, especially those stimulating cell growth. Example from Neurospora crassa: database code DCOR_NEUCR, 484 amino acids (53.24 kDa). ornithine transacetylase see glutamate N-acetyltransferase. ornithine-urea cycle or ornithine cycle or arginine-urea cycle or urea cycle a cyclic metabolic pathway, present in mammals and other ureotelic animals, that converts waste nitrogen, in the form of highly toxic ammonium, to essentially nontoxic urea, which may then be excreted. Urea is formed by hydrolysis of L-arginine to L-ornithine, the cycle being completed by conversion of ornithine to L-citrulline by carbamoylation with carbamoyl phosphate (previously formed by enzymic combination of carbon dioxide and ammonium with phosphate from ATP), reaction of the citrulline with L-aspartate to form L-argininosuccinate, and cleavage of this to produce fumarate and regenerate arginine. The cycle is also sometimes called the Krebs cycle or the Krebs-Henseleit cycle, after its discoverers. The role of argininosuccinate was revealed by the US biochemist, Sarah Ratner (1903- ), in 1954. ornithuric acid N,N' -dibenzoylornithine; a detoxication product of benzoic acid found in the excreta of birds.

00

H~yO I

,)+0.81 V; the oxidized form, P680+, is a powerful oxidant that can abstract electrons from water with the evolution of dioxygen. See also chlorophyll. P700 or pigment 700 a type of chlorophyll a, having an absorption maximum at 700 nm, that constitutes the reaction centre of photosystem I. It has a redox potential of approximately +0.5 V, its electron being used ultimately to reduce NADP via ferredoxin. See also chlorophyll. PS70 the special pair of bacteriochlorophyll a in the photosynthetic reaction centre of bacteria, so named because they have an absorption maximum of 870 nm. P960 the special pair of bacteriochlorophyll b in the photosynthetic reaction centre of bacteria, so named because they have an absorption maximum of 960 nm. Pa symbol for pascal. pA2 the negative logarithm to the base 10 of the molar concentration of antagonist that makes it necessary to double the concentration of agonist needed to elicit the original submaximal response. p[A]5o the negative logarithm to the base 10 of the [Also of an agonist. pEC 50 is the corresponding term for the ECso of an agonist (often used interchangeably with [Also). PAB or PABA abbr. for para-amino benzoate; para-aminobenzoic acid. See p-aminobenzoic acid. PABA test an indirect test of pancreatic function in which the synthetic peptide N-benzoyl-L-tyrosyl-p-aminobenzoic acid (BT-PABA) is administered orally, usually with a small amount of [l4C]-p-aminobenzoic acid (PABA). Normally the peptide is hydrolysed by chymotrypsin to PABA, which is absorbed and excreted in the urine, but in pancreatic insufficiency hydrolysis is much reduced. pacemaker reaction any metabolic reaction whose rate depends on factors other than the amounts of enzyme or substrate. An enzyme catalysing such a reaction may be termed a pacemaker enzyme. pachyman see callose. pachytene the third phase of prophase I in meiosis. package I (in cell biology) to surround (one or a number of macromolecules) with a membrane in the formation of a mature secretory granule. 2 (in virology) to enclose the nucleicacid core of a virus particle with a protein shell (the capsid) to form a mature virion; to encapsidate. packing (in chromatography) the material (whether active solid, liquid held on solid support, or swollen gel) that is introduced into a column and that consists of or contains what is to become the stationary phase during a chromatographic separation. packing density the ratio of the minimum (or actual) volume of an object, such as a molecule in a crystal or in solution, to the total volume it occupies. For a macromolecule or region of

481

packing fraction a macromolecule, it is the ratio of the volume enclosed by the van der Waals envelope of all atoms in the molecule or region to the total volume of the molecule or region. Theoretical values are 0.74 for close-packed spheres, 0.91 for infinite cylinders, and 1.0 for a continuous solid. packing fraction the ratio of the relative atomic mass of a particular nuclide minus its nucleon number divided by its nucleon number. It is positive for the lightest and heaviest nuclides and negative for nuclides of intermediate mass. Paclitaxel a proprietary name for taxol. PAF abbr. for platelet-activating factor. PAGE abbr. for polyacrylamide gel electrophoresis. PAGIF abbr. for polyacrylamide gel isoelectric focusing. See polyacrylamide gel electrophoresis. PAH abbr. for para-amino hippurate; para-aminohippuric acid. pair see base pair. paired the gene for a sequence-specific DNA-binding homeobox segmentation protein in Drosophila melanogaster. It is one of a number of pair-rule genes, each of which specifies a simple alternation with a repeat distance of two segments. Their protein products are characterized by four motifs, referred to as the paired box. Example from D. melanogaster: database code HMPR_DROME, 613 amino acids (65.43 kDa). paired box see paired, Pax genes. pair-rule gene see paired. PaJaMa experiment the nickname for a bacterial mating experiment carried out at l'Institut Pasteur, Paris, that showed that induction and repression of the enzyme p-galactosidase in Escherichia coli are regulated by two closely linked genes, one of which produces a cytoplasmic repressing substance that blocks the expression of the other. [From the names of the experimenters: Pardee, Jacob, and Monod.] Palade, George Emil (l912~ ), Romanian-born US cell biologist; Nobel Laureate in Physiology or Medicine (1974) jointly with A. Claude and C. R. M. J. de Duve 'for their discoveries concerning the structural and functional organization of the ceiL' palindrome 1 any linear arrangement of symbols, such as letters or digits, that has the same sequence from either end; e.g. noon, radar; 75311357; 'Madam, in Eden I'm Adam'. 2 (in molecular biology) or palindromic sequence a popular name for a DNA sequence with a twofold rotational axis of symmetry (dyad symmetry). Confusingly the term is used in at least two distinguishable senses: (I) to describe a region of local twofold rotational symmetry in duplex DNA, e.g. 5'-GAATTC-3' 3'-CTTAAG-5' and (2) to describe a sequence in a single polynucleotide strand that contains an inverted repeat, e.g. 5'-TGA-AGT-3'. It is also sometimes applied to a region of either a single- or a double-stranded polynucleotide that is capable of forming one or more hairpins containing palindromes of the first type; an example is shown at cruciform. Examples of palindromes are operators and restriction sites but, in general, any stem-loop in RNA must have a corresponding palindrome in the DNA from which the RNA was transcribed. -palindromic adj. pallidin any of a group of endogenous carbohydrate-binding proteins (Iectins) produced by cells of the slime mould Polysphondylium pallidum during differentiation. Similar to discoidin, they may be concerned in cell adhesion. palmitate 1 numerical symbol: 16:0; the trivial name for hexadecanoate, CH 3-[CH zl I4-COO-, the anion derived from palmitic acid (i.e. hexadecanoic acid), a saturated straightchain higher fatty acid. 2 any mixture of free palmitic acid and its anion. 3 any salt or ester of hexadecanoic acid. See also palmitoyl. palmitate synthase see fatty-acid synthase complex. palmitic acid hexadecanoic acid; a saturated straight-chain fatty acid having sixteen carbon atoms per molecule, and a major component of plant and animal fats. See palmitate.

pancreatic hormone palmitoleate 1 numerical symbol: 16:1(9); the trivial name for (Z)-hexadec-9-enoate, CHdCHzls-CH=CH-[CHzh-COO-, the anion derived from palmitoleic acid, (Z)-hexadec-9-enoic acid, a monounsaturated straight-chain higher fatty acid. 2 any mixture of free palmitoleic acid and its anion. 3 any salt or ester of 9-hexadecenoic acid. See also palmitoleoyl. palmitoleic family (of polyunsaturated fatty acids) a series of polyenoic acids in which the hydrocarbon chain terminates with the alkenyl grouping CHr[CHzls-CH=CH- (as in palmitoleic acid (see palmitoleate»); there are three other series of such acids, i.e. the linoleic family, linolenic family, and oleic family. Members of the palmitoleic family can be synthesized from palmitic acid via palmitoleic acid by chain elongation andlor desaturation, but in mammals not from linoleic, (9,12,15)linolenic, or oleic acids; the series includes cis-vaccenic acid. palmitoleoyl symbol: ,JPam; the triJ!ial name for (Z)-hexadec9-enoyl, CHdCHzls-CH=CH-[CHzh-CO- (cis isomer), the acyl group derived from palmitoleic acid (i.e. (Z)-hexadec-9enoic acid). It is a relatively minor component of plant and animal lipids. The chain is synthesized metabolically by the action of a ,J9-desaturase on palmitoyl-CoA. palmitoyl symbol: Pam; the trivial name for hexadecanoyl, CHr[CHzlt4-CO-, the acyl group derived from palmitic acid (i.e. hexadecanoic acid). This is one of the major fatty-acid components of plant and animal lipids; together with stearic acid it represents a high proportion (often around 30%) of the fatty-acid content of dietary and other lipids. It acts as a precursor in mammals for a family of unsaturated fatty acids in which all double bonds are nine or more carbons from the methyl terminus. The chain is synthesized metabolically from acetyl-CoA as palmitate (in mammals) or palmitoyl-CoA (in yeast), the product of fatty-acid synthase. See fatty-acid synthase complex. palmityl 1 or cetyl a common name for hexadecyl, CHr[CHzl!4-CHr, the alkyl group derived from hexadecane. 2 aformer name (now incorrect) for palmitoyl. palytoxin any of a group of structurally very similar potent neurotoxins isolated from the marine zoanthid Palythoa toxica or other Palythoa spp. Each consists of a single carbon chain of 115 carbon atoms containing 64 chiral centres and seven double bonds, and terminating in nitrogen-containing groups; there are 128 carbons in all and a further double bond in a methylene group. The chain bears numerous hydroxyl groups and a number of methyl groups, and in several places it is folded and formed into pyran rings. Palytoxin is the most deadly nonproteinaceous material isolated, having 50 times the toxicity of tetrodotoxin in mice. The number of stereoisomers is 264 = 18446744073709551 620 (not including possible EIZ variations at the double bonds!). Pam symbol for palmitoyl (i.e. hexadecanoyl). pancreas a compound gland, occurring in the abdominal cavity of most vertebrates, that has both exocrine and endocrine functions. The major (exocrine) part consists of acinar tissue, which secretes pancreatic juice into the upper part of the gut (duodenum in mammals). Within this acinar tissue are scattered numerous (endocrine) islets of Langerhans, containing notably A cells, secreting glucagon, B cells, secreting insulin, and D cells, secreting somatostatin. -pancreatic adj. pancreastatin a 49-residue peptide hormone that acts as an inhibitor of glucose-induced insulin release from the pancreas. It also inhibits exocrine pancreatic excretion. It was originally isolated from porcine pancreas, where it is colocalized with insulin, glucagon and somatostatin, but is synthesized as part of the sequence of chromogranin A and is thus found in tissues where the chromogranin gene is expressed, including most endocrine cells. pancreatic cholera an alternative name for Verner-Morrison syndrome. pancreatic diabetes an older term for insulin-dependent diabetes mellitus. pancreatic hormone or pancreatic polypeptide abbr.: PP; a

482

PAP

pancreatic islet crystallizable polypeptide present in the PP cells of the pancreas, first detected as an impurity in insulin preparations. Avian pancreatic polypeptide, known as aPP, has been isolated from chicken and turkey pancreas; bovine, human, ovine, and porcine homologues, known as bPP, hPP, oPP, and pPP, respectively, have also been identified. All have 36 amino-acid residues with C-terminal tyrosinamide and show considerable sequence homologies. The PP level in the plasma rises rapidly after feeding, especially with protein foods; the hormone appears to act as a regulator of pancreatic and gastrointestinal functions; sequence from human: APLEPVYPGDNATPEQMAQYAADLRRYINMLTRPRY(NH z); database code (precursor) PAHO_HUMAN, 95 amino acids (10.43 kDa) also contains an icosapeptide of uncertain physiological role (residues 69-88). pancreatic islet an alternative name for islet of Langerhans. pancreatic juice a slightly alkaline digestive juice secreted by the exocrine pancreas into the upper part of the small intestine. It contains numerous enzymes and inactive enzyme precursors including a-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, pro phospholipase A z, ribonuclease, and trypsinogen. Its high concentration of hydrogencarbonate ions helps to neutralize the acid digesta from the stomach. pancreatic lipase a Ca2+- requiring triacylglycerol lipase (EC 3.1.1.3) that is secreted into the intestine by the exocrine pancreas when this is stimulated by cholecystokinin in response to ingestion of food. Its role is to degrade triacylglycerols, partially or completely, to fatty acids and glycerol in the intestine; it acts at an ester-water interface. It is a glycoprotein with sequence similarity with other lipases. Example (precursor) from human: database code LlPP_HUMAN, 465 amino acids (51.10 kDa). pancreatic polypeptide abbr.: PP; another name for pancreatic hormone. pancreatic thread protein or pancreatic stone protein (abbr.: PSP); a C-type lectin that may inhibit spontaneous calcium carbonate precipitation, and one of the major secretory proteins of the human exocrine pancreas. It is fOjlnd in acinar cells of pancreas and (in smaller amounts) in the brain. It is a major soluble protein of human pancreatic calculi and a Ca z+binding phosphoprotein present in zymogen granules of pancreatic acinar cells and secreted in pancreatic juice of normal subjects and calculus formers. It inhibits calcium carbonate precipitation from the juice. The protein is rich in aromatic amino acids. Between pH 5.4 and 9.2 it undergoes reversible fibril formation. It is also typically characteristic of infant brains. There is increased expression of PSP-like proteins in Down's syndrome and Alzheimer's disease. Example (precursor) from human: database code LITH_HUMAN, 166 amino acids (18.71 kDa). pancreatic trypsin inhibitor abbr.: PTI; a serine proteinase inhibitor, correctly known as pancreatic secretory trypsin inhibitor. A crystallizable protein trypsin inhibitor isolated from bovine pancreas, it forms a crystalline complex with trypsin and is relatively heat-stable in trichloroacetic acid solution. Its physiological role is to control trypsin activation of zymogens. The bovine protein is of known sequence: NILGREAKCTNEVNGCPRIYNPVCGTDGVTYSNECLLCMENKERQTPVLIQKSGPC. The 3-D structure is also known, and it is a favoured model for testing protein-folding algorithms. Example (bovine): database code IPST_BOVIN, 56 amino acids (6.16 kDa). It was also formerly known as Kunitz and Northrop inhibitor. pancreozymin abbr.: PZ; a putative hormone having secretagogic activity on the exocrine pancreas and extractable from duodenal mucosa. It is now known to be identical with cholecystokinin. panose an oligosaccharide, GIc(al-6)G1c(al-4)GIc; it is found in the fungus Aspergillus niger.

~o"

H~O-~CH2 OH

QHOCH20H 0

OH

HO OH

OH

panose

pantetheine N-pantothenylcysteamine; the D-enantiomer is a growth factor for Lactobacillus bulgaricus, and is an intermediate in the pathway for the biosynthesis of coenzyme A in mammalian liver and some microorganisms.

pantoate 1 the anion, HO-CHz-C(CH3h-CH(OH)~COO,derived from pantoic acid (i.e. (R)-2,4-dihydroxy-3,3-dimethylbutyric acid). 2 any salt or ester of pantoic acid.

pantoic acid

pantothenate 1 the anion, HO-CHz-C(CH3)Z-CH(OH)-CO~ NH-CHz-CHz-COO- (i.e. N-pantoyl-fJ-alanine anion), derived from pantothenic acid, a B vitamin complex; only the D-(R)enantiomer is biologically active. 2 any salt of pantothenic acid.

pantothenic acid

pantothenyl the acyl group, HO-CHz-C(CH3h-CH(OH)CO~NH-CHz-CH2-CO-, derived from pantothenic acid; coenzyme A is a D-(R)-pantothenyl derivative. pantoyl 1 the acyl group, HO-CHz-C(CH3)Z~CH(OH)-CO-, derived from pantoic acid, 2,4-dihydroxy-3,3-dimethylbutyric acid. PAP abbr. for peroxidase-antiperoxidase.

483

paramagnetism

papain papain or papaya peptidase I EC 3.4.22.2; a cysteine endopeptidase obtained from the latex, leaves, and unripe fruit of the papaya (or pawpaw) tree, Carica papaya. It will preferentially hydrolyse peptide bonds at the carbonyl end of Arg, Lys, and Phe residues (but never Val), with preference for large hydrophobic residues at the P2 position. It also has esterase, thiolesterase, transamidase, and transesterase activity. Papain is unusually stable to elevated temperatures and to denaturing agents and consists of a single polypeptide chain of 212 amino-acid residues. Example from C. papaya: database code NRL_IPPD, 212 amino acids (23.40 kDa); 3-D structure known; a and ~ regions. papaverine 1-[(3,4-dimethoxyphenyl)methyl]-6,7-dimethoxyisoquinoline; a constituent of opium that acts as a smooth muscle relaxant; this action is thought to be due to phosphodiesterase inhibitory activity and blockade of membrane calcium channels. OCH s OCHs

HsCO

HsCO

paper chromatogram the visible result of a chromatographic separation effected on paper. paper chromatography abbr.: PC; a technique of chromatography, applicable to microgram quantities of soluble substances, in which specially prepared filter paper, chromatography paper, forms the support for the stationary phase. The latter is commonly a film of water held by adsorption on the cellulose fibres of the paper and in equilibrium with a water-immiscible liquid or liquid mixture, which forms the mobile phase. A solution of a sample is applied near one end of a strip of paper, allowed to dry, and the mobile phase allowed to flow over the strip from that end. If the sample consists of only one component, development using an appropriate method of detection will reveal a single spot at a characteristic distance from the origin relative to that travelled by the mobile phase; in general, a mixture will give rise to a number of spots each occupying a different and characteristic position. Separations occur essentially by partition between the mobile and stationary phases, with some contribution, under certain conditions, attributable to adsorption or ion-exchange onto the paper support. An elaboration of the technique uses a square of paper on which two successive separations are effected at rightangles using mobile phases of differing separatory powers to produce a two-dimensional pattern of spots on the paper. With suitable treatment of the paper and an appropriate choice of the composition of the two phases, reversed-phase partition chromatography on paper may be effected. Since cellulose is chiral, some enanti orner separations are possible. paper electrophoresis a type of zone electrophoresis on (filter) paper. Papovaviridae a family of DNA viruses, most or all of which are, under suitable conditions, oncogenic in vertebrate hosts. The virion, 45-55 nm in diameter, consists of a nonenveloped icosahedral capsid with 72 capsomeres, and contains a circular DNA genome. papovavirus any virus belonging to the family Papovaviridae. The name derives from papilloma, polyoma, and vacuolating agent, an early name for simian virus 40. PAPS abbr. for 3'-phosphoadenosine-5'-phosphosulfate; i.e. adenosine 3' -phosphate 5'-phosphosulfate. par+ a variant form of para+ (before a vowel).

para 1 characterized by or relating to (substitution at) two ring-carbon atoms separated by two others in a monocyclic aromatic compound. 2 (followed by to) at a position in a benzene ring next but two to a particular (specified) substituent. See also para-. para+ or (before a vowel) par+ prefix indicating beside or near; beyond; resembling; defective or abnormal. para- abbr.: p-; prefix (in chemical nomenclature) denoting an isomer of a disubstituted monocyclic aromatic compound in which the substituents are attached at positions I and 4 of the ring. Compare meta-, ortho-. parabiont either individual of a pair united in parabiosis. parabiosis the state or condition of two individual animals being functionally united, either naturally, as in Siamese twins, or as a result of an experimental procedure. -parabiotic adj. paracasein an alternative name (esp. US) for casein (def. 2). paracetamol see acetaminophen. paracrine 1 describing or relating to a regulatory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produces it; describing or relating to such an agonist. 2 such an agonist; a paramone. Compare endocrine, neurocrine, neuroendocrine. paracrystal any assemblage of molecules or particles having a certain degree of order but one that is insufficient for it to be considered a true crystal. -paracrystalline adj.; paracrystallinity n. paradaxin or pardaxin any of several ichthyotoxic, neurotoxic peptides, isolated from the defence secretion of the Red Sea Moses sole fish, Paradachirus marmoratus, or the Pacific sole, Paradachirus pavoninus, that act as a shark repellent. Each consists of 33 amino acids, with hydrophilic C-terminal and hydrophobic N-terminal regions and with physical and pharmacological similarities with melittin but no sequence homology. Example, paradaxin P-2 from P. pavoninus: database code PAP2_PARPV, 33 amino acids (3.32 kDa). paraffin 1 an obsolete term for alkane. 2 or paraffin oil or kerosene or kerosine any liquid mixture, consisting mainly of alkanes, with a boiling point range of 150-300 °c and relative density range of 0.78-0.82. 3 an alternative name for paraffin wax. Compare liquid paraffin. paraffin wax any waxy mixture of higher alkanes, obtained as a residue from the distillation of petroleum, with a relative density of zO.9 and a melting point range of 45-65 °c. Parafilm the proprietary name for a flexible, moisture-proof, thermoplastic tissue useful for temporarily sealing small containers. parafollicular cell an alternative name for C cell (when found in the thyroid gland). parafusin an evolutionarily conserved phosphoglycoprotein involved in exocytosis. It is rapidly dephosphorylated via a Ca 2+-dependent process when secretagogues induce exocytosis in competent cells. Example from Paramecium tetraurelia: database code PARPARAFUS, 475 amino acids (52.94 kDa). parahematin or (esp. Brit.) parahaematin a former name for ferrihemochrome. parallel 1 (in biochemistry) describing a pair of linear structures, such as two polynucleotide or polypeptide chains, that are polarized or asymmetric in the same direction. 2 (in physical chemistry) denoting the spins of a pair of electrons, occupying the same atomic or molecular orbital, that are described by the same spin quantum number. Compare antiparallel. 3 (in electricity) describing an electrical component that is connected to the same two points in a circuit as another component; describing two or more components that are so connected. parallel dichroism see dichroic ratio. parallelism the quality or state of being parallel; similarity in corresponding details or in evolutionary pattern. paramagnetism the property displayed by substances that have a positive but small magnetic susceptibility, due to the presence in them of atoms with permanent magnetic dipoles

paramecium

484

caused by unpaired electron spins (with a contribution from the orbital motion of the electrons). These dipoles tend to align themselves in the direction of an applied magnetic field but no permanent magnetism is conferred on such substances. Compare diamagnetism, ferromagnetism. -paramagnetic adj. paramecium (pl. paramecia) any freshwater protozoan belonging to the genus Paramecium. Typically 50-300 /lm in length, they are ovoid and uniformly ciliated. See also kappa particle. parameter 1 (in mathematics) an unknown quantity that is a constant in a particular context but that may have different values in other (similar) contexts; e.g. the coefficient b in the general equation, y = bx + c, representing a family of straight lines. 2 (in statistics) a numerical characteristic of a population (as opposed to that of a sample of such a population). 3 any distinguishing characteristic of something, especially one to which a measured value is or can be ascribed. -parametric adj. paramomycin an amino glycoside antibiotic produced by Streptomyces paromomycinus. Its actions are similar to those of neomycin. paramone a proposed name for paracrine agonist, derived as a contraction of 'paracrine hormone'. paramylon a storage polysaccharide occurring in Euglena gracilis. It comprises a backbone of Pi ~3-glucopyranose units with side chains joined by al ~6 linkages. paramyosin a two-chain, coiled-coil, a-helical ~200 kDa protein that forms the core protein of the thick filaments of a number of invertebrate muscles. paramyxovirus any of a group of RNA animal viruses of the family Paramyxoviridae (distinguish from the genus Paramyxovirus), in class V of the Baltimore classification, consisting of enveloped, pleomorphic particles ~150 nm in diameter with helical nucleocapsids, 1000 nm long and 18 nm in diameter. They contain single-stranded RNA (minus strand) of 7 MDa plus virion polymerase. The group includes viruses causing mumps, measles, Newcastle disease of chickens, and distemper of dogs, and the morbilliviruses, pneumoviruses, and parainfluenza viruses. paranemic describing the nature of the coiling of a doublestranded helix in which the two strands are not intertwined, i.e. they may be separated without uncoiling. Compare plectonemic. parapepsin I an alternative name for pepsin B. parapepsin II an alternative name for porcine gastricsin (i.e. pepsin C). paraprotein name originally given to any plasma protein that gave an abnormal band on electrophoresis, derived from para+ + protein. Usually such a protein is a monoclonal immunoglobulin derived from neoplastic plasma cells and present at abnormally high concentration in the blood plasma. Such proteins are seen as a discrete band in the gamma-globulin region, but they may appear elsewhere if the paraprotein is IgA or IgM. Examples are proteins characteristic of a myeloma, e.g. Bence·Jones protein, amyloid proteins, Waldenstrom's macroglobulinemia, or cryoglobulins. Some paraproteins are not abnormal, e.g. the immunoglobulin that arises as a result of a severe bacterial infection. paraproteinemia or (esp. Brit.) paraproteinaemia the presence in blood plasma of paraprotein. Paraquat methyl viologen; I, I'-dimethyl-4,4'-bipyridynium dichloride; a nonselective herbicide whose action requires direct contact with the plant. It is highly toxic to humans and other animals if ingested in undiluted form. parasite any organism that spends all or part of its life cycle in (endoparasite) or on (ectoparasite) another living organism of a different species (its host), from which it obtains nourishment and/or protection, and to which it is usually detrimental. Compare symbiont. parastatin a 73-amino-acid peptide hormone, M r 11 000, that inhibits parathyrin secretion. Porcine parastatin has the aminoacid sequence: LSFRAPAYGFRGPGLQLRRGWRPSSRED-

parinaric acid SVEAGLPLQVRXYLEEKKEEEGSANRRPEDQELESLSAIEAELEK. Activity resides in a 19-amino-acid N-terminal fragment; that from rat has the sequence: LSFRARA YGFRDPGPQLRR. It is synthesized as part of the sequence of chromogranin A. paratartaric acid an old name for racemic (DL}-tartaric acid. The resolution of this acid into the D- and L-enantiomers by Pasteur was a landmark experiment in stereochemistry. See tartaric acid. parathion O,O-diethyl O-p-nitrophenyl phosphorothioate; a compound that acts as an inhibitor of cholinesterase through covalent bonding to the esteratic site of the enzyme. It is used as a chemical warfare agent and insecticide.

Parathormone a proprietary name for parathyrin. parathyrin or parathyroid hormone (abhr.: PTH); a 9.5 kDa polypeptide hormone, consisting of a single chain of 83 amino-acid residues (bovine). It is synthesized in parathyroid tissue by proteolysis of a 12.5 kDa prohormone. Parathyrin acts in conjunction with calcitonin and other hormones to control calcium and phosphate metabolism; it elevates the blood calcium level by dissolving the salts in bone and preventing their renal excretion. Example (precursor) from human: database code PTHY_HUMAN, liS amino acids (12.85 kDa). Proprietary name: Parathormone. parathyroid 1 situated near the thyroid gland. 2 of, pertaining to, or produced by the parathyroid gland. 3 the parathyroid gland. parathyroid gland an endocrine gland of higher vertebrates; there are typically two pairs, located near or within the thyroid. They develop from the gill pouches, and secrete parathyrin. parathyroid hormone abbr.: PTH; an alternative name for parathyrin. paratope the part of an antibody, formed by the hypervariable loops of the variable regions, that binds to an epitope. paratose 3,6-dideoxY-D-glucose; 3,6-dideoxY-D-ribo-hexose; a monosaccharide that occurs in type A O-antigen chains of the lipopolysaccharide on the outer membrane of certain species of Salmonella. Parazoa a subkingdom of multicellular invertebrate animals comprising the sponges (phylum Porifera). parenchyma 1 (in botany) in higher plants, any soft tissue consisting of thin-walled, relatively undifferentiated living cells. 2 (in zoology) the tissue constituting the essential or specialized part of an organ, as distinct from supportive tissue, blood vessels, etc. -parenchymal adj.; parenchymatous adj. parenchymal liver cell see hepatocyte. parent 1 any organism that has given rise to another such Ofganism, whether sexually or asexually. 2 a precursor of some derived entity; applied, e.g., to a cell, a virus, a chromosome or molecule of DNA, or a radionuclide. 3 parent compound (in chemical nomenclature) the member of a group of related compounds that has the simplest chemical structure and that forms the basis for naming the others. -parental adj. parenteral 1 located or occurring outside the intestine. 2 any route other than via the gastrointestinal tract, especially by injection. -parenterally adv. parietal 1 of, pertaining to, or forming part of the wall of a body cavity or similar structure; e.g. the hydrochloric-acidsecreting parietal cells of the gastric mucosa, also known as oxyntic cells. 2 of or relating to the parietal bones of the skull. parietal layer see serous membrane. parinaric acid any octadeca-9, 11,13, 15-tetraenoic acid; two isomers are found in Parinarium laurinum, namely the (9Z, liE, 13E, 15Z)-isomer (a- or cis-parinaric acid) and the

485

partition function

Parkinson's disease (9£,11 E, 13E, 15Z)-isomer (~- or trans-parinaric acid). Both are useful as probes in membrane studies, trans-parinaric acid especially, as it partitions preferentially into the less fluid regions of membrane lipids with increased quantum yield. They inhibit neutrophil elastase.

9~COOH

~CH 11

13

15

3

a-parinaric acid

~COOH

~ 9 11 13 15 CH 3 p-parinaric acid

Parkinson's disease or parkinsonism a progressive disorder of

the central nervous system characterized by tremor and impaired muscular coordination, thought to be due to defective dopaminergic transmission in some parts of the brain. There is a loss of dopaminergic neurons connecting the substantia nigra with the striatum, resulting in loss of dopaminergic inhibition in the striatum, with resulting cholinergic hyperactivity. Therapy is aimed at replacement of dopamine, achieved by administration of L-dopa, which is converted to dopamine within the brain (dopamine itself does not cross the blood-brain barrier). See also MPTP. [After James Parkinson (1755-1824), British palaeontologist and surgeon, who first described the disease in 1817.] Park nucleotide UDP-N-acetylmuramyl pentapeptide; an intermediate in the biosynthesis of peptidoglycan in the cell walls of most bacteria. [After James Theodore Park (1922- ).] parotid gland either of a pair of salivary glands situated near each ear in mammals. The duct runs forwards and empties into the oral cavity. PARP abbr. for 1 procyclin. 2 proline/arginine-rich protein. parsimony l(in computing) an algorithm used for determining sequence relationships in macromolecules. 2 (in genetics) the construction of evolutionary trees from protein and nucleicacid sequences. It maximizes the genetic likeness associated with common ancestry, whilst minimizing the incidence of convergent mutation, and provides a way to find the best genealogical hypothesis from sequence data. parthenocarpy the formation of fruit without the setting of seeds. It occurs naturally, but can be induced by spraying flowers with gibberellic acid (see gibberellin) to produce crops of seedless fruit. parthenogenesis the development of a new individual from an unfertilized female gamete. -parthenogenetic adj.; parthenogenetically adv. partial agonist an agonist that is unable to evoke the maximal response of a biological system, even at a concentrations sufficient to saturate the specific receptors. partial derivative (in mathematics) the derivative of an expression containing two or more independent variables that is obtained by differentiating the expression with respect to only one of them, the remaining variable or variables being considered constant. partial hydrolysate any mixture of monomers and oligomers resulting from a limited degree of chemical hydrolysis of a biopolymer or from its exposure to a specific hydrolytic enzyme.

partial inhibition (sometimes) a type of nonlinear enzyme in-

hibition in which saturation of the enzyme with inhibitor does not decrease the rate of the enzyme-catalysed reaction to zero. partial inverse agonist an inverse agonist that evokes a submaximal response in a biological system, even at a concentration sufficient to saturate the specific receptors. At high concentrations it will diminish the actions of a full inverse agonist. Compare antagonist, partial agonist. partially overlapping code see overlapping code. partially overlapping gene see overlapping gene. partial molar quantity a function of any particular extensive property (e.g. enthalpy, entropy, Gibbs energy, heat capacity, internal energy, volume) of a specified component of a singlephase multicomponent system that describes how that property varies, at constant pressure and temperature, with variation of the concentration of the component when the change in the property is expressed per mole of the component. Partial molar Gibbs energy is more usually known as chemical potential. Compare partial specific quantity. partial pressure symbol: PB or p(B) (for a gas B); the pressure exerted by one particular gas in a mixture of nonreacting gases. It is defined as the pressure the gas would exert if it alone were present and occupied the whole volume of the mixture at the same temperature, and is equal to the product of the amount-of-substance fraction of the gaseous component in question and the total pressure of the gaseous system. Compare tension. See also p5Q. partial pressures, law of see Dalton's law of partial pressures. partial specific quantity a function of any particular extensive property (e.g. enthalpy, entropy, Gibbs energy, heat capacity, internal energy, volume) of a specified component of a single-phase multicomponent system that describes how that property varies, at constant pressure and temperature, with variation of the concentration of the component when the change in the property is expressed per unit mass of the component. Compare partial molar quantity. partial specific volume (of a solute) symbol: VB; an instance of a partial specific quantity, defined as the change in volume of a solution on addition of a small amount of a solute B, expressed per unit mass of added solute and extrapolated to infinite dilution. The cgs unit (in which values are often listed) is cm 3 g-l and the 81 unit is m 3 kg-to particle 1 an extremely small piece or portion of (esp. solid or colloidal) matter. 2 elementary particle. -particulate adj. particulate enzyme any enzyme that is bound to an insoluble cellular or subcellular structure or that has been artefactually or artificially attached to particulate material. particulate radiation any form of radiation consisting of a stream of particles, especially alpha radiation, beta radiation, or neutron radiation emanating from a radioactive source. partition 1 (in chemistry) or distribution the equilibration of a solute between two phases (usuall;' of differing composition); the result of such a process. 2 (in genetics) the events that lead to the separation of chromosomes or to the segregation of plasmids into daughter cells in prokaryotic organisms. partition chromatography any form of chromatography in which separation of the components of a mixture is based mainly on differences between the solubilities of the components in the stationary phase (in gas chromatography) or on differences between the solubilities of the components in the mobile and stationary phases (in liquid chromatography). partition coefficient or distribution coefficient symbol: a or Ko ; the ratio of the equilibrium concentrations of a pure substance dissolved in two phases that are in contact, at a specified temperature. The partition coefficient is independent of the concentrations provided that no chemical interaction occurs with either (or both) of the phases and that the presence of the solute does not affect their immiscibility. partition function symbol: Z; a dimensionless mathematical function, derived by the application of statistical mechanical theory, that can be used to derive the average distribution of

partition law

486

the internal energy of a system in terms of its partition between all its molecular inhabitants. partition law or distribution law the principle that a solute, when added to a system consisting of two phases, will, at a given temperature, distribute itself between the two phases in proportion to its solubility in each of the two phases separately. Henry's law is a particular case of the partition law. See also Nerost distribution law. parturition the act or process of giving birth to offspring. parvalbumin any of a group of closely related ~ 12 kDa muscle proteins that bind calcium ions. Parvalbumin a is a muscle EF-hand Ca 2 +-binding protein, that may be involved in muscle relaxation. Example from human: database code PRVAHUMAN, 109 amino acids (11.93 kDa). Parvalbumin ~ is known as oncomodulin. parvovirus any of a group of small, animal viruses, in class II of the Baltimore classification, consisting of a naked capsid, 20-25 nm in diameter, and containing linear, single-stranded DNA of 1.2-1.8 MDa. Parvoviruses are highly resistant to chemical and physical agents. parvulin a peptidvlprolvl isomerase isolated from Escherichia coli. lt does not have any function as an immunophilin. Database code CYPC_ECOLI, 92 amino acids (10.10 kDa). PAS abbr. for 1 p-aminosalicylic acid. 2 periodic acid-Schiff; see periodic acid-Schiff reaction. pascal symbol: Pa; the SI derived unit of pressure or stress. It is equal to a force of one newton per square metre; i.e. I Pa = I N m- 2 = I J m- 3 . [After Blaise Pascal (1623-62), French mathematician and philosopher, who discovered the relationship between barometric pressure and altitude.] passage (in biology) the action or process of (serially) subculturing cells or microorganisms, especially with a view to adapting them to a changed environment. passage number (in cell culture) the number of subcultures performed after the original isolation of the cells from a primary source. passenger or passenger DNA any specific DNA fragment introduced into a cloning vector or other cloning vehicle. passive diffusion an alternative name for simple diffusion (used especially to emphasize its distinction from active transport). Compare facilitated diffusion. passive immunity immunity in an individual due to the presence of antibody or primed lymphocytes derived from another, already immune, individual. Pasteur. Louis (1822-95), French chemist, microbiologist, and immunologist; distinguished for his pioneer work in stereochemistry (in terms of symmetry rather than molecular constitution), for his recognition of the role of microorganisms in fermentation, for his invention of the technique of heat treatment of certain fluids to prevent microbial spoilage, now known as pasteurization, and for devising methods of immunization against certain diseases. Pasteur effect or (formerly) Pasteur-Meyerhof effect either the phenomenon that occurs in facultatively anaerobic cells whereby oxygen inhibits glycolysis or fermentation, or its converse whereby the rate of glycolysis or fermentation increases when oxygen is excluded. Compare Crabtree effect. pasteurization or pasteurisation a method of heat-treating milk or similar fluids to improve storage qualities and destroy pathogenic bacteria, without markedly altering taste and nutritional characteristics. Pasteurization of milk involves heating to 65°C for 30 minutes or to 72 °C for 15 minutes followed by rapid cooling to below 10°C. -pastenrize or pasteurise vb. Pasteur pipette or pasteur pipette a simple, disposable, ungraduated, dropping or transfer pipette constructed by drawing out a short length of narrow glass tubing to form a long fine tip and operated commonly by means of an attached rubber or PVC bulb or teat. Analogous devices are available

Pauli moulded in low-density polyethylene, with integral bulb and sometimes calibrated. Also (esp. US): Pasteur pipet, pasteur pipet. Pasteur reaction the putative chemical reaction once considered to link fermentation and respiration and to account for the Pasteur effect. patatin any of a family of glycoproteins that form 40% of the soluble protein of potato tubers. They serve as potato somatic storage proteins, and also have enzyme activity involved in host resistance. They have lipid acylhydrolase activity. Example (precursor): database code PATO_SOLTU, 386 amino acids (42.44 kDa). patch an intermediate stage in the formation of a cap (def. 2) on the surface of a cell, e.g. of a lymphocyte. patch-clamp technique a technique whereby the conductance change of a single ion channel of an excitable membrane is measured directly. A very small electrode tip is sealed onto a patch of cell membrane, thereby making it possible to record the flow of current through individual ion channels in the patch. See also Neher, Sakmann. path see light path. +pathic see +pathV. patho+ or (before a vowel) path+ comb. form denoting disease or clinical disorder. pathobiochemistry 1 the study of the biochemical processes associated with disease. 2 the processes themselves. pathogen any agent, especially any living organism, that can cause disease. pathogenesis the generation and production, or the origin and development, of a disease. -pathogenetic adj. pathogenesis-related proteins proteins synthesized in plants in response to attack by fungal or bacterial pathogens. They are small proteins that belong to a limited number of families, characterized by six motifs. Example, pathogenesisrelated leaf protein PI4 from tomato: database code PRI4_LYCE, 130 amino acids (14.24 kDa). pathogenic (capable of) causing or producing disease. -pathogenicity n. pathological or pathologic 1 of, or pertaining to, pathology. 2 causing, relating to, involving, or caused by disease. pathology 1 the branch of medical science concerned with the causes and nature of disease and with the effects of disease on the structure and functioning of the organism. 2 the sum of the changes that occur in an organism as the result of a specific disease. -pathologist n. pathophysiology 1 the study of the physiological processes associated with disease. 2 the processes themselves. pathway 1 the chain of reactions undergone by a given molecular entity or class of such entities in a particular ecosystem. 2 metabolic pathway. pathway engineering the use of genetic engineering to change either the kinetics or the products of a metabolic pathway. +pathy comb. form denoting 1 feeling, sensitivity. 2 disease of a (specified) part or kind. 3 a method of treating disease. pathic adj. patulin 4-hydroxy-4H-furo[3,2-c]pyran-2(6H)-one; a carcinogenic metabolite with antibiotic activity isolated from several fungi, particularly Aspergillus and Penicillium spp.

lY°,>=o

o~ OH

pauci+ comb. form indicating few. paucidisperse describing a colloidal system whose dispersed phase consists of particles of only a few sizes. -paucidispersity n. Pauli. Wolfgang (1900-58), Austrian-born US physicist; Nobel

487

Pauli exclusion principle Laureate in Physics (1945) 'for the discovery of the Exclusion Principle, also called the Pauli Principle'. Pauli exclusion principle or exclusion principle or Pauli principle the principle that no two electrons in an atom can be described by the same set of four quantum numbers. Pauling, Linus Carl (1901-94), US chemist and peace campaigner; Nobel Laureate in Chemistry (1954) 'for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances'; Nobel Laureate for Peace (1962). Paulus filtration method a method for studying the binding of a ligand microsolute to a macrosolute. It is applicable to small amounts of material and is particularly useful for a system having a relatively low binding constant. It involves equilibration of a series of mixtures of macrosolute and ligand in a suitable solvent, then separation of unbound ligand from macrosolute-plus-bound-ligand by ultrafiltration through anisotropic membrane filters of an appropriate retentivity. The amount of microsolute retained with the macrosolute on each filter is then estimated by, e.g., radioactivity measurement or another sensitive technique. [After H. Paulus.] Pauly's reagent a chromogenic reagent for imidazoles and phenols, consisting of a freshly prepared solution of diazotized sulfanilic acid (or other aromatic amine). In the presence of alkali, this reacts with histidine to give a red colour and with tyrosine to give an orange colour. It is useful for the identification of these amino acids on paper chromatograms. Pavlov, Ivan Petrovich (1849-1936), Russian physiologist and experimental psychologist; Nobel Laureate in Physiology or Medicine (1904) 'for his work on the physiology of the saliva glands'. See also salivary juice. Pax genes abbr. for paired box genes. The paired box is a conserved DNA sequence that plays a role in development. Pax genes encode a family of transcriptional regulators specifically expressed during the development of a wide range of structures and organs, including: Pax-I, paraxial mesoderm derivatives; Pax-2, urogenital system; Pax-3, neural crest and pre-myoblast migration; and Pax-6, eye and nose. paxillin an adhesion protein, associated with vinculin. that becomes phosphorylated in response to a number of stimuli, phosphorylation being associated with focal adhesion. It is also associated with dysfunction of cadherin-dependent cell-cell contacts and with cell spreading. Example from human: database code HSU14588, 557 amino acids (60.87 kDa). Pb symbol for lead. PBD see biphenylylphenyloxadiazole. PBG abbr. for porphobilinogen. PBI abbr. for protein-bound iodine. PBP abbr. for pencillin-binding protein. pBR322 a cloning vector. PBS abbr. for phosphate-buffered saline. PC abbr. for 1 paper chromatography. 2 phosphocreatine. 3 phosphatidylcholine. 4 personal computer. pCa symbol for the negative logarithm of the concentration (or strictly the activity) of calcium ions in a specified solution. PCA abbr. for perchloric acid. P-cadherin placental cadherin. PCB abbr. for pyruvate carboxylase. PCCase abbr. for propionyl-CoA carboxylase. PCMB abbr. for p-chloromercuribenzoate, or p-chloromercuribenzoic acid. PCMBS abbr. for p-chloromercuribenzenesulfonate, or pchloromercuribenzenesulfonic acid. PCP abbr. for 1-(1-phenylcyclohexyl)piperidine (see phencyclidine). PCR abbr. for polymerase chain reaction. p.d. abbr. for (electric) potential difference. Pd symbol for palladium. PDB abbr. for protein database; a database containing 3-D protein and nucleic-acid structures. A database of the files that

pectinesterase include the atomic coordinates is referred to as 'PDB format' or 'Brookhaven format' (after the Brookhaven National Laboratory at Upton, Long Island, New York, USA). PDBu abbr. for phorbol 12, 13-dibutyrate, a phorbol ester. PDD abbr. for phorbol 12, 13-didecanoate, a phorbol ester. PD·ECGF abbr. for platelet-derived endothelial cell growth factor. PDGF abbr. for platelet-derived growth factor. pDNA abbr. for plasmid DNA. P domain a domain of highly conserved cysteine residues, disulfide-bonded in the pattern 1-5,2-4, 3-6, associated with highly conserved alanine, glycine, and tryptophan residues. Such domains are found in secretory polypeptides from animals. Pe symbol for the pentyl group. PE abbr. for 1 phosphatidylethanolamine. 2 potential energy. peak 1 a sharp increase followed by a sharp decrease in a physical quantity that varies with distance, frequency, time, etc. 2 (in chromatography) the portion of a differential chromatogram recording the changes in detector response or eluate concentration while a given component of the applied mixture emerges from a chromatographic column. 3 the maximum value of a peak (def. I, 2). pECso see p[Also. PEC-60 a 60-amino-acid endogenous regulatory polypeptide abundant in intestinal tissue and also found in the central nervous system. It inhibits the formation of cyclic AMP and activates Na+,K+-ATPase. It is structurally related to pancreatic secretory trypsin inhibitor and inhibits insulin secretion. Example from Sus scrofa (precursor): database code PE60_PIG, 86 amino acids (9.63 kDa). PECAM abbr. for platelet endothelial cell adhesion molecule; a class of adhesion molecules represented by PECAM-l (or CD31), a member of the immunoglobulin superfamily. It is constitutively expressed on endothelial cells, platelets, granulocytes, monocytes, and T cells, and participates in homophilic binding (i.e. binding to itself). It is required for transmigration of leukocytes across the endothelium during extravasation. Example from human (precursor): database code PECI_HUMAN, 738 amino acids (82.54 kDa), residues 1-27, signal; 28-738, PECAM. pectate any salt or ester of pectic acid. pectic acid the form of pectin (def. 1) that is essentially free of methyl ester groups. pectic substance an alternative name for pectin (def. 1). pectin 1 or pectic substance any mixture of complex, colloidal, macromolecular plant galacturonans containing a large proportion of o-galactopyranosyluronic acid residues in (al--->4) linkage, the carboxyl groups of which may be esterified to varying degrees by methyl groups or be partially or completely converted to salts; some o-arabinose and o-galactose residues nearly always occur in addition, and residues of certain other sugars are sometimes present. M, is usually in the range 1 x 104-4 X 10 5 . Pectins are important matrix polysaccharides of plant cell walls, especially those of higher plants, sometimes constituting as much as one-third of the dry matter; they also occur in some plant juices. Certain fruits are particularly rich in pectin. 2 (in commerce) a whitish, water-soluble powder prepared from the rind of citrus fruits or apple pomace by extraction with dilute acid and consisting essentially of pectin (def. 1). It is used inter alia in the preparation of jams because of its ability to form gels in the presence of sucrose at high concentrations. pectinase see polygalacturonase. pectinesterase EC 3.1.1.11; other names: pectin methylesterase, pectin methoxylase; an enzyme that hydrolyses pectin to methanol and pectic acid. It is found in plant cell walls. One role may be concerned with cell-wall metabolism during fruit ripening. Example from Lycopersicon esculentum (tomato): PMEl_LYCES, 317 amino acids (34.55 kDa).

pectinic acid

488

pectinic acid the form of pectin (def. I) in which a high proportion of the carboxyl groups are esterified with methanol. pectin lyase EC 4.2.2.10; an enzyme that catalyses a trans elimination to convert pectin to oligosaccharides with unsaturated (C-4,C-5) terminal residues. Although often described as 4-deoxy-6-methyl-a-o-galact-4-enuronosyl groups, they are more accurately termed 4-deoxy-6-methyl-p-L-threo-hex-4enopyranouronosyl groups. Example (precursor) from Aspergillus niger: database code PLYA_ASPNG, 379 amino acids (39.85 kDa). pectin sugar an old name for L-arabinose. PEG abbr. for polyethylene glycol. PEl abbr. for the poly(ethyleneimine) group, pelargonate another name for nonanoate. pelargonoyl another name for nonanoyl. pellagra a disease of animals, including humans, arising from a dietary deficiency of nicotinic acid, especially in the absence of sufficient dietary tryptophan to generate adequate amounts of nicotinamide coenzymes metabolically. This situation can occur when the diet consists largely of maize (corn). Pellagra is characterized by scaly dermatitis on exposed skin surfaces, diarrhoea, and depression. pellagra-preventative factor abbr.: PP factor or PPF; a former name for nicotinic acid or nicotinamide. pellet a small compressed mass of material, especially such a mass deposited at the bottom of a tube by centrifugation of a suspension. pellicle a thin skin, membrane, or film. pellicular 1 of, relating to, or being in the form of a pellicle. 2 describing a type of column packing, used in high-pressure liquid chromatography, in which the stationary phase is present as a thin layer on the surface of tiny glass beads. Peltier eHect the phenomenon whereby heat is given out, or absorbed, when an electric current passes across a junction between two dissimilar materials. See thermocouple. Compare Seebeck effect. [After Jean Peltier (1785-1845), French physicist.] penatin an obsolete name for glucose oxidase. penetrance (in genetics) the degree to which a particular genotype is expressed in a population phenotype. If every individual carrying a dominant mutant gene shows the mutant phenotype, the gene is said to show complete penetrance. penicillamine 3-mercapto-o-valine; p,p-dimethy1cysteine; 2-amino-3-methyl-3-mercaptobutyric acid; the o-enantiomer is a characteristic degradation product of penicillintype antibiotics. It is a potent chelator of heavy metal ions, hence it is used clinically in the treatment of Wilson's disease and of poisoning by metals such as copper, lead, and mercury.

penicillic acid 3-methoxy-5-methyl-4-oxo-2,5-hexadienoic acid (exists in equilibrium with lactone form); a toxic antibiotic metabolite obtained from several fungi. It bears no relationship to penicillin or its degradation products. (Illustrated opposite.) penicillin 1 the generic name for a range of related antibiotics, whether produced naturally during the growth of various microfungi of the genera Penicillium and Aspergillus or of semisynthetic origin, that contain the condensed p-Iactamthiazolidine ring system:

penicillinase

where R is anyone of a variety of acyl groups such as: phenylacetyl, C6H5-CHZ-CO- (in penicillin G, penicillin II, benzylpenicillin); phenoxyacetyl, C6H5-O-CHZ-CO- (in penicillin V); and n-adipyl, HOOC-CH(NHzHCHzh-CO- (in penicillin N, also called cephalosporin N). Only those enantiomers having the o-configuration at C-2 of the thiazolidine ring show antibiotic activity. The parent substance, 6-aminopenicillanic acid, in which R is H, has little intrinsic antibiotic activity but is important as the naturally occurring starting point for the semisynthesis of artificial penicillins, e.g. ampicillin, in which R is aminophenylacetyl, C 6H 5-CH(NH z)-CO- . All penicillins are readily inactivated by chemical or enzymic hydrolysis of the strained four-membered p-Iactam ring, cold dilute acid yielding penicillamine, and alkali or penicillinases and other plactamases forming the corresponding substituted penicilloic acids. The penicillins generally have extremely low toxicity to animals and a high antibacterial activity, especially against Gram-positive organisms, the spectrum of activity varying somewhat with the nature of the group R. They act by inhibiting cross-linking of peptidoglycan in the cell wall of growing bacterial cells, the consequent structural weakness of the wall rendering the cells sensitive to osmotic lysis. 2 the (hypothetical) substance 6-formamidopenicillanic acid, used only in combination in trivial names of certain penicillins (def. I), e.g. benzylpenicillin. penicillin acylase EC 3.5.1.11; recommended name: penicillin amidase; an enzyme that catalyses the hydrolysis of penicillin to a fatty-acid anion and 6-aminopenicillinate. There are several enzymes that differ in specificity for the fatty acid. Examples: penicillin V acylase (or penicillin V amidase), a homotetramer from Bacillus sphaericus, database code PAC_ BACSH, 338 amino acids (37.42 kDa); penicillin G acylase (or penicillin G amidohydrolase) from Escherichia coli, database code PAC_ECOLI, 846 amino acids (94.54 kDa) - the latter sequence represents a zymogen for a periplasmic enzyme comprising a signal (amino acids 1-26), an a subunit (27-235), a spacer (236-289) and a ~ subunit (290-846); the active enzyme is a heterodimer (a,~). See also 6-amino-penicillanic acid. penicillin amidase the recommended name for penicillin acylase. penicillinase a trivial name for any JJ-Iactamase that acts preferentially on penicillins.

penicillic acid

489

peplomer

penicillin-binding protein penicillin-binding protein abbr.: PBP; any of various bacterial proteins that are capable of binding penicillin(s) covalently. Such proteins appear to be located predominantly, if not solely, in the cytoplasmic membrane of all species of bacteria in which peptidoglycan occurs in the cell wall. These proteins are believed to catalyse reactions in the later stages of cell-wall synthesis and there is a strong presumption that at least one of them catalyses the insertion of nascent peptidoglycan into the cell wall. In Gram-negative bacteria some penicillin-binding proteins are known to be involved in the maintenance of cell shape or in cell elongation or septation. Another is a carboxypeptidase, example from Haemophilus injluenzae (precursor): database code DACA_HAEIN, 393 amino acids (43.41 kDa). penicillin G acylase see penicillin acylase. penicillin V acylase see penicillin acylase. penicilloic acid any of a range of compounds of structure:

and produced by cleavage of the ft-Iactam ring of penicillins (def. I) by enzymic or alkaline hydrolysis. penta+ or (before a vowel) pent+ comb. form denoting five, fivefold, five times. pentacosa+ comb. form denoting 25, 25-fold, 25 times. pentadeca+ comb.form denoting 15, IS-fold, IS times. pentafunctional arom polypeptide a polypeptide that catalyses five consecutive enzymatic reactions in prechorismate polyaromatic amino-acid biosynthesis, i.e the second to sixth steps in the biosynthesis from chorismate of the aromatic amino acids (the shikimate pathway). It occurs in some yeasts and other fungi and in Euglena gracilis. It contains: 3-dehydroquinate synthase, 3-dehydroquinate dehydratase, shikimate 5-dehydrogenase, shikimate kinase, and EPSP synthase. Example from yeast: database code AROL YEAST, 1588 amino acids (174.55 kDa). Residues 1-392 = 3-dehydroquinate synthase; residues 404-866 EPSP synthase; residues 887-1060 shikimate kinase; residues 1061-1293 = 3-dehydroquinate dehydrogenase; and residues 1306-1588 = shikimate dehydrogenase. pentagastrin the trivial name for (N-tert-butyloxycarbonyl-ftalanyl)- L- tryptophanyl- L-methionyl- L- aspartyl- L- phenylalaninamide; a synthetic analogue of gastrin that consists of the latter's C-terminal tetrapeptide amide sequence with an added protected N-terminal ft-alanyl residue. It is used in the pentagastrin test as a gastrin analogue to stimulate gastric-acid secretion, which is then measured. Secretion is sometimes high in patients with duodenal ulceration and low in patients with gastric ulcer, but this is too variable to be of great use in diagnosis. See also calcitonin. pentamer 1 any oligomer consisting of or derived from five monomers. 2 the group of five capsomeres in an icosahedral virus capsid. pentanoate another name for valerate. pentanoyl another name for valeryl. pentaose a pentasaccharide in which all the residues are of one type and uniform linkage. Compare pentose. pentaric acid any aldaric acid obtained by oxidation of a pentose at C-I and C-5. pentasaccharide any oligosaccharide composed of five monosaccharide units. Pentasaccharides occur in small amounts in plants, e.g. verbascose in soybeans. pentaxin or pentraxin any of a family of proteins with a discoid appearance under electron microscopy, having five non-covalently bound subunits. The family includes C-reactive protein, serum amyloid P-component, and neuronal pentaxins. Exam-

=

=

pie from human, neuronal pentaxin II (precursor): database code NPX2_HUMAN, 430 amino acids (46.81 kDa); residues I-IS are the signal, 16-430 neuronal pentraxin II; residues 226-430 contain the pentaxin domain. pentitol any alditol having a chain of five carbon atoms in the molecule. pentobarbital 5-ethyl-5-( I-methylbutyl)barbiturate; a major barbiturate drug. One proprietary name is Nembutal. pentolinium test a test in which pentolinium, a sympathetic ganglion blocking drug, is used to reduce catecholamine secretion; failure to achieve reduction may indicate a pheochromocytoma. penton a capsomere that is surrounded by five other capsomeres in an icosahedral virus capsid. pentonic acid any monocarboxylic acid (aldonic acid) formally derived from a pentose by oxidation at C-1. pentosan a glycan that yields only pentoses on hydrolysis. pentose any aldose having a chain of five carbon atoms in the molecule. Compare pentaose. pentose cycle an alternative name for pentose phosphate pathway. pentose nucleic acid abbr.: PNA; a former term for ribonucleic acid. pentose phosphate pathway or hexose monophosphate pathway a complex series of extramitochondrial metabolic reactions by which glucose 6-phosphate is oxidized with formation of carbon dioxide, ribulose 5-phosphate, and reduced NADP, the ribulose 5-phosphate then entering a series of reactions in which a number of sugar phosphates containing between three and seven (or eight) carbon atoms are successively interconverted. One consequence of these interconversions is the non oxidative regeneration of glucose 6-phosphate, which then can enter the pathway for another cycle of oxidative decarboxylation and skeletal rearrangement, the eventual result being the complete oxidation of one molecule of glucose with the formation of six molecules of carbon dioxide and 12 molecules of NADPH. The pathway thus provides (in some organisms or tissues) an alternative route to (or shunt of) part of the glycolytic pathway; it also provides ribose 5-phosphate for nucleotide synthesis and (in some organisms) other intermediates for biosynthesis. Of special importance is D-erythrose 4-phosphate, required for the biosynthesis of aromatic amino acids and many other materials by the shikimate pathway. In higher plants many of the enzymes of the pathway function in the reverse direction as part of the reductive pentose phosphate cycle. Other names: hexose mono phosphate shunt; pentose cycle; phosphogluconate (oxidative) pathway; Warburg-Dickens pathway; Warburg-Dickens-Horecker pathway. See also glucose-6-phosphate dehydrogenase, phosphogluconate, phosphogluconate dehydrogenase (decarboxylating), transaldolase, transketolase. pentosuria the presence of excessive amounts of pentose in the urine. Two types may be distinguished: (I) essential pentosuria, in which daily excretion of 1-4 g L-xylulose (normal :::::

: : :,. I

...9

CH3

H

5,8,11, l4,17-pentaenoate respectively. PGl z is the major product in vivo; it is produced by endothelial cells of blood-vessel walls, has potent platelet anti-aggregatory properties resulting from stimulation of adenyl ate cyclase, and induces vasodilation. It has a normal half-life of 2 min, being degraded by hydrolysis to 6-oxo-prostaglandin F Ja; this is then converted to the 6,15-dioxo-13,14-dihydro-PGF ja , and follows a similar degradative path to other prostaglandins. More stable but still active analogues have been synthesized, e.g. carbacyclin. (S)15-hydroperoxyeicosatetraenoate inhibits prostaglandin-I synthase. See also prostaglandin.

(S)-form

propressophysin the polypeptide precursor of vasopressin and neurophysin (see vasopressin-neurophysin 2-copeptin precursor). A clinical name for the product of the gene associated with familial neurogenic diabetes insipidus. proprotein an inactive form of a protein, having an additional sequence that is removed by a proteinase to yield the active protein; a classic example is proinsulin. A zymogen is a form of proprotein, sometimes referred to as a proenzyme. propyl symbol: Pr; n-propyl; the alkyl group, CH 3-CH r CH r , derived from propane. Compare isopropyl. pro-Rlpro-S convention stereochemical descriptors for paired, chemically-like ligands at a prochiral centre; they derive from an extension of the sequence rule used to assign R,S descriptors to a chiral centre. In the prochiral (but achiral) structure, Caahc, the chemically-like ligands are the two atoms (or groups of atoms), a. For the sake of example assume that the sequence rule gives the priority sequence, a > h > c. In the molecular model (or projection formula) arbitrarily label the a groups as a' and a" and arbitrarily assign higher priority to one of them, e.g., a' > a". The modified priority sequence, a' > a" > b > C, is then considered with the model viewed from the side remote from c. If this gives a right-handed ordering for a' ~ a" ~ b, thus leading to R chirality for the arbitrarily created chiral element, the promoted a' is designated the pro-R group; conversely, if the arbitrarily created chiral element reveals an S ordering, the promoted group is pro-So Example: glycerol, HOCHz-CHOH-CHzOH, contains two chemicallylike CHzOH groups, and the normal priority sequence is OH > CHzOH > H. In the Fischer projection formula with the central carbon atom having the OH group to the right and H to the left, arbitrarily assign the top C'HzOH group priority over that at the bottom, C"HzOH, giving the modified sequence, OH > C'HzOH (top) > C"HzOH (bottom) > H. When the model is viewed from the side remote from the lowest priority atom (H) the ordering, OH ~ C'HzOH (top) ~ CHzOH (bottom) is right-handed so that the arbitrarily created chiral element has R chirality; hence the top C'HzOH is the pro-R group. Subscript letters Rand S can be used to indicate whether an atom or group of atoms is pro-R or pro-So This is most commonly done for the two hydrogens of a methylene group, with H R indicating the pro-R hydrogen and H s the pro-S hydrogen. For a methylene group, replacement of IH R by zH or 3H gives a centre with R chirality; similar replacement of JH s gives a centre with S chirality. See also enantiotopic. pros a designator of position of a nitrogen in the histidine imidazole ring, being that nitrogen nearest to the side chain; often abbreviated to 71:, as in N". Compare ,ele. PROSITE a database of all documented protein motifs. prosolin see stathmin. prosome another name for proteasome. prostacyclin or prostaglandin I (abbr.: PGI) any of a group of prostanoids synthesized by prostaglandin-I synthase (EC 5.3.99.4) from prostaglandin H - which itself is the product of prostaglandin-endoperoxide synthase - as prostaglandin I z, I), or 13, depending on whether the substrate for the enzyme is arachidonate, dihomo-(6,9,12)-linolenate, or eicosa-

° CH 3

prostaglandin 12

prostacyclin synthase see prostaglandin-I synthase. prostaglandin abbr.: PG; any of a group of biologically active metabolites of arachidonate (PG z series), dihomo-y-linolenate (PG J series), or eicosa-5,8, 11,14, 17-pentaenoate (PG 3 series). They characteristically contain a cyclopentane ring due to formation of a bond between C-18 and C-12 of the fatty acid; hydroxy or oxo substitution at positions 9 and II is a major distinguishing feature between prostaglandin classes. They were originally discovered as a uterus-contracting activity in seminal plasma, and are now known to possess a protean array of highly potent biological activities that defy simplification. However, to give an indication of these roles, their pharmacological effects include: vasodilation (PGE z and prostacyclin) which is short-acting, and vasoconstriction (PGF za and thromboxane A z ); oxytocic activity (PGF 2a can be used to terminate pregnancy in the second trimester and PGE 2 induces labour at term); bronchodilation (PGE series) and constriction (PGF series). They are involved in inflammatory reactions, and the enzymes that are involved in their synthesis are targets for antiinflammatory agents such as aspirin and non-steroidal antiinflammatory drugs such as ibuprofen. They are also involved in the regulation of cell proliferation in normal and neoplastically transformed cells. Prostaglandins are formed from the precursors prostaglandin G), G 2, or G 3, the intermediate products of prostaglandin-endoperoxide synthase, depending on the substrate fatty acid; the same enzyme converts these to prostaglandins H, from which other enzymes form prostaglandins D, E, and F, and also prostacyclins (or prostaglandins I). These are, from the bioactive aspect, the end products of the system, but they have a half-life of minutes, being rapidly converted to metabolites with much weaker, or often inhibitory properties. The initial metabolites are the 15-oxo-13,14-dihydroprostaglandins, produced by the sequential actions of 15-hydroxyprostaglandin dehydrogenases (e.g. EC 1.1.1.196 and 1.1.1.197) and 15-oxoprostaglandin 13-reductase (EC 1.3.1.48); these are further degraded by beta oxidation and omega oxidation to urinary metabolites such as 7a-hydroxy-5, Il-dioxotetranorprostane-l, 16-dioate (from PGE 2) and 5, 7-dihydroxy-ll-oxotetranorprostane-l, 16dioate. The structures of prostanoic acid, with its carbon numbering, and of PGG 2 , PGH 2 , PGD 2 , PGE 2 and PGF 2a are shown.

538

prostanoate

prostaglandin-D synthase

prostaglandin D2

prostaglandin E2

prostaglandin F2a

H

prostaglandin G2

prostaglandin H2

1

OH

10

H 13

CH 3 15

17

19 20

prostanoic acid

prostaglandin-D synthase abbr.: PGD synthase; EC 5.3.99.2; other name: prostaglandin-H 2 D-isomerase; an enzyme that catalyses the conversion of (52,13E)-(l5S)-9a,11a-epidioxy15-hydroxyprosta-5,13-dienoate to (52, 13E)-(l5S)-9a, 15-dihydroxy-ll-oxoprosta-5, 13-dienoate (prostaglandin D). Glutathione is a cofactor in some cases. Example (precursor) from

human, PGD 2 synthase (glutathione-independent PGD synthetase or ~-trace protein): database code PGHD_HUMAN, 190 amino acids (21.00 kDa). prostaglandin-endoperoxide synthase EC 1.14.99.1; other names: prostaglandin synthase; prostaglandin G/H synthase. An enzyme whose reaction embraces the activity formerly referred to as cyclooxygenase; it catalyses a reaction between dioxygen, arachidonate and two molecules of reduced glutathione (GSH) to form prostaglandin H 2, oxidized glutathione (GSSG), and H 20. The enzyme acts as both a dioxygenase and as a peroxidase. It catalyses the formation of the precursor, prostaglandin G 2 (PGG 2), for the biosynthesis of all prostanoid compounds, by forming an endoperoxide bridge between C-9 and C-II, simultaneously bonding C-8 and C-12 to form the cyclopentane ring, and also forming the hydroperoxide at C-15. The latter is reduced by a reduced glutathione (GSH)dependent peroxidase activity of the enzyme to a hydroxyl group to form prostaglandin H 2 ; these, and their further metabolites, prostaglandins D, E and F, are highly potent bioactive compounds with a great diversity of actions (see prostaglandin). The enzyme can also act on dihomo-(6,9,12)linolenic acid, to form a series of prostaglandins (denoted by a subscript I, e.g. PGEd lacking the C-5 double bond, and on eicosa-5,8, 11,14, 17-pentaenoic acid, to form the 3 series of prostaglandins (e.g. PGE 3), with the additional double bond at C-17. Two isoenzymes, COX-I, constitutively expressed, and COX-2, inducible in inflammation by cytokines, are highly homologous membrane proteins, but selective inhibition of COX-2 is possible due to its larger inhibitor-binding site. Aspirin acetylates an active-site serine residue in both, the IC so being 10 to 100 times lower for COX-I than for COX2. Its inhibiton of COX-I is the basis of its antithrombotic effects. Examples, both from human, COX-l (precursor): database code PGHLHUMAN, 599 amino acids (68.58 kDa); COX-2 (precursor): database code PGH2_HUMAN, 604 amino acids (68.98 kDa). See also prostacyclin, thromboxane. prostaglandin-E 2 9-reductase EC 1.1. 1.189; an enzyme that catalyses the reduction by NADPH of (52,13E)-(l5S)-lla, 15dihydroxy-9-oxoprosta-5,13-dienoate (PGE 2) to (52,13E)(l5S)-9a, lla, 15-trihydroxyprosta-5, 13-dienoate (PGF 2a ) with formation of NADP+. The monomeric cytoplasmic human enzyme catalyses reduction of many carbonyl compounds. In addition to the activity of prostaglandin-E 2 9-reductase (also termed prostaglandin 9-ketoreductase) described here two other activities are present. They are that of carbonyl reductase (NADPH) EC 1.1. 1.184, and 15-hydroxyprostaglandin dehydrogenase (NADP+), EC I. 1.1.197: database code DHCA_HUMAN, 276 amino acids (30.21 kDa). prostaglandin-E synthase EC 5.3.99.3; other names: prostaglandin-H 2 E-isomerase; endoperoxide isomerase; an enzyme that catalyses the conversion of (52,13E)-(l5S)9a, Ila-epidioxy-15-hydroxyprosta-5,13-dienoate to (52,13E)(15S)-lla, 15-dihydroxy-9-oxoprosta-5, 13-dienoate (PGE 2). Glutathione is a cofactor. prostaglandin-F synthase EC 1.1.1.188; other name: prostaglandin-D 2 II-reductase; an enzyme that catalyses the formation of (52, 13E)-(I5S)-9a, Ila, 15-trihydroxyprosta5,13-dienoate and NADP+ from (52, 13E)-(15S)-9a, 15-dihydroxy-ll-oxoprosta-5,I3-dienoate and NADPH. It is a monomeric protein of the prostaglandin biosynthetic pathway. Example of bovine enzyme (precursor): database code PGFS_BOVIN, 322 amino acids (36.55 kDa). prostaglandin-I synthase EC 5.3.99.4; other name: prostacyclin synthase; an enzyme that catalyses the conversion of (52, 13E)-(l5S)-9a, Ila-epidioxy-15-hydroxyprosta-5, 13dienoate to (52, 13E)-( 15S)-6,9a-epoxy-11 a, 15-dihydroxyprosta-5,13-dienoate (PGI 2 , prostacyclin). This is a hemethiolate protein. Example from human: database code JC223 I , 500 amino acids (57.04 kDa). prostanoate the anion of prostanoic acid, 2-octylcyclopent-

prostanoid

539

aneheptanoic acid; the 8S,12S form is the parent compound for prostanoid nomenclature. For structure, see prostaglandin. prostanoid any compound based on or derived from the prostanoate structure, including the prostaglandins, prostacyclins, and thromboxanes. prostasin a serine protease with trypsin-like activity, found in human seminal fluid. prostate-specific antigen abbr.: PSA; a proteinase which is virtually prostate specific. Levels may be elevated in prostate hypertrophy but the release into the serum from cancer is higher than from normal tissue. It is a much better marker than acid phosphatase, being elevated at an earlier stage of the tumour. PSA is a serine endopeptidase belonging to the family of glandular kallikreins with a His-Asp-Ser charge-relay system. Its physiological substrate is the predominant protein of the seminal vesicle coagulum. It can be isolated from prostate epithelial cells and seminal plasma. Example from human (precursor): database code PROS_HUMAN, 261 amino acids (28.74 kDa); residues 1-18 are a signal sequence, 19-24 a propeptide, and 25-261 PSA. prostatic of, pertaining to, or related to the prostate gland. prosthetic group a nonprotein group that is combined specifically with a protein, in stoichiometric proportion. protachykinin II precursor a preproprotein from which certain polypeptide hormones are cleaved, not all by the same processing pathway. Example from human: database code TKNB_HUMAN, 129 amino acids (14.99 kDa). Derived peptides: substance P, residues 58-68; neurokinin A, residues 98-107; neuropeptide K, residues 72-107; residues 68 and 107 are C-amidated in the derived peptides. See also tachykinin. protamine any of a group of small peptides, containing arginine, alanine, and serine, that are isolated from the sperm of fish (e.g. salmon, herring, sturgeon, trout, and mackerel), but present in the sperm of all animals. They have a histone-like function in the chromatin of sperm, compacting sperm DNA into a condensed complex. Example, sperm protamine PI from Alouatta seniculus (howler monkey): database code HSPI_ ALOSE, 51 amino acids (6.82 kDa). protamine sulfate a sulfated derivative of a protamine. Protamine sulfates combine with, and inactivate, heparin, and are used to prevent bleeding in heparin overdose. protease a former name for any enzyme that catalyses the hydrolysis of peptide bonds in a protein or polypeptide. The specific names endopeptidase, aminopeptidase, and carboxypeptidase are now recommended. See also proteinase. protease inhibitor 4 see kallistatin. protease nexin I see nexin 1. proteasome or proteosome EC 3.4.99.46 recommended name: multicatalytic endopeptidase complex; other names: multicatalytic proteinase (complex); ingensin; macropain; prosome; lens neutral proteinase. Proteasomes are large multi-subunit protease complexes that selectively degrade intracellular proteins. Most of the proteins removed by these proteases are tagged for destruction by ubiquitination. Proteasomes playa role in controlling cellular processes, such as metabolism and the cell cycle, through signal-mediated proteolysis of key enzymes and regulatory proteins. They also operate in the stress response, by removing abnormal proteins, and in the immune response, by generating antigenic peptides. The proteolytic activity is due to a 26S protease, which is a 2 MDa complex. The ability of this 26S protease to degrade proteins generally depends on both the ubiquitination of the substrate and the presence of ATP. The core of the 26S protease is a 20S particle that carries the catalytic activity. It is this 20S particle that was first isolated, and was called 'multicatalytic proteinase' because it possessed trypsin-like, chymotrypsin-like and peptidyl-glutamyl activities, with the ability to cleave peptide bonds carboxy-terminal to basic, hydrophobic, and acidic residues. The 20S particle does not require ATP for activity. Following the determination of the crystal structure of this core from the Archaeon Thermoplasma acidophilum, the struc-

protegrin ture has been clarified. The proteasome itself is inactive and requires two specific subunits of a 19S particle to mediate recognition of ubiquitin-protein conjugates. The proteasome subunits are arranged in four heptameric rings which are stacked together to form a hollow cylinder with the protease activity on the inside. The active site nucleophile is threonine. The size of the channel in the cylinder is such that the protein substrate first must be unfolded and the disulfide bonds reduced. In Thermoplasma, the two outer rings of the 20S proteasome are composed of seven a subunits, and each inner ring contains seven ~ subunits, an organization that is likely also to apply in eukaryotic 20S proteasomes. The enzyme catalyses the cleavage at Xaa-I- bonds in which Xaa carries a hydrophobic, basic, or acidic side chain. Components (all examples are human): c2 (other names: macropain subunit c2; proteasome v chain; multicatalytic endopeptidase complex subunit c2; 30 kDa proteasomal protein): database code PRC2_HUMAN, 263 amino acids (29.52 kDa); c3 (EC 3.4.99.46; other names: macropain subunit c3; multicatalytic endopeptidase complex subunit c3): database code PRC3_ HUMAN, 233 amino acids (25.74 kDa); c5 (other names: macropain subunit c5; proteasome y chain): database code PRC5_HUMAN, 241 amino acids (26.46 kDa); pro teas orne chain 7 (other names: macropain chain 7; multicatalytic endopeptidase complex chain 7; ring 12 protein): database code PRC7_HUMAN, 219 amino acids (23.24 kDa); proteasome component c8 (other names: macropain subunit c8; multicatalytic endopeptidase complex subunit c8): database code PRC8_HUMAN, 254 amino acids (28.27 kDa); proteasome component c9 (other names: macropain subunit c9; multicatalytic endopeptidase complex subunit c9): database code PRC9_HUMAN, 261 amino acids (29.45 kDa); proteasome ~ chain (other names: macropain ~ chain; multicatalytic endopeptidase complex ~ chain (fragment»: database code PRCB_HUMAN, 28 amino acids (2.79 kDa); component cl3 (other names: macropain subunit cl3; multicatalytic endopeptidase complex subunit cl3): database code PRCC_HUMAN, 208 amino acids (23.03 kDa); /) chain (other names: macropain /) chain; multicatalytic endopeptidase complex /) chain): database code PRCD_HUMAN, 205 amino acids (21.68 kDa); Echain (other names: macropain E chain; multicatalytic endopeptidase complexE chain; proteasome chain 6 (fragment»: database code PRCE_HUMAN, 26 amino acids (2.32 kDa); component mecl-I (other names: macropain subunit mecl-l; multicatalytic endopeptidase complex subunit mecl-l): database code PRCF_HUMAN, 273 amino acids (28.90 kDa); l' chain (other names: macropain l' chain; multicatalytic endopeptidase complex l' chain; 27 kDa proteasomal protein (also in rat»: database code PRCLHUMAN, 246 amino acids (27.37 kDa); ~ chain (other names: macropain ~ chain; multicatalytic endopeptidase complex ~ chain): database code PRCZ_HUMAN, 241 amino acids (26.44 kDa). protectin see CD59. protecting group or protective group or blocking group any chemical group added to a reactive centre of a molecule to prevent it from reacting during chemical treatments in which it is not intended to participate. Such groups are commonly used during chemical synthesis of macromolecules or shorter polymers of amino acids or nucleotides. Reagents contributing protecting groups should react readily under mild conditions, with high specificity, and lead to addition of a group that can be removed highly specifically under mild conditions. For protein or amino-acid protecting groups see aminoethyl, Boc, citraconylation, DABITC, dabsyl, dansyl, Fmoc, maleylation, pipsyl, silylation, succinylation, tosyl, triphenylmethyl group. protegrin abbr.: PG; any of a group of leukocyte antimicrobial peptides, denoted PG-I to PG-5, that are active against Escherichia coli, Listeria monocytogenes, and Candida albicans in vitro. Like tachyplesins they contain two intramolecular cystine disulfide bonds and show homology to defensins. Example, protegrin I (precursor) from Sus scrofa: database code

540

protein PGl_PIG, 149 amino acids (16.67 kDa); protegrin 1 is residues 131-148. protein any of a large group of organic compounds found as major macromolecular constituents of living organisms. All enzymes are proteins, although catalytic activity is shown by some nucleic-acid molecules (see ribozyme). A protein is a linear polymer of amino acids linked by peptide bonds in a specific sequence. In the biosynthesis of the polypeptide chain, any of 20 different amino acids may be incorporated, according to the genetic instructions of the cell (see protein and peptide biosynthesis). The amino-acid residues may be modified subsequently so that the chains may contain a much wider variety of residues, amounting to nearly 200. The modifications may involve the covalent attachment of various groups such as carbohydrates and phosphate; these are the simple proteins. Other substances may be more loosely associated with the polypeptide chains, such as heme or lipid, giving rise to the conjugated proteins. Four hierarchies of structure may be detected in the polypeptide chains: primary structure is the order of the specific amino-acid residues; secondary structure is the way the aminoacid residues interact within a chain to form structures such as the alpha helix and the beta strand; tertiary structure signifies the way in which an entire single polypeptide chain (or chains linked by disulfide bonds) folds to form a three-dimensional structure; and quaternary structure is the interaction between intact chains to form multi-subunit proteins. The various ways in which the polypeptide chains fold have been elucidated, in particular with regard to the presence of alpha helices and betapleated sheets. Four types of proteins may be classified: allalpha; all-beta; alpha/beta; and alpha + beta. Some important protein types are listed separately in this dictionary and many others are listed individually: contractile proteins (actin, myosin, tropomyosin, tubulin), heat-shock proteins, hemoproteins (cytochromes, hemoglobin, myoglobin), lipoproteins, membrane proteins (ATPases, ion channels, rhodopsin), nonheme proteins (blood coagulation factors, serum albumin, serum globulin), nuclear proteins (histones), plasma proteins, and structural proteins (collagen, crystallin, keratin). Nutritional aspects of protein metabolism include the fact that higher animals cannot synthesize certain of the amino acids required for protein synthesis; such amino acids are referred to as essential amino acids. Plants and most microorganisms can synthesize all of the amino acids required for protein synthesis and many others. The nutritional value of different proteins depends on their composition. Some proteins are of poor nutritional value due to lack of essential amino acids, e.g. gliadin, which lacks lysine, and zein, which lacks lysine and tryptophan. -proteinaceous adj. 14-3-3 protein any of a highly conserved family of proteins, widespread in higher eukaryotes, that seem to act as regulators in signal transduction or phosphorylation. The name derives from the migration position on DEAE-cellulose columns, and on starch-gel electrophoresis, of certain brain proteins that were the first members of the family to be studied. Members of this family have been implicated in regulation of protein kinase C, transcriptional regulation in plants, exocytosis, cell-cycle regulation, and interaction with Raf in the MAP kinase cascade. For example, 14-3-3 protein ~ (other name: protein kinase C inhibitor protein-I) from sheep activates tyrosine and tryptophan hydroxylases in the presence of Ca2+/calmodulin-dependent protein kinase II. The bovine equivalent has an identical sequence: it is a homodimer: database code 143B_BOVIN, 244 amino acids (27.82 kDa). protein A a bacterial cell-wall protein, found in many strains of Staphylococcus aureus, that can bind, without masking the antigen-binding site, to the Fc region of IgG. It binds weakly to humanqgA, IgE, and IgM but fails to bind to human IgG 3 and IgD; it does not bind to cell Fc receptors. The purified protein or a preparation of cells of S. aureus that carry protein A is widely used as an immunochemical reagent, often in an immobilized form on affinity columns, for isolation and purification of immunoglobulins and, by forming ternary com-

protein and peptide biosynthesis plexes, of antigens and immune complexes. It is also used as a binding reagent in enzyme-linked immunoassay, in histochemistry, and in blotting techniques. protein and peptide biosynthesis the biochemical synthesis of proteins. Biochemists became actively concerned with the elucidation of the mechanism of protein synthesis from about 1950. The classical pathway was expected to involve the utilization of enzymes to synthesize peptide intermediates, which would sequentially be linked together, but it soon became apparent that the number of enzymes involved would be horrendous and, moreover, there was no evidence that such peptide intermediates existed in living cells. Although there was a suggestion that peptide bonds were synthesized by transpeptidation using proteolytic enzymes, on theoretical grounds there was increasing support for the concept that the amino acids would first be aligned on a template and then be sequentially linked by peptide bonds. Following the elucidation of one structure for DNA in 1953 it was confidently predicted that the template would be nucleic acid. Shortly after, in 1955, P. C. Zamecnik and his group in Boston demonstrated the synthesis of a polypeptide by the isolated microsome fraction from rat liver. This involved the presence of particles (ribosomes), a soluble extract of the cell, and ATP and GTP. As will be described, the synthesis of most peptides in living cells depends on the presence of ribosomes. This includes the small peptide hormones, such as oxytocin and vasopressin, which are synthesized as polyproteins. Other peptides are not synthesized by means of ribosomes. Thus glutathione is synthesized by soluble enzymes in two steps. Many biologically active peptides, especially cyclic structures, are products of microorganisms. These include such antibiotic peptides as gramicidin S, the tyrocidines, and the polymyxins. The systems responsible for their synthesis consist of interacting multienzymes in which activated amino acyl groups are transferred onto -SH groups to form intermediate thioesters. The multienzymes are unusual in size, ranging from 120 to 1700 kDa. The respective genes consist of repeating modules, each encoding the incorporation of one amino-acid residue. The genes are arranged in clusters associated with genes encoding auxiliary proteins for the synthesis of precursors, modifying enzymes, exporting proteins, and regulatory systems. In addition to the amino acids and ATP, S-adenosylmethionine is required as methyl group donor if N-methylated bonds are involved. Due to their complexity (cyclosporin synthase for example, integrates 40 reactions on one polypeptide chain), the multienzyme systems have low turnover numbers. It has been possible to set up cell-free systems for the production of various peptides and their analogues. With respect to the synthesis involving ribosomes it was shown that the first step was the activation of the amino acids to form amino-acid adenylates. The amino acids were then transferred to an RNA present in the soluble extract of the cell, and so named soluble RNA but later termed transfer RNA (tRNA) to which the amino acids became attached by an ester linkage. The template was then found to be messenger RNA (mRNA), which associates with the ribosomes themselves. Although the ribosomes themselves contain much RNA it came as a surprise that this did not serve as a template. The translation of the triplet codons in mRNA to provide a polypeptide involves three steps: chain initiation, chain elongation (see elongation factor), and chain termination (see release factor). Chain initiation normally starts with the codon for methionine, AUG. For this purpose a unique initiator tRNA is involved. Many protein factors play a part in the three processes and five molecules of ATP and GTP participate. The ribosomes participate in a cycle during which they subdivide into their two subunits only to reassemble. Hence the synthesis of a peptide bond is a surprisingly expensive process in terms of cell physiology. The targeting of the newly synthesized proteins to their final destination is termed protein kin-

541

proteinase esis. The mechanism of ribosomal protein synthesis is very

similar in all types of cell but there are subtle differences between prokaryotes and eukaryotes, which account for the differential action of antibiotics such as chloramphenicol and cycloheximide. Apart from differences in the number and properties of the soluble factors the main difference involves chain initiation: in prokaryotes this is by way of formylmethionine while in eukaryotes, apart from mitochondria, this involves methionine. proteinase name introduced in 1928 to distinguish a sub-class of proteases that catalyse the hydrolysis of peptide bonds more readily in an intact protein than in small peptides. It is still widely used. Endopeptidase is now recommended. proteinase K EC 3.4.21.64; recommended name: endopeptidase K; other name: Tritirachium alkaline proteinase. A serine proteinase enzyme that catalyses the hydrolysis of keratin, and of other proteins with subtilisin-like specificity. Example from the fungus Tritirachium album: database code NRL_2PRK, 279 amino acids (28.88 kDa); 3-D structure of this, and with inhibitor bound, is known. proteinase VB see glutamyl endopeptidase. protein B a cell-surface protein of group B Streptococcus species that binds specifically to the Fc region of human IgA, without affecting its antigen-binding capacity, but not to other immunoglobulins or serum proteins. It is used in enzyme-linked immunoassay and blotting techniques. protein biosynthesis see protein and peptide biosynthesis. protein-bound iodine abbr.: PBI; that fraction of iodinated molecules bound to protein in serum. It is due largely to thyroxine (T 4)' 99.97% of which in human serum is present bound to the binding proteins T4 -binding globulin, T 4 -binding prealbumin and albumin, but also to T 3, 99.7% of which is bound to the same proteins. Determination of PBI (now replaced by immunoassay) was used for estimation of blood thyroid hormones as a basis for assessment of thyroid function. protein C a vitamin K-dependent glycoprotein that is the zymogen of a serine endopeptidase in normal blood plasma; M r 62000 (human), 54300 (bovine). It is formed from a precursor, autoprothrombin lIA, which is cleaved into a light chain and a heavy chain held together by a disulfide bond to form protein C. Thrombin cleaves a tetradecapeptide from the amino end of the heavy chain; this reaction, which occurs at the surface of endothelial cells, is strongly promoted by thrombomodulin; protein C then becomes the enzyme protein C (activated), EC 3.4.21.69. This activated form specifically hydrolyses factors Va and VIlla to inactive forms (in a reaction requiring phospholipid, calcium, and protein S), thereby acting as a potent anticoagulation factor; it contains 10-12 y-carboxyglutamyl residues in the N-terminal 40 residues. Example (precursor) from human: database code PRTC_ HUMAN, 461 amino acids (52.01 kDa). A congenital deficiency of protein C (usually autosomal dominant) is often not compatible with survival, or leads to hemorrhagic disease of the newborn. Protein C is so named because it eluated from columns as the third of four peaks labelled A, B, C, and D. protein C23 see nucleolin. protein C-binding protein see apolipoprotein H. protein disulfide-isomerase EC 5.3.4.1; other name: disulfide rearrangase; an enzyme that enhances the rate of interchange in the groups attached to two or more intrachain or interchain disulfide bonds in a protein. It was originally described by Anfinsen in 1966 concerning the reversible denaturation of ribonuclease and then called 'rearrangase'. It has since been shown to be a luminal protein of the endoplasmic reticulum. It is a homodimer; two of its domains are homologous to thioredoxin of Escherichia coli. It is also the triacylglycerol transfer protein (MTP) that facilitates the incorporation of lipids into newly synthesized core lipoproteins within the endoplasmic reticulum. It serves as the ~ subunit of procollagenproline dioxygenase. Examples: probable protein disulfideisomerase er-60 precursor from human (other names: erp60; 58

protein-glutamine y-glutamyltransferase kDa microsomal protein): database code ER60_HUMAN, 505 amino acids (56.64 kDa); precursor (human) of this and also prolyl 4-hydroxylase ~ subunit (EC 1.14.11.2) and cellular thyroid hormone binding protein (p55): database code POI_HUMAN, 508 amino acids (57.04 kDa). protein engineering the process whereby a protein of any desired primary structure can (in principle) be created by the use of recombinant DNA technology. The ability to express DNA in a bacterium such as Escherichia coli creates the potential to synthesize a protein with the desired primary structure. Bacteria cannot effect post-translational modifications so if these also are required a eukaryotic host cell such as yeast must be employed. In principle there are no problems with the proteins of bacterial cells but introns present in the genome of eukaryotic cells present a potential problem. This can be overcome by preparing complementary DNA, eDNA, which is synthesized by the use of the mRNA as template and the enzyme reverse transcriptase. There are several ways whereby the DNA for the required protein may be prepared by modification of the base sequence of the natural DNA. DNA may be used that contains inserts of synthetic oligonucleotides, or stretches replaced by these. Oligonucleotide-directed mutagenesis may be used to modify a single base to produce a protein with a single amino-acid replacement. This is done by preparing an oligonucleotide primer with the modified sequence which will base pair with the natural DNA around the site to be altered; a single base substitution still permits satisfactory pairing. The primer is elongated by DNA polymerase and the doublestranded circle closed by DNA ligase. A specific deletion can be obtained by cleaving a plasmid at two sites with a restriction enzyme and religating to form a smaller circle. A smaller deletion can be obtained by cutting a plasmid at a single site. The ends of the linear DNA are then digested with an exonuclease that removes nucleotides from both strands and the shortened piece of DNA is religated. protein folding disease any disease that results from the abnormal folding of a protein. Prion diseases are examples of such diseases that can be inherited or acquired; Alzheimer's disease is a different type of disease, caused by alternative folding of proteins derived from the amyloid precursor. protein G a bacterial cell-wall protein isolated from group G streptococci. Its properties and uses are similar to those of protein A, but it does not bind to IgM, IgD, or IgA; it does bind to all subclasses of human IgG, and animal immunoglobulins with which protein A does not react well. protein gene product anyone of the proteins or protein subunits synthesized biochemically on the basis of information encoded in a genome, whether generated at translation or by post-translational modification; the pattern of protein gene products formed or capable of being formed by an organism is unique to anyone genotype. Individual proteins are often referred to using the symbol p followed by the relative molecular mass, e.g. p53. The protein may be further identified by adding an indication of its origin as a superscript, e.g. p2l'as. A protein gene product may also be referred to by the name of the gene that encodes it, but normal font is used instead of italics, with a capital initial followed by lower case characters, e.g. Src protein encoded by SRC gene. protein-glutamate methylesterase a chemotaxis protein encoded by cheB (see che). protein-glutamine y-glutamyltransferase EC 2.3.2.13; systematic name: protein-glutamine:amine y-glutamyltransferase; other names: transglutaminase, factor XlIla; the enzyme activity of blood coagulation factor Xilla. It forms inter- and intramolecular links between a y-carboxyl group of a glutamine residue of a protein and the a-amino group of a lysine residue, releasing ammonium ion. Its natural substrate is the fibrin monomer, and its function is to link these into polymers. The protein is a heterotetramer of two each of the A and B chain,

542

protein intron the A chain bearing the catalytic activIty. Examples from human, A chain: database code F13A_HUMAN, 731 amino acids (83.14 kDa); residues 1-37 are a propeptide that is cleaved from the A chain by thrombin in the conversion of factor XIII to XIIIa; B chain (precursor): database code F13B_HUMAN, 661 amino acids (75.49 kDa); residues 1-20 are the signal peptide; the molecule contains ten Sushi domains. protein intron see intein; splicing (def. 3). protein kinase any of a number of enzymes that phosphorylate one or more hydroxyl or phenolic groups in proteins, ATP being the phosphoryl-group donor. Two classes are recognized: those that phosphorylate seryl or threonyl hydroxyls, and those that phosphorylate tyrosyl phenolic groups. The first class contains enzymes that were classically identified as regulating pathways of intermediary metabolism (e.g. glycogen phosphorylase kinase); subsequently, protein kinase A (cyclic-AMP-dependent protein kinase) and protein kinase C were recognized in this class. Enzyme activity of the second class is found in some cytokine receptors such as platelet-derived growth factor receptor and epidermal growth factor receptor and in oncogene products such as that of SRC. Over 110 unique gene products are known to make up the protein kinase superfamily; important motifs include GXGXXG ...AHK and APE... DXWSXG, which are common to both serine/threonine- and tyrosine-specific activities. The tyrosine-specific kinase activity associated with the cytoplasmic domains of certain cytokine receptors forms part of an important signaltransduction mechanism implicated in cell growth (see tyrosine kinase). protein kinase A an alternative name for cyclic-AMP-dependent protein kinase. protein kinase C abbr.: PKC; any of a family of protein kinase enzymes identified following discovery of a protein kinase requiring anionic phospholipid for activity, and regulated by diacylglycerol and Ca2 +. They phosphorylate hydroxyl groups in substrate serine and threonine residues. Several isoforms have now been characterized: cr, ~], ~2, y, 8, E, 1;, e, 1], t, and J.I. Four conserved regions are recognized, C], C 2 , C 3 , and C4 ; C 3 and C4 comprise the C-terminal half of the molecule and bear the active site, including the ATP-binding sequence GXGXXG... K. PKC-E is Ca 2+-independent, and 8, E, and I; lack the homologous C2 region. Activation of PKC occurs when plasma membrane receptors coupled to phospholipase C are themselves activated, releasing diacylglycerol. Phorbol ester tumour promoters can substitute for diacylglycerol in enzyme activation, which may indicate their mechanism of action, and much evidence points to PKC activation being involved in cell-growth stimulation. Inhibitors of PKC attract considerable interest, and include bisindolylmaleimide, 1-0hexadecyl-2-0-methylglycerol, melittin, phloretin, polymyxin B, and staurosporine. Examples: u from Bos taurus: database code KPCA_BOVIN, 672 amino acids (76.84 kDa); ~2 from Oryctolagus cuniculus: database code KPC2_RABIT, 673 amino acids (76.97 kDa); 8 from Mus musculus: database code KPCD_MOUSE, 674 amino acids (77.59 kDa). protein kinesis the directed movement of proteins from their site of synthesis to specific targets within cells and the modulation by proteins of interactions among intracellular organelles. It is a factor in generating subcellular compartments and determining the way in which reactions are compartmentalized to control metabolic processes. It embraces the mechanisms for ensuring that proteins reach their site of action and that the amounts and locations of particular proteins are controlled during development, during the cell-division cycle, in combating pathological states of the cell, and during apoptosis. protein mapping the resolution of a mixture of proteins into a two-dimensional pattern (i.e. map) by successive use of two differing separative procedures, as in isoelectric focusing followed by gradient gel electrophoresis, the pattern being rendered visible by an appropriate detection method. protein phosphatase any enzyme that hydrolyses phosphate

protein

Z

groups from proteins. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity. Protein phosphatases are classified into several groups. Class I enzymes are mainly specific for seryl- or threonyl-phosphate. Within this class, phosphatase I is ATP,Mg 2+ -dependent (AMD phosphatase); it consists of a catalytic subunit of 38 kDa and a modulator subunit of 23 kDa, which is subject to phosphorylation, thus activating the phosphatase. Phosphatase 2A is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone HI; it constitutes a subclass of several enzymes activated by different histones and polylysine. These have a very high affinity for the tumour promoter okadaic acid. Phosphatase 2B (or calcineurin) is a heterodimer; one of the subunits, of 61 kDa, contains the catalytic site, a high-affinity calmodulin-binding site, and a binding site for the other subunit, a 19 kDa, Ca 2+_ binding protein. Phosphatase 2C is a Mg2+-dependent monomeric 43 kDa protein; it has been purified as myosin light chain phosphatase, but is active against the phosphorylated forms of glycogen synthase, 6-phosphofructo-l-kinase, pyruvate kinase, fructose 1,6-bisphosphatase, and 6-phosphofructo-2-kinase. Class II enzymes hydrolyse tyrosylphosphates, and are generally designated 'phosphatase 3'. They are subdivided into those that are cytoplasmic, and others that are membrane-bound and may have receptor properties. Example of phosphatase 2A from human: database code P2AA_ HUMAN, catalytic subunit 309 amino acids (35.55 kDa); same in rabbit. This enzyme can modulate the activities of phosphorylase kinase b, casein kinase 2, mitogen-stimulated S6 kinase, and MAP-2 kinase. It is a cytoplasmic enzyme that exists in several oligomeric forms, all of which contain a catalytic (C) subunit (36-38 kDa) associated with one or both of two putatively regulatory subunits, the A subunit (61-65 kDa) and the B subunit (51-55 kDa). Example of protein tyrosine phosphatase, leukocyte antigen-related PTPase precursor from human: database code LAR_HUMAN, 1897 amino acids (211.60 kDa). protein-N"-phosphohistidine-sugar phosphotransferase EC 2.7.1.69; systematic name: protein-N"-phosphohistidine:sugar N"-phosphotransferase; other name enzyme II; any of a group of related membrane-bound bacterial enzymes, part of the phosphoenolpyruvate-dependent sugar phosphotransferase system for the transport of hexoses across the cell membrane. It involves phosphorylation of a protein substrate (9.5 kDa), a phosphocarrier known as HPr. Individual enzymes are specific for a range of sugars. They catalyse the reaction: protein N"-phosphohistidine (HPr) + sugar = protein histidine + sugar phosphate; example from Escherichia coli: database code PT2G_ECOLI, 477 amino acids (50.62 kDa). protein S a single-chain glycoprotein occurring in blood, M r 69 000. It is a vitamin K-dependent protein (not a proteinase) that promotes the binding of protein C to platelets, and functions as a cofactor for the anticoagulant activity of activated protein C. It is named after Seattle, where it was discovered. protein splicing see splicing. protein synthesis 1 (in cell biology) see protein and peptide biosynthesis. 2 (in chemistry) see peptidesynthesis (def. 2). protein thiotemplate mechanism see thiotemplate mechanism. proteinuria the presence of protein in urine. Normal excretion of protein in human urine is less than 0.1 mg every 24 h, about half of which is Tamm-Horsfall glycoprotein, and about 20% is albumin. Protein may appear in urine due to extrarenal factors such as fever, strenuous exercise, or burns; direct involvement of the kidney occurs in the nephrotic syndrome, which may arise from several causes, such as diabetic nephropathy, cancer of the kidney, or various forms of glomerulonephritis of unknown etiology. protein Z a major protein of barley endosperm albumin. It is

543

proteoclastic

proton number

structurally similar to a serpin, but its main role is as a storage protein, being especially rich in lysine. Database code PRTZ_HORVU, 399 amino acids (22 lysine), 43.23 kDa. proteoclastic an obsolete term for proteolytic. proteoglycan any glycoprotein in which the carbohydrate units are glycosaminoglycans. proteolipid a term variously applied to describe certain hydrophobic membrane proteins, or any other protein, that has a lipid moiety covalently bound to one or more of its constituent amino acids. Many such proteins are soluble in chloroform-methanol, a property that was significant in their first identification. proteoliposome a Iiposome into which a specific protein, or group of proteins, has been incorporated. proteolysis degradation of a protein, usually by hydrolysis at one or more of its peptide bonds. -proteolytic adj. proteolytic enzyme see peptidase. proteome the complete expression profile of the proteins of an organism. See also proteomics. proteomics the study of the proteome by the analysis of protein structure and composition. proteosome a variant spelling of proteasome. prothrombin an alternative name for factor II; see blood coagulation. protide 1 symbol: 'H-; a hydride (def. I) ion derived from an atom of protium. 2 any hydride (def. 2) formed from protium. 3 or protid a generic name embracing protein, peptide, or amino acid, suggested by analogy with glucide and lipid(e). Its use in English is largely restricted to translations or abstracts from French. -protidic adj. protio+ comb. form indicating that one or more atoms of hydrogen in a hydrogen-containing chemical compound consists exclusively of protium. Protista a taxonomic grouping of eukaryotic organisms that are unicellular, coenocytic, or multicellular but that are not classified as fungi, animals, or embryophytes. protium symbol: IH; hydrogen-I, the nuclide of hydrogen, lH, of relative atomic mass 1.008. It is a stable isotope, having a relative abundance in natural hydrogen of 99.98 atom percent. The name is used especially when distinction from deuterium or tritium is required. protoalkaloid an alkaloid that does not contain a heterocyclic ring, e.g. damascenine in Nigella spp. protobiont one of the postulated first precursors of cells, supposed to have arisen when a boundary or membrane formed around one or more macromolecules possessing catalytic properties. Compare coacervate droplet. protochlorophyllide Mg2+-vinylpheoporphyrin As methyl ether; an intermediate in the synthesis of chlorophyll, it is formed from Mg2+-protoprophyrin, and converted to chloro-

protochlorophyllide a

phyllide by NADPH:protochlorophyllide oxidoreductase (EC 1.3.1.33). Protochlorophyllides may be suffixed with the letter of the related chlorophyll, e.g. protochlorophyllide a. protochlorophyllide holochrome a pigment protein complex that carries out a light-catalysed reduction of protochlorophyllide to chlorophyllide with an external hydrogen donor, which is probably strongly bound NADPH. The enzyme involved in regenerating NADPH is NADPH·photochlorophyllide oxidoreductase; it is a single polypeptide, M r 36 000, and is only one component of the complex protein entity of the holochrome. protocollagen collagen chains in which proline and lysine residues have not been hydroxylated. Protocollagens may be produced by experimental inhibition of the relevant hydroxylases either by use of a chelating agent or by imposed anaerobiosis. Compare procollagen. protoheme or (esp. Brit.) protohaem the iron-porphyrin prosthetic group of the cytochromes b. protohemin see hemin. protokaryon an obsolete term for prokaryon. protokaryote an obsolete term for prokaryote. protolysosome see primary lysosome. protomer any of the subunits of an oligomeric protein that are identical. See also monomer, oligomer. -protomeric adj. proton 1 symbol: IH+; the cation derived from an atom of protium; a hydrogen ion of nucleon number unity; used in this sense especially when distinction between 'H+, 2H+ (i.e. deuteron), and 3H+ (i.e. triton) is needed; any solvated species is included. 2 symbol: H+; commonly used term for the cation derived from any atom of natural hydrogen (of which a small proportion is deuterium) by loss of its orbital electron; any solvated species is included. See also hydrogen ion, hydron. 3 symbol: p; a nuclear particle of nucleon number unity, having a charge equal and opposite to that of an electron and having a mass of 1.007 276 470 (12) Da. -protonic adj.. proton magnetic resonance abbr.: PMR or pmr; see nuclear magnetic resonance spectroscopy. proton magnetogyric ratio symbol: yp; a fundamental physical constant, of value 2.675 221 28(81) x 10 8 S-1 T-'. See also gyromagnetic ratio. protonmotive indicating, or related to an ability to transport protons (Le. hydrons). protonmotive Q cycle a hypothetical mechanism put forward to explain the protonmotive and redox properties of certain components of the respiratory chain in the coupling membrane of bacteria, mitochondria, and chloroplasts. The Q cycle applies to the part of the respiratory chain involving passage of electrons through cytochrome b. Essentially, the cycle accepts two hydride ions from a reduced flavoprotein (e.g. of complex I or complex II of the respiratory chain; see complex I, II, III, IV) passes electrons singly to cytochrome Cl and releases the two hydrons to the intermembrane space. Ubiquinone is the molecule that accepts the hydride ions, and releases the electrons and hydrons. Cytochromes bS66 and bS62 are involved in shuttling electrons between different oxidation states of ubiquinone during the cycle. The property of ubiquinone that it can exist as a semiquinone is important in the switch from twoelectron to one-electron transfer. proton number or atomic number symbol: Z; a dimensionless physical quantity, with a unique integral value for each chemical element, that is equal to the number of protons contained in the nucleus of each atom of the element irrespective of the mass of any particular atom. It also is equal to the number of unit positive charges on the nucleus of each atom of a given chemical element, to the number of orbital electrons surrounding the nucleus of an un-ionized atom of that element, and, for a specific nuclide of that element, to the arithmetical difference between the nuclide's nucleon number, A, and its neutron number, N; i.e. Z = N - A. The proton number of an element determines the position of the element in the periodic

544

proton relaxation enhancement table. It may be attached to the symbol for the element as a left subscript, e.g. 6C, proton pump another term (esp. in pharmacology) for hydrogenion pump. proton relaxation enhancement abbr.: PRE; a technique that yields information concerning (macro)molecular motion. It depends on the enhancement of the solvent water-proton relaxation rates on addition of a macromolecule. protooncogene a normal gene, usually concerned with the regulation of cell proliferation, that can be converted into a cancer-promoting oncogene by mutation. For example, in the case of the Rous sarcoma virus the viral oncogene is v-src (see src). This is closely related to a normal gene, c-src. The appearance of v-src is believed to have followed the acquisition of a copy of c-src by an ancestor of the Rous sarcoma virus. Through many generations this ancestral gene was mutated and became dominant. Protooncogenes encode proteins involved in all aspects of controlling cell proliferation, including growth factors, growth-factor receptors, nuclear factors regulating gene expression proteins that generate second messengers, and protein kinases. protoplasm the living contents of a cell; i.e. the matter contained within (and including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm. protoplast a spherical, osmotically sensitive plant cell without its cell wall but retaining an intact cell membrane. The cell wall is degraded by digestion with different hydrolytic enzymes, as a mixture or sequentially, e.g. cellulase, hemicellulase. Protoplasts are used to create hybrid cells via protoplast fusion. In some cases they are totipotent, and are thus capable of yielding plants. Such protoplasts can be used in plant transformation. protoporphyrin IX the specific substrate for the enzyme ferrochelatase, which catalyses the insertion of iron to form protoheme. It is also probably the substrate for the insertion of magnesium in the formation of chlorophylls in plants. prototroph any strain of a microorganism (alga, bacterium, or fungus) that does not require any substances in its nutrition additional to those required by the wild type. Compare auxotroph. -prototrophic adj. Protozoa a phylum or subkingdom comprising single-celled eukaryotic microscopic organisms, usually classified as animals. Compare Metazoa, Parazoa. provirus a virus, e.g. a retrovirus, that is integrated into the chromosome of its host cell and can be transmitted through the generations without causing lysis of the host cell. provitamin a compound which is converted to an active vitamin in the body. In practice the term is only applied to carotenes. Pro-X dipeptidase EC 3.4.13.8; recommended name: proUnase; other names: prolyl dipeptidase; iminodipeptidase; proUnase; L-prolylglycine dipeptidase; an enzyme that catalyses the hydrolysis of Pro-I-Xaa dipeptides. It also acts on hydroxyprolyl analogues. proximal protein any protein that binds early in the assembly of complex structures, such as ribosomes. Their presence in the partially assembled structure is required for the binding of distal proteins. proximate carcinogen or proximate carcinogenic metabolite any metabolite of a chemical carcinogen that is itself carcinogenic; the term may embrace ultimate carcinogen. Prozac see fluoxetine. PrP abbr. for prion protein. PRP protein abbr. for pre-mRNA processing protein. PRPP abbr. (not recommended) for phosphoribosyl pyrophosphate (see (5-lphospho(-a-D-)ribosyl diphosphate). PRPP synthetase another name for ribose-phosphate pyrophosphokinase. prunasin (-)-(R)-mandelonitrile P-D-glucoside; a cyanogenic glycoside.

pseudouridine

prunasin

ps symbol for picosecond. P-selectin see selectin. pseudoalkaloid any alkaloid in which the skeleton is partly derived from a terpene. pseudoallele any of two (or more) mutations that are allelic functionally but not structurally. See allele. pseudoaxial (in chemistry) abbr.: a'; see conformation. pseudocholinesterase EC 3.1.1.8; recommended name: cholinesterase; other name: choline esterase II. An enzyme, found in blood and other tissues, that catalyses the hydrolysis of a variety of choline esters and a few other compounds. Compare acetylcholinesterase. pseudoequatorial (in chemistry) abbr.: e'; see conformation. pseudoexon a portion of an exon that is duplicated in an adjacent intron. pseudogene symbol: '1'; a sequence in DNA that is related to a functional gene but cannot be transcribed. This may be due to mutational changes that preclude it from being expressed in the form of functional products or the lack of some flanking control region in the promoter. Pseudogenes mayor may not contain the introns of the functional gene. Examples include pseudogenes for a, p, and 1; globulins in several species, VK chains of immunoglobulins, actin, and tubulin. Processed pseudogenes, or LINES (see LINE), occur in a genome somewhere other than the normal position of the corresponding functional gene and so cannot be expressed because of alterations in regulatory DNA sequences, or coding sequences, or both. pseudoglobulin a globulin that is soluble in solutions of low ionic strength or in pure water. Compare euglobulin. pseudointron an intron that contains 5' and 3' splice sites that are appropriate but not utilized in the excision of the intron. pseudoisoenzyme anyone of the epigenetically derived multiple forms of an enzyme. pseudo-operator a functional operator element within a structural protein-coding region of DNA. pseudopepsin see pepsinogen. pseudoplasmodium see Dictyostelium discoideum. pseudopodium (pl. pseudopodia) a temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm and serving for locomotion and feeding. pseudopodial adj. pseudouridine symbol: 'P; 5-P-D-ribofuranosyluracil; a component of transfer RNA (tRNA) containing a C-C bond between the ribose (C-I) and uracil (C-5). Typical of the minor nucleosides present in tRNA, it is formed by modification of uridine in the original transcript; the chemistry of this process is unclear. When peudouridine occurs in the anticodon of transfer RNA it base pairs with adenine. Compare uridine.

545

pUC vector

psi

OH

OH

pseudouridine

psi 1 symbol: IjI (lower case) or 'J! (upper case); the twenty-third letter of the Greek alphabet. For uses see Appendix A. 2 or p.s.i. abbr. for pounds per square inch (a unit of pressure in the Imperial and US systems of units). PSI abbr. for photosystem I (see photosystem). psicofuranine 6-amino-9-D-psicofuranosylpurine; an antibiotic produced by Streptomyces hygroscopicus, found to have antitumour activity. See also D-psicose. D-psicose a nonsystematic name for the keto-hexose D-ribo-2hexulose. The hydroxyl at C-3 has the opposite configuration to that of D-fructose. It is a component of psicofuranine.

{0;fH 0H 2

H6)-(bH OH OH

a-D-pyranose form

UDPgalactose and sphingosine by sphingosine p-galactosyltransferase, EC 2.4.1.23. It is acylated to a cerebroside by reaction with a long-chain acyl-CoA. psychrometer or wet-and-dry bulb hygrometer a type of hygrometer consisting of two thermometers, one with a wet bulb and one with a dry bulb. The cooling effect of evaporation from the wet bulb creates a temperature difference between the two thermometers, from which the relative humidity can be calculated. psychrophile an organism that grows best at low temperatures (below about 20 0q. -psychrophilic adj. P system a system of blood groups in which the antigenic determinants are oligosaccharides. The antigens are detected on erythrocytes, erythroblasts, platelets, megakaryocytes, fibroblasts, and endothelial cells; they are designated pk, P, and PI' The common phenotypes are PI (antigens PI and P positive) and Pz (P antigen positive); p k phenotypes are rare. Individuals with the p phenotype lack all of the above determinants, having only the core structure lactosylceramide, and have anti-P and anti-p k antibodies. The determinants are: p k (Gb 3Cer): Gal(al-4)Gal(pl-4)GlcCer p (Gb 4 Cer): GaINAc(pI-3)Gal(al-4)Gal(pl-4)GlcCer PI: Gal(al-4)Gal(pl-4)GlcNAc(PI-3) Gal(pl-4)GlcCer. Pt symbol for platinum. PTA abbr. for plasma thromboplastin antecedent (i.e. factor XI); see blood coagulation. PTC abbr. for 1 plasma thromboplastin component (i.e. factor IX); see blood coagulation. 2 phenylthiocarbamoyL Ptd symbol for the phosphatidylgroup. Ptdlns symbol for phosphatidylinositoL Ptdlns4P or Ptdlns-4-P symbol for phosphatidylinositol 4phosphate. Ptdlns(4,5)P2 or Ptdlns-4,5-P2 symbol for phosphatidylinositol 4,5-bisphosphate. pteridine pyrazino[2,3-djpyrimidine; the parent structure of pterins and the pteroyl group. See also xanthopterin.

PSI! abbr. for photosystem II (see photosystem). psilocin 3-[2-(dimethylamino)ethyl]-IH-indol-4-01; a hallucinogenic alkaloid extracted from the mushroom Psilocybe mexicana.

pteroyl 4-[[(2-amino-I,4-dihydro-4-oxo-6-pteridinyl)methyl]amino]benzoyl; the acyl group of pteroic acid, and the structural basis of folate and its derivatives.

P-site abbr. for a peptidyl-tRNA binding site of ribosome; in bacteria this involves the ribosomal proteins L2, L14, Ll8, L24, L27, and L33, and a region close to the 3' end of l6S rRNA. psoralen 6-hydroxy-5-benzofuranacrylic acid a-lactone; a furocoumarin present as a phytoalexin in many plants. It has photosensitizing and phototoxic effects in humans and animals, and is used in photochemistry, intercalating into DNA and forming cross-links on irradiation. See also methoxypsoralen.

PSP abbr. for pancreatic stone protein (see pancreatic thread protein). psychosine l-O-P-D-galactosylsphingosine; it is formed from

PTFE abbr. for polytetrafluoroethylene. PTH abbr. for 1 parathyroid hormone (Le. parathyrin). 2 phenylthiohydantoin; as in PTH-amino acid (i.e. the phenylhydantoin derivative of an amino acid). PTI abbr. for pancreatic trypsin inhibitor. PTM abbr. for post-translational modification. PTS abbr. for phosphoenolpyruvate-dependent sugar phosphotransferase system. ptyalin a substance in saliva, identified as a-amylase. Pu symbol for plutonium. pUC vector any of a series of plasmid cloning vectors having an

546

PUFA

purinoceptor

ampicillin resistance gene and part of the lacZ gene containing multiple cloning sites (MCSs). Different members of the series (e.g. pUCI8, pUCI9) vary in the restriction enzyme recognition sites included in the MCS. They are high copy number plasmids and so can be purified by rapid, small-scale methods of isolation. A related series of bacteriophage M 13 vectors, the M13mp vectors, contain the same MCS and are useful for DNA sequencing. See also Messing vector. PUFA abbr. for polyunsaturated fatty acid. puff any discrete, localized expansion occurring at specific sites in polytene chromosomes, e.g. the giant salivary gland chromosomes in Diptera. Typically a few micrometres long, they are believed to be a gene or group of genes that are actively synthesizing RNA, which accounts for a considerable part of the mass of the puff. See also Balbiani ring. 'pull' model a nickname for the Monod-Wyman-Changeux model (for ligand-induced changes in protein conformation) because, in this model, ligands influence the equilibrium between enzyme states by sequestering the enzyme in ligand-bound forms. Compare 'push' model. pull ulan an extracelhilar glucan elaborated by Aureobasidium pullulans (yeast form) and formed by other fungi. It is a linear structure with both (l--74)-a-o- and (I--76)-a-o-linkages. Pulhilan is used as a non"caloric material, a water-retention agent, and as a film and fibre former. pullulanase 1 isopullulanase EC 3.2.1.57; an enzyme that catalyses the hydrolysis of pullulan to isopanose (i.e. 6-a-maltosylglucose). 2 neopullulanase EC 3.2.1.135; an enzyme that catalyses the hydrolysis of pullulan to panose (i.e. 6-a-o-glucosylmaltose). 3 see a-dextrin endo-1.6-a-dlucosidase. pulsed field gel eleotrophoresis abbr.: PFGE; a type of gel electrophoresis in which large fragments of DNA can be separated by continuously altering the angle at which the electric current is applied. pulse radiolysis a technique whereby reactive chemical species are generated by pulses of high-energy radiation and the Subsequent reactions of these species are followed spectrophotometrically as a function of time. pump (in cell biology) any transmembrane protein that drives the active transport of ions and small molecules across the lip,id bilayer. See also hydhigen-ion pump, sodium pump. PUMP~1 see matrilysiil. pump-1 protease see matrilysin. Purcell. Edward Mills (1912-97), US electrical engineer, physicist, and radioastronomer notable for his discovery (independently of F, Bloch) of the phepomenon of nuclear magnetie resonance of cert.ain atomic nuclei and for being the first to report detection of the emission of 1420-Hz microwave radiation by interstellar dihydtogen; Nobel Laureate in Physics (1952) jointly with F. Bloch 'for their development of new methods for nuclear magnetic precision measurements and discoveries in connection therewith'. purine 1 IH-purine; 7H-imidazo[4,5-djpyrimidine; an organic nitrogenous base, sparingly soluble in water. 2 any of a class of derivatives of IH-purine; these form one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine. See also purine biosynthesis.

7f'p~, 9 ,,:::::~.J.-N N H

purine biosynthesis the biosynthesis of purine ribonuc1eotides. The pathway for the synthesis of purine ribonucleotides begins with the formation of 5-phospho-a-D-ribosyl diphosphate (5-phosphoribosyl-a-D-pyrophosphate, common abbr.: PRPP) by ribose-phosphate pyrophosphokinase, EC

2.7.6.1. This is converted to P-5-phosphoribosylamine (I) by reaction with glutamine, catalysed by amidophosphoribosyltransferase, EC 2.4.2.14; reaction of I with glycine, with hydrolysis of ATP to ADP and Pi, catalysed by phosphoribosylamine-glycine ligase, EC 6.3.4.13 (glycinamide ribonucleotide synthetase, common abbr.: GAR synthetase), brings about the formation of NI-(5-phospho-o-ribosyl)glycinamide (II, glycinamide ribotide, common abbr.: GAR); II reacts with 10-formyltetrahydrofolate to form 5'-phosphoribosyl-Nformylglycinamide (III, common abbr.: FGAR), the enzyme being phosphoribosylglycinamide formyltransferase, EC 2.1.2.2 (GAR transformylase); III is converted to 5'-phosphoribosylformylglycinamidine (IV, formylglycinamidine ribotide, common abbr.: FGAM) by phosphoribosylformylglycinamidine synthase, EC 6.3.5.3 (common abbr.: FGAM synthetase) by reaction with glutamine with ATP hydrolysis to ADP and Pi' IV is converted to 1-(5-phosphoribosyl)-5-aminoimidazole (V, 5-aminoimidazole ribotide, common abbr.: AIR), with hydrolysis of ATP to ADP and Pi, by phosphoribosylformylglycinamidine cyclo-Iigase, EC 6.3.3.1 (common abbr.: AIR synthetase); V is carboxylated to 1-(5-phosphoribosyl)-5-amino-4-imidazolecarboxylate (VI, carboxyaminoimidazole carboxamide, common abbr.: CAIR), by phosphoribosylaminoimidazole carboxylase, EC 4.1.1.21 (common abbr.: AIR carboxylase); VI reacts with L-aspartate, with hydrolysis of ATP to ADP and Pi, to form 1-(5-phosphori bosyI)-5-amino-4-(N-succinocarboxamide)-imidazole (VII, 4-(N-succinylocarboxamide)-aminoimidazole ribotide, common abbr.: SACAIR) catalysed by phosphoribosylaminoimidazolesuccinocarboxamide synthase, EC 6.3.2.6 (common abbr.: SACAIR synthetase); VII is converted, with loss of fumarate, to 1-(5-phosphoribosyl)-4-carboxamide-5-aminoimidazole (VIII, aminoimidazolecarboxamide ribotide, common abbr.: AI CAR) by adenylosuccinate lyase, EC 4.3.2.2 (VII is an alternative substrate for this enzyme); VIII reacts with 10formyltetrahydrofolate to form 5' -phosphoribosyl-5-formamido-4-imidazolecarboxamide (IX, formaminoimidazolecarboxamide ribotide, common abbr.: FAICAR), catalysed by phosphoribosylaminoimidazolecarboxamide formyltransferase, EC 2.1.2.3 (common abbr.: AlCAR transformylase); IX undergoes ring closure catalysed by IMP cyclohydrolase, EC 3.5.4.10, to form inosine monophosphate (iMP), from which other purine nucleoside mono phosphates are formed. Thus it is converted to AMP via adenylosuccinate, in steps catalysed by adenylosuccinate synthase, EC 6.3.4.4, and adenylosuccinate lyase, EC 4.3.2.2. It is converted to GMP via xanthosine monophosphat y, in steps catalysed by IMPdehydrogenase, EC 1.1.1.205, and GMP synthase, EC 6.3.4.1. A salvage pathway also exists, that reconverts purine bases released during nucleic-acid degradation to nucleoside monophosphates. The enzymes adenine phosphoribosyltransferase and hypoxanthine-guanine phosphoribosyltransferase are responsible for these reactions. purine-nucleoside phosphorylase abbr.: PNP; EC 2.4.2.1; systematic name: purine-nucleoside:orthophosphate ribosyltransferase; other name: inosine phosphorylase. An enzyme that catalyses the phosphorylysis of a purine nucleoside to a purine and a-o-ribose I-phosphate. It functions in the degradation of purines; decreased activity leads to accumulation of dGTP, which affects DNA replication. Enzyme deficiency is associated with moderate immunodeficiency. Example from Escherichia coli, homohexamer: database code DEOD_ ECOLI, 238 amino acids (25.79 kDa). purinergic describing a type of nerve in which synaptic transmission is brought about by purine-like transmitter substances. See purinoceptor. Compare adrenergic, cholinergic. purinoceptor or purinergic receptor a family of receptors (P" P 2X , P 2Y , P2Z , P2T , and P 2U ) classified according to the relative potency of purine nucleotides - ATP, ADP, AMP, and UTPin stimulating them and by their response to either adenosine (PI) or ATP (P 2). P 2Y and Pm have seven transmembrane domains and regulate turnover of phosphoinositides; example of

547

pyrimidine dimer

puromycin P zu from Rattus norvegicus: database code P2UR_RAT, 374 amino acids (42.26 kDa). P zx , P zz , and P ZT modulate the opening of an intrinsic cation channel but P 2T also stimulates release of intracellular Ca z+ and reduces synthesis of cyclic AMP. Example of P2X from R. norvegicus: database code P2XLRAT, 472 amino acids (52.62 kDa). puromycin a nucleoside antibiotic produced by the soil actinomycete Streptomyces alboniger. It interrupts protein synthesis by virtue of its structural similarity to the 3' end of aminoacyltRNA: it enters the A-site (see aminoacyl site) on the ribosome, and is incorporated into the growing polypeptide chain, thereby causing premature release of the puromycinyl polypeptide from the ribosome.

pyranold pyran-like, i.e. describing a molecular structure that consists of or contains a ring of five carbon atoms and one oxygen atom (as in pyran). pyranose symbol: p; any monosaccharide or monosaccharide derivative whose molecule contains a pyranoid ring. Compare furanose, septanose. pyridine-nucleotide coenzyme any of a group of coenzymes containing a nicotinamide nucleotide residue, e.g. nicotinamide-adenine dinucleotide (NAD+); now known as nicotinamide-nucleotide coenzymes. pyridoxal abbr.: PL; 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde; a compound with vitamin 8 6 activity.

pyridoxal kinase EC 2.7.1.35; an enzyme that catalyses the formation of pyridoxal 5'-phosphate from ATP and pyridoxal with release of ADP. Example (fragment) from sheep: database code A61483, 11 amino acids (1.24 kDa). pyrimidine 1 1,3-diazine; an organic nitrogenous base, sparingly soluble in water. 2 any of a class of derivatives of pyrimidine (def. I); these form one of the two categories of nitrogen-containing ring compounds found in DNA and RNA, which include cytosine, thymine, and uracil. See also pyrimidine biosynthesis. purothionin any of a group of basic peptides, isolated from grain and of M r "'5000, that contain a large number of cysteine residues and are toxic to bacteria and fungi by inhibiting DNA hanscription and RNA translation. Example purothionin y-l from Triticum aestivum: database code THG I_WHEAT, 47 amino acids (5.24 kDa). /:turple membrane part of the cell membrane of Halobacterium halobium containing bacteriorhodopsin. 'push' model a nickname for the Koshland model (for ligandinduced changes in protein conformation) because, in this model, binding of the ligands results in a conformational change and does not simply select a pre-existing state. Compare 'pull model'. putidaredoxin a ferredoxin, isolated from Pseudomonas putida, that is an electron carrier in a hydroxylase system acting on camphor and closely related monoterpenes. Compare adrenodoxin. putrescine 1,4-diaminobutane; the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine. PVA abbr. for 1 polyvinyl alcohol. 2 polyvinyl acetate. PVC abbr. for polyvinyl chloride. PVP abbr. for polyvinyl pyrrolidone. PWM abbr. for pokeweed mitogen. pycnometer an apparatus for measuring the density of liquids, and also sometimes of solids. It consists of a container whose volume can be accurately measured, and that can be filled with great precision, so that when filled with the liquid in question it can be weighed to determine the density. -pycnometric adj. Pyd symbol for a residue of an unspecified pyrimidine nucleoside (alternative to Y). pyr-1 the symbol for the pyrimidine I gene, which encodes CAD protein in several eukaryotes. pyran the trivial name for either of the hypothetical isomers apyran, 2H-pyran, oxacyclohexa-3,5-diene, or y-pyran, 4Hpyran, oxacyclohexa-2,5-diene, C sH 60. These pyrans are not known as such, but are the parent structures of various known pyranoid compounds such as dihydropyran, a- and y-pyrones, and pyranoses.

e

N

I) N

pyrimidine biosynthesis or pyrimidine ribonucleotide biosynthesis pyrimidines are formed from carbamoyl phosphate (see carbamoyl-phosphate synthase) after conversion to carbamoyl aspartate in a reaction with L-aspartate catalysed by aspartate transcarbamylase, EC 2.1.3.2. Carbamoyl aspartate is converted to orotate via dihydroorotate, in steps catalysed by dihydroorotase, EC 3.5.2.3, and dihydroorotate dehydrogenase, EC 1.3.99.11. Oro tate is phosphorylated to orotidine mono phosphate (OMP) in a reaction with 5-phospho-a-D-ribosyl diphosphate catalysed by orotate phosphoribosyltransfl!rase, EC 2.4.2.10. OMP is converted to uridine monophosphate by orotidine 5'-phosphate decarboxylase, EC 4.1.1.23. pyrimidine dimer any structure formed within a strand of DNA from two neighbouring pyrimidine residues through covalent cross-linking induced by ultraviolet irradiation. Two types are known. (1) Addition of one pyrimidine ring to the other at each end of their respective 5,6-double bonds generates a cyclobutadipyrimidine, a fully substituted cyclobutane. Such a dimer is formed most readily from two thymine residues (see thymine dimer), but may be formed also from two cytosine residues, or from one cytosine and one thymine residue. For each of these varieties there are four possible configurational isomers: if the pyrimidine rings have become linked in a parallel manner, i.e. by 5-5' and 6-6' bonds, the configuration is designated by the prefix syn-, but if they are linked in an antiparallel manner, i.e. by 5-6' and 6-5' bonds, it is designated by anti-; further, if the pyrimidine rings are both on the same side of the plane of the cyclobutane ring, the dimer is described as being in the 'doghouse configuration', designated by the prefix cis-, but if the rings are on opposite sides of the cyclobutane plane, the dimer is said to be in the 'chair configuration', designated by trans-. The presence of a

pyrimidine-nucleoside phosphorylase

548

cyclobutadipyrimidine in a DNA strand causes a local distortion of the DNA duplex and blocks the action of DNA polymerase, thus preventing replication; cell death may ensue unless repair is effected by photoreactivation. (2) Alternatively, addition may take place between position 6 of one pyrimidine residue and position 4 of an adjacent one, with creation of a single covalent link and generation of a (6-4)photoproduct. Such a dimer is usually formed between position 6 of a cytosine or thymine residue on the 5' side of a dinucleotide segment and position 4 of a cytosine residue on its 3' side. The (6-4)photoproduct is thought to be the main type of lesion in DNA responsible for mutations; it is not susceptible to photoreactivation, but can be eliminated by other DNA-repair mechanisms, e.g. excision repair. pyrimidine-nucleoside phosphorylase any of several enzymes that function in the catabolism of pyrimidines; examples are: (I) Uridine phosphorylase, EC 2.4.2.3; it catalyses the phosphorolysis of uridine to uracil and a-o-ribose I-phosphate. Example from Escherichia coli, homohexamer showing 4-, 6-, and 8-fold symmetry: database code UDP_ECOLl, 252 amino acids (27.00 kDa). (2) Thymidine phosphorylase, EC 2.4.2.4; it catalyses the phosphorylysis of thymidine to thymine and 2-deoxy-o-ribose I-phosphate. Example from E. coli, homodimer: database code DEOA_ECOLl, 441 amino acids (47.28 kDa). pyro+ or (before a vowel) pyr+ comb. form 1 of, relating to, caused, or produced by fire. 2 (in chemistry) indicating material derived by the action of heat; it often indicates an acid formed by loss of a molecule of water in a heating process, and hence also some anhydrides, e.g. pyrophosphate. pyrocatechol or pyrocatechin or (formerly) catechol 1,2-benzenediol; o-dihydroxybenzene. Compare catecholamine, 0benzoquinone, hydroquinone. pyrolysis the decomposition or dissociation of a chemical compound by the application of heat. See also thermolysis. -pyrolytic ad).; pyrolyse or (sometimes, US) pyrolyze vb. pyrophosphatase 1 an imprecise name for inorganic pyrophosphatase. 2 the generic name for any of a number of the enzymes within sub-subclass EC 3.6.1 (enzymes acting on diphosphate bonds); e.g. ATP pyrophosphatase (EC 3.6.1.8). pyrophosphate an older name for diphosphate (def. 1-5) (use no longer recommended although it is still used as an alternative in such terms as inorganic pyrophosphate, pyrophosphatase, etc.). See also inorganic diphosphate. pyrophosphokinase the general name for any enzyme belonging to the sub-subclass EC 2.7.6, diphosphotransferases, which transfer a diphosphate group from ATP to a named substrate; e.g. GTP pyrophosphokinase (EC 2.7.6.5), which converts guanosine 5'-triphosphate, GTP to guanosine 3'phosphate 5'-triphosphate, pppGpp. pyrrolidonecarboxylic acid symbol: - abbr. for racemo-. RACE abbr. for rapid amplification of cDNA ends; a variation on the polymerase chain reaction designed for amplification of cDNA corresponding to low-abundance mRNA. racemase any enzyme that interconverts the two enantiomers of a chiral compound; such enzymes are categorized in subclass EC 5.1 (which also includes epimerases). If more than one chiral centre is present, a racemase must invert configuration of all the chiral centres. Thus, the name methylmalonyl-CoA racemase, sometimes used for methylmalonyl-CoA epimerase (EC 5.1.99.1), is incorrect - the enzyme does not change configurations of the chiral centres of the CoA moiety.

racemate any homogeneous phase containing equimolar amounts of enantiomeric molecules. racemic symbol: (f)- or (formerly) dl-; denoting the presence of equimolar amounts of the dextrorotatory and levorotatory enantiomers of a compound, regardless of whether the (optically inactive) product formed is crystalline, liquid, or gaseous. A homogeneous solid phase composed of equimolar amounts of enantiomeric molecules is termed a racemic compound, and a mixture of equimolar amounts of enantiomeric molecules present as separate solid phases is termed a racemic mixture; see also racemate. A (f)-product may be resolved into its (+)- and (-)-components. The term is derived from racemic acid [from Latin racemus, bunch of grapes], the optically inactive mixture of (+)- and (-)-tartaric acids sometimes found during the manufacture of wine. By extension, the term is applied to DL- and (RS)-mixtures. See OIL convention, optical isomerism, sequence rule. See also racemo-. racemize or racemise to induce the formation of a mixture of the two possible enantiomers from one of the pure isomers of a chiral compound. -racemization or racemisation n. racemo- abbr.: rac-; prefix (in chemical nomenclature) designating a racemate. It may be used as an alternative to the symbol (f)- or (for certain classes of racemic compounds) the symbol DL-. Compare meso-. rachitic of, pertaining to, or afflicted with rickets. rachitis an alternative name for rickets. rachitogenic tending to cause rickets. rad 1 symbol for radian. 2 symbol: rad or (to avoid possible confusion with rad (def. I)) rd; the cgs unit of absorbed dose of ionizing radiation, equivalent to an absorption of 0.0 I joule of energy per kilogram (= 100 ergs per gram) of irradiated material. Whereas the rad represents, in practice, about the same amount of energy as the rontgen (the exact equivalence depending on the material irradiated), it applies to any type of ionizing radiation in any medium. I rad = 0.01 Gy. 3 abbr. for radiation. radial 1 of, resembling, or relating to a radius or ray; in rays. 2 emanating from the centre of a circle or a common central point. 3 spreading out uniformly in all directions on a surface. -radially adv. radian symbol: rad; the SI supplementary unit of plane angle. One radian is equal to the angle subtended at the centre of a circle by an arc whose length is equal to the radius. It is dimensionless. There are 211: radians in a circle; I rad = 57.29578°. radiant energy symbol: Q or W; the energy of any form of electromagnetic radiation. The SI derived unit is the joule. radiant intensity symbol: I; the radiant power of radiation from a point source per unit of solid angle; i.e. 1= d/dQ, where is the radiant power and Q is the solid angle measured in steradians. The SI unit is the watt per steradian (W sr- I ). radiant power or radiant flux symbol: P or ; the rate of flow of energy of radiation; i.e. = dQldt, where Q is the radiant energy. The SI derived unit is the watt. radiation 1 the emission of energy from a source and its transmission as particles, rays, or waves, especially as electromagnetic rays or waves, sound waves, or streams of subatomic particles. 2 energy so transmitted, especially the corpuscular and electromagnetic rays emitted in the decay of radionuclides. 3 ionizing radiation. 4 divergence from a common point, especially radially from a central point or source. radiation absorbed dose see absorbed dose, rad (def. 2). radiation biology an alternative name for radiobiology. radiation-chemical reaction any chemical reaction that is initiated by the absorption of radiation but is distinguishable from a photochemical reaction by its lack of specificity (i.e. by

554 radiation chemistry

giving rise to a variety of reaction products) and by occurring at higher radiation energies (i.e. by absorption either of electromagnetic radiation from the mid-ultraviolet region onwards or of high-energy particulate radiation) and thus by resulting always in the formation of detectable ions. radiation chemistry the branch of chemistry concerned with radiation-chemical reactions. Compare radiochemistry. radiation damage the totality of the harmful changes induced in a cell or tissue by radiation. The harmful effects may include formation of thymine dimers in DNA or of radicals from polyunsaturated acyl groups in lipids. radiation dose equivalent see dose equivalent. radiation inactivation method a technique, based on target theory, that enables the size of the functional unit of a biologically active macromolecule (or of its complexes with other molecules) to be estimated; it can be used on unpurified (e.g. membrane-bound) material. Determinations are made of the biological activity remaining in a sample after exposure to various large doses of ionizing radiation (electrons or X- or gamma radiation of at least I MeV), and the value, D 37 , of the radiation dose, expressed in Mrad, required to reduce the activity to 37% of (i.e. e- 1 times) its original value is obtained; the relative molecular mass, M" of such a macromolecule may then be found from the empirical relationship M r = 6.4 x 10 5/ D 37 , where D 37 is determined at 30°C. radiation source a quantity of radioactive material used as a source of ionizing radiation. radical (in chemistry) 1 any molecular entity, charged or uncharged, that possesses an unpaired electron (but normally excluding any paramagnetic metal ion); often formed by homolysis of a covalent bond. Radical character is indicated in a formula by a centred dot symbolizing the unpaired electron and placed (if possible) beside the symbol for the atom of highest spin density; e.g. HOO', ·CH 3. The term free radical is now preferably restricted to any radical that does not form part of a radical pair. 2 a former name for group (def. 2). radical anion see radical ion. radical cation see radical ion. radical centre the atom in any polyatomic radical (def. I) on which the unpaired electron is largely localized. radical ion any radical (def. I) that carries an electric charge. One carrying a negative charge is termed a radical anion (e.g. the benzene radical anion, C 6H 6'-); one carrying a positive charge is termed a radical cation (e.g. the benzene radical cation, C 6H 6'+). radical pair any two radicals (def. I) in close proximity in liquid solution, with a solvent cage. They may have been formed simultaneously, e.g. by homolysis, or have come together by diffusion. Whilst together, correlation of their unpaired electron spins occurs and manifests itself as a distortion of nuclear magnetic resonance spectra. radical scavenger any substance that can react readily with, and thereby eliminate, radicals. In biological systems or materials, radical scavengers may function as antioxidants or may protect from damage by ionizing radiation. Among the important radical scavengers that function in animal tissues at physiological concentrations are the water-soluble substances ascorbate, glutathione, and the purine bases, and the fat-soluble substances tocopherols, the retinols, the carotenes, and the ubiquinones. radioactivate to convert a stable nucleus into one undergoing radioactive decay by bombardment with high speed particles, including protons, alpha particles, neutrons, and deuterons. These are formed in a cyclotron or synchrotron from a radioactive source, and accelerated through a potential difference of a few thousand volts by a magnetic field before being focused on the substance to be converted. radioactivation analysis or activation analysis a method for the qualitative and/or quantitative estimation of the chemical elements in a sample. It depends on the identification and de-

radiography

termination of the radio nuclides formed when the sample is bombarded with neutrons or other particles. radioactive having the properties associated with a radioactive isotope. radioactive concentration the activity (def. 2) per unit quantity of any material in which a radionuclide occurs. See also specific activity. radioactive decay see decay (def. I b). radioactive isotope or radioisotope any isotope of a chemical element whose nucleus is unstable and emits alpha, beta, or gamma rays. The product is another element, which may be stable or unstable; if the latter, it decays further. Thus, the principal isotope of uranium, 23 8 U, emits an alpha particle and decays to 234Th, which emits a beta particle forming 234Pa; this chain continues to the formation of 206Pb, which is stable. radioactive label or radiolabel a radioactive isotope incorporated into a molecule to confer on it the property of radioactivity. radioactive tracer or radiotracer a radioactive substance that is added to a metabolic system in quantities (mass) too small to perturb the system, in order to follow, by isolating the radioactive intermediates formed, the sequence of transformations undergone normally by the same (nonradioactive) molecule under similar conditions. radioactivity 1 the emission of radiation from certain nuclides by the spontaneous transformation of their nuclei. 2 (loosely) the radioactive material itself or its emitted radiation. See activity (def. 2). radioallergosorbent test abbr.: RAST; a test used primarily for quantifying the levels of antigen-specific immunoglobulin E (IgE) in serum. A specific allergen, which has been covalently coupled to an insoluble Sephadex carrier, is incubated with serum containing the unknown amount of IgE. The carriers are then washed and further incubated with radiolabelled antibodies to IgE, the amount of radioactivity bound being a measure of the amount of IgE. The advantage of this method over the radioimmunosorbent test is that IgE specific to a particular antigen can be selectively quantified. radioassay any type of assay in which a radioactive isotope is used in the measurement. The term embraces, e.g., immunoradiometric assay, radioimmunoassay, and competitive proteinbinding assay. radioautogram or radioautograph or autoradiogram the pattern formed after development of an X-ray film that has been exposed to a paper, gel, or thin-layer chromatogram containing radioactive compounds. radioautograph 1 an alternative term for radioautogram. 2 to prepare a radioautogram. -radioautography n. radiobiology or radiation biology the study of the interaction between radiation and biological material. radiocarbon any radioactive isotope of carbon, usually carbon-II or carbon-14. radiochemical purity abbr.: Rep; the proportion of the total activity (def. 2) that is present in the stated chemical form in a radioactive material. radiochemistry the branch of chemistry concerned with the compounds of radioactive nuclides. Compare radiation chemistry. radiochromatogram a chromatogram of substances some or all of which contain a radioactive isotope. radiofrequency radiation electromagnetic radiation encompassing wavelengths in the region I mm (300 GHz) to 30 km (10 kHz) (frequencies in parentheses). This range includes microwave radiation and lies above that of infrared radiation. radiography the use of X-rays to examine the internal structures of a body. An X-ray film is placed behind the body, through which X-rays are passed. After exposure, there are areas of the film in which development has not occurred due to absorption of the X-rays by structures of the body, thus yielding a pattern of these structures. -radiographer n.; radiographic adj.; radiographically adv.

555

radioimmunoassay radioimmunoassay abbr.: RIA; a highly sensitive method of assay of nonradioactive material. A known amount of antibody (Ab) directed against the substance (antigen, Ag) to be assayed is saturated with a mixture of Ag and radioactive Ag (Ag*), so that total Ag (Ag + Ag*) is in excess. When nonradioactive Ag is added to Ab along with Ag*, Ag and Ag* compete for binding to Ab, so that less Ag* will be found in the antibody-antigen complex as the ratio Ag:Ag* increases. If the antibody-antigen complex is then separated from free antigen, the total amount of antigen (the substance being assayed) can be calculated from the ratio Ab-Ag*:Ag* and the known titre of antibody. It is often convenient to attach the antigen to plates so that the amount of ligand bound to the plate is proportional to the amount of test antibody. radioimmunosorbent test abbr.: RIST; a test used primarily for quantifying total serum immunoglobulin E (IgE) levels. Antibodies specific for 19B, covalently linked to an insoluble dextran, are incubated first with a known amount of radiolabelled IgE and then with the serum containing the unknown amount of IgE. From the decrease in the amount of radiolabel bound to the immobilized antibodies, due to competition by the unlabelled IgE in the serum, the total amount of IgE in the serum can be estimated. radioiodinate to incorporate one or more atoms of radioiodine (usually iodine-125 or iodine-131) into a molecule. radioiodine any radioactive isotope of iodine, notably iodine125 (half-life 60 days) and iodine-13l (half-life 8 days). radioisotope a radioactive isotope. ,adiolabel 1 a radioactive label. 2 to incorporate a radiolabel. radioligand any ligand containing a radioactive isotope; see also Scatchard plot. radiology the study and use of radiation and radioactive substances, especially in the diagnosis and treatment of disease. It includes the use of diagnostic X-rays in radiography, the therapeutic use of ionizing radiation to treat disease (radiotherapy), and the experimental and diagnostic use of radioisotopes introduced into the body. -radiological ad).; radiologically adv.; radiologist n. radiolysis the cleavage of chemical bonds by high-energy radiation. -radiolytic ad).; radiolyse vb. radiometer 1 any instrument used to measure radiant energy. 2 Crookes radiometer a specific type of radiometer in which the different behaviour of a polished surface, which reflects energy, and a blackened surface, which absorbs it, is utilized to cause a rotor to turn at a rate related to the intensity of radiation. [After William Crookes (1832-1919), British chemist and physicist.] -radiometric adj.; radiometry n. radiomimetic 1 describing any drug or other chemical substance, typically an alkylating agent, whose effects in living systems (e.g. carcinogenic, immunosuppressive, mutagenic) resemble those produced by ionizing radiation; more loosely, describing any such agent able to cause gene and chromosome mutations. 2 a radiomimetic (def. 1) substance or agent. radionuclide a radioactive nuclide. -radionuclidic ad). radionuclidic impurity any radionuclide, other than the nuclide that should be present, in a radioactive material. radionuclidic purity or radiopurity (of a radioactive material) the proportion of the total activity (def. 2) that is in the form of the stated radionuclide. radiotherapy see radiology. radiotracer an alternative name for radioactive tracer. radixin a protein of the erythrocyte band 4.1 family present in a variety of eukaryotic cells; it shares about 75% homology with human ezrin. It is an actin barbed-end capping protein, highly concentrated in the undercoat of the cell-to-cell adherens junction and the cleavage furrow in the interphase and mitotic phase. Example from human: database code RADCHUMAN, 583 amino acids (68.49 kDa). radyl (in chemical nomenclature) a term used to indicate any acyl, alkyl, or alkenyl group where this cannot be specified in detail.

Ramsay RAF any of a family of genes encoding Raf proteins; there are at least three Raf proteins, Raf-I, A-Raf, and B-Raf. These are protooncogene cytoplasmic serinefthreonine protein kinases (EC 2.7.1.-) of the Ras/Mos family; they show similarity to members of the protein kinase C family in both their conserved C-terminal catalytic and regulatory N-terminal domains. Example, Raf-l (human), which has binding domains for ATP, phorbol ester, and diacyl glycerol: database code KRAF_HUMAN, 648 amino acids (72.97 kDa). This protein is involved in transduction of mitogenic signals from the cell membrane to the nucleus. In the mouse, raf is the transforming gene of the mouse sarcoma virus, 3611, v-Raf having a truncated regulatory domain that causes constitutive activation of kinase activity. The c-Raf-I protein kinase, a 74 kDa protein, has been found in all mammalian cells tested. Raf-I is an important mediator of signals involving cell growth, transformation, and differentiation and is activated by a wide variety of extracellular stimuli. It has MAP kinase kinase kinase activity. In many cell types, Raf functions immediately downstream of the G-protein Ras (see HAS) in the activation pathway; although Ras does not directly activate Raf, it mediates translocation of Raf-I from cytoplasm to plasma membrane where it is activated. In some cells Raf may be phosphorylated and activated by members of the protein kinase C family. The first physiological substrate to be discovered for Raf kinase was a protein kinase (MEK) of yeast that is required for meiotic recombination and which on phosphorylation can activate MAP kinase. raffinose or gossypose or meJitose or melitriose the trisaccharide O-a-D-galactopyranosyl-( I ~6)-O-a-D-glucopyranosyl-( I ~2)­ p-D-fructofuranoside; it occurs in plants almost as commonly as sucrose, being present, e.g., in cereal grains, cotton seeds, and many legumes. It is the first member of a series in which galactosyl residues are attached to sucrose, others being the tetrasaccharide stachyose and the pentasaccharide verbascose; these are all synthesized from sucrose by transfer reactions in which an a-D-galactopyranoside of myo-inositol (i.e. galactinol) is the donor of the galactosyl residues. r.a.m. abbr. for relative atomic mass. Ramachandran plot or conformational map a plot that shows the ranges of bond angles that are permissible and the main types of structure of an L-polypeptide chain (e.g. a helix, ~­ pleated sheet). As the peptide bond, -C'O-NH-, is planar, a polypeptide chain has only two degrees of freedom per residue, the twist about the ca-N bond axis, ¢, and that about the ca_C' axis, f/I. Some foldings will be easily achieved; others will be impossible because they would bring neighbouring unbonded atoms or groups within van der Waals contact distances. The Ramachandran plot shows the permitted range within a plot of ¢ against f/I. [After G. N. Ramachandran (1922- ).] Raman, (Sir) Chandrasekhara Venkata (1888-1970), Indian physicist; Nobel Laureate in Physics (1930) 'for his work on the scattering of light and for the discovery of the effect named after him'. Raman scattering the inelastic scattering of a photon by a molecule, producing in the scattered light weak radiation of frequencies not present in the incident light. The sample does not have an absorption band at the wavelength of the incident light (compare fluorescence) and the frequency differences between the weak Raman lines in the spectrum and the exciting line are characteristic of the scattering substance and independent of the frequency of the exciting line. [After C. V. Raman.] Raman spectrum a plot of Raman scattering over a range of frequencies. Ram6n y Cajal, Santiago (1852-1934), Spanish anatomist and histologist; Nobel Laureate in Physiology or Medicine (1906) jointly with C. Golgi 'in recognition of their work on the structure of the nervous system'. Ramsay, (Sir) William (1852-1916), British physical and inorganic chemist; Nobel Laureate in Chemistry (1904) 'in recog-

556

rare earth metal

RAN nition of his services in the discovery of the inert gaseous elements in air, and his determination of their place in the periodic system'. RAN a gene encoding a small nuclear G-protein, first identified as a well-conserved gene distantly related to H-RAS. Its product, Ran, interacts with RCCt, and the complex is involved in regulating cell-cycle progression and messenger RNA transport. In the absence of RCCI, GDP-Ran predominates and this results in activation of M-phase-promoting factor and chromatin condensation. The presence of RCCI activates nucleotide exchange on Ran, increasing the amount of GTP-Ran and preventing premature chromatin condensation. Example from Mus musculus: database code RAN_MOUSE, 216 amino acids (24.42 kDa). See also nuclear pore. random coil the condition in solution of a linear polymer that exhibits little side group interaction, or resistance to rotation about the bonds in its chain. There are no preferred conformations. Quantitative expressions have been developed for the average radius of gyration. The term has formerly been incorrectly applied to various states of protein chains. random copolymer a polymer of more than one species of monomer, in which the sequence of species within the polymer is not predetermined by controlled steps during synthesis, but depends only on random collisions between the reactant molecules. An example is the sequence of bases in RNA synthesized from nucleoside diphosphates by polynucleotide phosphorylase. random mechanism or random pathway (for an enzymic reaction involving two substrates, A + B """" C) a mechanism in which the enzyme, E, may first react with either substrate and the resulting enzyme-substrate complex then reacts with the second substrate, e.g. A + E """" EA then EA + B """" EAB, or, B + E"""" EB then EB + A"""" EAB, subsequently EAB """" E + C. Compare ordered mechanism. random sample a selection of part of a population made in such a way that no individual is favoured over any other individual. See also sample, statistical sample. ranitidine a competitive antagonist at histamine Hz receptors, being the major and pharmacologically more selective analogue of the imidazole derivative, cimetidine. It inhibits histamiue- and pentagastrin-evoked gastric acid secretion and cardiac stimulation and also inhibits gastric secretion evoked by physiological stimuli, agonists at muscarinic cholinoceptors, and gastrin. It is used in the treatment of gastric and duodenal ulcers. One proprietary name: Zantac (hydrochloride).

RANTES abbr. for regulated upon activation, normal T-cell expressed and secreted chemokine; other names: smaU inducible cytokine A5; a chemokine secreted by T cells and macrophages on stimulation by mitogens, that acts as a chemoattractant, and stimulates basophils and eosinophils. Example from human (precursor): database code SISD_HUMAN, 91 amino acids (10.07 kDa); residues 1-23 are the signal, 24-91 RANTES. ranunculeic acid another name for columbinic acid. rapamycin an immunosuppressant (and antifungal agent) from Streptomyces hygroscopicus; it is used to reduce rejection of organ transplants. It is a lipid-soluble macrocyclic lactone, with the unusual feature of a cyclohexane ring with hydroxyl and methoxyl substituents. It competes with FK506 for a common binding site on FKBP. See also cyclosporin.

OH

1

~ H, ""

22

24

N17

0

25

o

o """CH 50 3

rapamycin

RAPD peR abbr. for random polymorphic DNA PCR; a variation of the polymerase chain reaction in which many short ("'10 nucleotide) primers are used. The products of the reaction from different sources can lead to recognition of polymorphisms and physical maps. rape or colza a herbaceous plant, Brassica napus, of the mustard family, Cruciferae; it resembles a turnip, and the seeds yield valuable rapeseed oil. rapeseed oil oil derived from the seed of rape; it is widely used as a lubricant and cooking fuel, and for the manufacture of animal foodstuffs, soap, and synthetic rubber. It contains erucic acid, which has cardiotoxic effects varying with species; rape varieties of low erucic acid content have recently been developed. rapid-reaction kinetics the kinetic analysis of an enzyme reaction before the steady state is reached. The stopped-flow method is commonly used, in which two independent sources of substrate and enzyme are mixed immediately before flow through a spectrophotometer cell. An opposing syringe stops the flow immediately before activating the detection and recording system, such that reaction times of a few milliseconds can be achieved. Characteristically, reaction rates may be appreciably faster than during the steady state. In the quenched flow modification of the method, a further reagent is added to stop the reaction immediately before detection and recording. See also relaxation kinetics. Rapoport-Liibering shunt a unique feature of erythrocyte glycolysis in which the glycolytic intermediate 3-phosphoglyceroyl phosphate is converted by bisphosphoglycerate mutase to 2,3-bisphosphoglycerate, which is in turn converted to 3phosphoglycerate and inorganic phosphate by bisphosphoglycerate phosphatase, both reactions being catalysed by a single enzyme molecule. The shunt bypasses the near equilibrium phosphoglycerate kinase reaction, one of the two ATPgenerating reactions of glycolysis. Since 2,3-bisphosphoglycerate is an important intracellular modulator of hemoglobin function, regulation of the Rapoport-Liibering shunt balances the energy needs and oxygen-transporting function of the red cell. [After Samuel Mitja Rapoport (1912- ) and J. Liibering.] rare earth (strictly) an oxide of a rare earth metal, or (more loosely), a rare earth metal itself. rare earth metal or rare earth element scandium, yttrium, or a lanthanoid.

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RAS RAS an oncogene (v-ras) first discovered in the retroviruses Harvey and Kirsten rat sarcoma viruses; three closely related (85% homology) oncogenes are now known, Ha-ras, Ki-ras, and N-ras. Their cellular counterparts encode 21 kDa guanine nucleotide-binding proteins that playa pivotal role in regulating growth and differentiation in nearly every eukaryotic cell studied. There are two subfamilies, the Rho and Rac proteins (involved in relaying signals from the cell-surface receptors to the actin cytoskeleton) and the Rab family (involved in regulating the traffic of intracellular transport vesicles). Ras proteins undergo a number of modifications of the Nand C termini that result in their localization to the plasma membrane. Ras binds both GTP and GDP with high affinity. It is considered active in the GTP-bound form and inactive in the GDP-bound form. The intrinsic rate of nucleotide exchange and GTPase activity is very slow. Ras·GDP predominates in resting cells, but when Ras is activated by occupied receptors, specific guanine nucleotide exchange factors (GEFs), e.g. Sos, enhance nucleotide exchange leading to Ras·GTP, GTP exceeding GDP in cytoplasm. Ras·GTP then activates downstream effector proteins such as Raf-l (see RAF). Activated GTPase activating protein (GAP) causes the formation of inactive Ras·GDP. The retroviral oncogene, v-ras, encodes a protein that differs from the c-ras product as a result of a point mutation. If this affects amino acids 12,13,59,61, or 63 the protein fails to hydrolyse its bound GTP and so persists abnormally in its active state, constitutively transmitting an intracellular signal for cell proliferation. Alternatively, some transforming mutations increase the rate at which Ras can exchange guanine nucleotides, e.g. when amino acids 116, 117, 119, or 146 are affected, again increasing the amount of Ras·GTP. Activated ras oncogenes have been found in up to 30% of all human tumours analysed, with the most common point mutations being at codons for amino acids 12 and 13. In some types of malignancy, the figure is nearly 100%. Two genes corresponding to H-ras occur in yeast; they encode Gproteins that inhibit adenylate cyclase. 3-D structure known (including GDP bound to guanine nucleotide-binding domain) for human protein H-Ras-I: database code NRL_4Q21, 168 amino acids (19.07 kDa). RAST abbr. for radioallergosorbent test. rate coefficient see rate constant. rate constant or rate coefficient symbol: k; a constant relating the concentration of a reactive species to the velocity of a reaction; thus for a first order reaction (see order of reaction) such as: EA -? E + A, the rate of reaction, v, is proportional to the concentration of the reactant EA, so v = k[EA], where k is the first-order rate constant. For a second order reaction, e.g. E + A -? EA, the rate is proportional to the product of the reactant concentrations, i.e. v = k[E][A] , where k is the secondorder rate constant. rate-determining step see rate-limiting step. rate-limiting step the slowest step in a reaction sequence; i.e. the step with the smallest rate constant. rate of consumption see rllte of reaction. rate of conversion symbol: ~; for a specified chemical reaction, the rate of increase of the extent of reaction at any moment in time, regardless of the conditions under which the reaction is carried out: ~ = dl;,ldt, where ~ is the extent of reaction and t is time. In the case of a reaction with one-to-one stoichiometry, such as a typical simple enzyme-catalysed reaction, the extent of reaction is equal to the amount of a reactant consumed or the amount of a product formed. Rate of conversion is an extensive quantity (see extensive property), its dimensions are (amount of substance) divided by time, and it is expressed in mol S-l (compare rate ofrellction). It is therefore independent of the volume of the system. Where this volume remains constant, as during a typical enzyme-catalysed reaction, the rate of conversion is equal to the rate of reaction multiplied by the volume: ~ = v V. The term was formerly known in physical chemistry as rate of reaction. See also catalytic activity.

RCC1 rate of formation see rate of reaction. rate of reaction or velocity of reaction or (sometimes) reaction rate 1 symbol: v; for a specified enzyme-catalysed reaction of a typical kind (i.e. one involving a single substrate, S, a single product, P, one-to-one stoichiometry between them, and constant-volume conditions), the rate of consumption of substrate or the rate of formation of product at any moment in time is given by: v =~d[S]/dt = d[P]/dt, where [S] and [PI are respectively the concentrations of substrate and product, and t is time. A similar set of relationships applies where there are several reactants in one-to-one stoichiometry, but if the overall stoichiometry is not one-to-onea situation rarely arising in enzyme kinetics - the relationships are more complicated. Where intermediates are formed in amounts comparable to those of the reactants, there is timedependent stoichiometry and a rate of reaction for the complete reaction cannot be specified. Rate of reaction is an intensive quantity (see intensive property), its dimensions are (amount-of-substance concentration) divided by time, and it is expressed in mol L- 1 S-I (compare rllte of conversion). See also initilll velocity, limiting rate. 2 (formerly, in physical chemistry) the extensive quantity now termed rate of conversion. rate theory of agonist action a theory of agonist action stating that the response to an agonist is proportional to the number of receptor-agonist associations per unit time, i.e. to the rate of receptor occupation, the binding of agonist to receptor being reversible. The response is therefore maximal at time zero and falls exponentially to an equilibrium value. Rayleigh see Strutt. Rayleigh ratio symbol: R; the ratio of the intensity of light scattered by particles (molecules) in solution at an angle () from the incident beam, Ie, multiplied by the square of the distance, r, from the particle to the detector, divided by the intensity of the incident light, 1o, i.e. R = ler2/lo' The reduced Rayleigh ratio, R e = ler2/loO + cos 2(). Many literature references do not distinguished between these two. See also Rayleigh scattering. [After J. W. Strutt, Lord Rayleigh.] Rayleigh scattering the elastic scattering of photons of light by molecules or atoms of the substance through which the light is passing. When light passes through a liquid or gas, atoms or molecules are polarized by the electric vector of the light, thus inducing a rapidly fluctuating dipole in the atoms or molecules in the light path. The fluctuating dipole leads to the emission of electromagnetic waves in various directions of the same frequency as the incident radiation, and this emission is seen as scattered light. See also Rayleigh ratio. [After J. W. Strutt, Lord Rayleigh.] Rb symbol for rubidium. RB a human tumour suppressor gene that encodes a nuclear phosphoprotein, retinoblastoma protein. Inactivation or loss of RB on both copies of the chromosome (l3qI4) leads to retinoblastoma. R band see Giemsa's stain. RBC or rbc or r.b.c. abbr. for red blood cell. See erythrocyte. Rbe abbr. for relative biological effectiveness (i.e. quality factor). RBS abbr. for Rene Borghgraef solution; the proprietary name for any of a range of general-purpose surfactants and decontaminating agents, especially for laboratory use, that have combined detergent and chelating properties. They are identified with a number or other designation, e.g. RBS 25, RBS 35, RBS solid. RCC1 a chromatin-bound guanine nucleotide release (or exchanging) factor. Its function is required for the normal coupling of the completion of DNA synthesis and the initiation of mitosis, and in its absence mitosis initiates before DNA replication is complete. RCCI therefore appears to be involved in the regulation of this process. It is also necessary for RNA export from the nucleus. It binds to and acts on the nuclear G-protein, Ran. Example from the yeast Candida albicans:

ReF database code RCC_CANAL, 464 amino acids (51.27 kDa). [From regulator of chromosome condensation.] RCF abbr. for relative centrifugal force. R chromophore a chromophore that gives rise to low-intensity absorption bands at long wavelengths. Compare Kchromophore. [From German Radikal.] RCP abbr. for radiochemical purity. RCS abbr. for rabbit aorta-contracting substance. rd symbolfor rad (def. 2) (alternative to rad). Rd abbr. for rubredoxin. rDNA 1 abbr. for ribosomal DNA. 2 (sometimes) abbr. for recombinant DNA; use not recommended because of possible confusion with ribosomal DNA. Re- prefix (in chemical nomenclature) denoting rectus (i.e. right, or clockwise) configuration of a face of a trigonal atom. See ReIS; convention. Re symbol for rhenium. Re symbol for Reynolds number. RE abbr. for (eukaryotic) response element. reactancy of enzymes the number of reactants involved in an enzyme-catalysed reaction in a given direction. The numbers of kinetically important substrates or products in an enzyme mechanism are designated by Uni (1), Bi (2), Ter (3), or Quad (4). Thus, e.g., Uni Uni indicates one substrate and one product, and Ter Bi indicates three substrates and two products. reactant any material participating in a chemical reaction in a given direction. reaction (in chemistry) any process in which molecules interact with one another, leading to chemical or physical change. reaction centre see photosystem. Compare photosynthetic reaction centre. reaction intermediate a transient chemical species, with a lifetime appreciably longer than a molecular vibration time, formed directly or indirectly from the reactants of a chemical (often enzymic) reaction, and that further reacts (directly or indirectly) to give the reaction products. reaction rate (sometimes) an alternative term for rate of reaction. reaction time an alternative name for latent period (def. 1). reactivate to restore activity to any enzymic or cellular system. reactive describing any molecular entity or centre that is capable of reacting readily. Thus, a reactive centre is the point in the molecule at which electron configurations favour a reaction. reactive oxygen a highly active oxygen species, such as superoxide ion. reactivity the degree to which a molecule or centre is reactive. reading (in molecular biology) the process of one-way linear decoding of a nucleotide sequence during, e.g., transcription or translation. reading frame any sequence of bases in DNA that codes for the synthesis of either a protein or a component polypeptide. The point of initiation of reading determines the frame, i.e. the way in which the bases will be grouped in triplets as required by the genetic code. For example, the sequence -ATGGTCAcould be grouped -A,TGG,TCAor -AT,GGT,CAor -ATG,GTC,Adepending on the point at which the reading frame begins. See also open reading frame. readthrough the continuation of DNA transcription beyond a normal termination sequence, due to a failure of RNA polymerase to recognize the termination signal. Readthrough may also occur in translation, where a mutation has caused a ter-

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receptor assay mination codon to be converted to a codon for an amino acid (a sense codon); this is the underlying etiology of several hemoglobinopathies. See also readthrough protein. readthrough protein a product formed by translation of a messenger RNA when one of its termination codons is misread or is recognized by a suppressor tRNA. Polypeptide-chain synthesis then continues until the next termination codon is reached, resulting in the production of a variant protein with a C-terminal extension. reagent 1 any chemical substance that reacts or participates in or is necessary for a reaction. 2 a substance used for the detection or determination of another substance by chemical or microscopical means, usually in solution; e.g. the Folin-Ciocaheu reagent. reagent grade a level of purity of a chemical; chemicals of this quality conform to the specifications established by the Committee on Analytical Reagents of the American Chemical Society and may often be sufficiently pure to use as primary standards in an analytical laboratory, with information concerning the actual percentage of impurities or at least the maximum limit of impurities being given on the label. reagin 1 a term originally used to describe a heat-labile antibody-like substance in the serum of many people suffering from atopic allergies and that has now been identified as immunoglobulin E (IgE). The immediate hypersensitivity (type I) generated by the binding of IgE to its specific antigen on the surface of mast cells involves the release of cell mediators via the reaginic or anaphylactic mechanism. 2 a special kind of antibody response produced by syphilitics that has specificity for cardiolipin antigens. real-time (in computing) indicating that a computer monitors a process continuously as it occurs, in distinction to the analysis of recorded data. rearrangase or S-S rearrangase an alternative name for protein disulfide isomerase. rearrangement reaction a reaction in which molecular bonds are rearranged without the loss of any atom from the molecule, e.g. as in the conversion of glucose 6-phosphate to fructose 6-phosphate. rseA a gene in Escherichia coli encoding a protein, RecA, involved in genetic recombination and in the SOS response for DNA repair (see SOS repair). The protein has two activities: (I) a DNA-dependent ATPase in the presence of single-stranded DNA that catalyses the ATP-dependent uptake of singlestranded DNA to form the heteroduplex required in recombination. (2) In the presence of DNA fragments it becomes a protease (RecA*; EC 3.4.99.37) that cleaves a specific Ala-IGly bond in certain repressor molecules, including its own repressor (see texA). This allows all the SOS genes to be activated. Example from E. coli and Shigella flexneri (identical sequences): database code RECA_ECOLI, 352 amino acids (37.80 kDa); 3-D structure known; eight motifs. See also exodeoxyribonuclease V, recombinational repair, recombinase. recalcitrance or persistence the ability of a substance to remain in a particular environment in an unchanged form. reeSe a gene in Escherichia coli for exodeoxynuclease V, an ATP-dependent nuclease specific for double-stranded DNA; it mediates genetic recombination. recDNA (sometimes) abbr. for recombinant DNA. receptor any cellular macromolecule that undergoes combination with a hormone, neurotransmitter, drug, or intracellular messenger to initiate a change in cell function. Receptors are concerned directly and specifically in chemical signalling between and within cells. Cell-surface receptors, e.g. the acetylcholine receptor and the insulin receptor, are located in the plasma membrane, with their ligand-binding site exposed to the external medium. Intracellular receptors, e.g. steroidhormone receptors, bind ligands that enter the cell across the plasma membrane. receptor assay 1 the determination of receptor numbers and the dissociation constant of receptor-ligand binding. The

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receptor cross-talk binding at various concentrations of ligand is measured, often by use of a radioactive ligand, and is analysed by means of a Scatchard plot. 2 the determination of the concentration of a ligand by utilizing a purified receptor in a manner similar to that used in radioimmunoassay; in this case the receptor, rather than an antibody, performs the role of specific binding agent. receptor cross-talk interaction between two receptors such that one receptor, when activated, modulates the action of the other. This type of interaction often involves the production by the first receptor of a second messenger, which then modulates the action of the second receptor. receptor-destroying enzyme an enzyme that brings about chemical change in a (usually membrane-bound) receptor, leading to inactivation of the receptor. Knowledge of the specificity of the enzyme provides information about the nature of the groups or linkages exposed to enzyme attack, and thus to receptor structure or orientation in the membrane. Examples are sialidase and trypsin. receptor-effector complex the complex that results when an occupied receptor binds to another protein (the effector), the activation of which by the occupied receptor leads to signal transduction. receptor-mediated describing a response that requires the intermediary action of a receptor, especially one located in a membrane. receptor-mediated endocytosis a form of endocytosis involving the internalization (i.e. passage into the cell interior) of stretches of membrane into which receptors have clustered after binding of ligand. The cytoplasmic surfaces of these stretches of membrane are coated with clathrin and are termed coated pits. See also endosome. receptor transformation see translormation (def. 3). recessive describing an allele that lacks effect when accompanied in the same diploid by a dominant form of the same gene. Most (not all) defective mutant genes are recessive to their normal functional counterparts. -recessivity n. recipient bacterium see bacterial conjugation. reciprocal 1 expressed in the reverse direction, in response to an initial application of any force or stimulus. 2 (in mathematics) the inverse value, obtained when the values of numerator and denominator are reversed; the reciprocal of x is obtained by evaluating I/x. reciprocal plot a plot in which the units of both the ordinate and the abscissa are reciprocals of the values that have been determined. Compare Uneweaver-Burk plot. recircularization or recircularisation the restoration of circularity to a plasmid vector following the insertion of recombinant DNA. The plasmid used for gene cloning is a small circular molecule. This is cut with a restriction endonuclease to create linear DNA molecules. The foreign DNA fragment with the same cohesive ends is then annealed to the cut plasmid to form a recombinant DNA circle. The DNA molecule containing the foreign DNA insert is then covalently sealed with DNA ligase. Recircularization also occurs during the replication of some DNA phages by a rolling circle replication mechanism. recognition any specific binding interaction between molecules. Such interaction between two molecules is based on the existence of recognition sites, one (or more) on each of the interacting molecules, that are tailored to fit in such a way that highly specific binding occurs; i.e. the two molecules uniquely 'recognize' each other. See also chiral recognition, molecular recognition. recognition sequence the part of the sequence of a macromolecule that is able to recognize and bind to a particular sequence in another macromolecule. recognition site 1 (in proteins) a site for recognition of another protein, involving a specific sequence of amino acids; the latter may be in a single chain (e.g. target sites for protein phosphorylation), or may involve amino acids in separate chains brought into juxtaposition by quaternary structure. 2 (in nucleic acids) a site for recognition of a protein, involv-

recombinational repair ing a specific sequences of bases; see restriction endonuclease. 3 (in pharmacology) a region of a receptor macromolecule to which an endogenous agonist binds. recombinant clone a population of bacteria or other host derived from a single cell into which a vector containing recombinant DNA has been introduced. recombinant DNA a fragment of deoxyribonucleic acid (DNA) that has been inserted into a cloning vector, thereby leading to its use in the isolation of a clone of cells characterized by the presence of the fragment. The term is derived from the concept that insertion into the vector is a form of genetic recombination. [Note: The abbreviation rDNA has sometimes been applied to recombinant DNA, but this use is discouraged (rDNA having been pre-empted for ribosomal DNA); while alternatives such as recDNA or rtDNA have been suggested, IUBMB considers a standard abbreviation unnecessary.] See also recombinant DNA technology. recombinant DNA technology an area of biotechnology concerned with the manipulation of recombinant DNA. It has many important applications, including (1) DNA sequencing, which may lead to the ability to predict the primary structure of a protein where this is the product of a cloned gene, (2) the synthesis of recombinant protein by a suitable expression system, and (3) the production of DNA probes (def. 3) for use in hybridization techniques. The technology has led, e.g., to the production of human insulin for the treatment of diabetics, human growth hormone for administration to children with growth defects, and a vaccine for hepatitis B. DNA probes are essential for the detection of aberrant genes which are the cause of numerous diseases and the technique has the potential for gene therapy. See also genetic engineering. recombinant protein a protein coded for by a gene - recombinant DNA - that has been cloned in a system that supports expression of the gene and translation of messenger RNA (see expression system). Modification of the gene by recombinant DNA technology can lead to expression of a mutant protein. Proteins coexpressed in bacteria will not possess post-translational modification, e.g. phosphorylation or glycosylation. Eukaryotic expression systems are needed for this; see, e.g., baculovirus. recombinase 1 an enzyme that recognizes specific sites involved in the joining of V-region gene segments in L- and Hchain gene segment pools in the generation of antibody. 2 RecA protein (see recA) is also a recombinase, the activity of which is increased in Escherichia coli following damage to DNA. RecA binds to a region of single-stranded DNA and catalyses the formation of duplex DNA; hydrolysis of ATP is involved. A recombinase recognizes and binds to each of two recombinant sites on different DNA molecules or within the same DNA. One DNA strand in each site is cleaved at a specific point within the site, and the recombinase becomes covalently linked to the DNA at the cleavage site through a phospho tyrosine (sometimes a phosphoserine) bond. The transient protein-DNA linkage preserves the phosphodiester bond lost in cleaving the DNA; cofactors such as ATP are unnecessary in subsequent steps. The cleaved DNA strands are rejoined to new partners, with new phosphodiester bonds created at the expense of the protein-DNA linkage. The result of the initial breakage and rejoining process is the Holliday junction. To complete the reaction, the process must be repeated at a second point within each of the two recombination sites. In summary the recombinase can be viewed as a site-specific endonuclease and ligase in one package. recombination see genetic recombination, recombinant DNA, immunoglobulin synthesis. recombinational heteroduplex see heteroduplex. recombinational repair a mechanism to restore the integrity of DNA when replication of DNA stops at a thymine dimer but resumes after the dimer is passed, creating a gap. The undamaged parental strand recombines into the gap, a process promoted by RecA protein (see recA). The new gap in the parental

recoverin strand is filled by the action of DNA polymerase and DNA ligase. The thymine dimer itself is not repaired in this process but time is allowed for the excision system to repair this damage later. recoverin an EF-hand Ca 2+-binding protein, apparent molecular mass 26 kDa; also known as cancer-associated retinopathy protein. It selectively localizes to the retina and pineal gland and is implicated in the activation of retinal rod guanylate cyclase by rhodopsin, possibly being involved in the blocking of the phosphorylation of rhodopsin, by forming an inhibitory complex with rhodopsin kinase. It has been identified as an autoantigen in cancer-associated retinopathy, a putative autoimmune process. Example from human: database code RECO_ HUMAN, 199 amino acids (22.97 kDa). recovery the portion of material or activity that remains after any extraction or purification, usually expressed as a percentage of the amount that was present as starting material. recruitment the action by any cell, cell constituent, or molecule that brings about the cooperation of any other component in performance of any function. recrystallize or recrystallise to dissolve a crystalline substance and subsequently crystallize it from the solution, usually to increase the purity of the substance. -recrystallization or recrystallisation n. rectangular hyperbola a hyperbola whose asymptotes are at right angles. It is sometimes said that, for enzymes that follow so-called Michaelis kinetics, the plot of initial rate against substrate concentration has the shape of the curve of a rectangular hyperbola. It is true that the Michaelis-Menten equation does yield a curve that is part of a rectangular hyperbola, but the axes of the hyperbola must be rotated through 45°, and displaced, if they are to coincide with the axes of the Michaelis-Menten plot. rectification 1 (in physics) the process of obtaining a direct current from an alternating electrical supply. 2 (in physiology) the regulation of membrane conductance by the voltage across the membrane; strong rectification implies that ionic channels carrying current are open at some membrane potentials and shut at others. Conductance is low at very negative membrane potentials, but increases as the potential becomes less negative. 3 (in chemistry) the process of purifying a liquid by distillation. rectus Latin right; used to describe the right, or clockwise, configuration of one of the two faces of a compound containing a trigonal carbon atom. It is designated by the prefix Re-. Compare sinister. See also RelSi convention. recycle to pass again through a system one or more times after return to a starting condition or state. red drop a phenomenon in photosynthesis, in which the quantum yield is relatively constant in light of wavelengths between 500 and 600 nm, but drops dramatically at longer wavelengths. redistil or (US) redistill to distil again that which has already been distilled, usually as an aid to purification of liquids. red marrow see bone marrow. red muscle dark, skeletal, voluntary muscle that is relatively rich in myoglobin and cytochromes, and derives energy for contraction from a high oxidative capacity, in contrast to white muscle, which has a high glycolytic capacity. The distinction between muscle types should more strictly be based on muscle-fibre types. Type I fibres have a high oxidative capacity based on a high activity of tricarboxylic-acid cycle and respiratory chain enzymes. Type IIA fibres have high oxidative and high glycolytic capacity. Type lIB fibres have low oxidative and high glycolytic capacity. The proportions of these fibres vary in different muscle types; accordingly the muscle may have the ability to engage in very rapid but quickly exhausted 'fast twitch' contractions characteristic of white muscle, or less powerful but more sustained contractions typical of red muscle. redox abbr. for reduction-oxidation; see oxidation-reduction.

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reductive alkylation redox balance the ratio of the number of reductions to the number of oxidations in a given metabolic pathway. Compare redox state. redox couple the oxidized (electron acceptor) and the reduced (electron donor) forms of the species of a given redox reaction; e.g. NAD+ and (NADH + H+). The potential of any redox couple in solution can be measured against a reference electrode, and a table of relative potentials constructed. See redox potential. redox hypothesis a now discounted model for the Pasteur effect in glycolysing muscle extracts. Addition of redox indicators that changed the redox state in the direction of oxidation decreased the rate of lactate formation; it was therefore suggested that the effect of oxygen might be connected with a change of the redox state in the same direction. redox indicator see indicator (def. 3). redox potential or oxidation-reduction potential symbol: Eo; for a particular redox couple at a given pH and temperature, the potential of an electrode (usually bright platinum) immersed in a solution containing I M oxidant and I M reductant, relative to a standard hydrogen electrode. The more 'reducing' the couple, the more negative is Eo; the convention in biochemistry is that the more 'oxidizing', the more positive is Eo. Some standard potentials, measured against the hydrogen electrode, are: NAD+/NADH + H+, -0.32 V; fumarate/ succinate, +0.032 V; cytochrome b(Fe 3 +)/cytochrome b(Fe 2+), +0.22 V; cytochrome c(Fe3+)/cytochrome c(Fe2+), +0.25 V; O 2 + 2H+/H2' +0.82 V. redox reaction a chemical reaction in which the oxidation of one reactant is coupled to the reduction of a second reactant, electrons being transferred from the reactant being oxidized to that being reduced. redox state the ratio of the concentration of the oxidized member of a redox couple to the concentration of the reduced member; e.g. [NAD+]/[NADH] or [Fe 3+]/[Fe 2+]. The term should only be applied to a particular redox system and not to a heterogeneous system. red shift any shift of the peaks of a spectrum to longer wavelengths (i.e. towards the red end of the spectrum), including a shift from the red to infrared. Compare blue shift. red tide a bloom of the dinoflagellate Ptychodicus brevis (Gymnopodium breve), an organism that produces brevetoxins and causes epidemics of food poisoning. reduce to cause or undergo reduction. reduced Rayleigh ratio see Rayleigh ratio. reducing agent any substance acting as a reductant. Compare oxidizing agent. reducing end the end of an oligo- or polysaccharide molecule that carries a potential hemiacetal or hemiketal (reducing) group. reducing sugar any sugar that will reduce heated alkaline solutions of cupric salts, such as Fehling's or Benedict's solutions, due to the presence of a hemiacetal or hemiketal group. reductant the chemical species that donates an electron in an oxidation-reduction reaction; i.e. the species that undergoes oxidation in such a reaction. Compare oxidant. reductase a donor:acceptor oxidoreductase enzyme (EC class I) when named after the more oxidized alternative substrate and when O 2 is not a substrate. See oxidoreductase. reduction the chemical process by which oxygen is withdrawn from, hydrogen is added to, or (more generally) an electron is added to (with or without addition of a proton) a molecular entity. Compare oxidation. -reductive ad}.; reduce vb. reduction division the first division of meiosis. reduction potential the electrode potential that measures the tendency of one half of a redox reaction to proceed so as to gain electrons. See oxidation potential, redox potential. reductive alkylation the reaction of amino groups with an alkyl carbonyl group, followed by reduction of the resulting Schiff base with a reducing agent such as sodium borohydride. See reductive amination.

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reductive amination reductive amination the process whereby ammonia or a primary or secondary amine reacts with ketones and aldehydes in the presence of reducing agents such as H 2 and a metal catalyst, or more conveniently, NaBH 4 or its derivative NaBH 3CN, to produce primary, secondary, or tertiary amines. In a formal sense, the amine is alkylated in this reaction while the carbonyl group is reduced, hence the term reductive amination, or alternatively reductive alkylation. Amino acids have been made from oxo acids by this process. A variation of reductive amination, termed the Escbweiler-Clarke reaction, involves the methylation of an amine to the tertiary amine stage using formic acid as the reducing agent and formaldehyde as the methylating reagent. reductive carboxylic-acid cycle or reductive tricarboxylicacid cycle a metabolic cycle used by members of the Chlarobiaceae for CO 2 fixation. The usual operation of the tricarboxylic-acid cycle is reversed, with three enzyme replacements, and other supplementary reactions are used. Initially one CO 2 reacts with succinyl-CoA to form oxoglutarate; oxoglutarate synthase (EC 1.2.7.3) replaces the usual oxoglutarate dehydrogenase complex. A second CO 2 converts oxoglutarate to isocitrate with use of isocitrate dehydrogenase, and isocitrate proceeds to citrate. Citrate is then cleaved by ATP citrate (pro-S) lyase to acetyl-CoA and oxaloacetate; the latter recycles to succinylCoA with fumarate reductase (NADH) replacing succinate dehydrogenase. These operations reverse the usual tricarboxylicacid cycle and convert two CO 2 to acetyl-CoA. A net gain of oxaloacetate is possible by conversion of acetyl CoA and one CO 2 to pyruvate (pyruvate synthase), pyruvate to phosphoenolpyruvate (phosphoenolpyruvate synthase) and phosphoenolpyruvate and one CO 2 to oxaloacetate (phosphoenolpyruvate carboxylase). The overall result is that four CO 2 yield a net gain of the four-carbon oxaloacetate. reductive methylation a specific form of reductive alkylation, in which the alkyl group is methyl. Formaldehyde is often used as a reagent in this case. reductive pentose-phosphate cycle or Calvin cycle other names: carbon reduction cycle; C 3 cycle/pathway; more appropriately, Calvin-Bassham cycle; the cyclic set of reactions, occurring in chloroplasts in the majority of higher plants (C3 plants), that results in the fixation of CO 2 as glucose using the ATP and the NADPH formed in the light reactions of photosynthesis. Briefly, CO 2 reacts with ribulose 1,5-bisphosphate under the action of ribulose-bisphosphate carboxylase (Rubisco), EC 4.1.1.39, to form two molecules of 3-phosphoglycerate; these are phosphorylated (by ATP) to 1,3-bisphosphoglycerate, which in turn is reduced (by NADPH) to glyceraldehyde 3-phosphate. This is then converted by aldolase, transketolase, and other enzymes to fructose 6-phosphate and ribulose 5-phosphate; the latter being phosphorylated (ATP) to ribulose 1,5-biphosphate, completing the cycle. See also HatchSlack pathway. reductone any reducing substance with a chemical structure containing the stabilized enediol -C(OH)=C(OH)-. Reductones are generated when monosaccharides are heated for prolonged periods with strong alkali, whereby the enols originally produced are broken down to strongly reducing fragments. Another notable example is ascorbic acid, and in some contexts reductones are described as 'apparent ascorbate', i.e. the reductive acids that are present in certain processed foods and react similarly to ascorbate, interfering with its determination. Re-face (of an atom or molecule) see Rs/Siconvention. reference something that acts as a standard in relation to quality, quantity, or type against which other values or characteristics can be compared; e.g. reference spectrum. reference electrode any electrode, selected by convention, against which the electronegativity of compounds is measured. The standard biochemical reference is the hydrogen electrode, normally a platinum electrode in hydrochloric acid through which hydrogen gas is passed. A cell is constructed such that another electrode is immersed in a test solution and the poten-

regeneration tial difference between these two half-cells is measured. For convenience, however, the reference electrode is often a calomel electrode, and after measurements have been made against this, the electronegativity against the hydrogen electrode can be calculated from the known difference between this and the hydrogen electrode. reflect to change the path of electromagnetic radiation, when it meets a surface, such that it returns partially or completely in a direction on the same side of the surface as the source. reflectometer see densitometer (def. I). reflex (in physiology) an automatic or involuntary response of the nervous system to a stimulus. A reflex may be a monosynaptic spinal reflex (e.g. a simple motor response to a sensory stimulus), involving transmission through the spinal cord only, or polysynaptic and involving synaptic transmission in the brain. A conditioned reflex is one that is learned through repeated association of a stimulus with either rewarding (e.g. food) or aversive (e.g. punishment) events. refolding (for proteins) the restoration of three-dimensional structure in a manner that mayor may not achieve a full return to the native state following denaturation. refraction the change in direction undergone by a wave of electromagnetic radiation on passing through a boundary between two media in which its velocity differs. Snell's law states that nlsin{lj = n2sin{l2, where nj and n2 are the refractive indices of the two media, and {II and {l2 are the angles between the radiation and the normal to the boundary in the corresponding media. [After Willebrord Snell (1591-1696), Dutch astronomer and mathematician.] refractive index abbr.: RI; symbol: n; for a given medium, a measure of the degree of refraction induced by the medium when light or other electromagnetic radiation passes through it. The refractive index of a medium is the ratio of the speed of light in a vacuum, Co, to the speed of light in the medium, c; i.e. n = co/c. For many practical purposes the speed of light in air may be used instead of that in a vacuum. refractivity a measure of the extent to which a medium will cause the deviation of a ray of light or other electromagnetic radiation entering its surface. If the refractive index of a medium is n, its refractivity is (n - I). The specific refractivity is given by (n - I)/p, where p is the density of the medium. The molecular refractivity is the specific refractivity multiplied by the relative molecular mass. refractometer an instrument for measuring refractive index. refractory 1 (of a clinical condition) resistant to treatment. 2 (of a cell or tissue) resistant to stimulation, as by a drug, hormone, or nerve impulse, especially during a period following previous stimulation. See also tachyphylaxis. 3 (of a substance or material) resistant to heat, corrosion, mechanical deformation, or other aggressive agents causing alteration. 4 a substance or material having such resistance. Refsum's disease a rare autosomal recessive inherited disease with neurological symptoms, including retinitis pigmentosa, peripheral neuropathy, cerebellar ataxia, and nerve deafness. It is caused by a defect in alpha oxidation of fatty acids, which is important for the oxidation of phytanic acid. The defect results in the accumulation of this acid in tissues and serum of patients. The symptoms are reduced by restriction of dietary dairy products and meat from ruminants, which contain phytanic acid. regeneration 1 (in chemistry) the process of restoring to a state of preparedness for use, as in the case of an ion-exchange resin washed with acid or alkali to restore it to the H+ or OHform. 2 (in biology) the growth of new tissues or organs to replace ones lost or damaged, e.g. through injury or surgery. In some tissues, such as liver, epithelial tissue, or pancreas, regeneration occurs by simple duplication of cells, with the regeneration time varying from one week to a year. In other systems, such as epidermis, renewal is from specialized stem cells. Regenerating liver can be used as a model in which systems involved in proliferation are more highly activated than

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in normal liver. It is a unique property of liver that it is possible to remove two thirds of the organ yet it regenerates to form an organ of similar total weight to the original, albeit with somewhat different organization of the lobes. Many plants can regenerate a complete plant from a shoot segment or a single leaf or from tissue culture cells. regeneration time the time taken for a tissue or organ to regain its former size or weight following damage or removal. For example, if two-thirds of the liver of a rat is removed surgically the liver regains its former weight in about two weeks. The proliferation of cells can be measured by the use of [3H]thymidine to label the cells synthesizing DNA. regio+ comb. form denoting, or relating to, an area or site. regioselective pertaining to a chemical change that occurs with greater frequency at one site than at a number of other possible sites of similar type, usually involving a structural or positional isomer. regiospecific describing a chemical reaction that occurs specifically in only one of two possible ways, but not including stereospecificity (see stereospecific). registration peptide one of the postulated extensions of the a chains of tropocollagen, when synthesis has just been completed; two a I extensions and one a2 extension interact to form a stable assembly with the correct chains brought together into register. regression coefficient see regression line. regression line a line fitted to a series of two variable quantities, x and y, so as to minimize the sum of the squares of the distances parallel to the y axis of the observations from the line. The regression line of y on x has the equation (regression equation): y = a + bx where a = LY - bLxln and b, the regression coefficient, is the slope of the line and is given by: b = (nLxy - LXLy)/(nLx 2 - (Lx)2) where n is the number of pairs of observatioris. In an analogous manner a regression equation, line, and coefficient may be obtained for x on y. regucalcin a hepatic Ca 2+-binding protein, and also a GTPbinding protein, that modulates the hormonal regulation of plasma membrane Ca 2 \Mg 2 +-ATPase. regulation (in metabolism) control of the rate of a metabolic system, especially in intact organs and cells as a result of interaction from components of related systems. -regulatory adj. regulator gene or regulatory gene any gene that does not contribute structural information to the proteins whose synthesis it controls, but that determines the production of a specific cytoplasmic substance, a repressor, that inhibits information transfer from a structural gene (or genes) to protein. It may control the synthesis of several different proteins, which are determined by a coordinated group of structural genes (see operon). Although, when it was put forward, the concept of the regulatory gene was helpful, it is now realized that the genome codes for many different proteins that control the transcription of the structural genes (see, e.g., attenuators, transcription factors), and that can be classed as gene-activator proteins; these will possess two domains, one to recognize a specific regulatory DNA sequence, the other to contact the transcription machinery. regulator-site hypothesis a hypothesis to explain the control of insulin release from pancreatic islet B cells by glucose. It postulates that the glucoreceptor is an enzyme that is activated (or inhibited) by glucose and catalyses the production from a precursor of an activator, which controls the release process. Compare substrate-site hypothesis. regulatory enzyme an enzyme that regulates the rate of a metabolic pathway; under regulating conditions, it is the enzyme of lowest activity in the pathway. Commonly, the rate is altered either by variation in the amount of regulatory enzyme (as a result of increased or decreased synthesis or degradation), or by variation in its activity by covalent modification (often by phosphorylation or dephosphorylation by kinases or

relative centrifugal force phosphatases) or by allosteric modifiers. Classic examples are phosphofructokinase and glycogen phosphorylase (see phosphorylase). regulatory gene see regulator gene. regulatory sequence a sequence in a DNA molecule concerned with regulating the expression of a gene; e.g. a promoter or operator. regulatory site a specific site on an enzyme that is distinct from the substrate-binding site and that binds a feedback inhibitor or other regulatory molecule. Compare allosteric site. regulatory subunit any of the subunits of a multimeric enzyme (composed of nonidentical subunits) that has a regulatory rather than a catalytic function. regulon a group of genes, whether linked in clusters or unlinked, that respond to a common regulatory signal. rehydrate to restore water to material that has been lyophilized (see freeze-dry) or otherwise dehydrated. Reichstein, Tadeus (1897-1996), Polish-born Swiss chemical engineer, organic chemist, and botanist renowned for his isolation and study of 29 different steroids from the cortex of the adrenal gland and (in 1933) for devising a method of synthesizing ascorbic acid, vitamin C, from glucose that is still in use industrially; Nobel Laureate in Physiology or Medicine (1950) jointly with E. C. Kendall and P. S. Hench 'for their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects'. reiterated describing nucleotide sequences that occur many times within a genome. These occur especially in higher organisms. See also repetitive sequences. REL a gene family encoding transcription factors of the KB family; v-rei is the oncogene of avian reticuloendothelial virus strain T (REV-T), encoding p69 v- rel . Rei and v-ReI form homo- or heteroditners that bind to NF-KB motifs. v-Rei has lost two N-terminal amino acids and 118 C-terminal residues compared with ReI. Example of ReI product from mouse: database code REL_MOUSE, 587 amino acids (64.96 kDa). Example of p69 v -rel : database code TREL_AVIRE, 503 amino acids (55.91 kDa). "etA a gene in Escherichia coli, mutations in which can lead to a 'relaxed' phenotype in which amino-acid starvation fails to switch off ribosomal RNA biosynthesis. The gene product is an enzyme active in the presence of ribosomes and uncharged tRNA, and called GTP pyrophosphokinase, EC 2.7.6.5; systematic name: ATP:GTP 3'-pyrophosphotransferase; other names: pppGpp synthetase I; stringent factor; guanosine 3',5'polyphosphate synthase; it catalyses a reaction between ATP and GTP to form guanosine 3'-diphosphate 5'-triphosphate and AMP. The product is referred to as pppGpp and is converted to ppGpp (guanosine 3'-diphosphate 5'-diphosphate), which is the active nucleotide in evoking the stringent response. Database code RELA_ECOLI, 744 amino acids (83.76 kDa). relative atomic mass or (formerly) atomic weight abbr.: r.a.m.; symbol: A,. 1 (of an atom) the ratio of the mass, ma , of the atom in question, to the atomic mass constant, m u , which is one-twelfth of the mass of the nuclide 12e; i.e. A, = ma/m u ' A r is a mass ratio, a pure number with no units. 2 (of an element) the ratio of the average mass, rna, of the atoms in a specified sample of the element in question, E, to the atomic mass constant, m u ; i.e. Ar(E) =ma(E)/m u • Since, in general, elements are mixtures of isotopes of differing nucleon numbers (mass numbers), an average mass of the atoms is required in this definition. Furthermore, the isotopic composition of many elements can vary with the origin of the sample and its treatments. Hence there are limits to the precision with which the values of the relative atomic masses of many elements can be given. relative band rate or relative band speed see RB value. relative biological effectiveness abbr.: RBE; an alternative term for quality factor. relative centrifugal force symbol: G; the force acting on a particle in a centrifugal field expressed in multiples of the ac-

563 relative density celeration due to gravity, g. G = w 2r, where w is the angular velocity in rad s-1 and r the radial distance from the axis of rotation in m. (G = 1440 x 1t 2w 2r where w is in revolutions per minute and r in cm.) relative density symbol: d; the ratio of the mass density of a substance, p, at a given temperature, to the mass density of a reference substance (usually water), pO at a reference temperature (usually 4°C); i.e. d = plpo relative formula mass the relative molecular mass as calculated from the formula of a compound. relative molecular mass or relative molar mass or molecular weight abbr.: r.m.m.; symbol: M r; the ratio of the mass of a molecule, mr, to the atomic mass constant, m u, which is onetwelfth of the mass of the nuclide J2C; i.e. M r = mrlmu' M r is a mass ratio, a pure number with no units. The convention for indicating the size of a protein is thus' Mr' followed by a number without units, e.g. M r 10000; the equivalent molecular mass, i.e. its mass in daltons, would be 10 kDa. See also dahon, relative atomic mass, unified atomic mass unit. relative permittivity symbol: Gr;formerly called dielectric constant, the ratio of the permittivity of a substance, G, to the permittivity of vacuum, GO, i.e. Gr = Gleo. relaxation (in chemistry) the process of self-adjustment of a molecular system to a new state of minimum free energy following a disturbance. relaxation kinetics a technique used to study rapid reactions in which a mixture at equilibrium is rapidly adjusted to a new set of conditions. The system is then observed as it approaches its new equilibrium, a process known as relaxation. The temperature-jump method is often used, whereby an electric discharge is used to increase the temperature by several degrees in a period of about I IlS. See also rapid-reaction kinetics. relaxation spectrometry the use of spectrometry to follow the kinetics of a reaction undergoing relaxation from a perturbation. See relaxation kinetics. relaxed control a mechanism of control of plasmid replication in which replication of plasmids greatly exceeds that of the chromosome. Compare stringent control. relaxed DNA circular DNA that is not supercoiled (see supercoil), and instead has an unwound loop. The supercoiled form is energetically favoured over the relaxed form. Since the supercoiled DNA is more compact it moves faster when centrifuged or upon electrophoresis, and so the two forms of DNA can be separated. relaxed form abbr.: R form; one of two alternative quaternary structures of a protein, the other being the tense form (or taut form, abbr.: T form). These forms derive from the concept of two conformational states of a protein, which differ in their affinities for a ligand. Factors affecting the conformational equilibrium also influence the affinity of ligand-binding and vice versa. Such factors may include the ligand itself, which could enhance or reduce the affinity of the protein, giving rise to positive cooperativity or negative cooperativity of binding respectively. The T form has a lower affinity for the substrate. For example, oxyhemoglobin is R, and deoxyhemoglobin is T; the binding of O 2 to the heme group causes the iron atom to move with respect to the heme plane, and this favours the move from T to R. See also allosteric constant, Monod-WymanChangeux model (for allosteric compounds). relaxed mutant a bacterial mutant that lacks the rel (relaxed) gene, which exerts a critical control over the stringent response. The rel- mutant is unresponsive to amino-acid starvation, so that rates of RNA synthesis, for example, continue as before. See also reiA. relaxin a protein hormone (M r ~5600) that is responsible in most mammals (including humans) for dilation of the symphysis pubis, softening of the cervix, and various other physiological changes prior to parturition. It is synthesized and stored in the corpus luteum. Like insulin, the hormone consists of two polypeptide chains linked by two disulfide bonds, with

renin an intrachain disulfide bridge also present. Although otherwise dissimilar in primary structure, the two proteins have very similar tertiary structures. As with insulin, synthesis is thought to occur via an inactive, single-chain precursor, in this case prorelaxin, and storage is as granules in vesicles. Example from human (precursor): database code RELI_ HUMAN, 185 amino acids (21.12 kDa). See also insulin-related growth factors. release factor abbr.: RF or (formerly) R factor; proteins that participate in the release of a nascent polypeptide chain from a ribosome. There are two classes of release factors, one codonspecific and the other non-codon-specific. In bacteria two codon-specific factors have been identified, RF -I, specific for UAGIUAA, and RF-2, specific for UGA/UAA. In eukaryotes one such factor has been found, eRF-1. These factors act at the ribosomal A-site and require polypeptidyl-tRNA at the P-site. In bacteria the action of RF-I and RF-2 are aided by the non-codon-specific RF-3 which binds to guanine nucleotides. In eukaryotes a similar factor, eRF-3, has been identified. The genes encoding RF-I (prfA) and RF-2 (prfB) have been identified. Mutations in these genes often cause misreading of termination signals, increased frameshifting, and temperature-sensitive growth of the cells. Examples from Escherichia coli: RF-I, database code RFLECOLI, 360 amino acids (40.41 kDa); RF-2, database code RF2_ECOLI, 365 amino acids (41.19 kDa). See also ribosome recycling factor. release-inhibiting factor or release-inhibiting hormone any polypeptide that inhibits the release of a hormone or hormones. An example is somatostatin. releasing hormone or releasing factor any of a group of peptide neurohortnones that are synthesized in various distinct regions of the hypothalamus. They are released in nanogram amounts into the capillaries of the portal vessels of the median eminence of the hypothalamus, then carried to the anterior pituitary where they regulate the production arid secretion in microgram amounts of the tropic hormones, e.g. thyrotropin, somatotropin, and the gonadotropins. In the anterior pituitary they act via the adenylate cyclase system and are then degraded by proteolysis. rem symbol: rem; a non-SI unit of (radiation) dose equivalent, equal to 0.01 J kg- 1 of irradiated human (or other mammalian) tissue. It is being superseded by the sievert; I rem = 10-2 sievert. [Acronym for rontgen equivalent man (or mammal).] REMI abbr. for restriction enzyme-mediated integration (see insertational mutagenesis). remnant a fragment of a molecule or other entity remaining after partial degradation especially chylomicron remnant. renal pertaining to, or of, the kidney. renal rickets a condition occurring in older children and characterized by the skeletal changes of rickets, due to impairment of renal function allowing excessive loss of calcium and phosphate into the urine. renaturation the return of denatured macromolecules (protein, DNA, etc.) to the conformation they maintained before denaturation. In the case of proteins, reversible denaturation is brought about by disulfide reducing agents and urea, for nucleic acids by heat or salts. See also native state. renewal (of tissue) see regeneration (def. 2). renin or angiotensin-forming enzyme or angiotensinogenase EC 3.4.23.15; a labile proteolytic enzyme, M r "'40000, formed from prorenin in plasma and kidney, and secreted into the blood by the kidney. It is also produced in relatively large amounts by the submaxillary gland of certain strains of mice. A glycoprotein aspartic endopeptidase, it is highly specific for the Leu-i-Leu bond in angiotensinogen, which it cleaves to generate angiotensin 1. Despite its high specificity it resembles other eukaryotic aspartyl proteinases. Example, precursor from human: database code RENCHUMAN, 406 amino acids (45.01 kDa). It is a preproprotein; residues 1-23 are the peptide signal and 24-66 are the propeptide. 3-D structure is known. Compare rennin.

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renin-angiotensin system a system involved in the control of blood pressure. Renin, secreted into the blood by the kidney in response to osmotic changes, anoxia, or kidney trauma, acts on angiotensinogen to release angiotensin I (AI) (see angiotensin). Angiotensin-converting enzyme forms angiotensin II (All) from AI by release of His-Leu from the C-terminal end. All stimulates release of the mineralocorticoid aldosterone from the glomerulosa cells of the adrenal cortex. Various nonapeptide analogues of AI inhibit converting enzyme and are used in the treatment of renin-dependent hypertension. See also captopril. rennet an extract obtained from the stomachs of young mammals living on milk. It contains rennin (i.e. chymosin), an enzyme that clots milk and is used in cheese-making. rennin an alternative name for chymosin (which is preferred because of possible confusion with renin). See also rennet. Reoviridae a family of double-stranded RNA viruses (class III in the Baltimore classification) with a segmented genome, infecting vertebrates, arthropods, and plants. The virion consists of a "nonenveloped icosahedral particle, 60-80 nm across, and containing 10-12 segments of RNA together with RNA-directed RNA polymerase; the latter serves to transcribe the negative strand of each RNA molecule into mRNA. This family comprises six groups: the orthoreoviruses, orbiviruses, rotaviruses, cytoviruses, phytoreoviruses, and Fijiviruses. No pathology is associated with the orthoreoviruses infecting humans, but rotaviruses cause gastroenteritis, and orbiviruses cause the disease blue tongue in sheep. reovirus see Reoviridae. rep an obsolete unit of absorbed dose of ionizing radiation of any kind, equal to the dose of radiation that, upon absorption by a given mass of living tissue, causes the same energy deposition as I rontgen of X- or gamma radiation, i.e. about 96 ergs per gram (0.0096 J kg~l) of tissue. See also rad, rem. [Acronym for rontgen equivalent physical.] REP abbr. for repetitive extragenic palindromic sequence. RepA the protein product of the Escherichia coli gene repA which has a role in the replication of DNA in E. coli. Although the principal DNA helicase in E. coli is DnaB helicase, there is also a different 68 kDa monomeric protein, which has some helicase activity during certain life-cycle stages of the replication of single-stranded phages. The contribution of RepA protein to the host cell is less clear, but the rate at which E. coli replication forks propagate is reduced in rer mutants. repairase an enzyme concerned in the repair of an interrupted polynucleotide chain. repair enzyme any of the enzymes making up the enzyme complex responsible for the excision of pyrimidine dimers which are formed on exposure of DNA to ultraviolet light, when adjacent pyrimidine residues on a DNA strand become covalently linked. Three enzymic activities are essential for the repair: (I) an enzyme complex comprising the three proteins encoded by the uvrABC genes (see uvr) that detects the distortion produced by the pyrimidine dimer: (2) the UvrABC enzyme complex also has another activity, described as a specific excinuclease, which cuts the damaged DNA strand eight nucleotides away from the dimer on the 5' side and four nucleotides away on the 3' side; (3) the 12-residue oligonucleotide excised by this specific excinuclease diffuses away and DNA polymerase I enters the gap to effect repair synthesis. Gaps are filled by DNA ligase. See also DNA repair enzyme, excision repair, recombinational repair, mismatch repair. repeated genes see repetitive sequences. repeat-induced point (mutation) see RIP. repeat sequence or repeat 1 (in DNA) see repetitive sequences. 2 (in proteins) any sequence of the same amino-acid residue or group of amino-acid residues that is repeated in a polypeptide. Thus in some cases there are runs of glutamine or cysteine. In Drosophila melanogaster there is a protein with a string of I I cysteine residues, and human androgen receptor protein has a string of 2 I glutamine residues. In fact there are at present in

replica plating composite databases 44 proteins with this number of glutamine residues. In other proteins, e.g. tropocollagen, there is a regular sequence, except in this case for the last 20 amino-acid residues at each end of the chain. In tropocollagen every third residue is glycine usually followed by proline or hydroxyproline. The intrachain hydrogen bonds involve glycine. 3 the repeats of sugar residues often found in complex polysaccharides. repeat unit a major periodicity in the structure of a molecule as deduced from X-ray diffraction patterns. repetitive extragenic palindromic sequences or palindromic units palindromic sequences in repetitive DNA in Escherichia coli and Salmonella typhimurium. These are never found within a coding sequence. They are topoisomerase substrates and potential transcription terminators. repetitive sequences repeated sequences of nucleotides found in the DNA of eukaryotes. There are various types. (I) Satellite DNA typically consists of tandem (head-to-tail) repeats of a few hundred nucleotides. It is so called because those first discovered had an unusual ratio of bases that made it possible to separate the satellite DNA from the bulk of the cell DNA in a centrifuge. (2) Minisatellite DNA consists of shorter tandem repeats. The restriction fragment length polymorphisms linked to many genes have short sequences of bases in common. rDNA (see ribosomal DNA) probes for these sequences are useful in the preparation of a profile of the genome of an individual (fingerprinting). (3) Transposons (transposable elements) are also characterized by repeated sequences, often numbering several hundred copies. Primate DNA has large numbers of two types of transposable elements, LI transposable elements and Alu sequences, which comprise about 300 bases. (4) Repeated genes for rRNA and histones are also found. In many cases repetitive sequences seem to be maintained solely by their ability to replicate within the genome (the 'selfish DNA hypothesis'). Rather than conferring benefits their behaviour can sometimes result in loss of fitness to the host, as in some human genetic diseases; mutations can arise due to insertion of transposable elements, to chromosomal rearrangements induced by recombination between repeated sequences, or to amplification of microsatellite sequences. replacement vector a cloning vector in which part of the normal genome is replaced by foreign DNA. It contrasts with an insertion vector where the foreign DNA is merely incorporated into the normal genome. For example, a mutant of lambda phage, called A.gt-A.~, contains only two EcoRI cleavage sites and so the middle segment of the DNA can be removed leaving 72% of the normal genome. A suitably long DNA replacement between the two ends of lambda DNA enables such a recombinant DNA molecule to be packaged into a lambda particle. replica (in electron microscopy) a reproduction of the surface of an object. There are various ways by which the surface of an object, e.g. membrane of an organelle, may be examined by transmission electron microscopy by means of a replica. Such a replica may be obtained by evaporating a thin film of a heavy metal such as platinum on to the dried specimen. The metal is sprayed from an oblique angle in order to deposit a coating of uneven thickness because a shadow effect is created that gives the image a three-dimensional appearance. The organic material may be dissolved away to provide a replica of the surface of the specimen. Two other methods, freeze-etching and freeze-fracturing, employ frozen sections. replica plating a technique for the production of identical patterns of bacterial colonies on a series of agar plates. The method uses velveteen or other fabric stretched on a pad, which is then pressed onto a plate of bacterial cultures so that some bacteria from each colony are transferred to the pad, preserving the spatial pattern of the colonies (in mirror image). If this pad is then pressed lightly onto a fresh culture plate, it will transfer colonies in the same formation to the new plate. This new plate may be prepared using media that will be selective for certain mutants, fermentation reactions, or anti-

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replicase biotic sensitivity. A similar technique can be used in the screening of hybridomas for antibody production. replicase a loose term/or certain polymerase enzymes; e.g. certain viral RNA-directed RNA polymerases can be referred to as RNA replicases. replicate 1 to make an exact copy of something, as in the replication of DNA. 2 (in electron microscopy) to make a replica. replication complex the complex of replication proteins that are linked together as a single large unit, of total mass 10 6 daltons, that moves rapidly along the DNA during replication of DNA. It enables DNA to be synthesized on both sides of the replication fork in a coordinated and efficient manner. That part of the complex that contains DNA primase and DNA helicase is known as the primosome. replication-error mutation a mutation that arises during DNA replication as a result of the incorrect copying of the sequence of nucleotides in the parent DNA. Probably fewer than one mistake occurs in 10 9 nucleotides added. replication fork or replicating fork the Y-shaped region of a replicating DNA molecule or chromosome, resulting from separation of the DNA strands and in which synthesis of new strands takes place. The process requires the participation of helicases that open the duplex. replication of DNA the means whereby new strands of deoxypolynucleotides are synthesized. The structure of doublestranded DNA, with two strands of complementary base pairs, led Watson and Crick to propose a possible means of copying DNA: the two strands could unwind and each act as the template for a new strand, thus forming two helices, each containing one parental strand and one new one. The elegant Meselson-Stahl experiment demonstrated that DNA replication was indeed semiconservative. Other mechanisms of replication, 'conservative' and 'dispersive', have been proposed but there is no evidence that they occur. The helix of the doublestranded parental DNA must be unwound and this requires more than 20 proteins in a complex known as a primosome. All DNA-dependent DNA polymerases synthesize the new strands in the direction 5' to 3' using as substrates deoxynucleotide triphosphates with the production of pyrophosphate. The new strands are antiparallel to the parental template strand. At low resolution both strands of a double-stranded DNA appear to be synthesized in the same direction in spite of the fact that the polymerases only synthesize the strands in one direction. The problem is resolved by the fact that one strand, the leading strand (or continuous strand), is synthesized in a continuous fashion whereas the other strand, the lagging strand (or discontinuous strand), is synthesized discontinuously to give Okazaki fragments (1000-2000 nucleotides long in prokaryotes and 100-200 nucleotides long in eukaryotes) which are eventually joined by DNA ligase. The DNA ligases cannot start a chain and must rely on a priming device which is provided by RNA primase which again synthesizes an RNA primer in the direction 5' to 3' using nucleoside triphosphates as substrate. The continuous strand needs to be primed only once whereas the discontinuous strand must be primed repeatedly. Three principal DNA polymerases for Escherichia coli were discovered in the laboratory of A. Kornberg. DNA polymerase I, in addition to possessing synthetic activity in vitro, is also a 3'-5' exonuclease which gives it an editing function. It also has 5'~3' nuclease activity. DNA polymerase II participates in DNA repair but is not required for replication. DNA polymerase III is the predominant polymerase for replication of E. coli DNA in vivo. Eukaryotic cells have at least four DNA polymerases. replicative able to be replicated. See also replicative form. replicative form abbr.: RF; the intracellular form of viral nucleic acid that is active in replication. A single-stranded viral nucleic acid, be it RNA or DNA, is first converted into a double-stranded form - the replicative intermediate - to enable the viral strand to be replicated preferentially. In the case of a retrovirus a hybrid of RNA and DNA is formed. replicative intermediate see replicative form.

RER replicon 1 a structural gene that controls the initiation and replication of DNA. 2 by association, the whole DNA sequence (such as the bacterial chromosome) that is replicated under the influence of a single replicon system. replisome a replication complex hypothesized to account for the initiation of chromosome replication within a living cell. replitase a particulate fraction that can be isolated from the nuclei of S phase Chinese hamster embryo fibroblasts and containing some of the enzyme activities required for DNA synthesis. reporter gene a gene used to disclose the function of potential regulatory sequences. The sequences are placed in plasmids, upstream of the reporter gene; these chimeric plasmids are then introduced into cells and the expression of the reporter gene is measured as an index of the function of the regulatory sequences under the conditions being investigated. The lacZ (~-galactosidase) gene, the CAT gene (see chloramphenicol 0acetyltransferase), and the gene encoding firefly luciferase have been used in this way. reporter group a chemical group that acts as a probe. repress to check or restrain; the effect may be partial or total. See repression, repressor. repressible describing a metabolic reaction that is capable of undergoing repression. repression (in genetics) the act of inhibiting gene expression. An example is catabolite repression of the lac operon by glucose, mediated through binding of cyclic AMP to catabolite (genel activator protein (CAP). By extension, the gene product itself (enzyme or other protein) and thus any associated metabolic reaction is said to be repressed. See also repressor. repressor (in genetics) a molecule that specifically prevents the transcription of regulatory genes under control of an operator. When the repressor is bound to the operator, transcription cannot occur. An inducer can induce transcription by binding to the repressor to form a complex that has a low affinity for the operator. The classic example of a repressor is the lactose repressor protein, which controls the expression of the lac operon in Escherichia coli. The protein binds to a specific sequence of 21 nucleotide pairs (called the operator) that overlaps an adjacent RNA polymerase binding site (the promoter) at which RNA synthesis begins. In the presence of lactose, allolactose is formed, which binds to the repressor. This induces a conformational change that causes the repressor to loosen its hold on the DNA so that the gene is derepressed. In other examples, the binding of a signalling molecule may increase the affinity with which the repressor binds to the DNA; e.g. the trp operon, encoding enzymes that produce tryptophan in E. coli (see trp gene). See also repression. reproducibility the ability to carry out a series of identical experiments to yield results that fall within a small range of error derived by statistical analysis (see standard deviation, standard error of the mean). The limits of error that are acceptable depend on the limitations of experimental technique and the inherent variability of the system under investigation. reproduction (in biology) the production by an organism of new individuals that are more or less similar to itself. Reproductive strategies can be divided broadly into two categories: sexual reproduction, which requires the participation of male and female gametes and gives rise to genetic variation among the offspring; and asexual reproduction, which does not involve gametes and leads to the formation of offspring that are genetically identical to the parent. The latter takes various forms; examples include budding, fragmentation, parthenogenesis, spore formation, and vegetative reproduction. reptation a term invoked to rationalize the movement and thermodynamics of linear polymers, dividing the chain conceptually into sections (reptons), which form the basis for statistical mechanical calculations of the relaxation time of the polymer and viscosity of polymer solutions. repton see reptatian. RER abbr. for rough endoplasmic reticulum.

566

reseal reseal to join again the ends of ruptured components, as in,

e.g., the resealing of plasma membranes after whole cells have been rendered permeable by various techniques, or of fractionated membrane fragments, which may reseal to form closed vesicles. The term can also refer to ligation of the cut ends of DNA after insertion of foreign DNA into a vector. reserpine (3P, 16p,17a, 18p,20a)-11 ,17-dimethoxy-18[(3,4,5trimethoxybenzoyl)oxy]yohimban-16-carboxylic acid methyl ester; an alkaloid isolated from the roots of certain species of Rauwolfia and noted for its antihypertensive and CNS depressant actions. These arise from its inhibition of the intraneuronal Na+, Mg 2+-ATPase pump, which maintains the neuronal vesicular stores of biogenic monoamines (dopamine, norepinephrine, and serotonin).

reserve polysaccharide any polysaccharide that is stored to

provide an energy source at times of need. Examples are starch granules in plants, and glycogen granules in animals. RefS; convention a nomenclatural system for specifying the stereoheterotopic faces of a trigonal atom using the sequence rule in two dimensions. This is used to establish a priority sequence for the three ligands, e.g. of Cabc. The plane containing C and the first atoms of the ligands is then inspected from an arbitrarily chosen side. Starting with the highest priority ligand, it is determined whether the priority sequence is clockwise, hence Re (from Latin rectus, right), or counterclockwise, hence Si (from Latin sinister, left); e.g. for acetaldehyde, CH 3 CHO, if the face inspected shows a clockwise ordering, o -7 CH 3 -7H, that face is designated Re. There are a number of extensions of this general principle, and the specialist literature should be consulted for details. residence time the averaged time that a site is occupied by any designated molecule. resident protein see luminal protein. residual body a membrane-lined cytoplasmic inclusion characterized by undigested residues (e.g. membrane fragments or whorls, ferritin-like particles). The term embraces telolysosome and (hypothetical) post-lysosome. residue 1 any of the incorporated amino-acid moieties in a peptide or protein. 2 material that remains after any procedure to remove something. residue mass the relative molecular mass of a residue; i.e. the sum of the relative atomic masses of all the atoms composing the residue. residue weight the molecular weight of a residue; i.e. the sum of the atomic weights of all the atoms composing the residue. Residue mass is the preferred term. resin 1 or rosin any of a group of naturally occurring amorphous solids or semisolids, typically light yellow to dark brown in colour. Usually brittle and insoluble in water, they are found as plant exudates, often on trees such as pines and firs. 2 the polystyrene base of certain ion-exchange materials used in chromatography. The polystyrene is modified to carry sulfonic acid or carboxyl groups (cation exchangers), or primary or quaternary ammonium groups (anion exchangers). resistance 1 the ability of a living organism, particularly a bacterium, to resist the effect of a disadvantageous environment or substance, especially an antibiotic. A bacterium may

resonance hybrid possess one or more resistance plasmids. 2 see electric resistance. resistance donor a strain of an organism, usually a bacterium, that is capable of transferring resistance, usually by conjugation, to a suitable recipient. resistance factor abbr.: R factor; an alternative name for resistance plasmid. resistance plasmid abbr.: R plasmid; a plasmid that carries ge-

netic information for resistance to antibiotics or other antibacterial drugs. Other name: resistance factor (abbr.: R factor). resolution 1 the degree of separation between two compounds being subjected to a transport method such as chromatography or sedimentation equilibrium (i.e. being resolved); complete resolution yields two compounds each uncontaminated by the other. 2 (in physics and biophysics) the extent to which closely juxtaposed objects can be distinguished as separate objects using an optical instrument, e.g. a microscope. The degree of resolution is dependent on the resolving power of the system. The fineness of detail with which objects can be seen is limited by the wavelength of light used. Only those objects similar in dimensions to the wavelength of the light (or larger) can be resolved. The wavelength of X-rays is from about 10-8 m to 10 II m and they can thus be used to resolve structures at the atomic level. Thus a structure can be said to have been determined at 3 A resolution, 7 A resolution, etc. resolvase an enzyme that, together with transposase, is involved in the replicative transposition of genetic elements in Escherichia coli. The 3' ends of the target chromosome, after the first cutting and splicing, serve as replicative primers for copying both the gaps and the two strands of the transposable element (which contains transposase) itself. Ligase action generates a cointegrate, a large circular structure containing both donor and target chromosomes with two freshly replicated copies of the transposable element. Resolvase now catalyses the site-specific recombination between the two elements, resulting in one copy of the transposable element inserted in each of the two chromosomes. Example, tnpA gene product from Tn3 which confers resistance for ampicillin; database code TNP3_ECOLI, 185 amino acids (20.59 kDa); it contains a helix-turn-helix motif. resolving power 1 (in chromatography) the power to resolve individual compounds (see resolution (def. I)). It depends on (I) the efficiency of the system employed; for columns this is given by the theoretical plate number; and (2) the relative affinities of different compounds for the stationary and mobile phases. 2 (in physics) a the ability of an optical instrument, e.g. a microscope or telescope, to produce separate images of objects placed close together. b the ability of a spectrometer to separate adjacent peaks in a spectrum. resonance 1 (in physics) the induction or amplification of one vibration by another vibration of a periodicity equal to the natural oscillation frequency of the first, which is then said to resound. In an electronic circuit, resonance occurs when an applied emf equals the natural frequency of oscillation of the circuit (used, e.g., in tuning a radio receiver). 2 (in chemistry) a phenomenon shown by any molecular entity to which more than one contributing structure can be assigned, when these structures are of similar energy and differ only in the distribution of the valence electrons; the entity then oscillates between the two structures and adopts, in effect, an intermediate state. Resonance always results in a different distribution of electrons than would be the case if there were no resonance. See also resonance energy, resonance hybrid. 3 see electron spin resonance spectroscopy, nuclear magnetic resonance. -resonant adj.; resonate vb. resonance energy the difference in energy of an actual molecule and the contributing structure of lowest energy. resonance hybrid the structure that results when a chemical entity exhibits resonance (def. 2), such as occurs by the sharing of one or more electrons over several bonds. It has a lower en-

567

resonance stabilization ergy than any of the possible formal nonresonance contributing structures, giving additional stability of which the so-called resonance energy is a measure. A classic example is carbon dioxtde, whi~h m.!!y be r~presented by t~e Lewis formula for each as O::OC::O, ::O:C:::O:, and +:O:::C:O:-. Compare mesomerism. resonance stabilization or resoDllnce stabilisation stabilization of molecular structure by resonance; see also resonance hybrid. resonate see resonance. re80rb to absorb again. -resorbent ad).; resorption n.; resorptive ad). resorcinol m-dihydroxybenzene; a compound used in the Seliwanoff test for ketoses. re8orption see resorb. respiration 1 the process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen and remove carbon dioxide. In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. These organs possess respiratory surfaces, across which gases are exchanged with the blood or other transport medium. This then carries dioxygen to the body tissues, and removes carbon dioxide. 2 or oxidative metabolism the various energy-yielding reactions of cells or organisms that require oxygen as the final electron acceptor. See respiratory chain. -respiratory ad). respiratory burst a phase of elevated metabolic activity, during which oxygen consumption increases, that occurs in neutrophils, monocytes, and macrophages shortly after phagocytosing material. This is associated with increased activity of the hexose monophosphate shunt and production of NADPH (see pentose phosphate pathway). An oxidase takes electrons from the NADPH and transfers them to O 2 creating the reactive superoxide (02-) ion and H 20 2 in the vacuole. Patients with chronic granulomatous disease never produce a respiratory burst. In some cases this is due to lack of an essential cytochrome b. The patients suffer an accumulation of mononuclear cells at sites of chronic inflammation, forming granulomas. respiratory chain or electron-transport chain the sequence of enzymes and other proteins within the mitochondrion and prokaryotic cell membranes by which substrates, including NADH and succinate, are oxidized by dioxygen. It is fundamental to tissue respiration (def. 2) which has the function of maintaining tissue metabolism through oxidative phosphorylation. The chain can be separated into a number of particles (see respiratory complex) each of which contains individual elements of the chain. The mechanism involves, in the case of NADH, removal by NADH dehydrogenase of a proton plus two electrons. In the case of succinate, there is a transfer of two hydride ions (i.e. two protons plus two electrons) by succinate dehydrogenase to the enzyme-bound FAD; other flavoproteins can similarly oxidize fatty acyl-CoA or p-hydroxybutyrate or a-glycerophosphate. The protons are initially released to the intermembrane space, and the electrons are transferred by the appropriate flavoprotein to ubiquinone, from which they are transferred singly in sequence to cytochrome b, cytochrome Cb cytochrome c, and cytochrome a/a3 at which point they reduce molecular oxygen to promote formation of water with the protons that were formed earlier. Many other components are also involved. In tightly coupled mitochondria, the protons released to the intermembrane space reach the mitochondrial matrix (the space in which they react with molecular oxygen) by transfer through the inner mitochondrial membrane by the F of 1 complex of the mitochondrial ATPase (see W-transporting ATP synthase), with concomitant phosphorylation of ADP to ATP. See also chemiosmotic coupling hypothesis. re8piratory complex any of several groups of physically associated components of the respiratory chain. The concept arose

response coefficient during experiments to purify individual components, when it was found that membrane particles could be isolated each with a consistently characteristic composition. Four main complexes have been identified: complex I, which contains primarily NADH dehydrogenase; complex II, which contains succinate dehydrogenase; complex III, which contains cytochromes band CI; and complex IV, which contains cytochrome a/a3 together with copper-containing proteins. Complexes I, II, and III all contain additionally a number of proteins rich in iron and sulfur. The F o and F 1 subunits of the ATPase associated with the respiratory chain have been termed complex V (see H+-transporting ATP synthase). See also complex I. II. III. IV. re8piratory control the regulation, in coupled mitochondria, of the rate of oxidative phosphorylation by the level of ADP. As the ADP level increases, and the ATP level falls, electron flow through the respiratory chain and coupled ATP synthesis are enhanced. The respiratory control ratio, or respiratory control index, represents the ratio of the rate of oxygen consumption of mitochondria in the presence of both substrate and ADP to the rate in the presence of substrate but the absence of ADP; i.e. the ratio of the rate in respiratory state 3 to respiratory state 4 (see respiratory state). re8piratory pigment any of a number of pigmented proteins, associated with respiratory processes, that derive their colour from a prosthetic group, usually heme in red proteins such as cytochrome C, or flavin nucleotides in flavoprotein dehydrogenases, which are yellow. respiratory quotient or respiratory ratio abbr.: RQ; a ratio of the rate of carbon dioxide evolution by any cell, tissue, or organism to its rate of dioxygen uptake. respiratory state or state of the respiratory chain anyone of the possible steady states of the phosphorylating respiratlJry chain in mitochondria. In state I both ADP and respiratory substrates are lacking. State 2 is a 'standard state' in which ADP has been added to exhaust the endogenous respiratory substrate; in state 2' substrate has been added to exhaust the endogenous ADP. In state 3, the 'active' state of rapid respiration, all required components are present and the respiratory chain itself is the rate-limiting factor. State 4, an anaerobic 'resting' state, is characterized by a low respiration rate. In state 5, only oxygen is lacking, the respiration rate then being at zero. State [0 2] [ADP] Substrate Respiration Ratelevel rate limiting factor I

>0

low

low

slow

2

>0

high

0

slow

ADP substrate

2'

>0

low

high

slow

ADP

3

>0

high

high

fast

respiratory chain

4

>0

low

high

slow

ADP

5

0

high

high

0

O2

respirometer an instrument for measuring the uptake of oxygen during incubation experiments. The Barcroft apparatus and the Warburg apparatus were examples of this type of instrument. response the events brought about by a stimulus, especially in a cell, tissue, or organism. See stimulus-response coupling, sensiti· zation, desensitization. response coefficient symbol: R; an overall measure of the control exercised by a specific enzyme inhibitor, at its concentration, I, on the overall flux, F, of a muItienzyme system. Hence, Rf::: (fJF/F)/(fJI/l)

or R == fractional change in flux/fractional change in inhibitor.

A response coefficient can also be determined for the effect of Ion the concentration of a metabolite S. Thus

568

restriction mapping

response element R~ = (dS!S)!(dI!l)

It is the product of the elasticity coefficient and the flux control coefficient. response element abbr.: RE; a DNA sequence (sometimes called a 'module') that is common to promoters/enhancers of genes whose expression is coordinately regulated (see coordinate induction/repression). Examples: the estrogen response element (ERE) has the consensus sequence GGTCANNNTG[A/T]CC; the glucocorticoid response element (GRE) has the consensus sequence TGGTACAAATGTTCT; the heat-shock response element (HSE) has the consensus sequence GNNGAANNTCCNNG; the metal response element (MRE) has the consensus sequence CGNCCCGGNCNC; the serum response element (SRE) has the consensus sequence CATATTAGG; and the thyroid response element (TRE), which is common to several enhancers, has the consensus sequence TGACTCA. response time the interval between initiation of a process and the commencement of the action that it induces. responsiveness (in physiology) the ability of a cell, tissue, or organ to undergo a response. Maximal response normally corresponds to the healthy in vivo state, so that the degree of response is an indication of the integrity of the preparation. However, negative regulators may be removed during tissue preparation, thus giving enhanced activity in vitro. restin Reed-Sternberg cell intermediate filament-associated protein; other name: cytoplasmic linker protein-l70 0.-2 (ahbr.: CLIP-l70); a protein that is highly expressed in such cells in Hodgkin's lymphoma and having a large coiled-coil a-helical domain similar to those in myosins. Example from human: database code REST_HUMAN, 1427 amino acids (160.81 kDa). resting potential the potential difference across the membrane of a cell in the unstimulated state. See also membrane potential. resting state an inactive or unstimulated state, especially of a cell. See also cell-division cycle. restricted DNA DNA that has been cut by a restriction endonuclease within a bacterium; bacteria are protected from the propagation within them of foreign DNA, usually viral DNA, by the possession of restriction endonucleases which degrade the invading DNA. Each nuclease recognizes a specific sequence of 4-8 nucleotides in the DNA. The cleaved sequences, where they occur in the genome of the bacterium itself, are protected from cleavage by methylation at the amino group of an adenine, or either the 5 position of a cytosine or the amino group of a cytosine. The newly replicated strand of the bacterial host DNA, which is protected from degradation by the methylated parent strand with which it forms a duplex, is modified before the next cycle of replication (see restrictionmodification system). Such sequences in the viral DNA are usually not so methylated and hence are degraded first by the restriction enzymes and then by bacterial exonucleases. Invading DNAs are only rarely modified and enabled to reproduce in their new host. Its progeny are, however, no longer modified in the way that permits them to propagate. See also hostcontrolled modification. restricted phage or restricted bacteriophage see restricted virus. restricted virus a virus whose host range is limited by hostcontrolled modification so that when it infects a related but nonidentical host cell its DNA is degraded by the new host cell's restriction endonucleases. restriction (in molecular biology) the action or use of restriction endonucleases. See also restrictive. restriction analysis another term for restriction mapping. restriction endonuclease or restriction enzyme or restriction nuclease any of a group of enzymes, produced by bacteria, that cleave molecules of DNA internally at specific base sequences. They, therefore, act to 'restrict' the replication of foreign, usually viral, DNA entering the bacterial cell (see restricted DNA). Some of them also methylate the host bacterial

DNA to protect it from degradation. There are three known types of restriction enzymes. Types I and III each carry activity for both the endonuclease and methylase function whereas type II enzymes do not carry the methylase activity. Type I enzymes cleave the DNA at a random site located at least 1000 bp from the recognition sequence, type III do so 24-26 bp distant from the recognition site. In contrast type II enzymes cleave DNA at specific sites within the recognition sequence. This makes type II enzymes indispensable for DNA manipulation. Around 2500 species of type II restriction enzymes with some 200 differing sequence specificities have been characterized. A restriction endonuclease is named by the first letter of the genus of the bacterium that produced it and the first two letters of its species, followed by its serotype or strain designation, and a roman numeral if the bacterium contains more than one type of restriction enzyme. Type I (EC 3.1.21.3) restriction and modification enzymes are complex, multifunctional systems that requin.: ATP, S-adenosyl methionine, and Mg2+ as cofactors; in addition to their endonucleolytic and methylase activities, they are potent DNA-dependent ATPases. The subunit composition, three subunits designated R, M, and S, is similar to that of ATPases. They catalyse the endonucleolytic cleavage of DNA to give random doublestranded fragments with terminal 5'-phosphates; ATP is simultaneously hydrolysed. Example, R protein from Escherichia coli, enzyme EcoR124/3: database code TIRl_ECOLI, 1033 amino acids (119.52 kDa). Type II enzymes have activity as site-specific deoxyribonucleases (EC 3.1.21.4), which catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates; Mg2+ is a cofactor. Example from E. coli, enzyme EcoRV: database code T2E5_ECOLI, 244 amino acids (28.49 kDa). Such enzymes are the basis of restriction mapping. Type III enzymes have activity as site-specific deoxyribonucleases (EC 3.1.21.5). The protein has two subunits, products of the res (from 'restriction') and mod (from 'modification') genes; these are respectively, responsible for binding the system-specific DNA recognition site in the restriction and the methylation of one of the adenosyl residues in the recognition site. A list of restriction endonucleases is given in Appendix F. See also restriction-modification system. restriction enzyme an alternative name for restriction endonuclease. restriction fragment a fragment of DNA produced by the action of a restriction endonuclease. It usually refers to the product of a type II enzyme that recognizes specific base sequences in double-helical DNA and cleaves both strands of the duplex at specific sites. restriction fragment length polymorphism abbr.: RFLP; polymorphism within a population of organisms of the size of the fragments of DNA produced as the result of the action of a type II restriction endonuclease. It results from a corresponding polymorphism of restriction sites in the genome, due to slight differences in base sequence between individual members of the population. RFLP is exploited in constructing physical maps of the genome, and widely used for localizing specific genes and detecting genetic differences between closely related individuals. The analysis of restriction fragments can reveal the presence of a mutation that may itself cause disease or be closely linked to one that does; for example, genetic diseases such as sickle-cell anemia, cystic fibrosis, and Huntington's diseasae can be detected by RFLP analyses. See also restriction mapping. restriction map a pattern obtained as the result of restriction mapping. restriction mapping the use of type II restriction endonucleases to cleave genomic or other DNA to produce a characteristic pattern of fragments. The fragments are resolved by gel electrophoresis and visualized. Every DNA molecule produces a unique pattern, which accords with the specificity of the particular restriction enzyme. By comparing the patterns ob-

569

retinal

restriction-modification system tained from two or more different DNAs, differences between closely similar DNA molecules, such as arise from mutations, may be detected. The use of DNA probes, such as rDNA, to identify particular fragments may often be of value. restriction-modification system any system whereby host DNA is methylated to render it resistant to the action of the cell's restriction endonucleases (see restricted DNA); methylation involves the adenine or cytosine residues at the restriction sites. Several enzymes have been implicated in this action: (I) EC 2.1.1.72; recommended name: site-specific DNA-methyltransferase (adenine-specific); other names: N-6 adenine-specific DNA methylase; modification methylase; it catalyses a reaction between S-adenosyl-L-methionine and DNA adenine to form S-adenosyl-I-homocysteine and DNA 6-methylaminopurine. (2) Another type is EC 2.1.1.73; recommended name: site-specific DNA-methyltransferase (cytosine-specific); other names: C-5 cytosine-specific DNA methylase; modification methylase; it catalyses a reaction between S-adenosyl-Lmethionine and DNA cytosine to form S-adenosyl-Ihomocysteine and DNA 5-methylcytosine. Examples: (1) EcoR V methylase from Escherichia coli: database code MTE5_ECOLI, 298 amino acids (34.60 kDa); (2) EcoPl5 mod gene product of a type III system (see restriction endonuclease); this methylates one of the A residues in 5'-CAGCAC-3'; it is a homotetramer: database code T3MO_ECOLI, 645 amino acids (74.22 kDa). restriction negative describing an organism that does not contain any restriction endonuclease. restriction site a sequence of bases in a DNA molecule that is recognized by a restriction endonuclease. restrictive 1 describing a strain or line of cells that does not permit the replication of a particular viral DNA, and is thus resistant to infection. 2 describing a set of conditions, such as a temperature range, in which a mutant phenotype is expressed, thus limiting the growth of the organism or causing its death. Compare pennissive. See also conditional lethal mutation, temperature-sensitive mutation. restrictive conditions see conditional lethal mutation. restrictive temperature see temperature-sensitive mutation. restrictocin an anti tumour polypeptide, M r 16 000, from Aspergillus spp. It cleaves the large RNA of the eukaryotic 60S ribosomal subunit and inhibits protein synthesis in picornavirus-infected cells. RET a human transforming oncogene derived through fibroblast transfection with T-cell lymphoma DNA. It encodes two forms of receptor tyrosine kinases of unknown ligand; the cytoplasmic oncogenic forms (p76 RET, p81 RET) are constitutively phosphorylated on tyrosine; they form homo- and heterodimers, and have autophosphorylation activity. A number of variants have been associated with multiple endocrine neoplasia and Hirschprung's disease. Example (precursor): database code RET_HUMAN, 1114 amino acids (124.32 kDa). retentate or dialysis residue or residue (in dialysis) the moiety of the dialysed material that has not traversed the membrane; the liquid containing this moiety (which mayor may not still be entirely in solution). Some authorities prefer the term nondiffusible material. retention coefficient (in column chromatography) the ratio of the void volume to the elution volume for a specific solute. It is a measure of the partition of the solute between the column material and the solvent, and is independent of column size. retention time the time taken by a compound to traverse the length of a gas-liquid chromatography column. The retention time is a characteristic of each compound under defined conditions. It can be used to aid in identification within a series of homologues, e.g. fatty acids, which are characterized by their carbon number derived from the retention time. retention volume a parameter of liquid chromatography, related to the volume at which each compound elutes under defined conditions. reticulate 1 or reticular resembling a net; in the form of a net-

work. 2 to create in the form of a net or network. -reticulation n. reticulocalbin a Ca 2+-binding luminal protein of the endoplasmic reticulum. It has six EF-hands, a 20-residue N-terminal signal sequence, and the C-terminal sequence HDEL. Example (precursor) from mouse: database code RCALMOUSE, 325 amino acids (38.07 kDa). reticulocyte an immature erythrocyte that is capable of protein synthesis, most of the protein synthesized (about 90%) being hemoglobin. It retains intracellular organelles, including mitochondria, and histologically stains for the presence of ribosomes. The name implies misleadingly that it has a reticulum (def. 1), which is characteristic of cells that secrete protein, a function not possessed by the reticulocyte. reticulocyte lysate the preparation obtained by suspending reticulocytes in distilled water so that the cells are lysed by osmotic shock. The reticulocytes are usually obtained from rabbits in which reticulocytosis has been induced by the administration of phenylhydrazine. The residual RNA is usually removed by the addition of a ribonuclease that is calciumdependent and is thereby inactivated by the addition of EDTA. Such a lysate is often used for the in vitro translation of added mRNA. reticulocytosis enhanced levels of reticulocytes in the blood, often due to experimentally-induced increased production. See also reticulocyte lysate. reticuloendothelial system a former name for mononuclear phagocyte system. reticulum 1 the endoplasmic reticulum, a netlike structure of membranes found in the cytoplasm. 2 the most anterior chamber of the ruminant stomach. retina the light-sensitive layer lining the inside of the posterior wall of the eye in vertebrates and some classes of molluscs. The inner nervous layer of the vertebrate retina is transparent and contains photoreceptive cone cells andlor rod cells together with their associated nerve cells and fibres, glia, and blood vessels; the outer layer, next to the choroid, is darkly pigmented and prevents back-reflection of light. retinal 1 pertaining to the retina. 2 the recommended trivial name for (2E,4E,6E,8£)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-l-en-I-yl)nona-2,4,6,8-tetraen-I-al; other names: retinalj; retinaldehyde; vitamin A aldehyde; vitamin Al aldehyde; retinene; retinenel; a compound that plays an important role in the visual process in most vertebrates (compare 3,4-didehydroretinal). In the retina this (all-E)-isomer, commonly distinguished as all-trans-retinal, is converted by retinal isomerase to its (2E,4Z,6E,8£)-stereoisomer, generally termed Il-cis-retinal, which then combines (as a Schiffs base) with an opsin to form (in cone cells) iodopsin or (in rod cells) rhodopsin. Interaction with a photon brings about dissociation of iodopsin or rhodopsin, to regenerate all-trans-retinal and the opsin, thereby completing the visual cycle. Retinal is formed in the retina by enzymic oxidation of retinol; in addition, most vertebrates can convert dietary a-, po, and y-carotenes to retinal by oxidative cleavage of the polyprenyl chain at its midpoint. [Note: (I) The numbering system of the systematic name is different from that of the trivial name, the latter following the rules used for carotenoids. (2) The fuller name retinaldehyde is recommended if confusion with def. 1 may occur.]

CHO

all-trans-retinal

570

retinal,

retinal, (sometimes) an alternative name for retinal (def. 2) (especially to distinguish it from retinal2; not recommended). retinal2 (sometimes) an alternative name for 3.4-didehydroretinal (especially to distinguish it from retinal!; not recommended). retinal cone see cone cell. retinaldehyde see retinal. retinal isomerase EC 5.2.1.3; systematic name: all-transretinal II-cis-trans-isomerase; other name: retinene isomerase; an enzyme that catalyses the conversion of all-trans-retinal to ll-cis-retinai. Example from Todarodes pacificus (Japanese flying squid): database code REIS_TODPA, 301 amino acids (33.45 kDa). See also retinal (def. 2). retinal rod see rod cell. retinene or retinenet an alternative name for retinal (def. 2) (not recommended). retinene2 an alternative name for 3,4·didehydroretinal (not recommended). retinene isomerase an alternative name for retinal isomerase. retinitis pigmentosa a relatively common genetic disorder which in humans affects I in 4000 people and is caused by the premature death of photoreceptors. The result is progressive night blindness, contraction of the visual field and finally complete loss of sight. One form of autosomal dominant disease results from an abnormality on chromosome 3. In this, there is a single amino-acid substitution in the rhodopsin molecule caused by a base transversion of C to A, which results in the change of a proline to a histidine residue at position 23 in the opsin molecule, causing the characteristic retinal degeneration. Another severe form of the disease, affecting up to around 20% of some populations, is X-linked; it usually becomes manifest within the first two decades of life and progresses to blindness within 10-20 years. The gene, named RPGR, for this form has now been found on the short arm of the X-chromosome. The predicted 90 kDa protein product of the RPGR gene bears significant homology to the RCC1 family. retinoate 1 the anion of retinoic acid. 2 any salt or ester of retinoic acid. retinoblastoma a childhood cancer of the developing retina. The offspring of surviving victims have a high incidence of this disease as well as several other types of malignancies. Retinoblastoma is associated with the inheritance of a copy of chromosome-13 from which a particular segment has been deleted. It develops through a mutation in a retinoblast (a retinal precursor cell). The affected chromosomal segment contains the RB gene which specifies a factor that restrains uninhibited cell proliferation. Thus the RB gene is a tumour suppressor gene. See also retinoblastoma protein. retinoblastoma protein abbr.: pRb; the product of the retinoblastoma gene, RB. pRb is a 105 kDa DNA-binding protein that is localized in the nucleus of normal retinal cells but absent in retinoblastoma cells. The protein is phosphorylated in the cell cycle by protein kinase CDC2. It appears that the interaction of pRb with various transcription factors suppresses cellular proliferation. Example: database code RB_HUMAN, 928 amino acids (106.04 kDa). retinoic acid the recommended trivial name for (2EAE,6E,S£)3, 7-dimethyl-9-(2,6,6-trimethylcyclohex-I-en-I-yl)nona-2A,6,Stetraenoic acid; other names: tretinoin; vitamin A acid; vitamin Al acid; it is formed from retinal by enzymic oxidation in kidney and other tissues, and is active in preventing some, but not all, of the symptoms of vitamin A deficiency. It is a morphogen and regulator of differentiation during embryogenesis. See also retinoic acid receptor, vitamin A. H3

~ ~

CHs ~

all-trans form

~

OH

0

retropepsin

retinoic acid receptor a nuclear receptor for retinoic acid that mediates its effects on cells. These receptors bind retinoic acid and directly regulate gene expression. The proteins belong to the steroid/thyroid/retinoic acid family of nuclear receptors for hormones. The ligand-binding domain is in the C-terminal region, the zinc-finger DNA-binding domain in a central region, and a function-modulating domain in the N-terminal region. Binding of hormone induces changes in receptor conformation that control transcriptional activation and repression, and also regulates homo- or heterodimerization. In the absence of ligand, these receptors repress basal gene expression, probably through co-repressor proteins. a, fl, y and -

HN:-( OH

);'

OH

OH OH

scinderin or adseverin a Ca 2 +-dependent cytosolic actin filament severing protein present in chromaffin cells, platelets, and a variety of secretory cells. Example (bovine): database code BBSCINDE, 715 amino acids (80.68 kDa). scintillant 1 (of a phosphor) exhibiting scintillation. 2 ajargon term for scintillator. scintillate 1 to give off sparks, to sparkle. 2 (of a phosphor) to emit quanta of light discontinuously, by fluorescence, when struck by a charged particle or a high-energy photon. scintillation 1 the act of scintillating. 2 the flash of light produced in a phosphor when it is struck by a charged particle or a high-energy photon. scintillation autoradiography an alternative term for fluorography (def. 2). scintillation cocktail or scintillation fluid any mixture, containing a scintillator, to which beta emitters can be added for the purpose of scintillation counting; the radiation excites the scintillator to emit light. Many scintillation cocktails are based on hydrophobic solvents, since for the most part scintillators sparingly soluble in aqueous solutions have been used. The first scintillator to be widely used was 2,5-diphenyloxazole (PPO), often used in conjunction with 1,4-bis(5-phenyl-2-oxazolyl)benzene (Po PoP), which is excited by the light emitted by PPO to emit light of a higher wavelength more suitable for measurement. Subsequently many other scintillators, especially biodegradable compounds and others more compatible with water, have been developed. See also biphenylylphenyloxadiazole, bismethylstyrylbenzene. scintillation counter an instrument for the detection and measurement of the intensity of high-energy radiation. Instruments for detecting gamma radiation contain a detector, normally a crystal of sodium iodide containing a small amount of thallium, and this is encased in a metal 'top hat' lined with a

white reflector, the open end being sealed with Perspex. When the sodium iodide absorbs y rays it emits a flash of light. For the counting of p- emissions, the radioactive substance is dissolved or suspended in a scintillation cocktail contained in a glass or plastic vial, which is inserted into a chamber in the counter. Sometimes a solid scintillant is used for this also, e.g, for the effluent from chromatography columns. In the case of both types of instrument, the flashes of light produced are detected by a photomultiplier and converted into pulses of electric current which may be counted by an electronic counter. scintillation fluid an alternative term for scintillation cocktail. scintillation spectrometer another name for scintillation counter. scintillator or scintillant any phosphor that fluoresces when struck by a charged particle or a high-energy photon. See scintillation cocktail. scintillon a subcellular, crystal-like structure, found in bioluminescent organisms, that emits light on acidification in the presence of oxygen. scissile capable of being split easily or cut smoothly, especially of an easily cleaved chemical bond. scission a division or splitting; an act of dividing a nonisometric object orthogonally to its longest axis, especially a chemical bond or a fibrous molecule; cleavage (def. 2). scleral pertaining to the sclera, the fibrous outer layer of the eyeball. scleroprotein any of a group of simple, generally fibrous proteins that are insoluble in aqueous solutions; examples include keratin and silk fibroin. sclerosis hardening of a tissue as a sequel to inflammation; especially an increase of connective tissue in the nervous system. See also arteriosclerosis. -sclerotic ad). scopolamine see hyoscine. scorbutic of, pertaining to, or affected with scurvy. scotophobin a IS-residue peptide that accumulates in the brains of rats trained to avoid the dark; administration is said to elicit a similar response in untrained animals. It is thought to be the first memory-directing substance isolated and identified. scotopia adaptation to darkness; the adjustment of the eye to vision in dim light or the dark. It is considered to involve mainly retinal rod cells. Compare photopia. ~scotopic ad). scotopsin an opsin that is the apoprotein of a rhodopsin. SCP abbr. for single-cell protein. scrapie a spongifonn encephalopathy of sheep and goats, and the first to be identified of a group once thought to be 'slow virus' infections occurring naturally and caused by an unconventional agent. Scrapie has similarities to two other animal diseases, transmissible mink encephalopathy and bovine spongiform encephalopathy, and three transmissible human dementias, kuru, Creutzfeldt-Jakob disease, and Gerstmann-Striiussler syndrome. All these diseases are now accepted as being caused by alterations in the prion proteins in the nervous system. The disease has been known since its first reported occurrence in merino sheep in Spain in 1732, which was rapidly followed by reports of other cases in Britain and Germany. The incubation period for the scrapie agent is usually 1-3 years. Different breeds of sheep exhibit markedly different susceptibilities to scrapie. As many as 20 different strains of scrapie agent, each with distinct properties in terms of incubation period in a given host and location of damage within the brain have been identified and transferred to mice. It would appear that the strains are passed to the progeny, so any explanation of the nature of the infective agent and process must take this into account. screen 1 to protect from; esp. from harmful agents or radioactivity using sheets of lead, glass, or plastic; or from radiofrequency interference using a copper sheath or wire net. 2 to sift data, often using a limited or general assay, for selection of a particular phenomenon or result; samples selected by preliminary screening can be isolated for more detailed study. 3 (in clinical chemistry) to carry out any diagnostic procedure on a

589

screw axis large cohort of patients with a view to detecting hitherto asymptomatic disease; see also genetic screening. 4 any device or material that acts to screen. screw axis a crystal or an oligomeric protein molecule is said to possess an n-fold screw axis if it presents exactly the same appearance after rotation about that axis of 360 o /n coupled with a translation parallel to the axis. Compare rotation axis. scRNA abbr. for small cytoplasmic RNA. scRNP abbr. for small cytoplasmic ribonucleoprotein. scurvy avitaminosis C; a deficiency disease caused by lack of ascorbic acid (vitamin C) in the diet. It is characterized by anemia, sponginess and ulceration of the gums, hemorrhages into the skin and subcutaneous tissues, and delayed wound healing. scute a gene in Drosophila for AS-C protein. scutelarin EC 3.4.21.60; other name: taipan activator (being from the venom of the taipan (snake), Oxyuranus scutellatus). An enzyme that catalyses the selective cleavage of Arg-I-Thr and Arg-l-Iie in prothrombin to form thrombin and two inactive fragments; its specificity is similar to that of factor Xa (see blood coagulation). Compare scutellarin. scutellarein 4',5,6,7-tetrahydroxyflavone; the aglycon of scutellarin. Compare scute/arin.

HO

HO OH

scutellarin the glucuronide of scutellarein, from Scutellaria spp. Compare scutelarin. scyrp colloquialism for scRNP (i.e. small cytoplasmic ribonucleoprotein). SO abbr. for standard deviation. SOS abbr. for sodium dodecyl sulfate. SO sequence abbr. for Shine-Dalgarno sequence. SOS-PAGE abbr. for SDS-polyacrylamide gel electrophoresis. SOS-polyacrylamide gel electrophoresis or SDS gel electrophoresis abbr.: SDS-PAGE; a rapid and inexpensive method for resolving a protein into its subunits and determining their relative molecular masses (M, values), based on the ability of sodium dodecyl sulfate to cause dissociation of oligomeric proteins and to bind to the subunits to form complexes of constant charge-to-mass ratio. On zone electrophoresis in polyacrylamide gel, such complexes often have mobilities directly related to their M r values, which, if unknown, may thus be obtained by comparison with standards. Other name: detergent gel electrophoresis. Se symbolfor selenium. SE abbr. for standard error; see standard error of astimate of tha mean. SEA a gene family encoding membrane receptor tyrosine kinases having strong homology with the insulin receptor family. The acutely transforming virus, avian erythroblastosis virus (abbr.: AEV) strain 13, contains the oncogene v-sea; this transforms fibroblasts and erythroblasts, but not avian myeloid cells. Sea, the product of c-sea, the cellular homologue of v-sea, phosphorylates She (see SHe) on tyrosine residues. Example from AEV strain 13: database code KSEA_AVIET, 370 amino acids (41. 70 kDa). sealase a former name for DNA ligase (ATP); see DNA ligase. sea-urchin-hatching proteinase see envelysin. sebaceous gland any of the single or branched glands in the skin that produce the oily substance, sebum. They open into the hair follicles. sebum the oily secretion of the sebaceous glands in the skin. It

secondary hyperlipidemia

contains lipids such as waxes, squalene, and triacylglycerols; the triacylglycerols are broken down by anaerobic bacteria during secretion to form fatty acids. Sebum helps to form an effective barrier against water loss. sec symbol for secant (def. I). sec. abbr. and obsolete symbol for second (def. I). sec- abbr.: SO; prefix (in chemical nomenclature) signifying secondary(def.la). secant 1 abbr. and symbol: sec; the reciprocal of the cosine of an angle. 2 a straight line cutting a curve at two or more points. seco- prefix (in chemical nomenclature) denoting cleavage of a ring with addition of one or more hydrogen atoms at each terminal group thus created. The numbering of the skeletal atoms of the parent molecule is retained. seco-carotenoid a carotenoid in which one of the rings has undergone fission by breakage of a carbon-carbon bond; e.g. semi-p-carotenone (5,6-seco-p-p-carotene-5,6-dione). second 1 symbol: s; the Sl base unit of time, equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium-133 atom. 2 symbol: "; a unit of plane angle equal to 1/60 of a minute; i.e. 4.848 14 microradian (1t/648 000 rad). See angle (def. 1). secondary (in chemistry) 1 a prefix: sec- (abbr.: so); describing an alkyl compound (e.g. an alkanol) in which the functional group (e.g. a hydroxyl group) is attached to a carbon atom linked to two others. b describing the carbon atom bearing the functional group in such a compound. 2 describing an amide or amine in which two appropriate groups are attached to a nitrogen atom. 3 describing a salt formed by replacing two of the ionizable hydrogen atoms of a tribasic acid by one or two other cations of appropriate valency. Compare primary, tertiary. secondary bond a loose term to describe any of the weak attractive forces between atoms and/or molecules, especially when these stabilize a three-dimensional structure. It includes hydrogen bonds, hydrophobic interactions, and van der Waals forces. secondary cell wall deposition (in plants) the deposition of microfibrils and noncellulosic polysaccharides on the primary cell wall. It provides additional conducting and supporting tissue and frequently makes up the greater part of the mature cell wall. secondary charge effect an effect seen in the hydrodynamic study of charged macromolecules when the positive and negative ions of the supporting electrolyte have different sedimentation (or diffusion) coefficients, leading to the establishment of local electric fields due to charge separation. These local fields act as an additional force on the macromolecules, either accelerating or retarding their movement. secondary cytotoxic T cell-inducing factor abbr.: SCIF; an alternative name for interleukin 2. secondary deficiency a nutritional deficiency occurring when the dietary content of some essential nutrient is known to be adequate in normal conditions. It may be caused by a failure of absorption from the gut due to disease, diminished synthesis of a vitamin by the intestinal flora during treatment with an antibacterial agent, or increased requirement, e.g. in pregnancy. secondary electron an electron emitted from a solid as a result of the impact of another electron. If the energy of the incident primary electron is sufficient, more than one secondary electron may be emitted, an effect exploited in an electron multiplier. See also photomultiplier. secondary emission the phenomenon of emission of secondary electrons. secondary F'-containing strain see F' plasmid. secondary fluor a second fluorescent agent that absorbs the fluorescent light emitted by a primary fluor and is thus excited to emit light at a higher wavelength, which may be more convenient for detection. secondary hyperlipidemia see hyperlipidemia.

590

secondary immune response secondary immune response an immune response to an immunogen to which an animal has previously been exposed and to which its lymphoid tissue has been primed. It consists characteristically of the rapid production of large amounts of antibody over a few days, following which the level of antibody slowly declines in an exponential manner. Compare primary immune response. secondary lysosome or phagolysosome a lysosome that contains not only the specific acid hydrolases but also their substrates taken up from the environment or sequestered from the cell's own cytoplasm. Secondary Iysosomes are formed by fusion of a primary lysosome with a phagosome or a vesicle containing endocytosed matter. Compare telolysosome. secondary messenger a variant form of second messenger. secondary metabolism the formation of end products of metabolism - secondary metabolites - that often have no readily apparent use in the producing organism. secondary metabolite any of a group of chemically very diverse natural products that have a restricted taxonomic distribution, usually possess no immediately obvious function in cell growth, and are often (but not always) synthesized by cells that have stopped dividing; typically they exist as members of closely related chemical families, usually of M r < 1500, but some bacterial toxins are considerably larger. An example of a secondary metabolite is penicillin. secondary response see secondary immune response. secondary structure I (of a protein) the arrangements of the polypeptide chain that form more-or-Iess regular hydrogenbonded structures, in particular a-helical and ~-pleated sheet structures; see alpha helix, beta strand. 2 (of a nucleic acid) the arrangement of one or two polynucleotide chains in bihelical structures, stabilized by hydrogen bonds between complementary bases (see complementary base sequence); compare clover-leaf structure. See also primary structure, quaternary structure, tertiary structure. second law of thermodynamics see thermodynamics. second messenger or secondary messenger a mediator that is caused to accumulate in an effector (target) cell by the action of a hormone, growth factor, or other agonist, and that brings about the action of that agonist on the cell. The major second messenger systems are currently recognized to include: synthesis of cyclic AMP by adenylate cyclase (the first of such systems to be discovered); synthesis of cyclic GMP by guanylate cyclase; opening of ion channels; the phosphoinositide system, (see phosphatidylinositol cycle) involving activation of phosphoinositide-specific phospholipase C (see phospholipase), or 1-phosphatidylinositol 3-kinase; and protein phosphorylation by serinelthreonine-specific or tyrosine-specific protein kinases. An important component in several of these systems involves coupling of activated receptor to the effector system through a G-protein. second-order rate constant see rate constant. second-order reaction see order of reaction. seco-steroid a steroid in which one of the rings has undergone fission by breakage of a carbon-carbon bond. secretagogue or secretogogue an agent that stimulates secretion (usually of a named hormone, juice, or other glandular product). See also +agogue. secretase a type of enzyme that cleaves the extracellular domain of a number of membrane proteins of type I or type II topology, releasing the extracellular part of the protein into the circulation. Cleavage normally occurs close to the extracellular face of the membrane. Proteins on which secretases act include Alzheimer's amyloid precursor protein, angiotensin converting enzyme, transforming growth factor-a, and the tumour necrosis factor ligand and receptor superfamilies. Secretase activity is inhibited by a number of metalloproteinase inhibitors, suggesting that secretases may be metalloproteinases. secrete to elaborate and emit a secretion from a cell or, particularly, from a gland. secretin a digestive hormone, discovered in 1902 by William

secretory protein I Maddock Bayliss (1860-1924, British biologist) and Ernest Henry Starling (1866-1927, British physiologist) (the first hormone to be discovered). It has the sequence (human): HSDGTFTSELSRLREGARLQRLLQGLV-NH 2 (3.04 kDa), and is formed from a 134-amino-acid precursor, which is synthesized in specific endocrine cells, S cells, in the mucosa of the small intestine. It stimulates the release of bicarbonate, enzymes, and potassium ions from the pancreas and stimulates the secretion of enzymes and electrolytes in the gut; it also inhibits HCI production by the stomach. Secretin lends its name to a superfamily that on structural grounds includes gastric inhibitory peptide, GHRH, glucagon, peptide HI, and vasoactive intestinal polypeptide. Example of precursor from Mus musculus: database code SECR_MOUSE, 133 amino acids (14.91 kDa). secretin receptor any of several membrane proteins that bind secretin and mediate its intracellular effects. These are seventransmembrane-domain, G-protein-coupled, adenylate cyclase stimulating receptors, not structurally related to other G-protein-coupled receptors. Example from human (precursor): database code SCRC_HUMAN, 440 amino acids (50.23 kDa). secretion I the process of elaborating, segregating, and emitting a substance or juice from a cell, organ, or organism; e.g. the secretion of insulin by the B cells of the islets of Langerhans, or the secretion of urine by the kidneys. At the cellular level there are three basic types of secretion: apocrine, holocrine, and merocrine. 2 a product of secretion (def. I) from a cell, organ, or organism. secretogogue a variant spelling of secretagogue. secretogranin I another name for chromogranin B (see chromogranin). secretor any person who secretes water-soluble glycoproteins with A, B, or H blood-group specificities into their mucous secretions, e.g. saliva and gastric juices. Over 80% of humans are secretors, their status being determined by the allelic constitution of a secretor gene in their genomes. secretor gene a gene determining secretor phenotype in humans. Whether a person is a secretor or nonsecretor is determined by a pair of allelic genes, Se and se. Secretors are either SelSe or Selse while nonsecretors are se/se. These alleles occur at a different locus from the ABO locus and do not affect the A, B, and H specificities of the red blood cells. secretory describing a molecule or molecular fragment destined for secretion from a cell, such as secretory protein, polypeptide, etc. secretory actin-binding protein abbr.: SABP; also called prolactin-inducible protein; gross cystic disease fluid protein 15; a glycoprotein that has been isolated in several different studies (as the alternative names indicate) but whose function remains unknown. As the prolactin-inducible protein, it was identified as a highly specific and sensitive marker of primary and metastatic breast cancer. Example from human (precursor): database code SABP_HUMAN, 146 amino acids (16.55 kDa). secretory component another name for secretory piece. secretory granule a small subcellular vesicle, surrounded by a single-layered membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules. Compare zymogen granule. secretory piece (abbr.: SP) or secretory component (abbr.: Sc) the 58 kDa polypeptide that joins together the two identical monomers comprising the secretory form of immunoglobulin A. It has strong affinity for mucus, thus prolonging retention of IgA on mucous surfaces, and may protect this class of immunoglobulin against proteolytic destruction in the digestive tract. Other names: T chain; transport piece. secretory protein I abbr.: SP-I; a glycoprotein of the parathyroid gland that is co-secreted in vitro with parathyrin. It consists

591

selectively labelled

sector of at least two homologous glycoproteins of similar size (Mr 72 000 and 70 000), related to chromogranin A (see chromogranin). sector any portion of a circle bounded by two radii and the included arc. -sectoral adj. sector cell or sector-shaped cell a cell used in an analytical ultracentrifuge to contain the sample. It is sector-shaped when viewed parallel to the rotation axis. Since the accelerating force is radial, sedimenting molecules move along radii and this cell shape minimizes the collision of sedimenting molecules with the cell walls. sediment 1 to undergo sedimentation. 2 the accumulation of material resulting from sedimentation. sedimentation the setting of solid particles (or solute) through a liquid (or solution) under the influence of a gravitational or centrifugal field. sedimentation coefficient symbol: s; the rate of sedimentation of a particle in an ultracentrifuge or other system. For a particle or solute sedimenting in a system at constant applied field, temperature, and pressure, s = vIa, where a is the acceleration of free fall or centrifugation and v is the velocity of sedimentation. In centrifugation s = vlw 2r, where w is the angular velocity in rad s-1 and r is the distance of the particle or solute from the axis of rotation. It has the dimensions of time. The sedimentation coefficients of macromolecules and cellular particles are often expressed in svedbergs. sedimentation equilibrium a technique in which compounds of interest are centrifuged for a period sufficiently long for the system to come to equilibrium. The technique has a number of applications. In one, used for molecules that have a density greater than the solvent, centrifugation is carried out at relatively slow speeds so that sedimentation of the molecule is slow enough to be counterbalanced by diffusion. At equilibrium, the concentration is lower at the meniscus and higher at the bottom of the cell, but is unchanging. The relative molecular mass, M r, of the compound in question, often a protein, can be calculated from the expression: M r = 2RT In(c2Ic])lw2(l - vp)(r/ - r I 2), where R is the gas constant, T is the thermodynamic temperature, v is the specific volume of the component, p is the density of the solution, w is the angular velocity of the rotor, and Cj and C2 are the concentrations of the component at distances r1 and r2 from the centre of rotation. Ideally, determinations should be done at several concentrations and extrapolated to zero concentration. sedoheptulose a nonsystematic name for D-altro-2-heptulose. HOCH2

CH20H

~ HO

OH

HO

OH

a-o-pyranose form

sedoheptulose-bisphosphatase EC 3.1.3.37; a chloroplast enzyme of the reductive pentose phosphate cycle that catalyses the reaction: sedoheptulose 1,7-bisphosphate + H 20 = sedoheptulose 7-phosphate + orthophosphate. Example from Arabidopsis thaliana (precursor): database code SI7P_ARATH, 393 amino acids (42.41 kDa). sedoheptulose '-phosphate the 7-phosphate ester of sedoheptulose; it is a component of the pentose phosphate pathway. Seebeck effect the phenomenon whereby an electromotive force is generated in a circuit containing junctions between

dissimilar metals if these junctions are not all at the same temperature. See thermocouple. Compare Peltier effect. [After Thomas Johann Seebeck (1770-1831), Estonian-born German physicist.] segmentation 1 (of an ovum) see cleavage (def. 3). 2 (of an animal's body) see metamerism. segregation (in genetics) 1 the separation of homologous genetic elements (i.e. allele pairs) during meiosis in diploid cells. 2 the separation of sister chromatids during mitosis; by extension, the separation of any two independent genetic elements during cell division in prokaryotes. 3 (of plasmids) the partitioning of plasmids into daughter cells at cell division. Naturally occurring plasmids contain a partitioning function, par, which ensures correct partitioning into the two daughter cells. segresome a membrane-bound, cytoplasmic aggregate of a dye, formed either by passage of the dye through the membrane of a pre-existing phagosome or lysosome, or by some process leading to the de novo formation of a membrane around the dye aggregate. Seitz filter a filtration apparatus that removes microorganisms from a liquid. It formerly consisted of a flat pad of asbestos, or asbestos and cellulose, suitably mounted between the sample container and the receiving flask, filtration being assisted by reducing the pressure in the receiving flask. It has now been superseded by a sintered-glass filter. [After Seitz-Filter-Werke, T. and G. Seitz Gmbh & Co., Bad Kreuznach, Germany.] selachyl alcohol 3-(octadec-9-enyloxy)-1 ,2-propanediol; a 1octadec-9-enyl ether of glycerol, and a hydrolysis product of ether lipids. selected-ion monitoring or mass fragmentography or molecular fragmentography a type of gas chromatography/mass spectrometry in which the intensities of one or more molecular or fragment ions selected from the mass spectrum of a particular compound are monitored continuously as a means of quantifying that compound. selectin any of a group of leukocyte surface molecules that act as leukocyte adhesion molecules; they are classed as CD62 in the CD marker system. All have lectin family carbohydrate-binding domains and EGF-repeats, with four motifs. They are expressed on the surface of platelets and endothelial cells as well as leukocytes. E selectin (CD62E), M r 107-115 000 in various glycosylated forms, is expressed on endothelial cells, being induced by cytokines such as interleukin I~ and tumour necrosis factor a in 3-6 hours. It mediates endothelial cell binding to neutrophils, monocytes, and some memory T cells. Example from human (precursor): database code LEM2_HUMAN, 610 amino acids (66.58 kDa). L selectin (or lymph node homing receptor; CD62L), M r 74 000 (on lymphocytes), is constitutively expressed on monocytes, lymphocytes (thymocytes, NK cells), neutrophils, eosinophils, and basophils. It mediates the adherence of lymphocytes, neutrophils, and monocytes to endothelium, including that of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. It binds to MadCAM and CD34. Example from human (precursor): database code LEM1_HUMAN, 372 amino acids (42.14 kDa). P-selectin (or PADGEM; abbr. for platelet activation dependent granule external membrane protein), M, 140000, is expressed at the surface of activated platelets and endothelial cells, and is inducible within minutes by thrombin, histamine, or peroxides from a granules of platelets or Weibel-Palade bodies of neutrophils. It mediates the adhesion of neutrophils and monocytes to platelets and endothelial cells. Example from human (precursor): database code LEM3_HUMAN, 830 amino acids (90.74 kDa). selection (in microbiology) a laboratory method in which a mixture of microorganisms is cultured under particular growth conditions that permit only cells with certain characteristics to survive, thereby enabling their isolation. selection pressure the intensity with which natural selection operates; it is often measured by the change in gene frequency per generation due to the effects of natural selection. selectively labelled indicating an isotopically labelled mol-

592

selective medium ecule in which the position(s) of the labelling is known, but the number of labelling nuclides at that (those) position(s) is not known; e.g. selectively labelled ethanol is designated as [1,2ZHjCH 3-CH r OH, which indicates that some, or all, of the hydrogen atoms on carbon atoms I and 2 are zH atoms. selective medium a culture medium designed either to encourage or to inhibit the growth of certain types of organisms, especially microorganisms. selective theory of immunity or elective theory of immunity any theory that ascribes to antigens a selective function in immunity by which antigens select cells genetically prepared to respond specifically and cause them to multiply and differentiate. They include the clonal-selection theory and the natural-selection theory of immunity. Compare instructive theory of immunity. selenium symbol: Se; a metalloid element of group 16 of the (IUPAC) periodic table; atomic number 34; relative atomic mass 78.96. Its main oxidation states are -2, +2, +4, and +6, with properties similar to those of sulfur, but more metallic. It occurs in various allotropic forms (grey, red, black); the grey form shows some electrical conductivity, which is enhanced by light, and it is used in 'selenium cells' to measure light intensity. There are several isotopes, the most abundant being selenium-80 (mass 79.916; relative abundance 49.8%); others are selenium-74 (0.9%), selenium-76 (9.0%), selenium-77 (7.6%), selenium-78 (23.5%), and selenium-82 (9.4%). Radioactive isotopes are selenium-72, selenium-73, selenium-75, and selenium-79. Selenium is an essential trace element, required for the formation of selenoproteins, notably glutathione peroxidase. Gut absorption is poor, but selenium deficiency is rare (seen, e.g., in some parts of China with low soil selenium). The most obvious clinical feature of dietary deficiency is myopathy (especially cardiomyopathy). Measurement of red-cell glutathione peroxidase activity gives an index of selenium status. selenium-72 a radioactive nuclide of selenium, USe, mass 71.927; it emits gamma radiation (0.046 MeV) and has a halflife of 8.4 days. selenium-73 a radioactive nuclide of selenium, ;~Se, mass 72.927; it emits a ~+ particle (1.32 MeV) and gamma radiation (0.361 Mev) and has a half-life on.1 h. selenium-75 a radio nuclide of selenium, ~~Se, mass 74.923; it emits gamma radiation (0.481 MeV) and has a half-life of 118.5 days. selenium-79 a radio nuclide of selenium, ~~Se, mass 78.918; it emits an electron (~- particle, 0.16 MeV), no gamma radiation, and has a half-life of 6.5 x ]04 years. selenoamino acid an amino acid in which selenium replaces a sulfur atom; see selenocysteine, selenomethionine. selenocysteine H-Se-CHrCH(NHz)-COOH; an essential component of glutathione peroxidase and some other proteins (see selenoprotein). For its synthesis, a special tRNA charged with serine responds to a UGA codon. The serine is converted to selenocysteine just before its use on the ribosome. It is assumed that the neighbouring base sequence indicates a special sense for this codon, which is normally a 'stop' codon. selenomethionine CHrSe-[CHzh-CH(NHz)-COOH; a selenoamino acid used as an antimetabolite, competing with methionine; it is also found in proteins; see selenoprotein. selenoprotein a protein containing selenium, almost invariably as selenocysteine, although selenomethionine can occur, apparently as a random substitute for methionine. Well-known selenoproteins include the mammalian glutathione peroxidases and tetraiodothyronine 5'-deiodinase, and bacterial formate dehydrogenases and glycine reductase. self 1 the individuality of a person or thing; the totality of components intrinsic to an individual or thing. 2 (in immunology) the components of an individual's own tissues that can be distinguished from foreign substances by the individual's immune system, and towards which immunological tolerance is shown. self-absorption the absorption of any emission by the emitting molecules.

semantophoretic molecule self antigen any (potentially) antigenic molecule originating in an individual that is recognized as nonforeign by the individual's immune system, and towards which immunological tolerance is normally shown. See also autoimmunity, self-tolerance. self-assembly the formation of a complex entity from more simple, identical units without intervention from any external agency. self-assembly doctrine a doctrine elaborated by Caspar and Klug to explain the assembly of small viruses and subcellular organelles. It is postulated that the structure assembles as a result of specific binding sites on proteins that interact to form a scaffold on which other components form. self-catabolite repression repression of gene expression by a catabolite formed within the same organism. self-cloning the cloning of a gene within the species from which it was derived, a technique that in some countries attracts less stringent government restrictions than when a gene is cloned in another species, being considered the less hazardous of the two approaches with respect to the genetic environment. self determinant a determinant originating from the tissue of an organism and thus treated as self (def. 2) by the immune system of that organism (except in the case of autoimmune pathology; see autoimmunity). self-fertilization the union of male and female gametes of the same organism. self-hybridization hybridization between nucleic acids that exhibit complementarity. selfing (in microbiology) the production of wild-type 'transductants' by infection of an auxotrophic strain with a transducing phage grown on the same auxotroph as the donor. selfish DNA hypothesis a hypothesis put forward to account for the presence in eukaryotic genomes of large amounts of repetitive DNA (see repetitive sequences). Because there is no confirmatory evidence that much of such DNA serves any useful purpose for its host, this DNA has been termed selfish DNA or junk DNA, and is suggested to be a molecular parasite that, over many generations has disseminated itself throughout the genome. If this is true, it remains a mystery why natural selection has not eliminated 'selfish DNA'. self tolerance the state in which the immune system of any particular individual lacks reactivity against potentially antigenic molecules originating within that individual. Self tolerance develops during perinatal life. See also acquired tolerance, autoimmunity, immunological tolerance. Seliwanoff test a test for ketohexoses based on the production of a red colour when the sample is boiled with a solution of 0.05% w/v resorcinol in 3 M hydrochloric acid. The test relies on the fact that ketoses are dehydrated more rapidly than aldoses to yield furfural products. [After Feodor Feodorowitsch Seliwanoff (1859-1938), Russian chemist.j SEM or S.E.M. 1 abbr. for standard error of estimate of mean. 2 abbr. for scanning electron microscope; see electron microscope. sem-5 the gene for Sem-5, sex muscle abnormal protein 5, in Caenorhabditis elegans. Sem-5 acts both in vulval induction and sex myoblast migration, and is linked in a signalling chain from tyrosine kinase receptors (e.g. EGF-type Let-23). It contains SH2 and SH3 domains (see SH domain) characteristic of tyrosine kinase binding proteins. Mutations of the sem-5 gene block signalling pathways from several tyrosine kinase receptors in the worm. Database code SEM5_CAEEL, 228 amino acids (26.18 kDa). semantide or semantophoretic molecule or informational macromolecule any of the different types of macromolecules that carry the information of the genes or a transcript (or a translation) thereof. The genes themselves are primary semantides, messenger RNA molecules are secondary semantides, and most polypeptides are tertiary semantides. semantophoretic molecule an alternative name for semantide.

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semen semen the fecundating fluid of male higher animals, consisting of spermatozoa suspended in seminal plasma - secretions of the accessory glands. semenogelin one of two major gel-forming proteins of semen. These proteins have 80% of their amino-acid residues in common, and their genes are localized to the long arm of chromosome 20. They are hydrolysed by a kallikrein-like proteinase. Example (precursor) of the predominant human protein of this type, semenogelin 1: database code SEMI_HUMAN, 462 amino acids (52.07 kDa). semi+ prefix 1 half. 2 partial or partially; intermediate. SEMI abbr. for specific endogenous mitotic inhibitor; see chalone. semialdehyde any of a class of organic compounds formed by the reduction of one carboxyl group of a dicarboxylic acid to an aldehyde group, as in glutamic semialdehyde. semiconductor any material, e.g. germanium or silicon, whose electrical conductivity lies between that of conductors and insulators and increases with increasing temperature. Its crystal structure has atomic bonds that allow the conduction of electric current by either positive or negative carriers when the appropriate additives (dopants) are present. semiconservative replication of DNA see replication of DNA. semiconstitutive mutant a mutant in which negative regulation is partially lost, so that a gene is expressed in the absence of inducer, but at a lower level than in the fully constitutive mutation, yet in the presence of inducer the expression reaches the fully constitutive level. See also constitutive mutation. semi-micro 1 describing or concerning something moderately small; applied to a scale of operation, an item of equipment, a quantity of material, etc. 2 (in analytical chemistry) a term originally used to indicate analysis of amounts of substance in the range 10-100 mg. Compare micro (def. I). See also microanalysis. seminal 1 a pertaining to seed. b of, or relating to, semen. 2 (of an experiment, idea, or publication) germinating new concepts; fundamentally original. seminal plasma the suspending fluid in which semen is ejaculated. seminal plasmin another name for caltrin. semiochemical any chemical substance that delivers a message or signal from one organism to another. The two broad classes into which such substances are divided are known as pheromones and allelochemics, depending on whether the information transfer occurs between, respectively, individuals of the same species (intraspecific) or between members of different species (interspecific). See also allomone, kairomone. semiotics functioning as sing. 1 the practice of symptomatology; a term that became obsolescent, but has been reintroduced in connection with CT, NMR, and other imaging techniques. 2 the philosophical theory of signs and symbols, having three branches: syntactics, semantics, and pragmatics. semipermeable membrane a membrane that allows the passage of only certain solutes, usually small molecules, but is freely permeable to solvent. semipolar double bond an alternative name for dipolar bond. semiquinone any free radical derived from a quinone or quinoid compound by the removal from it of a single hydrogen atom. Compare quinone. semisolid medium (in cell culture) a medium of consistency between those of a solution and a full gel. semisynthesis the partial synthesis of a chemical compound, especially a novel substance, by chemical orland enzymic modification of one isolated from natural sources or produced biotechnologically (e.g. by fermentation). The procedure has been applied with conspicuous success in the manufacture of new pharmaceuticals such as artificial penicillins and cephalosporins. -semisynthetic adj. semisystematic name or semitrivial name (in organic-chemical nomenclature) a name of a molecular entity that has only a part of it used in a systematic sense; e.g. (meth)ane, (but)ene,

Sephadex (calci)diol (in each of which only the part of the name outside the parentheses is systematic). Most names in organic chemistry are of this type. Compare systematic name, trivial name. senescence the process of ageing. -senescent adj. senile aged, to a point of severely decreased capability. -senility n. senna a preparation of the dried leaves of Cassia angustifolia or C. senna used as a laxative. It contains glycosides of hydroxyanthracene (sennoside B), which are metabolized to purgative anthraquinones by colonic bacteria. sense DNA see coding strand. sense strand (of duplex DNA) see coding strand. sensitivity 1 an index of the ability of any analytical method or other detection procedure to make quantitative determinations at very low levels. 2 (in metabolic control theory) the susceptibility of flux through a pathway to change in response to change in the level of one of the component enzymes, expressed quantitatively in terms of the flux control coefficient. An alternative meaning arises when an allosteric ligand acts at several points in a pathway, where a plot of the fractional modification in flux versus ligand concentration yields a sigmoidal curve for a positive effector; the sensitivity in this case can be derived from the slope of the sigmoidal curve. sensitivity coefficient former name for flux control coefficient. sensitization or sensitisation 1 enhanced reactivity to any treatment (such as exposure to an agonist) of any tissue, cell, or molecular system resulting from prior experience or treatment (often by the same agonist). 2 the conditioning of an animal by antigen in such a way that hypersensitivity reactions occur on subsequent exposure to the antigen. 3 the attachment of antibody to sheep red blood cells to make them susceptible to lysis by complement in the complement-fixation test. Red blood cells treated in such a way are commonly referred to as sensitized cells. -sensitize or sensitise vb. sensitizer or sensitiser see allergen. sensor any device that records the level of a substance of interest or under investigation, using physical parameters (heat, conductivity) or chemical methods. Sensors are often applied to continuous monitoring in flow systems; biosensors utilize the reactions of enzymes immobilized on a probe and often coupled with a second substrate that yields a coloured or fluorescent prod uct. sensory transducer any component of bacterial systems involved in signal transduction. An example is the ntrBlntrC system, which occurs in several bacteria (the following examples are from Escherichia coli). Under nitrogen limitation the product of the ntrB gene, NtrB (EC 2.7.1.-), activates NtrC - the ntrC gene product - by phosphorylating it; in nitrogen excess it reverses this. Examples: NtrB, database code NTRB_ECOLI, 349 amino acids (38.51 kDa); NtrC, database code NTRC_ ECOLI, 469 amino acids (52.19 kDa); NtrC contains an ATPbinding domain that interacts with sigma factor cr 54 . Another instance of a sensory transducer is sensory rhodopsin I transducer from archaebacteria. Example from Halobacterium halobium: database code HTRCHALHA, 536 amino acids (56.61 kDa); this is a typical seven-transmembrane-domain opsin-type protein used for sensing light. See also ehe. separation (in genetics) the break-up of a cointegrate into two or more replicons of similar sizes. Compare excision. Sephacel proprietary name for a gel-filtration medium based on cellulose cross-linked using epichlorohydrin so that a mesh results, the size of the apertures in the mesh being determined by the extent of cross-linking. Sephacryl proprietary name for a gel-filtration medium prepared from allyl dextran covalently cross-linked using N,Nmethylene bisacrylamide, to yield a mesh; the size of the apertures in the mesh depend on the degree of cross-linking. Sephadex proprietary name for a gel-filtration medium based on dextran cross-linked using epichlorohydrin so that a mesh results, the size of the apertures in the mesh being determined by the extent of cross-linking.

594 Sepharose Sepharose proprietary name for a gel-filtration medium based on agarose cross-linked using epichlorohydrin so that a mesh results, the size of the apertures in the mesh being determined by the extent of cross-linking. septanose the form of any monosaccharide, or monosaccharide derivative, in which the molecule contains a ring consisting of six carbon atoms and one oxygen atom. In monosaccharide symbolism the septanose form may be indicated by the suffix s; e.g. Glcs symbolizes glucoseptanose. Compare furanose, heptose, pyranose. septate divided by, or involving, a septum or septa. septation the process of forming the septum that cuts a cell into two at the end of the cell cycle in bacteria. septum I (in anatomy) a wall of tissue, sheet of cells, or other membrane-like structure that partitions two compartments. 2 a disk of silicone rubber, PTFE, or similar material used in any apparatus to seal an injection port. The needle of a syringe can be punched through the septum for the purpose of injection, and on withdrawal of the needle the elasticity of the septum ensures that the hole reseals. Sequenase proprietary name for a chemically modified T7 DNA polymerase with high processivity. It is the usual choice for DNA sequencing by the chain-termination method. sequenator an apparatus for determining the sequence of monomeric residues (e.g. amino acids) in an ordered linear polymer (e.g. an oligopeptide) by repeating a chemical process. sequence 1 the ordinal arrangement of the constituent parts of a biopolymer, e.g. the order of amino-acid residues in a polypeptide chain or of the nucleotide residues in a polynucleotide chain; the known arrangement of such units in any biopolymer or fragment. 2 any particular segment, occurring in or derived from a biopolymer, having a known order of its constituent parts; a synthetic polymer composed of parts equivalent to those occurring naturally and present in a particular known order. 3 to determine the order of residues in a biopolymer or fragment. -sequential adj. sequence compression see band compression. sequence homology similarity (often to an indicated degree) of sequences of residues in encoded macromolecules or specified segments of them. The term is often used synonymously with conservation (when used of primary structure) if the sequences occur in corresponding locations in specimens of any particular macromolecule obtained from genetically differing sources. Homology is discussed more fully in Appendix E. sequence hypothesis the hypothesis, formulated by F. H. C. Crick in 1958, that 'the specificity of a piece of nucleic acid is expressed solely by the sequence of its bases, and that this sequence is a (simple) code for the amino-acid sequence of a particular protein.' sequence ladder the ladder-like bands of separated components occurring in the chromatographic gel that result from DNA sequencing experiments. sequencer an apparatus for automatically determining the sequence of monomeric residues in an ordered linear polymer. sequence rule or Cahn-Ingold-Prelog rule or R/S convention (of configuration specification) a system for specifying the absolute molecular chirality of a chemical compound. This system considers the sequence of the proton numbers of the atoms directly attached to a chiral centre (see chirality); if two or more of these atoms have the same proton number, their substituents are then taken into account, the group with substituents of highest proton number taking precedence. When a multiple bond to a substituent is present, the substituent is arbitrarily considered to occur twice, or thrice; an isotope of higher nucleon number takes precedence over one of lower number. The priorities of some common ligands are tabulated in Appendix G. For a tetrahedral centre (e.g. a carbon atom) the substituent with the lowest priority is placed away from the observer (behind the chiral atom) with the other three projecting towards the observer; if these three substituents lie in a clockwise (right-handed) array of decreasing priority, then the

serial dilution chiral centre is designated with the stereochemical descriptor R, denoting Latin rectus, right; if the substituents lie in an anticlockwise (left-handed) array of decreasing priority, then the chiral centre is designated with the stereochemical descriptor S, denoting Latin sinister, left. For the name of a compound consisting of molecules with a single chiral centre the descriptor R or S, with a preceding locant if needed, is formed into a prefix by placing it in parentheses and adding a linking hyphen; a racemate with a single chiral centre in its molecules is labelled with the prefix (RS)-. When a molecule contains more than one chiral centre the prefix to the name is composed of multiple descriptors, each preceded by an appropriate locant; e.g. (2R,3R)-2,3-dihydroxybutanedioic acid (= Lg-tartaric acid). If only the relative, but not the absolute, configurations of two or more chiral centres in a molecule are known, these centres may be designated with the descriptors R* and S* (spoken as R star, S star), preceded when necessary by appropriate 10cants, on the arbitrary assumption that the chiral centre first cited (which usually is the one with the lowest locant) has an R configuration; for examples, compare the systematic names of allothreonine and threonine. See also o/L convention. Extensions of the sequence rule are the E/Zconvention, the pro-E/pro-Zconvention, the pro-R/pro-S convention and the ReIS; convention. [After Robert Sidney Cahn (1899-1981), British natural-products chemist, editor, and scientific semanticist, (Sir) Christopher Kelk Ingold (1893-1970), British physical organic chemist, and Vladimir Prelog, who jointly developed the system and described it in a series of three papers published in 1951, 1956, and 1966.] sequence-tagged site abbr.: STS; a short, single-copy DNA sequence that characterizes a mapping landmark on the genome. Such sequences provide unambiguous identification of DNA markers generated by the Human Genome Project (see HUGO). STSs are short segments of DNA of known (and unique) sequence which bind to VACs. If two YACs contain the same STS they must overlap. The YACs can be built up into an overlapping series of clones (a contig) covering an entire gene. sequencing the act or process of determining the sequence (def. I) of proteins or nucleic acids. See chain-termination method, chemical cleavage method, solid-phase technique. sequencing by hybridization see SBH. sequencing gel a polyacrylamide gel run to resolve oligonucleotides produced in a DNA sequencing procedure. See chain-termination method, chemical cleavage method. sequential analysis the analysis of a protein or nucleic-acid sequence (def. 1). sequential mechanism an enzyme reaction involving two or more substrates in such a way that all the substrates must be bound to the enzyme to form the central complex before any products can be released. A sequential mechanism may be an ordered mechanism or a random mechanism. sequestering agent see chelating agent. sequestration 1 the process of removal or separation. 2 (in chemistry) the effective removal of ions from solution by coordination with another kind of ion or molecule to form a firm complex molecule with different properties from the original ion. Compare chelation. 3 (in cell biology) the intracellular enclosing of material in an organelle. -sequester vb. Ser symbol for a residue of the a-amino acid L-serine (alternative to S). SER abbr. for smooth endoplasmic reticulum (see endoplasmic reticulum) . sera a plural of serum. SERCA abbr. for sarcoplasmic/endoplasmic reticulum calclumtransporting ATPase, EC 3.6.1.38; any of a family of Ca 2+ pump integral membrane protein isoforms of sarcoplasmic or endoplasmic reticulum. They catalyse the hydrolysis of ATP coupled with Ca2+ transport. Example from Drosophila melanogaster: database code ATCB_DROME, 1002 amino acids (109.47 kDa). serial dilution a method of achieving dilution of a liquid by se-

595

serinate quentially transferring a sample of predetermined volume into another, empty, vessel (usually a tube), which is then made up with diluent to the same total volume as the first. The overall dilution achieved is (vls)X-fold, where v is the chosen total volume in each tube, s is the size of the sample, and x is the number of times the procedure is repeated. serinate 1 serine anion; the anion, HO-CH r CH(NH 2)-COO-, derived from serine. 2 any salt containing serine anion. 3 any ester of serine. serine the trivial name for a-amino-p-hydroxypropionic acid; 2-amino-3-hydroxypropanoic acid; HO-CHz-CH(NH z)COOH; a chiral a-amino acid. L-Serine (symbol: S or Ser), (S)2-amino-3-hydroxypropanoic acid, is a coded amino acid found in peptide linkage in proteins; codon: AGC or AGU; UCA, UCC, UCG, or UCU. In mammals it is a nonessential dietary amino acid and is glucogenic. D-Serine (symbol: D-Ser or DSer), (R)-2-amino-3-hydroxypropanoic acid, in both free and combined forms occurs in silkworms and earthworms; residues of D-serine occur in certain peptide antibiotics, e.g. polymyxins D 1 and D z. [Note: The absolute configuration of D-serine (and hence that at the a-carbon atom of other aamino acids of the D series) is identical with that of D-glyceraldehyde (and hence with that at the reference carbon atom of other monosaccharides of the D series).]

L-serine

L-serine dehydratase EC 4.2.1.13; systematic name: L-serine hydro-lyase (deaminating); other names: serine deaminase; Lhydroxyaminoacid dehydratase. An enzyme that catalyses a reaction between L-serine and water to form pyruvate and ammonium ion. It is a pyridoxal-phosphate enzyme. The enzyme for gluconeogenesis from serine in Escherichia coli is a 4Fe-4S protein: database code SDHL_ECOLl, 454 amino acids (48.85 kDa). serine hydroxymethyl transferase see glycine hydroxymethyltransferase. serine-like carboxypeptidase see serine endopeptidase. serine C-palmitoyltransferase EC 2.3.1.50; an enzyme of the pathway for the biosynthesis of sphingoid bases. It catalyses the formation of 3-dehydro-D-sphinganine from palmitoyl-CoA and L-serine, releasing CoA and CO 2 , Pyridoxal-phosphate is a coenzyme. Example from yeast (long-chain-base biosynthesis protein), two forms: database code LCBLYEAST, 558 amino acids (62.16 kDa); and database code LCB2_YEAST, 561 amino acids (63.04 kDa). serine peptidase any enzyme characterized by having a residue of serine (and one of histidine) at the active centre and by being irreversibly inhibited by organic fluorophosphates (which phosphorylate the serine's hydroxyl group). Serine peptidases are of two types: (I) serine-type carboxypeptidases, and (2) serine endopeptidases, sub-subclass EC 3.4.21. During catalysis by serine peptidases an acyl-enzyme intermediate is formed by esterification of the hydroxyl group of the reactive serine with the carbonyl group of a sensitive peptide bond of the substrate. The serine endopeptidase group includes chymotrypsin, most elastases, kallikrein, thrombin, trypsin, and a number of microbial proteinases. See also serine-type carboxypeptidase. serinelthreonine kinase a protein kinase that phosphorylates serines or threonines on its target protein. serinelthreonine-specific protein phosphatase EC 3.1.3.16; recommended name: phosphoprotein phosphatase; other names: protein phosphatase-I; protein phosphatase-2A; protein phosphatase-2B; protein phosphatase-2C. This name

serum includes a group of enzymes that hydrolyse the serine- or threonine-bound phosphate group from many phosphoproteins. Examples from yeast: PP2a-1 catalytic subunit: database code P2AI_YEAST, 369 amino acids (41.89 kDa); PP2a-2 catalytic subunit: database code P2A2_YEAST, 377 amino acids (43.00 kDa). serine transhydroxymethylase see glycine hydroxymethyltransferase. serine-type carboxypeptidase EC 3.4.16.1; this name includes many enzymes that hydrolyse protein with release of a C-terminal amino acid; they have a broad specificity.Exampies (3-D structures) from wheat (chains a and b, respectively): database codes NRL_l WHSA, 255 amino acids (28.38 kDa), and NRL_I WHSB, 153 amino acids (17.28 kDa). serinium serine cation; the cation, HO-CH z-CH(NH 3+)COOH, derived from serine. serino+ prefix denoting the group, HO-CHrCH(NH-)-COOH, derived from serine by loss of hydrogen from the amino group. sero+ comb. form denoting a connection within or origin in serum. serological pertaining to, or originating in, serum; connected with the study of serum. serology the study of serum; in particular, the immunological phenomena involving circulating antibody that may be observed in vitro. serosa a serous membrane, especially the peritoneal covering. serosal adj. serotonergic 1 describing a nerve that is activated by serotonin. 2 describing a nerve that acts by the release of serotonin from the nerve endings. Compare adrenergic, aminergic, cholinergic, peptidergic, purinergic. serotonin 5-hydroxytryptamine (abbr.: 5-HT); a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties; it is also found in mast cells, platelets, brain, and the enterochromaffin cells of the gastrointestinal tract, and is capable of causing vasoconstriction, increased vascular permeability, and contraction of smooth muscle. It is formed from tryptophan, after hydroxylation to 5-hydroxytryptophan, by tryptophan 5monooxygenase (EC 1.14.16.4) followed by decarboxylation by aromatic-L-amino-acid decarboxylase (EC 4.1.1.28). It is a substrate for monoamine oxidase. serotonin receptor see 5-hydroxytryptamine receptor. serotransferrin see transferrin. serous 1 relating to or resembling serum (or similar watery fluid). 2 producing a fluid resembling serum. serous membrane or serosa a thin connective-tissue membrane lining certain closed body cavities and reflected over the viscera. The peritoneum of the abdomen, pleura of the chest, and pericardium of the heart are all serous membranes. Each consists of a parietal layer, lining the walls of the cavity, and a visceral layer covering the organs. The two are continuous, forming a closed sac. Compare mucous membrane. serpentine domain any sequence of transmembrane segments of a single polypeptide chain of a membrane protein that traverses the membrane several times, as, e.g., in seven-transmembrane-domain proteins. serpin any of a superfamily of proteins, many of which inhibit serine proteinases and exhibit a high degree of homology with classical serine proteinase inhibitors such as at-antitrypsin or antithrombin. The superfamily is now considered to extend beyond compounds that are known to be proteinase inhibitors and, based on homology, includes proteins such as ovalbumin and angiotensinogen, which have no inhibitory function. [From serine proteinase inhibitoL] Sertoli cell or sustentacular cell a supporting cell of the mammalian testis that surrounds and nourishes developing sperm cells. [After Enrico Sertoli (1842-1910), Italian histologist.] serum (pl. sera or (esp. US) serums) the liquid extruded after blood has clotted and the clot has retracted (syneresis (def. 2». Compare plasma.

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serum albumin

sex factor

serum albumin or plasma albumin the smallest and most abundant of the plasma proteins; M r 65 000-68 000 for the bovine form, 69 000 for the human. It is involved in the regulation of osmotic pressure and in the transport of sparingly soluble metabolites. The serum albumins belong to a multigene family of proteins that includes lX-fetoprotein and vitamin Dbinding protein. Human serum albumin has three homologous domains which assemble to form a heart-shaped molecule. It consists of 28 helices, ranging from five to 31 amino-acid residues each, formed into six subdomains; two each of these subdomains form one of the major domains. There is no beta structure. Bovine (serum) albumin (abbr.: BSA) and human (serum) albumin (abbr.: HSA) are widely used as standards in protein estimations. These include fatty acids, amino acids (such as tryptophan), steroids, metals (e.g. calcium, copper, and zinc), and hydrophobic drugs. See also albumin. serum amyloid P-component abbr.: SAP; a precursor of amyloid component P. Amyloid component P is found in basement membranes and is associated with amyloid deposits. serum converting enzyme a former name for angiotensin converting enzyme. serum globulin any serum protein that is also a globulin. An early classification of globulins was according to their mobility on electrophoresis. Serum albumin moves the fastest; behind albumin on paper electrophoresis or cellulose acetate strips are two bands known as the al- and a2-globulin bands, followed by a ~-globulin band with the y-globulins forming a diffuse band near the origin. The ai-globulins include thyroxine-binding protein, transcortin, aI-glycoprotein, alipoprotein, and antitrypsin. The az-globulins include haptoglobin, az-glycoprotein, macroglobulin and ceruloplasmin. The ~-globulins include transferrin, ~-lipoprotein and ~-gly­ coprotein. The y-globulins comprise the immunoglobulins. serum protein any protein contained in serum; the term is usually applied to those proteins present in high quantities. The most prominent of these is albumin, which is present in the normal serum of human adults in the range 34-48 g L-I. See also serum globulin. serum response element abbr.: SRE; a stretch of DNA that regulates promoters for a group of genes that are activated by addition of serum to cell cultures. Such elements have the consensus sequence CCATATTAGG. serum spreading factor see vitronectin. seryl the acyl group, HO-CHz-CH(NH2)-CO-, derived from serine. sesqui+ comb. form 1 denoting one-and-a-half times; in a ratio of three parts to two. 2 (in chemistry) indicating a compound having one-and-a-half molecular proportions of the specified element group, or unit, either in relation to a second component, as in sesquioxide (e.g. chromium sesquioxide, C0 20 3), or in relation to a reference compound, as in sesquiterpene; it also sometimes denotes a compound intermediate in constitution between two others, as in sesquicarbonate (e.g. sodium sesquicarbonate, Na2C03·NaHC03·2H20). sesquiterpene any terpene formed from three isoprene units, i.e. having 15 carbon atoms per molecule as compared with a monoterpene which has 10 carbon atoms per molecule and is formed from two isoprene units. sesquiterpene lactone any sesquiterpene (15 carbon atoms) containing a lactone structure. Several are derived from

o artemesinin

Artemisia spp., including artemesinin (qinghaosu) from A. annua (qing hao). Qing hao has been used for almost 2000 years as an antimalarial; its mechanism of action is unknown. sester+ comb. form 1 denoting two-and-a-half times; in a ratio of five parts to two or 10 parts to 4. 2 (in chemistry) indicating a compound having two-and-a-half molecular proportions of the specified group or unit in relation to a reference compound, as in sesterterpene. sesterterpene any terpene formed from five isoprene units, i.e. having 25 carbon atoms per molecule as compared with a monoterpene, which has 10 carbon atoms per molecule and is formed from two isoprene units. An ophiobolin is an example. S6V symbol for sevenless gene; see Sevenless protein. Sevag method a method for removing proteins from nucleic acids during purification of the latter. The proteins are precipitated after repeated denaturation by shaking with a solution of octanol in chloroform. Sevenless protein abbr.: Sev; a protein, encoded by the sevenless (sev) gene, that is part of a system for differentiation of R 7 photoreceptors in Drosophila. Sev is a receptor for an extracellular signal; it has tyrosine kinase activity and belongs to the family of insulin receptors. Sev has a ligand, Boss, the product of the bride of sevenless (boss) gene; it is expressed by R8 photoreceptor cells and internalized (as a transmembrane protein) in a Sev-dependent manner. Examples, Sev: database code 7LES-DROME, 2554 amino acids (286.79 kDa); Boss: database code BOSS_DROME, 896 amino acids (99.81 kDa). seven-minute phosphate see labile phosphate. seven-transmembrane-domain protein or seven-transmembrane-segment protein or seven-transmembrane-helix protein a type of receptor protein that contains, in a single polypeptide chain, seven hydrophobic domains that traverse the lipid bilayer. This structural characteristic is typically used to describe the structures of receptors that couple to effector systems through G-proteins. These are also sometimes referred to as serpentine receptors. The structures of only a few membrane proteins have been determined at high resolution, and this structural characteristic has been attributed to other proteins mainly on the basis of sequence comparison. Thus, for the majority of proteins, the name 'seven-transmembranedomain protein' is a tentative one. The suggestion that the transmembrane domains are helical is even more tentative. seven-up a receptor required for photoreceptor cells during eye development. It is a zinc-finger DNA-binding protein with two forms (I and 2) generated by alternative splicing. Example (type 1) from Drosophila melanogaster: database code 7UPL DROME, 543 amino acids (57.92 kDa). sex chromatin a condensed mass of chromatin that represents an inactivated X chromosome. In mammalian nuclei, each X chromosome apart from the activated one forms a sex chromatin body or Barr body. sex chromosome a chromosome involved in sex determination. In many species, these are the Xchromosome and Ychromosome. They are distinguished from the autosomes i.e. all the other chromosomes of that species. In some species, however, e.g. fish of the genus Xiphophorus, sex determinants are spread over a number of chromosomes. sex determination the specification of the sex of an individual organism by genes. In many animal species, these genes are located on the X chromosome and the Y chromosome. Their effects are manifested as a result of secretion of androgens and estrogens. sex factor or fertility factor or F factor or F agent an episomal genetic element (see episome) in bacteria that enables the cell to act as a genetic donor. Cells of such donor strains are able to form stable unions with cells devoid of such factors and to transfer to them extrachromosomal material, including the sex factor, and sometimes segments of bacterial chromosomes (see conjugation (def. 4)). The F plasmid is the prototypical sex factor, responsible for conjugation in certain strains of Escherichia coli.

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sex hormone sex hormone any steroid hormone that is responsible for controlling sexual characteristics and reproductive function. Estrogens and progesterone are the female sex hormones, while androgens are the male sex hormones. They are produced mainly by the ovaries or testes, with contributions from the adrenals and placenta. sex linkage a special type of gene linkage occurring when a gene producing a certain phenotype (often unrelated to primary or secondary sexual characters) is located on a sex chromosome. Such a gene, or the character it determines, is said to be sex linked. One consequence of a mutation of genes on the X chromosome is that they may often be apparent only in male offspring, which have only one X chromosome. The mutation may be masked in the female because of the presence of a second, unaffected X chromosome. sexual conjugation see conjugation (def. 4). S-form abbr. for smooth form; describing bacterial colonies with a smooth appearance. Compare Rform (def. 2). SGF abbr. for skeletal growth factor. SGOT abbr. for serum glutamic-oxaloacetic transaminase (name not now recommended; see aspartate transaminase). SGPT abbr. for serum glutamic-pyruvic transaminase (name not now recommended; see alanine transaminase). shadow casting a procedure used in the preparation of specimens for electron microscopic examination. The specimen is placed in a vacuum and a heavy metal is applied by evaporation - the metal is evaporated with an electrically heated tungsten filament. In high vacuum the metal atoms travel in straight lines and so, if evaporation is from an acute angle, metal will condense on only one side of the features of the specimen leading to variations in electron-density over the specimen, creating a 'shadow' effect. sham operated describing a control procedure in which all the operations employed in a surgical technique are imitated with the exception of the experimental lesion that is the subject of study. Shardinger enzyme see xanthine oxidase. shark's tooth comb a plastic device for creating wells in an electrophoretic gel. It is shaped like a comb with the teeth coming to a point. Sharp, Phillip Allen (1944- ), US molecular biologist; Nobel Laureate in Physiology or Medicine (1993) jointly with R. J. Roberts 'for their discovery of split genes'. Sharples super centrifuge a, now superseded, efficient centrifuge with a flow-through rotor in which the sedimentation path was short. It is used for harvesting bacteria, blood cells, etc. The version powered with an electric motor turned at 21 000-23000 rpm while the air-turbine-driven version turned at 50 000 rpm. The instruments of this type have been superseded by others that can operate continuous flow rotors. SHe a gene family that was identified by screening eDNA libraries for genes encoding SH2-containing proteins (see SH domain). The mammalian gene encodes two overlapping, widely expressed proteins with a C-terminal SH2 domain that binds activated growth factor receptors, and which are phosphorylated on tyrosine in growth factor activated cells. These She proteins are transforming when overexpressed in fibroblasts. Phosphorylated She forms a complex with Grb2, and may form a link between certain tyrosine kinases and the Grb2/Ras signalling pathway. Example of gene product from human: database code SHC_HUMAN, 473 amino acids (51.61 kDa). SH domain abbr. for Src homology domain; the SH2 domain is a protein module consisting of about 100 residues found in many proteins involved in signal transduction. Apart from Src, which contains the prototype SH2 domain (see src), these include among many others phospholipase C, products of protooncogenes such as ASL, FYN, and FGR, GTPase-activating protein, and protein tyrosine phosphatases. The SH2 domain has also been found in structural proteins such as fodrin. One function of the domain is to bind to the autophosphorylated site of growth factor receptors, e.g. PDGF and EGF recep-

shikimate pathway tors. Proteins with SH2 domains are frequently found also to have SH3 domains. The SH3 domain is composed of approximately 50 amino acids and was originally identified in Src, but has since been found within a number of other proteins. SH3 domains mediate protein-protein interactions through their ability to recognize and bind proteins containing specific amino-acid sequences rich in proline and hydrophobic residues. To date, there are known to be at least two general classes of ligand to which SH3 domains can bind: class I, which comprises proteins containing the consensus sequence PXLPPZP; and class II, with the sequence XPPLPXR (where X is any amino acid and Z appears to be a residue specific to the type of SH3 domain involved). Given the nature of the proteins possessing SH3 domains and SH3-binding domains, it is clear that the protein interactions mediated by these motifs are important to the operation and maintenance of cytoskeletal architecture and intracellular signalling pathways. shear 1 to disrupt or fracture (an entity) using forces acting parallel to a plane, rather than perpendicularly, as with tensile or compressive forces. For example, shear forces can be used to disrupt DNA or other macromolecules by enclosing the molecules between two closely applied plane surfaces moving rapidly in opposite directions. Homogenization techniques depend on shear forces. 2 the deformation or fracture produced by such forces. shear gradient see viscosity. shear rate see viscosity. shear stress see viscosity. shikalkin the racemic mixture of alkannin and its (+)( R) enantiomer, shikonin. shikimate the anion of shikimic acid; [-)3a,4a,5p-trihydroxyI-cyclohexene-l-carboxylic acid; (3R,4S,5R)-trihydroxy-lcyclohexenecarboxylic acid; an important intermediate, in microorganisms and plants, in the pathway for the synthesis of phenylalanine, tyrosine, tryptophan, and many other substances (e.g. tocopherol, vitamin K, folic acid, ubiquinone, enterobactin, and some antibiotics); this is known as the shikimate pathway. The enzyme 3-phosphoshikimate 1-carboxyvinyltransferase (EPSP synthase) in higher plants is specifically inhibited by the compound glyphosate, which inhibits growth and can thus be used as an effective and readily degraded broad-spectrum herbicide. Shikimic acid was first isolated from the plant Illicium religiosum (star anise) in 1885. The name is derived from the Japanese name for this plant, shikimi-no-ki. See also shikimate kinase. shikimate 5-dehydrogenase EC 1.1.1.25; systematic name shikimate: NADP+ 5-oxidoreductase; an enzyme of the shikimate pathway that catalyses the reduction by NADPH of 3-dehydroshikimate to shikimate with formation of NADP+. The description of the enzyme as a 5-dehydrogenase derives from the older numbering system for shikimate. With the nowaccepted chemical numbering, it is in fact a 3-dehydrogenase. See also pentafunctional arom polypeptide. shikimate kinase EC 2.7.1.71; systematic name: ATP:shikimate 3-phosphotransferase; an enzyme of the shikimate pathway that catalyses the phosphorylation by ATP of shikimate to shikimate 3-phosphate with formation of ADP. The product, shikimate 3-phosphate, is the precursor of 5-enolpyruvylshikimate 3-phosphate (5-0-(1-carboxyvinyl)-3-phosphoshikimate) from which chorismate is formed. Example, shikimate kinase I from Escherichia coli: database code AROK_ECOLI, 172 amino acids (19.39 kDa). See pentafunctional arom polypetide for another example. See also shikimate. shikimate pathway the 'classical' shikimate pathway in plants and microorganisms led to the production of the aromatic amino acids (phenylalanine, tyrosine, tryptophan) from carbohydrate precursors, with a requirement for chorismate as well as shikimate. Chorismate was regarded as a (single) branch point, being converted to phenylalanine and tyrosine via prephenate (see also arogenate) and to tryptophan via anthranilate. Chorismate can also be converted to ubi quinones,

59S

shikonin plastoquinones, and tocopherols. Moreover, on isomerization it yields isochorismate, from which are derived many naphthoquinones (including the vitamins K), 3-carboxy aromatic amino acids, salicylate, and dihydroxybenzoate (for enterobactin formation). Certain non-aromatic cyclohexane compounds are produced from shikimate itself. The pathway is now recognized to contain multiple branch points at many (possibly all) of the pathway intermediates, and has been termed a 'metabolic tree with many branches'. The carbohydrate precursors are phosphoenolpyruvate and o-erythrose 4phosphate; they yield 2-dehydro-3-deoxY-D-arabino-heptonate 7-phosphate (I, more commonly termed 3-deoxy-o-arabinoheptulosonate 7-phosphate, abbr.: DAHP) by action of EC 4.1.2.15, 2-dehydro-3-deoxyphosphoheptonate aldolase (DAHP synthase). I is converted to 3-dehydroquinate (II) by 3-dehydroquinate synthase, EC 4.6.1.3, and II is then converted to 3dehydroshikimate (III) by 3-dehydroshikimate dehydratase, EC 4.2.1.10. Shikimate is then formed from III by shikimate 5dehydrogenase, EC 1.1.1.25, and converted to shikimate 3phosphate (IV) by shikimate kinase, EC 2.7.1.71. Phosphoenolpyruvate is used again to convert IV to 5-enolpyruvylshikimate 3-phosphate (V, abbr.: EPSP) by 3-phosphoshikimate I-carboxyvinyltransferase, EC 2.5.1.19, and V yields chorismate (VI) by action of chorismate synthase, EC 4.6.1.4. Chorismate leads to prephenate by action of chorismate mutase, EC 5.4.99.5, and in another branching undergoes isomerization by isochorismate synthase, EC 5.4.99.6, to form isochorismate. Organization of the various enzymatic activities varies considerably in plants, bacteria, yeasts, and other fungi. In yeasts and other fungi, and also in Euglena gracilis, the conversion of DAHP to EPSP requires a complex pentafunctional polypeptide specified by the arom gene cluster (see perttafuctiona I arom polypeptide). shikonin the (+ )-(R) enantiomer of alkannin. Shine-Dalgarno sequence a sequence for the formation of the correct preinitiation complex between a 30S ribosomal subunit and a messenger RNA (mRNA) molecule. It is suggested that a seven-nucleotide, pyrimidine-rich sequence near the 3' terminus of 16S (prokaryotic) or ISS eukaryote ribosomal RNA, found in many organisms, can form base pairs with a complementary three- to seven-nucleotide, purine-rich sequence (the Shine-Dalgarno sequence) preceding the initiation codon in many mRNA molecules, thereby allowing the initiating ribosomal subunit to bind the mRNA so as to discriminate between many AUG or GUG (i.e. initiation) triplets and to select only the one at the beginning of a cistron. [After John Shine (1946- ) and Lynn Dalgarno (1935- ).] shockate the preparation that is obtained when (bacterial) cells are suspended in an osmotically stabilizing medium and lysed by osmotic shocking through the sudden addition of water, followed by immediate centrifugation. short-chain describing an aliphatic compound of any type with a chain length of less than 10 carbons. short-patch repair a type of excision repair of DNA in which the average size of excised DNA is about 20 nucleotides. It contrasts with very-short-patch repair, which deals with mismatches between specific bases, and long-patch repair, in which relatively long stretches of DNA are involved, mostly about 1500 nucleotides long, but in some cases up to 9000 nucleotides or more. See also DNA repair enzyme, uvr. shotgun cloning a method, first used for cloning an entire genome, in which the DNA is randomly broken into fragments of approximately the average size of genes. The fragments are then cloned into suitable vectors, to give a genome library. shotgun collection see genomic library. showdomycin 2-(fJ-o-ribofuranosyl)-maleimide; an antibiotic produced by Streptomyces showdoensis and active against a number of Gram-positive bacteria. It is sometimes used in biochemical studies as a thiol-reactive agent. Compare N-ethylmaleimide.

sialo-

OH

OH

shuttle (sometimes) an intracellular metabolic cycle concerned in the transfer of, e.g., reducing equivalents or carbon chains across membranes. Different carriers operate each way across the membrane. Examples include the 3-hydroxybutyrate cycle, the glycerol-3-phosphate cycle, and the malate-aspartate cycle. shuttle vector a DNA molecule, e.g. a plasmid, that is able to replicate in two different host organisms and can therefore be used to 'shuttle' or convey genes from one to the other. shuttle vesicle an endocytotic vesicle that transfers proteins across an epithelial cell from one face to another e.g. from the sinusoidal to the bile-canalicular face of a hepatocyte. sl symbol for a residue of the ribonucleoside thioinosine; mercaptopurine ribonucleoside (alternative to Sno). Si symbol for silicon. Si- stereochemical descriptor denoting sinister (i.e. counterclockwise, or 'left-handed') configuration of face of a trigonal atom. See RelSi convention. SI abbr. for Systeme International (d'Unites); International System (of Units); a rationalized coherent system of metric units, in which the magnitude of any physical quantity may be expressed, that is recommended for use by scientists throughout the world. The system is founded on seven SI base units: ampere, candela, kelvin, kilogram, metre, mole, and second. There are also 21 SI derived units, which are expressed in terms of the base units, and two SI supplementary units, radian and steradian, which are now regarded as dimensionless derived units. A series of prefixes signify decimal multiples and submultiples of any SI unit. Sia symbol for the sialoyl group. sial+ a variant of sialo+ (before a vowel). sialagogue or sialogogue any agent that stimulates the flow of saliva. -sialagogic or sialogogic ad). sialate the anion of sialic acid. sialic of, or relating to, saliva or a salivary gland. sialic acid any of the N- or O-substituted derivatives of neuraminic acid found as components of complex carbohydrates, e.g. N-acetylneuraminic acid (5-(acetylamino)-3,5-dideoxy-oglycero-D-galacto-non-2-ulosonic acid, (abbr.: Neu5Ac; see also NeuNAc). Linkage of sialic acids is through C-2 to monosaccharides at the ends of glycosylation chains of glycolipids and glycoproteins. Neu5Ac can also be linked at its C-S and C-9 hydroxyl groups to another Neu5Ac residue, often forming multiple repeats as in mammalian NCAM. Hydroxyl groups at C-4, -7, -8, and -9 can be O-acylated (see also NeuOAc). Other common derivatives are N-glycoloylneuraminic acid (in mammals, but not normally in humans; abbr.: NeuGc), and Nketodeoxyoctanooylneuraminic acid (e.g. in bacteria). sialidase EC 3.2.1.18; recommended name: exo-a-sialidase; former name: neuraminidase; a glycosidase enzyme that hydrolyses 2,3-, 2,6-, and 2,S-glucosidic linkages joining terminal nonreducing N- or O-acylneuraminyl residues to galactose, Nacetylhexosamine, or N- or O-acylated neuraminyl residues in oligosaccharides, glycoproteins, or glycolipids. Example from Clostridium perfringens: database code NANH_CLOPE, 3S2 amino acids (42.S1 kDa). sialidosis another name/or mucolipidosis I. sialo- or (be/ore a vowel) sial+ comb. form I of, or relating to, saliva or a salivary gland; sialic. 2 denoting the presence in a

599

sigmoid kinetics

sialoadhesin compound of one or more residues of sialic acid. Compare asialo+. sialoadhesln a macrophage-restricted sialic-acid-dependent glycoprotein receptor of several forms. It contains 17 immunoglobulin-like domains. It is an adhesion molecule that recognizes oligosaccharides terminating in NeuAc(a2-3)Gal in N-linked and O-linked glycans. Example, 16-domain form from the mouse: database code MMSIALl, 1598 amino acids (172.68 kDa). sialogogue a variant spelling of sialagoglie. slalosyl the glycosyl group derived by removal of the exomeric hydroxyl group from sialic acid or sialate. sialoyl the acyl group derived from sialic acid by removing the hydroxyl group from its carboxyl group. sickle cell an abnormal red blood cell obtained from an individual exhibiting sickle-cell anemia. At low oxygen tensions such cells adopt a crescent shape reminiscent of the blade of a sickle. The defect originates in a mutation leading to replacement of Glu by Val at position 6 in the hemoglobin ~ chain. In its deoxygenated state the hemoglobin forms long rodlike helical fibres, which cause the deformation of the red cells because the ~6 Val can pack into a pocket at the EF corner (between helices E and F) of another ~ chain, a pocket which is lost in conformational changes resulting from oxygenation. Sickling can also result from ~121 Glu ~ Lys replacement, a site that lies close to ~6. sickle-cell anemia an inherited disease of humans arising in individuals homozygous for a mutation resulting in replacement of Glu by Val at position 6 of the hemoglobin ~ chain. It is particularly common in populations indigenous to or orginating from subtropical areas, including the Mediterranean region, parts of Saudi Arabia and India, and in those of African origin. The resultant abnormal red blood cells, called sickle cells, are removed from the circulation, leading to anemia. There is no satisfactory treatment, and early death often results. Less serious consequences occur in heterozygotes i.e. individuals with sickle-cell trait; these survive longer and benefit from greater resistance against the malaria parasite, which is adversely affected by sickle-cell trait during the red-cell phase of its life cycle. This results from the fact that, when the heterozygous sickle cells pass through capilliaries, they sickle, causing them to lose K+ and killing the malaria parasite, which needs high levels of K+. See also glucose-&phosphate dehydrogenase. side-by-side model abbr.: SBS model or SBS; a model of duplex DNA consisting of an alternating arrangement of righthanded and left-handed segments of duplex DNA, or other double-stranded polynucleotide, with five base pairs per segment. This produces a structure similar to the Watson-Crick model of DNA except that the two antiparallel strands are side by side rather than intertwined in a double helix. side chain 1 any part of an organic molecule based on an aliphatic carbon chain that can be regarded as branching from a main chain. 2 the part of an amino acid that extends from the a-carbon atom and is unique for that amino acid. sideramine one of the two main categories of siderochrome. See also sideromycin. siderochrome or siderophore or ironophore any of various lowmolecular-mass Fe(m)-chelating substances elaborated by aerobic or facultatively anaerobic microorganisms, especially when growing in iron-deficient media. Fe3+-siderochrome complexes have very high stability constants (103°_1050 dm 3 mol-I). They are taken up by specific transport systems in the microorganisms; subsequent intracellular release of iron requires enzymic action. A siderochrome is thus an iron ionophore. Siderochromes are of two main categories, one or both of which may be formed by any particular organism: (I) catechol derivatives, e.g. enterobectin; and (2) hydroxamic acid derivatives (or sideramines), e.g. mycobactin (see also ferrichrome). It is curious that the transport systems for ferrichrome or ferric enterobactin in certain strains of bacteria

appear to be identical with the membrane receptors for colicin M or B respectively (see colicin), and in the former case for the antibiotic albomycin and various phages as well. aideromycin any of a class of iron-containing antibiotic substances elaborated by certain actinomycetes. They are structurally related to sideramines (see siderochrome), by which their antibiotic action can be antagonized. siderophage an alternative name for siderophore D. siderophilin an alternative name for serotransferrin, serum transferrin. sid,rophof. 1 or siderophage a macrophage containing granules of hemosiderin. 2 an alternative name for siderochrome. aiderosom. a membrane-bound organelle found in spleen macrophages and containing aggregates of hemosiderin. Siderosomes may be derived from lysosome•. siemens symbol: S; the SI derived unit of electric conductance, defined as the electric conductance between two poillts on an electric conductor when an electric potential difference of one volt causes an electric current of one ampere to flow; i.e. I S = I a-I. It was formerly called the mho or the reciprocal ohm. [After (Ernst) Werner von Siemens (l816-92),German electrical engineer, industrialist, inventor, and metrologist.) sievert symbol: Sv; 1 the SI derived unit of (radiation) dOlle equivalent, equal to one joule per kilogram of living tissue; i.e. I Sv 1 J kg-I. Also, I Sv 100 rem. Compare gray. 2 or intensity millicurie an obsolete non-SI uqit of intensity of gamma radiation, numerically eqllal to 8.4 rontgens per hour. [After Rolf Maximillian Sievert (1896-1966), Swedish radiation physicist.] sievorptive chromatography a form of chromatography in which absorption chromatography and molecular-sieve chromatography are combined within a single separative system. Si-face (of an atom or molecule) see ReIS; convention. SIF cell abbr. for small intensely fluorescent cell. sigma symbol: cr (lower case) or L (upper case); the eighteenth letter of the Greek alphabet. For uses see Appendix A. sigma bond see orbital. sigma factor an RNA polymerase initiation factor occurring in bacteria; a protein that promotes attachment of the RNA polymerase, of which it is a subunit, to specific initiation sites and is then released. The main sigma factor of Escherichia coli is cr 70 : database code RP70_ECOLI, 613 amino acids (70.18 kDa). An unrelated family is cr 54 (four motifs), with associated regulatory proteins; members of this are specific to certain operons; example from E. coli: database code RP54_ECOLI, 477 amino acids (53.93 kDa). Other sigma factors are involved in response to heat shock and respiratory stress; examples (E. coli), cr E ; database code Rl'OE_ECOLI, 191 amino acids (21.67 kDa); and cr 32 : database code RP3:CECOLI, 284 amino acids (32.43 kDa). Major switches in transcriptional control in bacteria, e.g. sporulation in bacilli, and transcriptional control in certain phages, involve modification to or replacement of sigma factors. sigma orbital see orbital. sigma receptor any of a class of receptors formerly regarded as opioid receptors but now generally regarded as nonopioid receptors because morphine has a very low affinity for them, and naloxone, the classical opioid antagonist, does not block the action of morphine. They are noted for their activation by powerful psychotomimetic drugs, e.g. phencyclidine. These receptors appear to mediate dis orientated and depersonalized feelings. sigma subunit a component of bacterial RNA polymerase; see sigma factor. sigmoid or sigmoidal S-shaped; especially as in a sigmoid flexure (e.g. of the large intestine); or a sigmoid plot, i.e. one similar to a skewed letter S, that is with slope increasing initially slowly, progressively increasing more rapidly, and then decreasing towards a plateau. -sigmoidicity n. sigmoid kinetics (in enzymology) a type of kinetics of en-

=

=

600

signal zyme-catalysed reactions characterized by a sigmoid plot of rate versus substrate concentration. Such kinetics are characteristic of allosteric enzymes, in that progressive activation occurs with increasing substrate concentration due to cooperativjty in binding of substrate. The presence of allosteric modifiers will alter the inflection of the curve, activators shifting it towards that found in Michaelis-Menten kinetics (see Michaelis kinetics). signal 1 any variable property or parameter that serves to convey information. 2 the message potentially to be transmitted by any agonist interacting with a cell membrane receptor. 3 a signal peptide. signalase see signal peptidase. signal averaging a method used to improve signal-to-noise ratios, particularly in spectroscopy, by summing repeated scans of the information. The signals are thereby reinforced while the background noise tends to average out. signal hypothesis a model proposed for the synthesis of secretory proteins on ribosomes bound to the rough endoplasmic reticulum. In 1971 the US cytologist Gunter Blobel (1936- ) and the US cell biologist David Domingo Sabatini (1931- ) suggested that secretory proteins would have a common sequence of amino-acid residues near the N terminus of the nascent chains and that the peptide, or a modification of it, would then be recognized by a factor mediating the binding to the membrane. Cesar Milstein and coworkers in 1972 proposed from experiments in which immunoglobulin light chain mRNA was translated in a reticulocyte lysate system, that light chains are initially synthesized as a precursor of slightly higher molecular weight, which is subsequently converted into the authentic product. From these experiments they proposed, independently of Blobel and Sabatini, that a short peptide at the N terminus of a precursor protein would be a simple way to provide a signal to ensure that secretory proteins were synthesized on membrane-bound ribosomes. This hypothesis has been largely substantiated (see signal peptidase, signal peptide, signal recognition particle). signalling molecule any extracellular or intracellular molecule, e.g. hormone, cytokine, or second messenger, that cues the response of a cell to the behaviour of other cells or objects in its environment. signal peptidase any of a group of endopeptidases that remove the signal peptide after insertion of membrane proteins into the membrane. In prokaryotes there are two types: 1 signal peptidase I, EC 3.4.99.36; recommended name: leader peptidase; other name: prelipoprotein signal peptidase; an endopeptidase that cleaves N-terminal signal peptides from secreted proteins and periplasmic membrane proteins. It is a protein of the inner membrane with a single transmembrane domain. Example from Salmonella typhimurium: database code LEP_SALTY, 324 amino acids (35.78 kDa). 2 signal peptidase II, EC 3.4.99.35; recommended name: premurein-leader peptidase; an endopeptidase that selectively cleaves the signal peptide from bacterial membrane lipoproteins, hydrolysing the protein on the N-terminal side of a specific Cys residue. Example from Haemophilus influenzae: LSPA_HAEIN, 171 amino acids (19.36 kDa). In eukaryotes, signal peptidases, EC 3.4.-.-, are endoplasmic integral membrane proteins with five subunits, numbered according to the approximate M" SPC25, SPC22123, SPC21, SPCI8 and SPCI2. Example, SPC21 from Canis familiaris: database code SPC3_CANFA, 191 amino acids (21.47 kDa). signal peptidase" see premurein-Ieader peptidase. signal peptide or leader peptide any sequence of amino-acid residues which when linked to a newly synthesized protein directs the protein to a location among the organelles of a eukaryotic cell and from the cytoplasm to the periplasmic space of prokaryotic cells. The term was originally applied to the Nterminal linked peptide that is responsible for the attachment of ribosomes which translate the mRNA for secretory proteins to the endoplasmic reticulum. Such peptides usually comprise

significant 20-30 amino-acid residues and are characterized by a central region of hydrophobic amino acids preceded by one or more basic amino-acid residues. An interesting feature is that at the junction of the signal peptide and the mature protein there is no consensus sequence of amino-acid residues, so the basis for the specificity of the protease at this position remains unclear (see signal peptidase). The term signal peptide is now more generally applied to any peptide that is responsible for the location of a newly synthesized protein within the organelles of eukaryotic cells (see protein kinesis). Thus it applies to the mitochondrial proteins synthesized in the cytoplasm, nuclear proteins and luminal proteins that are retained within the cisternae of the endoplasmic reticulum. In addition to the signal peptides described, which may be located either at the N terminus or C terminus of the nascent protein and which are subsequently cleaved, single-spanning membrane proteins also contain a signal sequence within the protein known as a stoptransfer sequence. This serves to anchor the protein within the membrane. The orientation of the protein within the membrane may be either type I or type II depending on whether the N terminus of the resulting protein is extracytoplasmic (type I) or cytoplasmic (type II). See also signal recognition particle. signal recognition particle abbr.: SRP; a ribonucleoprotein particle of 325 kDa composed of a 7S (300 nucleotide) RNA molecule and a complex of six different polypeptides. This binds both to the N-terminal signal peptide for proteins destined for the endoplasmic reticulum as they emerge from the large ribosomal subunit and also to the ribosome. This binding arrests further translation thereby preventing the proteins from being released into the cytosol. The SRP-ribosome complex then diffuses to the endoplasmic reticulum where it is bound to the signal recognition particle receptor, which allows resumption of protein synthesis and facilitates the passage of the growing polypeptide chain through the translocon. Through a process involving GTP hydrolysis, the SRP-SRP receptor complex dissociates and SRP returns to the cytosol. Of the six polypeptides of SRP the 54 kDa subunit (SRP54) is the central player. It contains an N-terminal GTPase domain and a C-terminal domain that binds directly to the signal peptide and the SRP RNA. signal recognition particle receptor abbr.: SRP receptor; a transmembrane heterodimeric protein (a subunit, 69 kDa; P subunit, 30 kDa), also known as docking protein, located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex. Example, a subunit (dog): database code SSRA_CANFA, 286 amino acids (31.94 kDa). The a subunits have an unusual charge distribution with a highly negatively charged N-terminus and a highly positively charged but phosphorylated cytoplasmic tail (C terminus). See also signal peptide, signal recognition particle. signal-to-noise ratio the proportional difference between the average level of values observed for a specific property under investigation (signal) measured against the average of nonspecific values (noise) in any record. See also signal averaging. signal transduction the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell. Typically, interaction of the extracellular signal - a hormone, growth factor, or other agonist - with a specific membrane receptor leads to synthesis within the cell of one or more second messengers, or to activation of other downstream cascades, e.g. by phosphorylation of proteins. signature an alternative term for motif (in protein sequences); the word is used in the PRINTS database. See Appendix E. significant (in statistics) reaching a degree of probability that experimental values lie on a distribution different from that of control values, such that the investigator will conclude that experimental and control samples differ, using tests such as Student's t-test or the chi-square test. The degree of probabil-

601

silane ity that will be accepted as indicating a significant difference depends on the type of investigation being conducted. If the tests indicate that the probability that the results are due to chance is ~5% (for biological or medical studies) or ::;;1% or, in some cases, ::;;0.1% (for biochemical studies), differences are considered significant. -significance n. silane 1 monosilane; silicon tetrahydride; SiH 4 ; the siliconcontaining analogue of methane. 2 any of a class of saturated silicon hydrides. Such compounds are silicon-containing analogues of alkanes or cycloalkanes; linear or branched silanes are of general formula SinH ln + l , and cyclic silanes, termed cyclosilanes, are of general formula [SiH 2]n (n > 2). The value of n, when >1, may be indicated by a specific or general numerical prefix; e.g. disilane, cyclohexasilane, oligosilane, polysilane. Silane and disilane are gases with a repulsive odour; higher silanes are liquids or solids. Silanes are spontaneously flammable in oxygen or air. 3 a term often loosely applied to any hydrocarbyl or other derivative of a silane. silanization treatment of a hydrophilic surface with a reactive silane (def. 3) such as dimethyldichlorosilane, trimethylchlorosilane, octyltrichlorosilane, or an octadecyltrialkoxysilane in order to render it more hydrophobic. Such a treatment is useful in particular for converting hydrophilic silanol (def. 4) groups on the surfaces of glassware or dried silica-gel particles into lipophilic alkylsiloxane moieties. When applied to glass, it reduces adsorption of polar compounds and minimizes the activation of lymphocytes, platelets, or other cells that can occur when untreated glass vessels are used; other benefits include promotion of drainage of aqueous liquids and minimization of electrical leakage (see also siliconize). Silanization has been applied to particles of dried silica gel for use in reversedphase adsorption chromatography (see also end capping) and to diatomaceous earth used as the support for the stationary phase in reversed-phase liquid-liquid partition chromatography or in some variants of gas-liquid (partition) chromatography. Compare silvlalion.-silanize vb.; silanized ad). silanol 1 silyl hydroxide; H 3SiOH; the silicon-containing analogue of methanol. 2 any monohydroxy derivative of a silane (def. 2); such compounds are silicon-containing analogues of alkanols and are of general formula SinHln+IOH. 3 a commonly used term for any Si-hydrocarbyl derivative of silanol, silanediol, or silanetriol; such derivatives are respectively of general formula R 3SiOH, RlSi(OHh, or RSi(OHh. 4 the trivalent group 7Si-OH occurring in hydrated silica (so-called silicic acid). Such groups occur also on the surfaces of dried silica-gel particles and of silica-based glasses under normal conditions (i.e. in equilibrium with undried air). sildenafil see Viagra. silent mutation or synonymous mutation or same-sense mutation a mutation in a codon of a DNA sequence that does not cause an amino-acid change in the translation product. The term 'silent' is also applied to a protein gene product arising from such a mutation, e.g. silent hemoglobin. Other names: silent site mutation; silent nucleotide change. silica silicon(Iv) oxide; silicon dioxide; SiOl; a colourless or white solid used as the basis of many chromatographic procedures; silicic acid contains silanol (def. 4) groups to some of which water is bound. For chromatographic use, it is heated to 100°C to drive out this water. Heating above 170°C causes formation of oxide linkages (Si-O-Si), and when heated to very high temperatures (800-1000 °C) it forms glass. Silicic acid is prepared for different uses in a variety of particle sizes. For chromatography, these range from 10 to 500 /lm, the larger sizes being used for column chromatography at normal pressures, the smaller sizes for thin layer chromatography and high-pressure liquid chromatography. Silicic acid precipitated as granules, about 3 mm diameter, is known as silica gel; in its dry state it takes up water and can be used as a drying agent, which can be re-used after heating to drive out water. A powder of very fine silica particles, 0.007-0.014 /lm, known as fumed silica, has thixotropic properties and was formerly em-

simian virus 40 ployed to create a gel in organic solvents, e.g. in scintillation cocktails to maintain hydrophilic materials in suspension during counting (this use is now superseded by cocktails that themselves form a gel with water). Silica is found in certain algae, notably in the hard shell, or test, of diatoms; it also serves to reinforce the stems of the primitive vascular plants known as horsetails. siliceous or silicious of, pertaining to, or containing silica. silicone the common name for any oligomeric or polymeric siloxane containing the repeating structural unit -O-SiRr , where R is a hydrocarbyl (e.g. methyl or phenyl) group. The molecules of an individual silicone are usually linear, but sometimes branched, crosslinked, or cyclic. Silicones are odourless and generally colourless, and are characterized by high hydrophobicity and by remarkably high chemical and thermal stability. Depending on their molecular size and configuration and on the nature of their R groups, silicones may be oils, greases, gums, elastomers, or resins. By virtue of their unusual and varied properties they have acquired a correspondingly wide range of clinical, electrical, engineering, industrial, and laboratory applications. In commercial usage, the term may be extended to include organosilicon compounds used for silanization and silvlation. siliconize to render (filter-paper, glassware, textiles, etc.) water-repellent by application of a coating of an appropriate silicone. See also silanizalion.-siliconized ad).; siliconizing n. siloxane any saturated silicon-oxygen hydride with unbranched or branched chains of alternating silicon and oxygen atoms in the molecule. Unbranched siloxanes are of general formula H 3 Si-[O-SiH l ln-SiH 3 ; each is named after its respective parent silane (def. 2), e.g. disiloxane (n = 0), tetrasiloxane (n = 2). By extension, hydrocarbyl derivatives are commonly included. See also silicone. silyl 1 strictly, H 3Si-, the group derived from silane (def. 1) by loss of a hydrogen atom. 2 a commonly used term for any hydrocarbyl derivative, R 3Si-, of the silVI (def. 1) group. silylation the process of converting organic compounds in general into their silyl (def. 2) derivatives by attachment of trimethylsilyl (or similar organosilicon) groups, or an instance of this process applied to a particular compound or mixture of compounds. Reagents frequently used for the purpose are trimethylchlorosilane and l-(trimethylsilyl)imidazole, although a number of others have particular applications. The classes of reactive compounds include those possessing amino, carboxyl, hydroxyl, or thiol groups, for which silylation is a means of selective protection in the course of synthetic work (see protecting group). Silylation is widely used also for conversion of mixtures of related compounds of such classes into derivatives capable of separation and analysis by gas chromatography/mass spectrometry. Compare silanization.-silylate vb.; silylator n.; silylated, silylating, adj. simian characteristic of, resembling, or belonging to the apes. simian immunodeficiency virus abbr.: SlY; a retrovirus, one of the lentiviruses, common in the sooty mangabey (a type of monkey) and many African green monkeys. SlY SM, a virus of the sooty mangabey, is closely related to - and probably gave rise to - HIY-2 (see HIV). HIY-1 is closely related to SlY from chimpanzees. Infection of sooty mangabeys and African green monkeys does not cause disease, but SlY infection has been found in macaques in captivity and is pathogenic. simian virus 40 abbr.: SY40; an icosahedral virus containing circular duplex DNA of about 5.2 kb associated with four histones (H4, H2A, H2B, H3) in a minichromosome. It infects monkeys and apes and is capable of inducing tumours in other species or their cells, its DNA being integrated into the host genome. It can enter two types of life cycle: in permissive cells (usually monkey permanent cell lines) replication occurs in normal infection; in nonpermissive cells there is no lytic infection, but growth transformation can occur. The virus is useful as an expression vector in recombinant DNA technology, having good promoter properties: it can be used either as a virion

602

simple diffusion

or as a construct maintained transiently in host cells at high copy number in unintegrated plasmid-like DNA molecules. See also small T-antigen. simple diffusion or passive diffusion a type of diffusion (def. 2) across a membrane in the absence of any specific transporting agent or carrier. Compare facilitated diffusion, active transport. simple radial immunodiffusion see single radial immunodiffusion. SIMS abbr. for secondary ion mass spectrometer. sin abbr. for sine. sinalbin a glucoside found in white or yellow mustard. See also sinapine. S-9lucose

I Dl 1Y

HO

~

N

~

'o-s-o-sinapine II

o

sinapine 2[[3-(4-hydroxy-3,5-dimethoxyphenyl)-I-oxo-2propenyl}oxy]-N,N,N-trimethylethanaminium; a component of sinalbin; it is also found in black mustard and other seeds.

sinaptobrevin a variant spelling ofsynaptobrevin. sine abbr.: sin; a trigonometric function, being the ratio of the side of a right-angled triangle opposite a given angle to the hypotenuse; the sine of an obtuse angle is numerically equal to that of its supplement. SINE abbr. for short interspersed element; a highly repeated sequence of DNA occurring interspersed in a mammalian genome; it is similar to a LINE but is shorter - typically less than 500 bp long - and is generated by RNA polymerase III. A family of closely related SINEs has of the order of 105 members, consisting of DNA segments that are similar if not identical in length and sequence. The function of SINEs is unknown. They appear to be processed pseudogenes derived from genes that encode small cytoplasmic RNAs including tRNAs. Thus the sequences of SINES are often homologous to the sequences of such RNAs. Singer-Nicholson model an alternative name for fluid-mosaic model. single-cell protein abbr.: SCP; a protein-rich material produced by the culture of bacteria, yeasts, other fungi, or algae and extracted for use as a protein supplement in animal or human foods. single-copy plasmid a plasmid that replicates at the same pace as the bacterial chromosome, and thus maintains equality in numbers with the chromosome. single nucleotide polymorphism abbr.: SNP; the occurrence of single-base variations in the genetic code that occur about once every 1000 bases along the human genome. single radial immunodiffusion or Mancini method an immunodiffusion technique in which holes (wells) are cut in a sheet of antibody-containing agar in a glass dish or on a slide. The wells are filled with antigen solution, which is then left to diffuse radially outwards; in doing so, it reacts with antibody to form a ring of precipitate. The diameter of the circle of precipitate is proportional to the concentration of antigen.

sinigrin

single-spanning describing an integral membrane protein anchored in the membrane by means of a single hydrophobic sequence embedded in the membrane lipid bilayer. single-strand binding protein abbr.: SSB protein; any of a group of proteins found in bacteria and mitochondria that have a greater affinity for single-stranded DNA than for doublestranded species. They are essential for replication, recombination, and repair. They bind tightly and cooperatively and do not catalyse associated activities such as the DNA-dependent ATPase activities of helicases and topoisomerases. They have been called 'unwinding', 'melting', and 'helix-destabilizing' proteins, but each of these names is somewhat misleading since these proteins have multiple functions. Example from Escherichia coli: database code SSB_ECOLI, 177 amino acids (18.82 kDa). single-strand conformation polymorphism analysis abbr.: SSCP analysis; a method for comparing mutations by the rate at which DNA migrates on denaturing gels, under conditions in which the conformation adopted by the DNA is critical. The technique involves amplification of a DNA sequence of interest using the polymerase chain reaction (peR); the rate of migration of this DNA is then compared with that of a known mutation on gels of differing composition, such that DNA conformation (and thus rate of migration) will depend on the gel conditions (e.g. varying glycerol concentration, ionic strength). If the DNA of unknown composition migrates the same as the known DNA under all conditions, it is an indication that a mutation of a similar character to the known mutation may have occurred. single-stranded DNA abbr.: ssDNA; a form of DNA consisting of a single chain of deoxyribonucleotides instead of the normal two chains. Single-stranded DNA occurs naturally in certain circumstances: (I) transiently, during replication (see replicate), when the duplex helical molecule of double-stranded DNA is unwound in the replication fork, initiated by helicase; (2) during replication of circular DNA, when in some circumstances only one strand is replicated, yielding a singlestranded product; as replication proceeds, the synthesized DNA unwinds as a single-stranded 'tail'. Replication may proceed around the unbroken circular DNA strand for more than one cycle, giving rise to the term rolling circle; (3) in certain filamentous coliphages, such as M13, fl, and fd, which contain a single-stranded circular DNA molecule. singlet oxygen a dioxygen molecule in which two 2p electrons have similar spin. It is more highly reactive than the form in which these electrons are of opposite spin. Singlet oxygen is produced in chloroplasts that, due to mutation, lack carotenoids; excited triplet chlorophyll reacts with oxygen to yield singlet oxygen, which is normally quenched by carotenoids. In the absence of carotenoids, lethal photodynamic damage occurs. single-turnover kinetics the study of the kinetics of an enzyme-catalysed reaction in conditions under which formation of the enzyme-substrate complex can be measured. Such conditions are required for the detection and analysis of transient enzyme-substrate and enzyme-intermediate forms in the investigation of the pre-steady state (see pre-steady state kinetics), and contrast with measurement of the multiple recycling of the enzyme in the steady state. Although the enzyme reaction is proceeding normally, only the first part of the reaction is studied, leading to the expression 'single-turnover conditions'. In this kind of study, a substrate is chosen such that the enzyme-substrate complex can be distinguished from substrate alone, e.g. in having a different absorption spectrum. The rate of formation of the complex can then be determined, often by stopped-flow methods. singly labelled describing a specifically labelled compound containing only one isotopically modified atom in a uniquely specified position, e.g CH 3-CH[2H]-OH. sinigrin I-thio-P-D-glucopyranose 1-[N-(sulfo-oxy)-3-butenimidate] monopotassium salt; a P-D-thioglucoside occurring in

603

sinister

SKI

mustard seeds and horseradish roots; it is used as a substrate for thioglucosidase.

sinister Latin left; used to describe the left, or counterclockwise, configuration of one of the two faces of a compound containing a trigonal carbon atom. It is designated by the prefix Si-. Compare rectus. See also Re/Siconvention. sintered glass or (rit small particles of glass that have been heated so that they just fuse but without extensive melting. The resultant material is porous, and is often used in glass filtration apparatus or as a support to retain packing materials in chromatographic columns. siroheme or (esp. Brit.) sirohaem a heme molecule discovered in bacterial sulfite reductase, EC 1.8.99.1. It is a tetrahydroporphyrin, having adjacent, reduced pyrrole rings. It is also a component of nitrite reductase (EC 1.6.6.4) from Nitrobacter. HOOC

COOH

HOOC

( COOH

siroheme synthase or (esp. Brit.) sirohaem synthase a multifunctional bacterial enzyme that contains uroporphyrin-III Cmethyltransferase, ferrochelatase and precorrin-2 oxidase. The latter activity results in the conversion of precorrin-2 into siroheme by oxidation and Fe2+ chelation. Example from Escherichia coli: database code CYSG_ECOLI, 457 amino acids (49.90 kDa). sirup a variant spelling (esp. US) of syrup. sis an oncogene (v-sis) from simian osteosarcoma virus that is also expressed in human disease. The related protooncogene, c-sis, encodes the B chain of platelet-derived growth factor (PDGF), and v-sis encodes a protein almost identical to the B chain, differing only in the amino acids at its Nand C termini. Cells are transformed by v-sis and produce the PDGF-related molecules, which stimulate the PDGF receptor in an autocrine fashion. Example, PDGF-related transforming protein p28 sis of simian sarcoma virus: database code TSIS_SMSAV, 226 amino acids (25.42 kDa). site-directed mutagenesis or site-specific mutagenesis the use of cDNA technology to generate a point mutation at a predetermined position in a genome. It may be achieved by stepwise synthesis of a strand of genomic nucleic acid with substitution of a mutagenic analogue of the base naturally pre-

sent (e.g. guanine for adenine) at a specific position in the nucleotide sequence. After purification this is replicated in vitro to allow the generation of base substitutions at the corresponding site in the complementary strand. site-specific DNA methyltransferase see DNA methylase. sitosterol 22,23-dihydrostigmasterol; a widely distributed plant sterol related to stigmasterol.

p-sitosterol

SI units see 51. SIV abbr. for simian immunodeficiency virus. sizing column a gel-filtration column that is used to provide information about the M r (size) of proteins. sizing gel a gel-filtration medium, especially one used in a sizing column. sizukacillin see peptaibophol. S2 kallikrein see tonin. SKALP abbr. for skin-derived antileukoproteinase; other name elafin; an inhibitor of serine proteinases; it probably inhibits elastase-mediated tissue proteolysis. Example, human protein sequence (precursor): database code ELAF_HUMAN, 117 amino acids (12.26 kDa). skatole 3-methylindole; a bacterial metabolic product of indoleacetic acid that contributes to the odour of feces. skeletal growth factor a protein that stimulates bone growth. Skeletal growth factor from human bone (hSGF) stimulates growth in human bone cells and embryonic chick bones in culture. The activity comprises insulin-like growth factors (IGFs) in association with IGF-binding proteins (IGFBPs). Example, precursor of human IGFBP-5: database code !BPS_HUMAN, 272 amino acids (30.53 kDa). skeletin (formerly) an alternative name for desmin. skeleton 1 (in zoology) any structure that provides support and protection for the soft tissues and organs of the body. An exoskeleton, such as the cuticle in arthropods, lies external to the body tissues, while an endoskeleton, such as the bony or cartilaginous skeleton of vertebrates, lies within the body. 2 (in chemistry) the carbon chain of a molecule, including any noncarbon elements that necessarily link carbon moieties of the chain. -skeletal ad). skew 1 asymmetric, biased, distorted. 2 oblique, slanting. 3 (of a statistical distribution) not symmetrical about the mean. 4 to become or make skew; to distort. See also skew conformation. -skewness n. skew conformation 1 any conformation of a six-membered ring form of a monosaccharide or monosaccharide derivative when three adjacent ring atoms and the remaining nonadjacent ring atom are coplanar. Such compounds may be designated by the conformational descriptor -S added to the name. The reference plane is so chosen that the lowest-numbered carbon atom in the ring, or failing that the atom numbered next above it, is exoplanar. Skew conformation is the median conformation through which one boat conformation passes during conversion to another boat conformation in the cycle of flexible forms; it is similar to twist conformation (def. 1). See also conformation. 2 a less common alternative term for synclinal conformation; see conformation. SKI a gene encoding a protein of unknown function but related to v-ski, the oncogene of Sloan-Kettering viruses; it has no marked homology with other oncogenes.

slab gel

604

slab gel a gel, usually polyacrylamide or starch, that is formed as a sheet rather than a rod. slaty a coat colour mutation in mice allelic for the tyrp-2 gene. The mice have a defect in melanin formation that causes darkgrey (slate-coloured) melanin to be formed. The enzyme affected is dopachrome A-isomerase. sleep peptide any peptide that brings about sleep when infused into the cerebrospinal fluid (CSF) of animals. Deltasleep-inducing peptide, isolated from CSF, has the structure Trp-Ala-Gly-Gly-Asp-Ala-Ser-Gly-Glu. A large number of endogenous substances isolated from the brain can likewise induce sleep, but it is not known if this is their physiological function. sliding filament model a model of muscle contraction that envisages contraction occurring as a result of thin filaments sliding past thick filaments. The mechanism of activation involves enhanced binding of Ca 2+ by troponin C (see troponin), one of the three troponin peptide components of the thin filament. In the resting state, troponins I and T inhibit the actintropomyosin complex of the thin filament from binding to myosin; increase in Ca 2 + concentration causes troponin C (each molecule of which binds up to four Ca 2 + ions) to release this inhibition, allowing the myosin headgroups to bind actin. Then, in the presence of ATP, the thin filaments slide over the thick filament myosin molecules to cause contraction. The myosin heads contain an active ATPase that hydrolyses the ATP; the latter must be continuously resynthesized for contraction to continue. sliding (of repressor) the mode of action of lac repressor in Escherichia coli. It first binds at a non-operator site, then slides along the DNA until it finds the target site, i.e. the operator. slime mould or (US) slime mold any of a group of organisms that exhibit features of both fungi and protozoa. Characteristically they exist as slimy masses on decaying wood or in damp soil, and have the ability to switch from an amoeboid single-celled phase, called a myxamoeba, to an aggregated or multicellular phase from which fruiting bodies may arise. In the so-called true slime moulds, the myxamoebae form an acellular mass called a plasmodium, whereas in the cellular slime moulds the myxamoebae aggregate to form a multicellular pseudoplasmodium, or 'slug'. A well-known example of a cellular slime mould is Dictyostelium discoideum; when the food supply is exhausted, its myxamoebae aggregate to form a small (1-2 mm) slug, containing up to 10 5 cells, which migrates to seek an area of food abundance. When nutritional conditions are favourable the slug undergoes differentiation to form fruiting bodies, from which spores are released. Germination of a spore leads to the formation of a myxamoeba. D. discoideum has a relatively small genome (about 10 times larger than that of a bacterium) and is popular with geneticists, providing insights into the nature of the inducible behaviour leading to aggregation, and the rapid cell division and differentiation that precede the formation of a fruiting body. slip a term used in regard to situations in which the mitochondrial enzyme, cytochrome c oxidase, may carry out its redox reaction without pumping protons into the intermembrane space. slope oy/ox, where results are expressed graphically as a continuous line, the ordinate (vertical axis) representing y, the abscissa (horizontal axis) representing x. slow-cycling rhodopsin a retinal-containing energy-transducing pigment present in small amounts in some of the strains of Halobacterium halobium in which purple membranes occur. It is distinct from bacteriorhodopsin and halorhodopsin and is believed to playa role in the characteristic variation in the phototactic response of such organisms at different wavelengths. Illumination with yellow light or with blue or near-ultraviolet light results respectively in accumulation of forms with absorption maxima at 375 nm and 590 nm. slow reacting substance (of anaphylaxis) or slow reacting substance A abbr.: SRS or SRS-A; one of a number of sub-

Smith stances that mediate anaphylaxis; it was identified as a polar, lipid-like compound not normally present in mammalian tissues but synthesized in them as a consequence of the combination of antibody with antigen. It increases vascular permeability and induces contraction of some types of smooth muscle, especially bronchial muscle. It is slow in action relative to histamine - hence its name - and is not antagonized by antihistamines. Leukotrienes C4, D4, and E4 are now known to be the active components. slurry a fluid suspension of particles having the consistency of cream. Sm symbol for samarium. small cytoplasmic ribonucleoprotein abbr.: scRNP (hence often colloquially termed 'scyrp'); any of various particulate complexes of proteins with molecules of small cytoplasmic RNA, found in the cytoplasm. Their function is unknown. small cytoplasmic RNA abbr.: scRNA; any of various lowmolecular mass (100-300 nucleotides) RNA molecules found in the cytoplasm as components of small cytoplasmic ribonucleoprotein. small intensely fluorescent cell abbr.: srF cell; a cell found in autonomic ganglia and containing dopamine. The name derives from the appearance of such cells after formaldehyde condensation in fluorescence microscopy. small nuclear ribonucleoprotein abbr.: snRNP (hence often colloquially termed 'snurp'); any of various particulate complexes of proteins with molecules of small nuclear RNA (snRNA), found in the eukaryotic nucleus; the particles are ",250 kDa. They are named according to the snRNAs they contain: the V4/V6 snRNP, e.g., contains V4 and V6 snRNA. They are involved in RNA splicing (see spliceosome). Patients with systemic lupus erythematosus make antibodies directed against one or more snRNPs. small nuclear RNA abbr.: snRNA; any of various low-molecular-mass (100-300 nucleotides) RNA molecules, designated VI, V2, ... VI2 RNA, found in the eukaryotic nucleus as components of small nuclear ribonucleoprotein. See also spliceosome. small nucleolar ribonucleoprotein abbr.: snoRNP (hence often colloquially termed 'snorp'); any of various particulate complexes of proteins with molecules of small nucleolar RNA, found in the eukaryotic nucleolus. They are possibly the same as processosomes. small nucleolar RNA abbr.: snoRNA; any of a class of small RNAs that are associated with the eukaryotic nucleus as a component of small nucleolar ribonucleoproteins and participate in the processing of ribosomal RNA. They contain a long stretch of sequence complementarity to conserved sequences in mature mRNA. Six have been identified in metazoan cells (87-280 bases) and 12 in yeast (125-605 bases). They exist as ribonucleoprotein (RNP) particles, which appear to assemble with a large multi-RNA RNP complex. small T-antigen see T-antigen (def. I). 51 mapping or 51 nuclease mapping a commonly used technique depending on the property of 81 nuclease to remove single-stranded DNA or RNA from double-stranded hybrids of DNA and RNA. It may be used to detect the coding region of genomic DNA that contains introns by a procedure in which either cDNA for a particular mRNA or the mRNA itself is hybridized to the genomic DNA, and the single-stranded DNA removed by the Sl nuclease leaving the hybridized coding DNA (the exons). The enzyme can also be used in a similar way to identify the 5' end of a mRNA. smectic (of a substance) being or having a mesomorphic state in which the molecules are arranged in parallel layers. The molecules in any layer can move in the plane of that layer but not into adjacent layers. Compare nematic. See also liquid crystal. smeetic mesophase see Iiposome, liquid crystal. Smith 1 Hamilton Othanel (1931- ), VS molecular biologist; Nobel Laureate in Physiology or Medicine (1978) jointly with W. Arber and D. Nathans 'for the discovery of restriction enzymes and their application to problems of molecular genet-

605 smooth ics'. 2 Michael (1932- ), British-born Canadian biochemist; Nobel Laureate in Chemistry (1993) 'for his fundamental contributions to the establishment of oligonucleotide-based, sitedirected mutagenesis and its development for protein studies' [prize (awarded 'for contributions to the developments of methods within DNA-based chemistry') shared with K. B. Mullis]. smooth describing a bacterial strain having shiny (smooth) colonies. See smooth-rough variation. smooth endoplasmic reticulum abbr.: SER; see endoplasmic reticulum. smooth muscle or involuntary muscle muscle that lacks striations, hence giving a 'smooth' appearance under the microscope; it produces slower, longer lasting contractions than striated muscle and is responsible for the contractile function of visceral organs such as stomach, bladder, intestine, and uterus, and the walls of arteries. The cells are mononucleate, and contain both thick filaments and thin filaments although these are not arranged in the pattern that leads to striations in skeletal muscle and cardiac muscle. The thin filaments are composed mainly of actin, polymerized into a double-helical strand, and associated with tropomyosin arranged along the length of the actin filament. The thick filaments are composed of aggregated myosin molecules. The thick and thin filaments comprise the contractile elements and are thought to function in an analogous manner to their striated muscle counterparts (see sliding filament model). Muscle contraction is regulated by the sarcoplasmic (cytosolic) free Ca 2+ concentration, which increases from resting levels of 120-270 nM to 500-700 nM in response to stimuli such as membrane depolarization, or the action of a-adrenergic or muscarinic agonists. Ca 2+ then binds to calmodulin, which activates myosin-light-chain kinase, which phosphorylates myosin at Ser l9 of each of the two 20 kDa light chains. This causes cycling of myosin cross-bridges along actin filaments and the development of force. Calponin, caldesmon, and protein kinase Care also thought to playa role in fine-tuning the contractile state. smooth-rough variation or S~R variation any of a number of types of cell-surface compositional variation that occur in bacteria, usually giving rise to changes in the appearance of colonies from that of the original strain. In the Enterobacteriaceae the colonies are typically shiny (smooth) and change to matt (rough), an S~R variation that may be accompanied by loss of surface antigens, reduction or loss or virulence, and changes in susceptibility to certain bacteriophages. sn- prefix (in chemical nomenclature) signifying stereospecifically numbered; it is used in designating the configuration of derivatives of certain classes of prochiral compounds (especially glycerol and its derivatives) to ensure differentiation from conventional numbering. Thus sn-l denotes Col of the glycerol moiety of a phospholipid under the stereospecific numbering system. C-2 and C-3 are similarly denoted sn-2 and sn-3 under the same system. Sn symbol for tin. SNAP abbr. for 1 S-nitroso-N-acetylpenicillamine. 2 synaptosome-associated protein; a number of these exist. The nomenclature has become somewhat confusing, since SNAPs exist with different but closely related roles. Thus SNAP-25 functions as a SNAP receptor, or SNARE, while other SNAP proteins such as a-SNAP (see def. 3) function to bind NSF proteins (see N-ethylmaleimide) to SNAREs such as SNAP-25. Example, SNAP-25 from chicken and mouse neurons: database code SN25_MOUSE, 206 amino acids (23.29 kDa). 3 soluble NSF attachment proteins, such as a-SNAP, ~-SNAP, etc. These are cytoplasmic proteins that mediate binding of N-ethylmaleimide-sensitive fusion protein to membranes. See also SNARE. SNARE hypothesis. SNARE abbr. for SNAP receptor; syntaxin, synaptobrevin, and SNAP-25 (see SNAP (def. 2» act as SNAREs; they bind in an ATP-dependent manner to NSF-SNAP complexes (SNAP in this case being the NSF attachment protein (see N-ethyl-

Soddy maleimide». Syntaxin, synaptobrevin, and SNAP-25 form a complex that is much more effective than the single proteins acting alone, leading to the concept of a core complex that bridges the synaptic vesicle and plasma membranes, and which may function in the docking and fusion process. See also SNARE hypothesis. SNARE hypothesis a suggested model of vesicular fusion, in which two types of SNARE are involved; v-SNAREs are found on vesicles and t-SNAREs are found on the target membranes, each transport vesicle having its own v-SNARE which recognizes a cognate t-SNARE on a target membrane and mediates docking; fusion is then mediated by N-ethylmaleimide-sensitive fusion protein and an attachment protein (SNAP (def. 3». Snell, George Davis (1903-96), US geneticist; Nobel Laureate in Physiology or Medicine (1980) (jointly with B. Benacerraf and Jean Dausset 'for their discoveries concerning genetically determined structures on the cell surface that regulate immunological reactions'). Snell's law see refraction. Sno symbol for a residue of the ribonucleoside thioinosine; mercaptopurine ribonucleoside; alternative to sl. snoRNA abbr. for small nucleolar RNA. snoRNP abbr. for small nucleolar ribonucleoprotein. snorp colloquialism for snoRNP, i.e. small nucleolar ribonucleoprotein. snRNA abbr. for small nuclear RNA. snRNP abbr. for small nuclear ribonucleoprotein. S1 nuclease EC 3.1.30.1; recommended name: Aspergillus nuclease SI; a single-strand endonuclease, purified from Aspergillus oryzae, that degrades single-stranded RNA or DNA to 5' mononucleotides; it has no apparent base specificity. It is useful for the removal of unpaired regions in hybridization technology (see also SI mapping). The enzyme is a monomer, and contains three zinc atoms. Database code NUSLASPOR, 267 amino acids (29.02 kDa). Similar enzymes occur in Penicillium spp. and barley. snurp colloquialism for snRNP, i.e. small nuclear ribonucleoprotein. snurposome any of at least three (A, B, and C) morphologically and biochemically distinct granules in the amphibian oocyte nucleus that contain one or more types of small nuclear ribonucleoproteins (snRNP). soap any salt formed between a hydroxide of a metal (usually an alkali or alkaline earth) and a higher fatty acid; such compounds are useful as detergents (def. 2). The meaning is sometimes extended to include the salt of any ionized lipid amphipath, e.g. of a long-chain amine or sulfate or of a sterol carboxylate. The common soaps of commerce were traditionally the mixed sodium salts (giving hard soaps) or the mixed potassium salts (giving soft soaps) of oleic, palmitic, and stearic acids, prepared by saponification of animal or vegetable fats or oils with sodium or potassium hydroxide respectively. Modern soap compositions are more complex, with solid or liquid soaps containing various additional detergents. soapstone see talc. SOD abbr. for superoxide dismutase. soda any of various compounds of sodium, especially sodium hydroxide (NaOH; caustic soda), sodium hydrogencarbonate (sodium bicarbonate, NaHC0 3 ; baking soda), or sodium carbonate decahydrate (Na2C03'IOH20; washing soda). The term may also indicate sodium monoxide (Na20). soda glass common glass, made from a mixture of silica, sodium oxide (soda), and lime, in approximate proportions Si0 2 70%, Na20 l5'Yo, CaO 10%. Its low melting point led to the production of more heat-resisting glasses, e.g. Pyrex. See also borosilicate (glass). Soddy, Frederick (1877-1956), British inorganic and physical chemist; Nobel Laureate in Chemistry (1921) 'for his contributions to our knowledge of the chemistry of radioactive substances, and his investigations into the origin and nature of isotopes'.

606 sodium sodium symbol: Na; a soft, silvery-white, highly reactive alkali metal of group I of the (IUPAC) periodic table; atomic number II; relative atomic mass 22.997. Sodium is widely distributed and is one of the most abundant elements of the Earth's crust; it exists in great quantity as sodium chloride (salt), especially in sea water. Apart from the nonradioactive, and most abundant, isotope, sodium-23, there are two radioactive isotopes, sodium-22 and sodium-24. In biochemistry, sodium (Na+) is the principal extracellular cation, and the one that largely determines the extracellular fluid volume. In humans the normal range for plasma sodium is 135-145 mmol L- 1• Sodium ions are actively pumped out of cells by sodium/potassium ATPase. Their concentration in the blood is regulated by the mineralocorticoid hormone aldosterone, which increases sodium reabsorption in the kidney distal tubule. In scientific and medical literature sodium was formerly given the Latin name 'natrium', hence the symbol Na and the term natriuretic. sodium-22 a radioactive nuclide of sodium, TTNa. It emits a ~+ particle (1.83 MeV) and gamma radiation (1.275 MeV). Its half-life is 2.605 years. sodium-24 a radioactive nuclide of sodium, nNa. It emits an electron (~- particle, 1.39 MeV) and gamma radiation (2.75 MeV). Its half-life is 15.02 h. sodium-alanine symporter see sodium/neutral amino acid cotransporter. sodium-ealcium ion exchanger a plasma membrane protein antiporter of muscle and nerve cells that promotes the exchange diffusion of sodium and calcium ions. Influx of Na+ to the cytosol drives the efflux of Ca 2+ from the cell. The affinity for Ca 2+ is low, so that it only functions at high intracellular Ca 2+ concentrations, transporting Ca2+, e.g., during excitationcontraction coupling. Example from human cardiac sarcolemma, type III membrane glycoprotein (precursor): database code NACA_HUMAN, 973 amino acids (108.42 kDa). sodium channel any of several types of structure that permit controlled (gated) passage of sodium ions through membranes. Two important types of gated sodium-ion channels are the voltage-gated channel and the transmitter-gated channel. Voltage-gated channels are involved in conduction and transmission of nerve impulses, whereas transmitter-gated channels respond only to neurotransmitters; a well-studied example of the latter type of channel is the acetylcholine receptor. Voltagegated sodium-ion channels consist of integral proteins in the plasma membranes of excitable cells. The proteins sense the membrane electric field, opening channels to permit an inward flux of sodium ions, thereby causing the membrane depolarization that is essential for the propagation of the action potential. Primary sequence data for the Electrophorus electroplax protein indicate that this channel consists of a single polypeptide chain of about 2000 amino-acid residues and contains four homologous repeats (domains I, II, III, and IV), each of which has six putative transmembrane segments (designated SI to S6) with extensive nonmembrane cytosolic and extracellular loops. This sequence shares significant homology to other ion channels, particularly the al subunit of the Ca2+ channel, segment S4 showing strong structural similarity to sequences in the Ca2+ and K+ channels. The cytoplasmic loop between repeats III and IV has been implicated in the rate of inactivation of the channel. As normally expressed the protein bears about 500 sugar residues (mostly N-acetylglucosamine and sialic acid) and 50 fatty-acyl chains (palmitoyl and stearoyl). Structural data are also available for enzymes of Drosophila and mammalian skeletal muscle and brain. The mammalian channels are heterooligomeric, consisting of a large a subunit similar to the Electrophorus protein, and several other smaller peptides; most of the functional properties reside in the a subunit. Example from rat brain (large subunit): database code CINI_RAT, 2009 amino acids (228.51 kDa); seven motifs. The a subunit is the target for polypeptide neurotoxins, e.g. from scorpions; other sodium-channel blockers include saxitoxin, tetrodotoxin, and veratridine.

sol sodium dodecyl sulfate or (esp. Brit.) sodium dodecyl abbr.: SDS; sodium lauryl sulfate; sulphate CHJ(CH2hoCH20S0J'Na; the sodium salt of the I-dodecanol half-ester of sulfuric acid (I-dodecanol was formerly known as lauryl alcohol). It is an anionic detergent and wetting agent; aggregation number 62 (0-0.1 M Na+), 101 (>0.1 M Na+); CMC 7-10 mM (0-0.05 M Na+), 1-2 mM (0.1-0.2 M Na+). The amphipathic dodecylsulfate anion is a powerful hydrophobic-bond breaker, hence it is much used in protein chemistry as, e.g., a denaturant, a dissociant of oligomers, and a solubilizer of membrane components. See also SOS-polyacrylamide gel electrophoresis. sodium-hydrogen ion exchanger a plasma membrane protein that functions as a Na+/H+ antiporter. Influx ofNa+ drives the efflux of H+. It functions to maintain intracellular pH, to which it is sensitive, its activity increasing as pH falls. Example from the gills of the crab, Carcinus maenas: database code CMU09274, 672 amino acids (75.89 kDa). sodium-ion channel see sodium channel. sodium/neurotransmitter transporter any of a family of integral membrane glycoproteins, having eight motifs and 12 putative transmembrane helices, that are involved in sodiumdependent transport of neurotransmitters. Examples (precursors) include sodium-dependent choline transporter from rat: database code NTCH_RAT, 635 amino acids (70.55 kDa); sodium- and chloride-dependent GABA transporter 1 from human: database code NTGLHUMAN, 599 amino acids (66.94 kDa). This latter protein is the target for cocaine and other psychomotor stimulants. sodium/neutral amino-acid cotransporter an integral membrane protein responsible for the Na+-dependent uptake of the neutral amino acids alanine, serine, glycine, cysteine, and proline. Example from pig: database code NAAA_PIG, 660 amino acids (72.66 kDa). Transporters with specificities for different types of amino acid are system A, system L, and systemN. sodiUm/potassium ATPase EC 3.6.1.37; recommended name: Na+/K+-exchanging ATPase; systematic name: ATP phosphohydrolase (Na+/K+-transporting); other names: sodium pump; Na+,K+-ATPase. An integral membrane protein that catalyses the hydrolysis of ATP to ADP and orthophosphate. Na+,K+ATPases are integral (cell membrane) proteins, and pump out approximately 3 Na+ ions for every 2 K+ ions that enter, with hydrolysis of 1 ATP. They are tetrameric proteins, consisting of two large a subunits and two smaller 13 subunits. The a subunits bear the active site and penetrate the membrane, while the 13 subunits carry oligosaccharide groups and face the cell exterior only. Ouebain is a specific inhibitor. Examples from rat; a-I chain: database code ATNLRAT, 1023 amino acids (112.92 kDa); 13 chain: database code ATNB_RAT, 304 amino acids (35.16 kDa); y chain: database code ATNG_RAT, 58 amino acids (6.49 kDa). sodium pump any of various transporters that transport sodium ions across membranes, especially enzymes of the Na+,K+ATPase type (see sodiUm/potassium ATPase). The Na+/K+ ratio across the plasma membrane of eukaryotic cells (outside: Na+ 140 mM, K+ 10 mM; inside: Na+ 10 mM, K+ 100 mM) requires that sodium ions be continually pumped out of the cell in exchange for potassium ions if the gradient is to be maintained; this is an energy-requiring process. See also active transport. software (in computing) programs used by computer hardware to execute commands keyed or otherwise supplied by the computer operator to bring about the completion of desired tasks. Most software is not permanently resident in the computer but is accessed from disks as instructed by the operator, operating systems, or other software. sol any fluid colloidal system composed of two or more components. The dispersed phase may be either particles of solid or droplets of liquid, and the continous phase either a liquid or a gas (see aerosol).

607 somatostatin

solanesol solanesol a 45-carbon polyprenol present in tobacco leaves.

OH 7

solation the (usually reversible) act or process of forming a sol from a gel. Compare gelation. -solate vb. solid a physical state of matter in which the constituent atoms, ions, or molecules have no translatory motion though they vibrate about fixed positions. In crystalline solids the constituents are arranged in a definite array, whereas in amorphous solids they are not. Solids, especially crystalline solids, commonly have characteristic melting temperatures at which they change to liquids. solid-phase peptide synthesis see peptide synthesis. solid-phase technique any technique in which reagents are immobilized on a support or in some other way insolubilized. In radioimmunoassay the insolubility or binding properties of an antigen-antibody complex are commonly exploited to remove labelled antigen. Enzymes immobilized on columns (immobilized enzymes) have many applications. In peptide synthesis, the growing peptide chain may be immobilized on a column. Socalled solid-phase extraction systems are in effect extractions using batch column chromatography techniques, in which the material to be extracted is bound to a column, then removed by batch elution. In peptide sequencing a peptide immobilized on a column may be degraded residue by residue, facilitating recovery of the undegraded remaining peptide at each cycle. solid scintillation fluorography a technique for visualizing radioactive materials in a specimen (e.g. a chromatogram) by covering the specimen with a solid fluor and allowing the ejected photons to darken an applied photographic emulsion. Compare fluorography (def. 2). solid-state (in electronics) describing any system in which current flow takes place entirely through solid materials, such as semiconductors and transistors, rather than through vacuum devices such as thermionic valves. solubility 1 the attribute of being soluble, of being able to dissolve. 2 the amount of a substance (solute) that can dissolve in a given amount of another substance (solvent) at a given temperature and pressure. solubility product symbol: K sp ; for a solute AxB y that ionizes in a stated solvent according to the equilibrium AxB y ~ xA + yB, at a given temperature and pressure, K sp = [aAlX[aBJY, where [aAl and [aBl are the activities of the two ions when the solution is saturated by the solute. In unsaturated solutions the product [aAlX[aBJY can have any value less than K sp , but if further amounts of either ion are added from whatever source, such that K sp is exceeded, precipitation from solution will occur to the extent that the relationship [aAy[aBJY = K sp is restored. In dilute solutions the concentrations CA and CB of A and B may be used as a good approximation. solubilize or solubilise to bring into solution any material, especially complexes that normally exist in the cell as part of membrane structures. Such materials usually have hydrophobic domains, and solubilization depends on masking these with detergents or similar substances, to bring the material into micellar suspension. soluble 1 capable of being dissolved in or as if in a fluid. 2 (of, e.g., a problem or mathematical equation) capable of being solved. soluble collagen see tropocollagen. soluble RNA abbr.: S-RNA or sRNA; an old term for transfer RNA (a 'soluble' RNA fraction from disrupted liver cells that did not sediment after centrifuging at 100000 g for several hours led to the discovery of transfer RNA). solute a dissolved substance, particularly a component of a solution that is present in a smaller amount than the solvent.

solution 1 a homogeneous molecular mixture of two or more substances, usually of dissimilar molecular structures, i.e. of a solid in a liquid. 2 the action or process of solving a problem. 3 the result of solving a problem, equation, etc. solvation the (loose) combination of solvent with molecules or ions of the solute. solvation effect the effect of solvent molecules on the behaviour of (especially) macromolecules in solution, especially during centrifugation. solvent 1 a substance or mixture, usually a liquid, that is able to dissolve other substances to form a solution. Typically it has the same physical state as the solution itself, and is the component of greatest extent in the solution. 2 (in chromatography) the liquid used to pass through a chromatography column, paper, or other support to 'develop' the chromatogram. solvent-perturbation method a technique in which some physical property of a macromolecule is measured in a polar and in a nonpolar solvent. For example, it can be determined whether an amino-acid residue in a protein is internal or external by measuring the absorption spectra of the protein in the two types of solvents. Difference spectroscopy is conveniently applied in such instances. soma (pl. somata or somas) 1 the whole of any plant or animal organism but excluding the germ cells. 2 the body, as opposed to the mind. See also somatic cell. -somatic adj. somat+ a variant form of somato+ (before a vowel). somatic cell any cell of an organism other than a germ cell. somatic cell genetic disorder a category of genetic disorders in which defects are restricted to specific somatic cells, e.g. cancer cells. This contrasts with the other types of genetic disorder - single gene, multifactorial, and chromosome - in which the abnormality is present in all cells, including the germ cells. somatic cell hybrid a hybrid cell formed from the fusion of different cells, usually from different species. Somatic cell hybrids obtained by the fusion of human and rodent cells are frequently used for gene mapping. See cell fusion. somatic crossing over an alternative name for mitotic recombination. somato+ or (before a vowel) somat+ comb. for denoting the body, or soma. somatocrinin another name for growth hormone releasing hormone (GHRH). somatogenic 1 originating in the soma (def. 1), or body tissues. 2 of organic, rather than mental, origin. somatoliberin the recommended name for growth hormone releasing hormone (GHRH). somatomammotropin human chorionic somatomammotropin; see choriomammotropin. somatomedin generic name for insulin-like growth factors (abbr.: IGF); in the human they comprise IGF-IA, IGF-IB, and IGFII. Somatomedins were isolated on the basis of several properties: (a) activity on cartilage (incorporation of sulfate and thymidine), (b) insulin-like activity in adipose and muscle, and (c) mitogenic activity in cell culture. Somatomedin A is IGFII, and somatomedin C is IGF-I (A and B). The term somatomedin should be used only when a generic term is needed, IGF-I (A or B) and IGF-II being used for the specific peptides. Somatomedin B is released from vitronectin, is a serum factor of unknown function, is increased in response to somatotropin, and has proteinase-inhibitory activity. somatostatin or somatotropin-release inhibiting factor (abbr.: SRIF) or (formerly) growth hormone-release inhibiting hormone (abbr.: GH-RIH) a hypothalamic cyclic l4-residue peptide discovered as an inhibitor of the release of the pituitary growth hormone somatotropin and of the release of glucagon and insulin from the pancreas of fasted mammals; it also inhibits the release of gastrointestinal hormones and other secretory proteins. It has the sequence Ala-Gly-Cys-Lys-AsnPhe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys, with a disulfide link

somatostatin receptor

608

between cysteines 3 and 14; this is called somatostatin 14. There also exists a bioactive 28-residue peptide - somatostatin 28 - in which the 14-residue peptide is extended from the N terminus (the N-terminal residues are SANSNPALAPRERKAG-). Both forms are derived from the 92 amino-acid precursor, prosomatostatin, by tissue-specific proteolytic processing. Somatostatin is widely distributed, occurring not only in the central nervous system, but also in peripheral tissues such as stomach, intestine, and pancreas. It has diverse effects that are tissue specific, and can function as a neurotransmitter. Example (precursor) from human and Macaca fascicularis (a crab-eating monkey): database code SMSL HUMAN, 116 amino acids (12.72 kDa). See also somatostatin receptor. somatostatin receptor any of several membrane proteins that bind different forms of somatostatin and mediate its ef-

fects. Pharmacological studies indicate that there are at least two subtypes of receptor. In appropriate systems somatostatin suppresses receptor-induced stimulation of adenyl ate cyclase by activating the inhibitory G-protein G j ; it can decrease intracellular Ca2+ concentrations and inhibit the voltage-dependent current, I ca , by a G-protein-dependent cyclic AMP-independent mechanism. Somatostatin 14 enhances and somatostatin 28 reduces potassium current, I K , also by G-protein-dependent cyclic AMP-independent mechanisms. There are several different types of somatostatin receptor; all are G-proteincoupled seven-transmembrane-domain proteins. The examples below are all from Rattus norvegicus. Type 1 has higher affinity for somatostatin 14 than 28 and is coupled to phosphotyrosine phosphatase and sodium-hydrogen-ion exchanger; example, database code SSRLRAT, 391 amino acids (42.75 kDa). Types 2 and 3 are receptors for somatostatins 14 and 28 and inhibit adenylate cyclase; examples, database code SSR2_RAT, 369 amino acids (41.20 kDa) and database code SSR3_RAT, 428 amino acids (47.15 kDa). Type 4 is a receptor for somatostatin 14 and inhibits adenylate cyclase; example, database code SSR4_RAT, 384 amino acids (42.09 kDa). Type 5 is a receptor for somatostatin 28 and inhibits adenyl ate cyclase; example, database code SSR5_RAT, 363 amino acids (39.97 kDa). Hybridization studies indicate these are members of a larger family of somatostatin receptors; they are G-protein-coupled adenylate cyclase activators. somatotrope or somatotroph a type of cell found in the lateral wings of the anterior pituitary and comprising about 50% of the hormone-producing cells of that part of the gland. Somatotropes are responsible for the production of somatotropin. Somatotrope adenomas cause acromegaly. somatotroph see somatotrope. somatotrophic 1 stimulating and maintaining the growth and development of any cell or tissue. 2 (sometimes) of or pertaining to somatotropin. somatotropic 1 of, or relating to, somatotropin. 2 stimulating the mechanisms connected with growth or development of a cell or tissue. Compare somatotrophic. somatotropic hormone see somatotropin. somatotropin or growth hormone (abbr.: GH); also called somatotropic hormone (abbr.: STH); a hormone secreted by the anterior pituitary whose main effect is to stimulate growth. The human hormone (hGH) is mostly synthesized as the precursor of a single-chain, 191-residue protein, M r 22 000, but 5-10% is a form of M r 20 000 resulting from alternative splicing that deletes codons for amino acids 32-46 from the mRNA. Genes encoding hGH, prolactin, and choriomammotropin form a family with high nucleotide homology with five coding exons. Somatotropin secretion is pulsatile, especially during fasting, when cycles of about four hours' duration occur; it is stimulated by fasting or hypoglycemia, and hormonally by glucagon, GHRH, estrogens, and arginine vasopressin, and during the first phase of sleep; secretion is inhibited by hyperglycemia, somatostatin, the insulin-like growth factor IGF-I, and glucocorticoids. It is secreted from

sorbitol storage granules. In vivo, somatotropin tends to promote synthesis of protein, and lipolysis or reduced fat deposition, and growth and mitosis of cartilage. Deficiency leads to pituitary dwarfism types I and IV. Its actions in vitro include stimulation of amino-acid uptake in muscle, and lipolysis in adipose tissue, but many of its actions in vivo may depend on its action in stimulating synthesis and secretion of somatomedins. hGH has 85% homology with human choriomammotropin and 35% homology with human prolactin. Example (precursor) from human: database code SOMA_HUMAN, 217 amino acids (24.82 kDa). See also GHRH, GHRH receptor, hypopituitarism. somatotropin-release inhibiting factor abbr.: SRIF; an alternative name for somatostatin. somatrem methionyl human somatotropin (growth hormone); somatotropin with an additional N-terminal methionine. It results from the production of somatotropin using cDNA technology in bacterial clones; methionine is involved in the initiation of bacterial protein synthesis. +some comb. form denoting body, esp. intracellular particle. somite any of a series of paired blocks of mesoderm that form during early development in vertebrate embryos and lie on either side of the notochord. -somital or somitic adj. sonicate to expose any material or sample to ultrasonic pressure waves (at or around 20 kHz). The immersion of vessels in a water bath and their exposure to ultrasound is used as a means of cleaning (see sonication bath). The insertion of a sonicator probe into a vessel containing a suspension of membranes or other large assemblies causes their dispersion to smaller aggregates or assemblies. sonication bath a water bath that is equipped with an oscillator, sited beneath the bowl, to produce ultrasound waves that permeate the water. It may be used for cleaning glass or other vessels or for degassing solvents. sonicator a device that produces ultrasonic pressure waves. It usually consists of a stainless-steel rod, of diameter from 1-2 mm to about 2 cm, that is activated by an oscillator to produce ultrasound waves and is inserted into a vessel to sonicate a sample. See also sonication bath. sonic hedgehog proteins analogues of hedgehog protein found in zebrafish and chickens and involved (in the latter case) in limb-bud pattern formation. The hedgehog proteins thus appear to be vital to pattern formation in several metazoan groups. The name sonic hedgehog is an allusion to a children's animated cartoon character. sophorose the disaccharide 2-0-p-o-glucopyranosyl-o-glucose; it occurs in a glycoside of Sophora japonica.

sorb in a heat-stable peptide isolated from porcine intestine

that increases water and sodium absorption in the intestine and gall-bladder. Example, database code SORB_PIG, 153 amino acids (17.46 kDa). sorbitol a nonsystematic name for o-glucitol, one of the ten stereoisomeric hexitols. It can be derived from glucose chemically or metabolically (by NADPH-requiring aldehyde reductase; other name: aldose reductase, EC 1.1.1.21) by reduction of the aldehyde group, and is converted to o-fructose by L-idi-

609 sorbose tol 2-dehydrogenase (EC 1.1.1.14). It is widely distributed in algae and higher plants, and was first discovered (1872) in the juice of berries from mountain ash (Sorbus aucuparia). It has a sweetening power about half that of sucrose, and is often used in sweeteners in conjunction with saccharin. Industrially it is of great importance in the food, pharmaceutical, paper, and textile industries. Its formation from excessive glucose concentrations in diabetics has been regarded as having pathological implications in lens tissue, which cannot convert it to fructose. sorbose trivial name for the ketohexose xylo-2-hexulose; the enantiomer, L-sorbose, is present in fermented juice of mountain-ash berries, being formed by the bacterial oxidation of sorbitol. It is produced commercially by fermentation and used as an intermediate in the manufacture of ascorbic acid. sorcin a protein, encoded in multidrug-resistant cells (see MDB), that binds calcium with high affinity. Example from human: database code SORC_HUMAN, 198 amino acids (21.68 kDa). See also grancalcin. Soret band an absorption band at about 400 nm, characteristic of porphyrins. See also cytochrome absorption bands. [After Louis Soret (1827-90), Swiss physicist.] sorocarp see Oictyostelium discoideum. sos symbol for son of sevenless, a gene encoding a guaninenucleotide releasing protein involved in neuronal development in Drosophila. When coupled to the activated Sev receptor (see Sevenless protein) the sos product, Sos, mediates activation of ras by stimulating release of GDP, thereby promoting uptake of GTP. Database code SOS_DROME, 1595 amino acids (177.64 kDa). SOS repair or error-prone repair a metabolic alarm system, occurring in bacteria, that helps the cell to save itself in the presence of potentially lethal stresses such as UV irradiation, thymine starvation, or the inactivation of genes essential for replication. Responses include mutagenesis, filamentation (cell elongation in the absence of division), activated excision repair, and activation of latent phage genomes. Mutagenesis occurs because under SOS conditions the gaps formed opposite thymine dimers can be filled by replication rather than by daughter-strand transfer. Replication of the dimer template is extremely inaccurate. The proteins involved include RecA protein (see recA) and the products of two other RecA-inducible genes; expression is regulated by the lexA gene product. Southern blotting a procedure for transferring denatured DNA from an agarose gel to a solid support membrane such as nitrocellulose or nylon. The procedure takes advantage of the property of nitrocellulose that it tenaciously binds singlestranded but not duplex DNA. The gel is soaked in 0.5 M NaOH, which converts the DNA to the single-stranded form. The gel is then overlaid with a sheet of nitrocellulose paper, which in turn is covered by a thick layer of paper towels and the entire assembly is compressed by a heavy weight. The liquid in the gel is forced (blotted) through the nitrocellulose so that the single-stranded DNA binds to it at the same position it had in the gel. The transfer to nitrocellulose can alternatively be accomplished by electrophoretic transfer. Nylon is now usually used in preference to nitrocellulose. DNA bands may be located' using a radioactive or otherwise labelled probe. The name led to a nomenclature for other types of blotting (see also Northern blotting, South-western blotting, Western blotting). [After E. M. Southern (1938- ), British molecular biologist.] South-western blotting a technique in recombinant DNA technology for detecting plaques expressing fusion proteins where the foreign sequence encodes a DNA-binding protein that binds specifically to a particular DNA sequence. After treatment of the plaques to ensure release of the protein, plaque-lift is carried out onto a nitrocellulose (or other) transfer membrane, which is then incubated with a radio labelled duplex DNA oligonucleotide that binds to the protein, which can then be detected by autoradiography. The term was derived by extension through the cardinal points from Southern blotting. Soviet gramicidin an alternative name for gramicidin S.

SPARe Soxhlet extractor an apparatus for exhaustive extraction of soluble components from a sample of solid material by recycling a solvent through it, whereby solvent vapour from a boiler is continually condensed and the condensate allowed to percolate through the sample in a solvent-permeable thimble, from which it is returned, usually periodically via a siphon, to the boiler, where the eluted substances accumulate. [After Franz Soxhlet (1848-1926), Belgian chemist, who devised it.] soybean or (esp. Brit.) soya bean a leguminous plant, Glycine max, originating in China (known from at least 2500 Be) and now cultivated widely in Asia, Europe, and America for forage and for its seeds. The bean has an oil content of 18-22%, and is also rich in protein - soybean protein is used as a human food and is the basis of tofu. See also soybean oil, soybean trypsin inhibitor. soybean oil an edible oil obtained from the seeds of the soybean plant and valued for its high content of linoleic acid. The composition is typically as follows: 18:2 co6, 44-62%; 18:3 co3, 4-11%; 18:1 co9, 19-30%; 16:0,7-14%. soybean trypsin inhibitor abbr.: STI; either of two different types of trypsin inhibitor, the Bowman-Birk and the Kunitz inhibitors. Both have given their names to a class of proteinase inhibitor. The two soybean inhibitors differ markedly from each other in size, structure, and properties. The Bowman-Birk inhibitor is a 71 amino-acid, 7.873 kDa protein: database code IBBLSOYBN. It has seven disulfide bridges. There are two active sites, one specific for trypsin and the other for chymotrypsin. Bowman-Birk type inhibitors are found in many cereals and legumes, and ancestrally may represent storage proteins. The soybean Kunitz inhibitors comprise three allelic proteins, A, B, and C, together with two Kunitz-type trypsin inhibitors, named KTil and KTI2. The A, B, and C proteins have 181 amino acids (20 kDa): database code (of A and C) ITRA_SOYBN. They have two disulfide bonds. They are heat-stable and resistant to proteases, and form a 1: I stoichiometric complex with trypsin, that is highly stable (Ka 5 x 109). They inhibit chymotrypsin to a much smaller degree and are inactive against other endopeptidases, but modification of Arg 63 to Trp converts them to strong chymotrypsin inhibitors with little action on trypsin. The Kunitz family of inhibitors embraces trypsin, chymotrypsin, cathepsin D, and subtilisin inhibitors (see Kunitz inhibitor). sp abbr. for synperiplanar; see conformation. sp. (pl. spp.) abbr. for species (singular). Sp abbr. for isomer of a thionucleotide. SP abbr. for 1 secretory piece. 2 substance P. SP-1 abbr. for secretory protein I. [S]pA symbol for adenosine 5'-thiophosphate (alternative to AdoP[S]. space or volume of distribution (in tracer kinetics) an apparent volume obtained as the amount of radioactivity retained divided by the concentration of the tracer in the plasma. The concept of space has the limitations discussed under apparent exchangeable mass. See also compartment. spacer 1 (in molecular biology) a sequence of bases of unknown function occurring in a DNA molecule and lying between sequences of transcribed DNA; spacer DNA is not usually transcribed. The term has also been used to refer to some stretches of primary transcript, e.g. a region in the mammalian primary transcript for rRNA, lying between l8S RNA and 28S RNA, that is not found in mature rRNA. 2 (in chromatography) an alternative term for spacer arm. spacer arm or spacer the (usually) hydrocarbon chain interposed, by covalent linkages, between the specific ligand and the supporting matrix in affinity chromatography. spacer gel (in electrophoresis) a small section of gel, polymerized above a polyacrylamide (or other) resolving gel, that lacks resolving power and serves to concentrate the material being electrophoresed as a tight band at the top of the resolving gel. SPARe abbr. for secreted protein acidic and rich in cysteine; also called osteonectin; a protein expressed in cells of tissues

spIre receptors

610

undergoing morphogenesis or wound repair and secreted into the basement membrane, where it interacts with other proteins, e.g. collagen and thrombospondin, and appears to have a role in regulating cell growth, It contains an EF-hand that binds one calcium ion and an acidic region that binds other calcium ions more loosely. Example from human (precursor): database code SPRC~HUMAN, 303 amino acids (34.63 kDa). spare receptors receptors that are in excess of those required to evoke a given response to a drug, hormone, or other agonist. For a given agonist, the size of the population of spare receptors (receptor reserve) can vary with the tissue and with the magnitude of the response being measured. For different drugs, the receptor reserve varies with drug efficacy. aparglng the bubbling of gas into a liquid medium. This technique may be applied to fermenters to introduce air directly into a culture, or it may be used to replace one dissolved gas by another, e.g. in displacing oxygen with an inert gas in liquid chromatography solvents. spatula a (usually) small, flattened, sometimes curved, utensil made of metal (often stainless steel), bone, or wood and used to dispense crystalline or powdered material. Spd abbr. for sphingoid. species (pl. species) abbr.: sp. (sing.) or spp. (pl.); a fundamental taxonomic category ranking below a genus and consisting of a group of closely related individuals that can interbreed freely to produce fertile offspring. species-specific confined to the one or several species referred to. specific 1 relating to a particular or specified thing. 2 (as a modifier of certain quantitative terms) indicating a relationship of the quantity to maSS and dimension in terms of standard (now normaIly S1) units; e.g. specific catalytic activity, specific enzyme activity, specific optical rotation. 3 of, or relating to, a species. See also specificity. specific acid ca.talysis a homogeneous catalysis in which the catalysts are free hydrons, H+ (or hydronium ions, H 30+). The catalysis is not affected by other acidic species present. Compare general acid-catalysis. specific activity the activity (def. I, 2) of, e.g., a radio nuclide or an enzyme, expressed as a function of mass. specifically labelled describing an isotopically labeIled com· pound in which both the position of labelling and the number of labelling nuclides at that position are known. Such a molecule is designated by a convention exemplified by CH[2H 2)- CHrOeH). specific base catalysis a homogeneous catalysis in which the catalysts are hydroxide ions, OH-. The catalysis is not affected by other basic species present. Compare general base-catalysis. specific catalytic activity the catalytic activity of an enzyme under specified conditions divided by the mass of an enzyme or enzyme preparation. It is a quantity useful for denoting the extent of purification of an enzyme; it may be expressed in katals per kilogram. specific dynamic action the increase in heat production above the basal level that occurs in animals after the ingestion of food, particularly of protein. specific enzymic activity the phenomenological coefficient that relates enzymic activity under specified conditions to the mass of an enzyme or enzyme preparation. It may be expressed in katals per kilogram of protein. Now obsolete, it has been superseded by specific catalytic activity. Compare molar enzymic activity. specific gravity a former name for relative density. specific heat capacity symbol: cp (at constant pressure) or Cv (at constant volume); the quantity of heatrequired to raise the temperature of unit mass of a substance by one degree. It is expressed (usually) in J K-I kg I. specificity an index of the degree to which an association between two molecular units or assemblies may be considered unique; in many applications it is judged by the magnitude of an effect (enzyme-substrate, ligand-receptor interaction, or

spectinomycin drug action). It is quantified in suitable units under defined conditions, in relation to the magnitude of effect of other substances with similar action, amplified by studies made when the substance under consideration is in a direct competitive interaction with other such substances. The success of other substances in competing with the subject of study is normally quantified by kinetic analysis (see competitive inhibition). The problem of quantifying specificity may be examined by referring to specificity constant. specifif;:jty constant the ratio of the catalytic constant, kear. to the Michaelis constant, K m . It can aid in comparing the activity of an enzyme in its action on different substrates. From Michaelis kinetics, using the Michaelis-Menten equation, v = (kea,1Km)[E)o[S) when [S) is very small (since then, little enzyme has bound substrate, so [El ~ [El o ' and [S) can be neglected in relation to K m ). Thus for substrate A, Va

= (kea,IKm)A[Elo[A),

and for substrate B, So ValVb = {(keatIKm)AX[AJ}/{(keatIKm)BX[BJ), and, at the same substrate concentrations, the activity of the enzyme against the different substrates reduces to a comparison of the respective specificity constants (k ea,!K m ); K m is not of itself a sufficient index of specificity. specific optical rotation symbol [a)~; the optical rotation of light of a specified wavelength (or frequency) achieved by a solution at a specified temperature. It is given by the relation [al1 = allp where a is the observed rotation in degrees, I is the length of the sample tube (in dm), p is the density of the liquid (in g mL- 1), A is the wavelength of the light (or other electromagnetic radiation) used, and (J is the Celsius temperature. For a solution of concentration c (in g solute per 100 mL solution), [al~= allc in degrees dm 2 g-l Compare molecular opticalrotation. specific refractivity see re'ractivity. specific viscosity symbol: I1s p; the fractional change in viscosity produced by adding a solute to a solvent. It is given by the equation: I1sp

= (111110) - I = A vc + Bv 2 c2 + CV 3c3 + .......

where 110 is the viscosity of the solvent, II is the intrinsic viscosity of the solution, A, B, and C are shape-dependent constants, c is the concentration of the solute, and v is the specific volume of one solute molecule. specific volume symbol: v; for a pure substance, the volume, V, of a sample, divided by the mass, m, of the sample; v = VIm = lip, where p is the mass density of the substance. The S1 unit is m 3 kg-I. See also partial specific volume. 'specifier' protein a protein that, when it combines with an enzyme or enzyme-substrate, modifies the catalytic specificity of the system. An example is a-lactalbumin, which modifies the substrate (acceptor) specificity of N-acetyllactosamine synthase (EC 2.4.1.90; other name: UDPgalactose:N-acetylglucosamine p-o-galactosyltransferase) from N-acetylglucosamine to glucose. spectinomycin an aminocyclitol antibiotic found in the growth medium of Streptomyces spectabilis. It has a wide

611

spectra range of activity against Gram-negative bacteria, with a more selective activity against Gram-positive bacteria. It is highly active against Neisseria gonorrhoeae. It inhibits protein synthesis by binding to the bacterial 30S ribosomal subunit. spectra the plural of spectrum. spectrin a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, a and ~, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers. Anchorage to the cytoplasmic face of the plasma membrane is mediated by another protein, ankvrin, which links ~ spectrin to transmembrane protein band 3, and by the binding of band 4.1 to glvcophorin. Interaction between spectrin and other proteins is thought to be responsible for the maintenance of the biconcave shape of human erythrocytes, for the regulation of plasma membrane components, and for the maintenance of the lipid asymmetry of the plasma membrane. Spectrin-like proteins have five domains. Example from human, a chain: database code SPCA_HUMAN, 2429 amino acids (280.74 kDa); ~ chain: database code SPCB_HUMAN, 2137 amino acids (246.04 kDa). spectrofluorometer an instrument used for measuring the fluorescence emitted by compounds excited by incident radiation produced within the instrument. The excitation radiation is produced by a lamp, and filters or diffraction grating monochromators are employed to isolate both the incident and emitted radiation to narrow wavebands. The emitted radiation is detected by photomultipliers. spectrogram a photographic record of a spectrum produced by a spectrograph. spectrograph a spectrometer or spectroscope with a facility for producing a photographic record of the spectrum under consideration. Compare spectroscope. -spectrographic ad).; spectrographically adv.; spectrography n. spectrometer any instrument used to produce and examine a spectrum, such as a spectrophotometer or a spectroscope. -spectrometric adj.; spectrometry n. spectrophotometer an apparatus to measure the proportion of the incident light (or other electromagnetic radiation) absorbed (or transmitted) by a substance or solution at each wavelength of the spectrum. -spectrophotometric adj.; spectrophotometry n. spectroscope an instrument for studying spectra, either qualitatively or quantitatively. -spectroscopic or spectroscopical ad).; spectroscopically adv. spectroscopy the investigation of the chemical composition, molecular structure, or atomic structure of a substance or solution by observation of its interaction with electromagnetic radiation using a spectroscope. spectrum (pl. spectra) (in physics) an arrangement of the components of a complex electromagnetic radiation (light, etc.) or sound in order of frequency or energy, thereby showing a distribution of energy among the components. -spectral adj. Spemann's organizer an embryonic signalling centre located in the dorsal lip of the blastopore. It plays a crucial role in the organization of the formation of the main body axis of a developing embryo. [After Hans Spemann (1869-1941), German zoologist and embryologist.] spermaceti or cetaceum a white, translucent, waxy solid, m.p. 42-50 "C, consisting mainly of the ester cetyl palmitate and obtained from oil in the head of the sperm whale (Physeter catodon) and related cetaceans. It is used in the manufacture of cosmetics, ointments, soaps, etc. spermadhesin or AQNl a secretory protein of male accessory glands that is found on the sperm surface and mediates sperm binding to the zona pellucida. Example from Sus scrofa: database code AQNLPIG, III amino acids (11.88 kDa). spermatogenesis the formation of spermatozoa in the male reproductive system. The sperms are formed from male germ

sphingolipid cells, spermatogonia, which line the inner wall of the seminiferous tubules in the testis. A single spermatogonium divides by mitosis to form primary spermatocytes, each of which undergoes the initial division of meiosis to form two secondary spermatocytes. Each of these then undergoes the second meiotic division to form two spermatids, which mature into spermatozoa without further cell division by a process called spermiogenesis. All these cell types are nourished and supported by neighbouring Sertoli cells. Spermatogenesis also requires the presence of testosterone-secreting LeVdig cells. spermidine N-(3-aminopropyl)-I,4-diaminobutane; NHz(CHzhNH(CHz)4NHz: one of the polyamines. spermidine synthase EC 2.5.1.16; other names: putrescine aminopropyltransferase; amino propyl-transferase; an enzyme that catalyses the formation of spermidine from S-adenosylmethioninamine and putrescine with formation of 5'-methylthioadenosine. Example from human: database code SPEE_ HUMAN, 302 amino acids (33.79 kDa). spermine N,N-bis(3-aminopropyl)-1,4-diaminobutane; NHz(CHzhNH(CHz)4NH(CHzhNH2; one of the polyamines. spermine synthase EC 2.5.1.22; other name: spermidine aminopropyltransferase; an enzyme that catalyses the formation of spermine from S-adenosylmethioninamine and spermidine with formation of 5'-methylthioadenosine. sperm tail see cilium. SPF abbr. for specific-pathogen-free. Sph symbol for sphingosine. S phase the phase of the eukaryotic cell cycle in which DNA is synthesized. See cell-division cvcle. spherocyte a rounded red blood cell that has lost its normal biconcave shape owing to damage to the surface membrane or to some disorder of metabolism. Spherocytes appear smaller and darker than normal red cells. spherocytosis the condition of having spherocytes in the blood. spheroid 1 a solid figure that is similar to but not identical with a sphere. 2 an ellipsoid of rotation, especially one in which the major axis of its parent ellipse is only slightly longer than its minor axis. -spheroidal adj. spheroplast the globular form of a bacterial cell in which the cell-wall structure has been modified (e.g. by growth in the presence of penicillin) rather than totally removed. The term also denotes a form of yeast cell obtained by partial hydrolysis of the cell wall. A prefix may be used to indicate the method of induction, e.g. penicillin-spheroplast. Compare protoplast. spherosome an organelle, generally spherical or oblate and 0.4-3 ~m in diameter, that occurs in lipid-storage tissues in plants, e.g. endosperm of castor-bean seeds. The nature of the surrounding membrane is still in doubt. sphinganine D-erythro-2-amino-I,3-octadecanediol; Derythro-dihydrosphingosine; the metabolic precursor of sphingosine. It is formed from palmitoyl-CoA and serine by, first, the action of serine C-palmitovltransferase, which forms 3dehydro-D-sphinganine, which is then reduced to sphinganine by 3-dehydrosphinganine reductase, EC 1.1.1.102. See also sphingolipids, sphingoid. sphingoid or sphingoid base symbol: Spd; any of a class of compounds comprising sphinganine and its homologues and stereoisomers, and derivatives of these compounds. sphingolipid any of a class of lipids containing the long-chain amino diol, sphingosine, or a closely related base (i.e. a sphingoid). A fatty acid is bound in an amide linkage to the amino group and the terminal hydroxyl may be linked to a number of residues such as a phosphate ester or a carbohydrate. The predominant base in animals is sphingosine while in plants it is phytosphingosine. The main classes are: (1) phosphosphingolipids (also known as sphingophospholipids), of which the main representative is sphingomvelin; and (2) glVcosphingolipids, which contain at least one monosaccharide and a sphingoid, and include the cerebrosides and gangliosides. Sphingolipids play an important structural role in cell membranes, and may be involved in the regulation of protein kinase C.

612 sphingolipid activator proteins

spin trapping

sphingolipid activator proteins see saposins. that have been formed move to opposite sides of the nucleus, sphingolipidosis (pI. sphingolipidoses) any of several inherited and form the two poles of the mitotic spindle. Microtubules grow away from the centrosomes towards the chromosomes, pathological conditions in humans in which one or more sphingolipids accumulate in the tissues because of a deficiency the minus ends being attached to the centrosome, and the plus of the corresponding degradative enzyme. They include ends growing towards the kinetochore. These micro tubules ceramidase deficiency, Fabry's disease, galactosylceramide lipidoeventually bind to kinetochores and are thus known as kinetochore microtubules. Other microtubules, known as polar sis, G M1 and G MZ gangliosidoses, Gaucher'S disease, metachromatic leukodystrophy, and sphingomyelin lipidosis. microtubules, grow towards the chromosomal region, but sphingomyelin N-acyl-4-sphingenyl-I-O-phosphorylcholine; eventually bind directly to other polar micro tubules growing any of a class of phospholipids in which the amino group of from the opposite centrosome. These push the poles of the sphingosine is in amide linkage with one of several fatty acids, spindle apart. Each centrosome eventually becomes attached through the kinetochore micro tubules to one of the sister mostly C zo or higher and either saturated or monounsaturated, while the terminal hydroxyl group of sphingosine is eschromatids of each chromosome, and pulls these away to efterified to phosphorylcholine. Sphingomyelins are found in fect the chromatid separation that occurs at anaphase. A similarge amounts in brain and other nervous tissue. They do not lar series of events occurs at the corresponding phases of occur in plants. meiosis. sphingomyelin lipidosis or Niemann-Pick disease a genetic spin hamiltonian a formulation in quantum mechanics used in the determination of the energy levels of the spin of an elecdisease of humans in which sphingomyelin accumulates in the tissues due to a deficiency of the enzyme sphingomyelin phosphotron or a nucleus in electron spin resonance spectroscopy or, less commonly, in nuclear magnetic resonance spectroscopy. See also diesterase. It is associated with mental retardation. sphingomyelin phosphodiesterase EC 3.1.4.12; other Hamiltonian operator. names: acid sphingomyelinase; neutral sphingomyelinase; a spin immunoassay or free-radical assay technique (of immunoassay) (abbr.: FRAT) a technique in which a spin label is lysosomal enzyme that catalyses the hydrolysis of sphingomyelin to N-acylsphingosine and choline phosphate. Defiattached to a specimen of the substance to be assayed and an ciency of the enzyme is the cause of Niemann~Pick disease antibody is raised against the substance. On mixing the antibody with the labelled substance there is a change in the elec(sphingomyelin lipidosis), in which there is an accumulation of sphingomyelin. Example (precursor) from human: database tron spin resonance (ESR) spectrum because of the inhibition code ASM_HUMAN, 629 amino acids (69.78 kDa). of tumbling caused by the antibody 'immobilizing' the labelled sphingophospholipid see sphingolipid. substance. On adding some of the unlabelled substance there sphingosine symbol: Sph; trans-D-erythro-2-amino-4is competition for the antibody, and the changes in the ESR octadecene-I ,3-diol; CH3(CHz)lZCH=CH~CHOH-CHNHr spectrum are partially reversed to an extent dependent on the CHzOH; a long-chain amino diol sphingoid base that occurs concentration of the added, unlabelled, substance. in most sphingolipids of animal tissues. See also phytosphingospin label 1 a synthetic paramagnetic organic free radical, sine. usually having a molecular structure and/or chemical reactivsphingosine N-acyltransferase EC 2.3.1.24; an enzyme of ity that facilitates its attachment or incorporation at some the pathway for synthesis of sphingolipids that catalyses the particular target site in a macromolecule, or assemblage of acylation of sphingosine by acyl-CoA to form N-acylsphingomacromolecules. 2 spin-label to effect labelling of a substance sine (ceramide) and CoA. or structure with a spin label (def. 1). spicule a roughly cone-shaped structure or tissue element, such spin-lattice relaxation time or longitudinal relaxation time as that projecting from the membrane of a red blood cell. Cal(in nuclear magnetic resonance spectroscopy) symbol: T 1; the careous or siliceous spicules are found in the skeletons of time taken for the upper electron spin state to dissipate its exsponges and corals. cess energy. Its reciprocal is the spin-lattice relaxation rate spin (in physics) 1 the quantized angular momentum of an ele(see correlation time). mentary particle, in the absence of orbital motion. 2 the quan- spinner culture the culture of cells in bottles or tubes that are tized angular momentum of an atomic nucleus, including continuously rotated. contributions from the orbital motions of nucleons. 3 the spin polarization or spin polarisation a phenomenon in which quantized angular momentum of an electron that adds to the the unpaired electron spin on one atom or part of a molecule is orbital angular momentum, thus producing fine structure in transferred to another atom, brought about by interaction beline spectra. tween the unpaired electron on the first atom and the paired spinal cord the part of the central nervous system that is enelectrons on the second atom (which lacks unpaired electrons) causing one of the paired electrons to have a lower energy closed in the vertebral column. Its function is to connect the innervation of most parts of the body via the spinal nerves to than the other. See also chemically induced dynamic nuclear polarization. the brain. spinal nerves the pairs of nerves that arise from the spinal spin-spin broadening an increase in line width in electron spin cord and are distributed to various peripheral parts of the resonance spectroscopy, caused by interactions between neighbody. In humans there are 31 pairs. bouring dipoles. spin coupling or spin-spin coupling (in nuclear magnetic res- spin-spin coupling see spin coupling. onance spectroscopy) the influence of one nucleus on another, spin-spin coupling constant (in nuclear magnetic resonance such that the nuclear spin of one nucleus is coupled via the spectroscopy) a measure of the specific interaction of one bonding electrons to the coupled nucleus, which experiences nucleus with another that gives rise to a splitting of the restwo different microenvironments and thus resonates at two onance bands produced by each nucleus. slightly different frequencies. This results in the splitting of spin-spin splitting splitting in the lines of a nuclear magnetic the resonance line into two lines (a doublet). resonance spectrum brought about by the interaction of the spin density the fraction of unpaired electron spin that is in magnetic moment of the nucleus of a given atom in a molecule the vicinity of a given atomic nucleus in a molecule. with those of neighbouring nuclei. It is used in the assignment spindle the array of micro tubules and associated molecules of particular nuclear resonances and in the determination of that forms between the opposite poles of a eukaryotic cell durmolecular conformations. See also hyperfine splitting. ing mitosis or meiosis and serves to move the duplicated chro- spin state the orientation, in a strong magnetic field, of an unmosomes apart. During mitosis the spindle starts to form paired electron or nuclear spin, e.g. parallel or antiparallel to outside the nucleus while the chromosomes are condensing the field direction. during prophase. At the start of M phase, the two centrosomes spin trapping a technique in which a reactive free radical is

613

spiro compound trapped by an addition reaction to produce a more stable radical, detectable by electron spin resonance spectroscopy, whose hyperfine coupling parameters permit identification of the initial radical trapped. spiro compound any compound containing two rings joined by one common atom, designated the spiro atom, as in the case of the y-Iactone ring of spironolactone. spironolactone 7-(acetyIthio)-17-hydroxy-3-oxo-pregn-4-ene21-carboxylic acid y-Iactone; a synthetic steroid lactone that is used as a diuretic. It is structurally similar to aldosterone, and competitively inhibits the renal tubular action of this hormone. It is metabolized to canrenone, the active compound, by removal of the acetylthio group and insertion of a 6,7 double bond.

spleen exonuclease see phosphodiesterase II. splenin seethymopoietin. splenopentin a synthetic peptide that corresponds to residues 32~36 of splenin (see thymopoietin). spliceosome a ribonucleoprotein complex, containing RNA and small nuclear ribonucleoproteins (snRNPs) that is assembled during the splicing of the messenger RNA primary transcript to excise an intron. snRNPs designated UI, U2, U4, U5, and U6 are variously involved; UI may bind the GU consensus sequence of the 5' splice site and U5 with U41U6 probably binds to the 3' splice site consensus sequence, AG. U2 may be part of a component binding the UACUA[AjC consensus sequence ([Aj is invariant) at a site slightly upstream from the 3' splice site, known as the branch site. The mechanism appears to involve cutting at the 5' side of the GU consensus sequence, which curls back to form a G5'-2'A bond with the invariant A of UACUA[A]C. This linkage generates the loop of the so-called lariat. Cutting out the 3' splice site follows on the 3' side of AG to release the complete intron (in the form of the lariat), and the cut ends of the exons are then ligated. splice site the sequence of bases at each end of an intron that determines the point of splicing. The 5' splice site (site at the 5' end of the intron) is termed the donor site, consensus sequence GU, while the 3' splice site is termed the acceptor, consensus sequence AG. splicing 1 (of DNA) the covalent linkage, by the action of a DNA ligase (EC 6.5.1.1, requires ATP, or EC 6.5.1.2, requires NAD+), of two fragments of duplex DNA at complementary single-stranded terminations. 2 (of RNA) the enzymic process in eukaryotic cells by which introns are excised from heterogeneous nuclear RNA (hnRNA) following its transcription from DNA, and the cut ends are rejoined to form messenger RNA (mRNA), in which the message is continuous, before its translation into polypeptide. In yeast, the splicing of transfer RNA involves cutting at the splicing junctions by an endonuclease followed by a process involving ATP whereby the two exon sequences are joined. Group I mitochondrial RNA is spliced by an autocatalytic mechanism, the RNA itself having the ability to catalyse its own splicing; nuclear mRNA precursor - the primary transcript - is spliced by a complex assembly incorporating snRNP and called a spliceosome; it involves the formation of a lariat. Splicing of group II mitochondrial RNA also involves the formation of a lariat but without formation

squalamine of a spliceosome. Splicing in which the cut ends are joined directly within the same RNA molecule is called cis-splicing; trans-splicing refers to situations in which the cut end from the splicing site rejoins to a splicing site on another RNA molecule. 3 (of protein) a post-translational modification of protein that includes two concerted proteolytic cleavages and one ligation that results in excision of an inner sequence of the original polypeptide chain to form one protein, and ligation of the two outer sequences to form a second protein. It is thought to be an autocatalytic process. The excised inner sequence is known as an intein, the ligated outer sequences as an extein. See also gene splicing. splicing factor 2 abbr.: SF2; a protein, present in nuclear extracts, that functions in an early step in splicing pre-mRNA. It is resistant to mild heat treatment, but inactivated by N-ethylmaleimide. It consists of two peptides, P32 and P33, and is involved in ensuring accuracy of splicing. Example, P32 from human: database code SP32_HUMAN, 282 amino acids (31.36 kDa). See also pre-mRNA processing protein. split gene a gene that is not represented by a continuous DNA sequence; an interrupted gene. spoke protein a protein associated with the filamentous structure of kinetochore microtubules in the mitotic spindle. Soluble and cytoplasmically localized during interphase, it becomes primarily associated with the mitotic spindle in mitosis. Example, spoke protein 4 (of five different ones) from Chlamydomonas reinhardtii: database code RSP4_CHLRE, 465 amino acids (49.74 kDa). spongiform encephalopathy any of a group of diseases of human and other animals characterized by the presence of many vacuoles in brain tissue, giving it a spongy appearance. The group includes bovine spongiform encephalopathy, scrapie in sheep, and Creutzfeldt-Jakob disease, Gerstmann-Straflssler syndrome, and kuru in humans. See also prion, prion protein. spontaneous generation see abiogenesis. spontaneous hypoglycemia see glycemia. spore a small, often microscopic, reproductive unit consisting of one or several cells. Spores are produced by fungi, bacteria, certain plants, and protozoa. They may variously serve as a means of rapid vegetative propagation, or as a dormant stage in the organism's life cycle. Spores have very low metabolic activity and give rise to a vegetative cell upon germination; they are usually more heat resistant than vegetative cells and are adapted for dispersal. Spores may be sexual or asexual. sporulation the formation of spores. spot 1 (in chemistry) or spot test to test for a substance by applying a small amount of detection reagent to a surface. 2 (in molecular biology) to detect, using radioactive oligonucleotide probes, oligonucleotides applied in spots onto hybridization fil ters (spot blots). spoT a gene in Escherichia coli for the enzyme guanosine-3',5'bis(diphosphate) 3'-pyrophosphohydrolase; EC 3.1. 7.2; other name: (ppGpp)ase; it catalyses the hydrolysis of guanosine 3',5'-bis(diphosphate) to guanosine 5'-diphosphate and pyrophosphate. The SpoT protein cycles ppGpp formed as a part of the stringent response. The name is jocular, ppGpp and pppGpp originally having been referred to as 'magic spot nuc1eotides'. Example from E. coli: SPOT_ECOLI, 702 amino acids (79.34 kDa). See also re/A, stringent factor. spp. abbr. for species (plural). SPP-1 see osteopontin. [S]ppA symbol for adenosine 5'-P-thiodiphosphate (alternative to AdoPP[S)). [S]pppA symbol for adenosine 5'-y-thiotriphosphate (alternative to AdoPPP[S)). spreading factor see hyaluronidase. SaOG abbr. for sulfoquinovosyldiacylglycerol (see sulfonolipid). sal abbr. for symbolic query language; a query language used with related databases, e.g. SYBASE. It is often pronounced 'sequel'. squalamine a water-soluble aminosterol isolated from the

614

squalene

stability constant

dogfish shark, Squalus acanthias. It has antibiotic properties against Gram-negative and Gram-positive bacteria and protozoa. It is an adduct of spennidine and a sulfate bile salt.

2,6, 10,15, 19,23-hexamethyl-2,6, 10,14, 18,22-tetracosahexaene; the linear triterpene precursor of all cyclic triterpenoids and the sterols. Although first isolated from shark-liver oils and later found in many other fish-liver and plant oils, squalene is widely distributed in plant and animal cells as a metabolic intermediate. It is formed from acetylCoA, via a pathway whose intermediates include mevalooate, isopeoteoyl diphosphate, geraoyl diphosphate, and farnesyl diphosphate. The latter is converted to presqualene diphosphate, which is then reduced to squalene by NADPH with loss of pyrophosphate; both steps are catalysed by farnesyltransferase. [From Latin squalus, marine fish, later specifically used to mean shark.]

squalene

2

squalestatin a fermentation product of Coelomycete spp. that

is a potent selective inhibitor of squalene synthase, and lowers serum cholesterol in vivo.

pp60 v-src . The Src family of tyrosine kinases is the largest of the nonreceptor tyrosine kinase families and is formed from a group of proteins that all share a high homology with the oncoprotein, v-Src, and the cellular counterpart, c-Src. Members of the Src family include Src, Yes, Fyn (see FYN'), Lck (see LCKj, Lyn (see Iyo), B1k (see blk), Hck, Fgr (see FGII), and Yrk, which range in size from 53 to 64 kDa. They all share a number of features including an N-terminal myristoylation site (a mechanism for promoting their association with membranes), a unique domain, two conserved segments known as Src homology 2 domain (SH2 domain) and Src homology 3 domain (SH3 domain(see SH domain», a tyrosine kinase domain, and a C-terminal regulatory domain. In vertebrates, the kinase activity of Src family members is normally inhibited by the phosphorylation of a tyrosine residue within the kinase domain. In v-src the region of the gene encoding the negative regulatory C-terminal tyrosine has been deleted, leading to v-Src having a higher constitutive tyrosine kinase activity than c-Src. Other mutations associated with oncogenic activation map to the SH2 and SH3 domains, supporting the proposal that in the resting cell Src is kept in an inactive state by the binding of its SH2 domain to the phosphotyrosine residue in its negative regulatory domain so keeping the kinase in an inactive conformation. SH3 domains may participate in this repression, possibly by binding proline-rich regions in the kinase domain. Activation of Src family members occurs by two potential mechanisms: (1) the co-presence of another protein containing a specific phospho tyrosine residue that has a higher affinity for the SH2 domain than the negative regulatory phosphotyrosine within the Src member; or (2) the dephosphorylation of the negative regulatory phospho tyrosine by a specific protein tyrosine phosphatase. Example from human: database code KSRC_HUMAN, 536 amino acids (59.77 kDa). Src homology domain see SH domain. Srd symbol for a residue of the ribonucleoside thiouridine (when the position of the thiol group in its thiouracil moiety is unknown or unspecified; alternative to S or sU). SRE abbr. for serum response element. SRF abbr. for serum response factor; a nuclear, dimeric transcription factor. It forms l\complex with Elk·' that is constitutively bound to the serum response element. Example from human: database code SRF_HUMAN, 508 amino acids (51.54 kDa). SRIF abbr. for somatotropin release-inhibiting factor (i.e. somatostatin). sRNA or S-RNA abbr. for soluble RNA (an early name for transfer RNA). SRP abbr. for signal recognition particle. SR protein any protein belonging to a family of pre-messenger

squalestatin 1 sr symbol for steradian. Sr symbol for strontium. SR abbr. for sarcoplasmic reticulum.

lire an oncogene (v-src), originally discovered in the Rous sar-

coma virus, the product of which is pp60v-src , a 60 kDa protein that undergoes phosphorylation/dephosphorylation. A normal cellular gene (or protooncogene), c-src, codes for a related protein; both proteins have tyrosine kinase activity. The viral oncogene product and its normal counterpart differ in aminoacid residues, especially at the C terminus where the last 19 residues of pp60c-src are replaced by 12 other residues in

RNA splicing factors possessing highly related primary amino-acid sequences. They share an N-terminal RNA recognition motif and a C-terminal domain that varies in length and consists almost exclusively of alternating serine (S) and arginine (R) residues, from which the proteins are named. Many animal cells possess a series of SR proteins of similar molecular mass: 20, 30,40, 55, and 70-75 kDa; as yet these have undetermined specificities. SRS or SRS-A abbr. for slow reacting substance (of anaphylaxis). S~R variation see smooth-rough variation. SSB protein abbr. for single-strand binding protein. SSCP analysis abbr. for single-strand conformation polymorphism analysis. ssDNA see DNA. St symbol for stokes (a cgs unit of kinematic viscosity). Sta symbol for statine. stability constant symbol: Kg; an equilibrium constant for the reversible formation of a complex chemical compound from two or more simpler entities; the reciprocal of the dissociation constant. In some cases, an apparent stability constant (symbol:

615

stable factor

starch synthase

K's), constrained with respect to certain variables (e.g. pH) is determined (for the distinction see equilibrium constant). The stability constant is also known as the a"ociation constant (symbol: Kass ) in cases where ions associate into a substance, e.g. for the reaction A+ + B~ = AB, the (concentration) stability or association constant is given by: K s [AB]/[A +][B~] K ass .

=

=

stable factor an alternative name for factor VII; see blood coagulation. stable isotope an isotope that is not radioactive. stachyose or lupeose the tetrasaccharide, O-a-D-galactopyranosyl-(I --? 6)-O-a-D-galactopyranosyl-(I --? 6)-O-a-Dglucopyranosyl-p-D-fructofuranoside. It is widely distributed, usually associated with raffinose (see that entry for synthesis) and sucrose; it is isolated from Stachys tuberifera rhizomes. stacking gel an alternative name for spacer gel. Staden, R. us molecular biologist; the author of a much used suite of computer programs for sequence analysis of nucleic acids and proteins, available for both VMS and UNIX. staggered conformation see conformation. stainless steel steel that is resistant to corrosion due to its high content of chromium and, often, nickel. It is highly resistant to all organic acids and weak mineral acids but is slowly attacked by concentrated mineral acids. It does not rust. Stains-all a proprietary name for l-ethyl-2-[3-(3-ethylnaphthor I,2-d]thiazolin-2-ylidene)-2-methylpropenyl]naphtho[ I,2d]thiazolium bromide; a cationic carbocyanine metachromatic dye used as a semiselective stain for locating nucleic acids, proteins, and polysaccharides. RNA stains bluish-purple, DNA blue, protein red, and phosphoprotein blue.

stamp collecting according to Lord Rutherford (1871-1937), one of the two branches of science (the other being physics). standard (in analytical chemistry) 1 primary standard a chemical that can be obtained in an unvarying state (e.g. of purity and/or stability) and used as an approved example against which other examples of the same chemical can be compared. 2 secondary standard a chemical that can be used for comparative purposes following calibration against a primary standard. Although its properties are less stringent than a primary standard, its ready availability makes for convenience of use. See also standard atmosphere, standard state, standard temperature and pressure. standard atmosphere an internationally established reference for pressure, defined as 101 325 pascals. The atmosphere (def. 3) (symbol: atm), equal to 101 325 pascals, was formerly used as a unit of pressure; its use is now discouraged. See also standard temperature and pressure. standard curve a plot of any appropriate parameter against known amounts (or concentrations) of detectable substance. Such a curve can be used to determine the amount (or concentration) of the same substance in an unknown solution given a reading for the parameter in the unknown solution. standard deviation abbr.: SD; symbol: s (for a sample) or a (for a distribution); the common measure of dispersion of a series of observations of x that is normally distributed. It is the root-mean-square average of the deviations of the observations from their mean and is in the same units as those of the observations. The standard deviation, $" is given by: sx

=

0/[1

'J

n

£

1=0

(x_X)2]

Where x is the arithmetic average of deviations of x and n is the number of observations; sx2 is called the variance of the sample of observations of x. Some authorities prefer the definition: sx=

"[nl_li~o(x-x)2]

so that Sx 2 is then the best estimate of the variance, a 2 , of the population from which the sample of observations ofx was made. See also degrees of freedom, standard error 01 estimate of the mean. standard error of estimate of the mean or standard error of the mean abbr.: SEM; a measure of the reliability of an estimate of the mean of a population. It is equal to the standard deviation, sx' of the observations divided by the sq uare root of the number of observations, n; i.e. SEM = sJ·./n. standard free energy see Gibbs energy. standardize or standardise to relate any instrument, vessel, or reaction to an absolute standard. -standardization or standardisation n. standard pressure symbol: p; an established reference for pressure. Since 1982 the recommended standard pressure for reporting thermodynamic data has been set at 10 5 pascals (1 bar). Before 1982 it was taken to be 101 325 pascals (I atmosphere). standard state a set of conditions, established by convention, under which a standard reference is determined or calculated. See chemical potential, enthalpy, entropy, Gibbs energy, hydrogen electrode, standard pressure, standard temperature and pressure. standard temperature and pressure abbr.: stp or s.t.p. or STP; the standard conditions for the comparison of properties of gases. Standard temperature is now 298.15 K (formerly 273.15 K, i.e. 0 0c) and standard pressure is 10 5 pascals. Former name: normal temperature and pressure (abbr.: ntp or n.t.p. or NTP). Stanley, Wendell Meredith (1904-71), US biochemist; Nobel Laureate in Chemistry (1946) jointly with J. H. Northrop 'for their preparation of enzymes and virus proteins in a pure form' [prize shared with J. B. Sumner]. Staphylococcus a genus of Gram-positive bacteria, commonly associated with wounds and generally causing localized infections. Staphylococcus aureus forms yellow or orange pigments and yields plasmids that are useful in recombinant DNA experimentation: S. aureus plasmids coding for resistance to various antibiotics can be transfected into Escherichia coli or into Bacillus subtilis where they are stable, replicate, and express antibiotic resistance. They have provided the basis from which improved vectors have been developed. starch the most important reserve polysaccharide found in plants. It is a glucan consisting of two components: amylose, which is a homopolymer of glucose units linked only by a(1 --? 4) bonds; and amylopectin, also a glucose homopolymer (branched) that contains a(l --? 6) bonds as well as a(l --? 4) bonds. Starch is synthesized as a temporary storage form of fixed carbon in chloroplasts during active periods of photosynthesis, accumulating as starch grains. The starch is subsequently converted to sucrose and translocated to storage organs, such as seeds and tubers, where it is re-formed. Compare glycogen. starch (bacterial glycogen) synthase EC 2.4.1.21; recommended name: starch synthase; systematic name: ADPglucose: 1,4-a-D-glucan 4-a-D-glucosyltransferase; other name: ADPglucose-starch glucosyltransferase. An enzyme that catalyses a reaction between ADPglucose and (I,4-a-D-glucosyl)n to form (1,4-a-D-glucosyl)n+! and ADP. It uses ADPglucose instead of the UDPglucose of glycogen synthase. Example from Escherichia coli: database code GLGA_ECOLI, 477 amino acids (52.48 kDa). starch phosphorylase see a-glucan phosphorylase. starch synthase EC 2.4.1.11; recommended name (example): glycogen (starch) synthase (the nature of the synthetic product should be included in the name); systematic name: UDPglucose:glycogen 4-a-D-glucosyltransferase; other name:

starch syrup

616

UDPglucose-glycogen glucosyltransferase. An enzyme that catalyses a reaction between UDPglucose and (1,4-a-D-glucosyl)n to form (1,4-a-D-glucosyl)n+) and UDP. Example (precursor) from maize chloroplasts: database code UGST_ MAIZE, 605 amino acids (65.89 kDa). See also glycogen synthase. Compare starch (bacterial glycogen) synthase. starch syrup an alternative name for corn syrup. Start an important checkpoint in the G j phase of the eukaryotic cell-division cycle. Passage through Start commits the cell to enter S phase. start codon the trinucleotide codon AUG that codes for Nformylmethionine, the first amino-acid residue in the synthesis of all prokaryotic and mitochondrial proteins. start kinase a complex of Cdc2 (see cdc gene) and a G, eyclin that functions as a serine/threonine protein kinase; its activation is necessary for the cell to pass Start. The G, cyclin that interacts with Cdc2 is thought to be any of several. The identity of the G, cyclin modifies the specificity of the complex. start point the base pair in DNA at which the first nucleotide is incorporated into an RNA transcript. It is most often a purine, and in many cases is the central base of the sequence CAT. It is sited at the downstream end of the promoter. Compare start codon. start protein any protein that is involved uniquely at the start of the cell cycle. Example, protein Cdc10 from Schizosaccharomyces pombe: database code CCIO_SCHPO, 767 amino acids (85.42 kDa). This protein (which has a close homologue in Saccharomyces cerevisiae) is probably a transcriptional regulator for cdc10 and also for cdc2, which encodes a component of start kinase. starve to deprive of nutrients. In animal experiments a minimum of 24 h deprivation is generally understood. Cultures may be starved of specified single nutrients. stasis arrest or stagnation of flow. +stasis comb. form denoting lack of movement; cessation of flow. -+static adj. STAT abbr. for signal transducer and activator of transcription; a family of eukaryotic transcription factors that mediate the response to many cytokines and growth factors. Upon receptor activation, STAT proteins dimerize, trans locate to the nucleus, and bind to specific promoter sequences on target genes. Seven different genes have been so far identified in mammals. Example: STALHUMAN, 750 amino acids (87.33 kDa). +stat comb. form indicating a device for maintaining a particular property at a constant value, e.g. cryostat, thermostat. +static adj. stathmin other names: phosphoprotein p19; oncoprotein p18; prosolin; an ubiquitous phylogenetically conserved cytoplasmic protein that serves as a phosphorylated intermediate in diverse second-messenger pathways. Stathmin undergoes phosphorylation; both phosphorylation and expression of the protein are regulated throughout development, in response to extracellular signals that control cell proliferation and differentiation. It is a major phosphorylation substrate in neurons. Example (precursor) from Rattus norvegicus: database code STHM_RAT, 148 amino acids (17.14 kDa). +static see +stasis, +stat. statics functioning as sing. the branch of applied mathematics dealing with the interaction of forces in nonmoving systems. statin 1 a phosphoprotein present specifically in the nuclei of nonproliferating cells. It forms a complex with a 45 kDa serinelthreonine protein kinase, and has structural similarity to the elongation factor EF-lu. Example from rat: database code STTN_RAT, 463 amino acids (50.28 kDa). 2 a variant spelling ofstatine. +statin word ending (in hormone nomenclature) denoting a hypothalamic release-inhibiting factor (or hormone). Compare +Iiberin. statine or statin symbol: Sta; [3S,4S]-4-amino-3-hydroxy-6methylheptanoic acid; a novel amino acid contained in positions 3 and 5 of pepstatin A.

stearate stationary phase 1 (in chromatography) the immobile phase to which the analyte adsorbs or partitions from the mobile phase. 2 (in fermentation) the phase of an in vitro culture of microorganisms or eukaryotic cells that follows the exponential growth phase and in which there is little or no growth. statistically significant see significant. statistical mechanics the theoretical analysis of molecular properties based on quantum theory. statistical sample a finite selection of items from a population of which the measurement of a variable will give a close approximation to the distribution of that variable in the whole population. See also random sample, sample. statistics 1 functioning as sing. the science of collecting, analysing, interpreting, and presenting quantities of numerical data. 2 functioning as pl. a collection of quantitative data. statistical adj. statyl the acyl group derived from statina. Staudinger, Hermann (1881-1965), German chemist; Nobel Laureate in Chemistry (1953) 'for his discoveries in the field of macromolecular chemistry'. Hew was particularly distinguished for his work on polymers such as polystyrene. staurosporine an antibiotic from Streptomyces spp., M r 466.2, best known as a potent inhibitor of protein kinase C.

Ste symbol for the stearoyl group, CH 3 -[CHzh6-CO-. steady state a condition in which the properties of any part of a system are constant during a process or reaction; Le. where the rate of formation or increase of a particular quantity is balanced by its rate of removal or decrease. steady-state fluorescence anisotropy a method in which a sample containing a fluorescent compound is irradiated with plane-polarized light, the emitted fluorescence being analysed to determine its degree of polarization both in the plane of the excitation radiation and in a plane at right angles to this. Only molecules of the fluorescent compound that are aligned in the plane of the incident radiation can absorb radiation and be excited to emit fluorescence. If, in the interval between absorption of the radiation and the emission of fluorescence, the molecule moves out of the plane of polarization of the incident radiation, the emitted radiation will lose polarization (be depolarized) to a degree that depends on the extent to which the molecule had moved. The technique is used to measure the degree to which fluorescent probes are tumbling in a sample. If the probes are held in a relatively rigid position, the extent of depolarization will be small, if tumbling freely it will be high. steady-state kinetics the analysis of an enzyme reaction in the steady state, Le. after the pre-steady state and when the intermediates have reached a steady concentration. The duration of the steady state is relatively short, and this state is in any case an approximation since the accumulation of products and the depletion of substrate occur continuously from the start of the reaction. See Michaelis kinetics. steapsin an old term for pancreatic lipase. stearate 1 a trivial name for octadecanoate, CH r [CH2])6-COO-, the anion derived from stearic acid, or octadecanoic acid, a saturated straight-chain higher fatty acid. 2 any

617

stereobase unit

stearin mixture of free stearic acid and its anion. 3 any salt or ester of stearic acid. See also stearoyl. stearin 1 an old name for any of the glyceryl esters of stearic acid, especially the triester, tristearin (tristearoylglycerol). 2 a commercial name for a grade of stearic acid containing other fatty acids, especially palmitic acid. stearoyl symbol: Ste; numerical symbol 18:0; a trivial name for octadecanoyl, CH3-[CH2h6-CO-, the acyl group derived from stearic acid (see stearate). It is one of the major fatty-acid components of plant and animal lipids; tallow and other hard animal fats contain up to 35%. Together with palmitate it represents a high proportion of the saturated fatty-acid content of dietary and other lipids. It is synthesized from palmitoylCoA by a microsomal chain-elongation enzyme. It was formerly and sometimes still is (incorrectly) referred to as steary!. stearoyl-CoA desaturase EC 1.14.99.5; systematic name: stearoyl-CoA,hydrogen donor:oxygen oxidoreductase; other names: acyl-CoA desaturase; fatty-acid desaturase; .J9-desaturase. An enzyme that catalyses a reaction between dioxygen, an electron donor and stearoyl-CoA to form oleoyl-CoA. It is an iron protein with a short half-life, and is the only inducible component of the endoplasmic reticulum fatty acyl-CoA desaturase system. It utilizes electrons from reduced cytochrome b s. Example from rat: database code ACOD_RAT, 358 amino acids (41.44 kDa). stearyl 1 a common name for octadecyl, CH3-[CH2l16-CH2-' the alkyl group derived from octadecane; octadecyl is recommended. 2 an old trivial name for octadecanoyl; stearoyl now used instead. steatite see talc. steato+ comb. form indicating presence or relation to fatty substances. steatorrhoea the presence of abnormally large amounts of fat in the feces. steatosis fatty degeneration of tissue. steel factor see stem cell factor. steel factor receptor see KIT. stefin see cystatin. Stein, William Howard (1911-80), US protein chemist; Nobel Laureate in Chemistry jointly with S. Moore (1972) 'for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule' [prize shared with C. B. Anfinsenl. In addition to this he, together with Moore, was responsible for devising the means for automatic analysis of the aminoacid constituents of protein hydrolysates, and free amino acids in body fluids, separated by ion-exchange chromatography. Stelazine see trifluoperazine. stellacyanin a blue copper-containing mucoprotein of low molecular weight obtained from the Japanese lacquer tree, Rhus vernicifera. It functions as an electron-transfer protein, accepting electrons from the cytochrome b6 -f complex and donating them to photosystem I, and has been much studied for the structure of the copper-binding site. STEM abbr. for scanning transmission electron microscope. stem cell any member of the various groups of reserve cells whose role is to replace cells that are destroyed during the normal life of the animal, e.g. blood cells, epithelial cells, spermatogonia, and skin cells. Stem cells can divide without limit; after division, the stem cell may remain as a stem cell or proceed to terminal differentiation. Although appearing morphologically unspecialized, the stem cell may be considered as having reached a state of differentiation where the possibilities for further differentiation are very limited. stem cell factor (abbr.: SCF) or mast cell growth factor or steel factor a cytokine that stimulates the proliferation of mast cells. It is produced by endothelial cells, fibroblasts, bone marrow cells, and Sertoli cells. A homodimer glycoprotein with type I membrane and soluble forms, it is able to augment the proliferation of both myeloid and lymphoid hemopoietic progenitors. It acts as a ligand for the product of the protooncogene

c-kit (see KIT). Example from human precursor: database code SCF_HUMAN, 273 amino acids (30.86 kDa). stem name any generic name of a category of similar compounds, enzymes, organisms, etc. that is used also as an affix in forming the specific names of individual members of such a category. steno+ or (before a vowel) sten+ comb. form indicating narrowness. stenohaline describing an organism that is unable to tolerate wide variations in environmental osmotic pressure. stenothermous describing an organism that is unable to tolerate wide variations in environmental temperature. step gradient a discontinuous gradient, formed in a tube by layering solutions of different densities carefully one on the other. In column chromatography the same effect is achieved by pumping buffers of different composition sequentially through the column. See gradient. steradian symbol: sr; the SI supplementary unit of solid angle. It is equal to the angle subtended at the centre of a sphere by an area of surface equal to the square of the sphere's radius. The surface of a sphere subtends an angle of 41t sr at its centre. stercobilin or stercobilin IXcx a linear tetrapyrrole formed in heme catabolism with a red brown colour. Structurally it is an oxidation product of stercobilinogen, comparable to the urobilinogen-turobilin conversion. Metabolically, it is a major product formed from urobilinogen by intestinal bacteria and is the major pigment of feces.

COOH stercobilinogen an alternative name for 1O,23-dihydrostercobilin; former name, stercobilinogen IXa. A product of heme catabolism; it is a linear tetrapyrrole and structurally is a urobilinogen molecule in which the double bonds between the methyl and ethyl substituents on the two end rings have been reduced.

sterculic acid see cyclic fatty acid. stereo+ comb. form denoting solid or three-dimensional. stereobase unit the smallest set of one, two, or more succes-

618

stereochemistry

steroid-hormone receptor

sive configurational base units that prescribes repetition in a polymer molecule. stereochemistry the branch of chemistry dealing with the three-dimensional properties of molecules; the study of the properties of stereoisomers. See cis-trans isomerism, RelSi convention, sequence rule, stereospecific numbering. stereoheterotopic a term describing chemically-like ligands (or faces of double bonds) whose separate replacement with an achiral ligand (or for faces, addition of an achiral reagent) gives rise to two stereoisomers. If the stereoisomeric products are enantiomers, the ligands (faces) are enantiotopic; if they are diastereoisomers, the ligands (faces) are diastereotopic. for more extensive descriptions, see diastereotopic, enantiotopic. stereoisomer any of two or more isomers that have the same molecular constitution and differ only in the three-dimensional arrangement of their atomic groupings in space. Stereoisomers may be diastereoisomers or enantiomers. Compare constitutional isomer. -stereoisomeric adj.; stereoisomerism n. stereology the body of mathematical methods dealing with the interpretation of the structure and dimensions of three-dimensional objects from information contained in two-dimensional representations, such as photomicrographs of tissue sections. stereoregular polymer a regular polymer composed of molecules having a regular repetition of identical stereobase units at all stereoisomeric sites of the main chain. stereoselective polymerization the formation of a polymer from a mixture of stereoisomeric monomer molecules by preferential incorporation of one species into a growing polymer chain. stereospecific (of an enzymatic or other reaction system) acting on or producing a particular stereoisomer; stereochemically specific. -stereospecificity n. stereospecific numbering a numbering system finding most application for prochiral compounds, Caabe, with two chemically-like atoms, or groups of atoms, a. It provides identifying numbers for the prochiral a groups and, by extension, a numbering system for their chiral derivatives. A stereospecifically numbered compound is designated by the prefix sn- to differentiate it from a conventionally numbered compound. Two systems have been described. That of Hirschmann was 1

2 3 (1) glycerol

(2) sn-glycerol-3-phosphate

yOOH

pro-R

I

COOH

1

2

CH 2 I HOOC-C-QH I CH 2

3 4 pro-S

(3) citric acid

5

devised particularly so that the 14C-Iabelled glycerol giving rise to [3,4-1 4C 2]glucose (in rats) could be termed [1_14C] glycerol and thus be related, biosynthetically and by nomenclature, to [l-14C]lactate. It uses the basic RIS system (see sequence rule) to set up a model, which is viewed away from the group with the lowest sequence priority. If this is e in Caabe, a counterclockwise ordering is examined for the remaining three groups, baa, starting with b. The first a group to be encountered receives the lower number. The numbering for glycerol is shown in structure I. By extension, the naturally occurring glycerol phosphate formed by the action of glycerol kinase becomes sn-glycerol 3-phosphate (structure 2). This structure has also been described as D-glycerol 3-phosphate, L-glycerol 3-phosphate, and L-a-glycerophosphate. The Hirschmann nomenclature has found wide acceptance in the lipid field. The other method, the Hanson and Hirschmann system, expands the RIS system in a logical fashion (rather than using the arbitrary counterclockwise ordering described for glycerol). The two chemically-like groups, a, of Caabe are first given pro-R and pro-S assignments. Then, following the established' R precedes S rule', pro-R precedes pro-S, and the pro-R group is assigned the lower number. This system has been applied to citric acid as shown in structure 3. Application of this system to glycerol unfortunately leads to the product of glycerol kinase being sn-glycerol I-phosphate. Although this system has a logical basis in terms of established nomenclature, it seems unlikely that the sn system for glycerol and derivatives will be brought into line. stereospecific polymerization a polymerization in which a tactic polymer is formed. steric relating to effects involving arrangements of atoms in space. steric hindrance 1 prevention of the free rotation of an atom or group in a molecular entity with respect to a connected one due to the relative sizes andlor spatial disposition of the atoms or groups in question. 2 restriction or prevention of the reaction of a molecular entity with another due to the relative sizes andlor spatial disposition of atoms or groups in either or both of the reactants. sterile 1 (of inanimate objects) free from microbiological or other life forms. 2 (of a living organism) incapable of sexual reproduction. sterilize or sterilise 1 to treat in such a way as to kill undesired microorganisms without damaging the material under treatment. Compare disinfetdon. 2 to render incapable of sexual reproduction. -sterilization or sterilisation n. Stern-Volmer equation an expression relating fluorescence quenching to the concentration of the quenching substance, e, and the fluorescence lifetime, r. It is: FolF = I + kef, where Fo is the fluorescence intensity when no quencher is present, F is the fluorescence intensity in the presence of quencher, and k is a constant that depends on the system; the concentration of the absorbing molecule must be the same in both quenched and unquenched systems. The Stern-Volmer plot is a plot of FolF against concentration of quenching substance, from the slope of which, if the fluorescence lifetime is known, the quenching constant can be obtained. [After Otto Stern (1888-1969) and M. Volmer]. steroid any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene. The group includes such natural products as bile acids, corticosteroids, sex hormones, sterols, and various plant steroids. See also vitamin D. steroid diabetes a condition involving decreased glucose tolerance, fasting hyperglycemia, and glucosuria, found in patients exposed to excessive quantities of glucocorticoids. It may thus accompany Cushing's syndrome. steroid-hormone receptor any member of a family of intracellular receptors that bind steroid hormones and mediate their effects; the family also includes receptors for thyroid

619

stoichiometry

steroid ..4-isomerase hormones, retinoids, and vitamin D. After binding steroid that has entered the cell, the steroid-receptor complex is translocated to the nucleus and binds to a specific DNA sequence, a response element. The receptors are composed of three domains: a modulating N-terminal domain, a DNA-binding domain, and a C-terminal steroid-binding domain. Their zinc fingers are characteristic (four motifs). Examples (human), steroid-hormone receptor ERR I: database code ERR 1_ HUMAN, 521 amino acids (55.68 kDa); estrogen receptor: database code ESTR_HUMAN, 595 amino acids (66.18 kDa). steroid il-isomerase EC 5.3.3.1; systematic name: 3-oxosteroid j5-j4-isomerase; other name: Ll5-Ll4-ketosteroid isomerase. An enzyme (dimer) involved in microbial transformation of steroids; it catalyses the reaction: 3-oxo-j5-steroid = 3-oxo-j4-steroid. Example from Comamonas testosteroni (Pseudomonas testosteroni): database code SDIS_COMTE, 125 amino acids (13.38 kDa). steroid 21-monooxygenase EC 1.14.99.10; other names: steroid 21-hydroxylase; cytochrome P450 2IAI; an enzyme that catalyses a reaction between dioxygen, an electron donor, and a steroid to form a 21-hydroxysteroid. It is a heme-thiolate protein. A deficiency underlies congenital adrenal hyperplasia: there is a failure to synthesize cortisol, and this results in overproduction of corticotropin, as well as of 17-hydroxyprogesterone and androstenedione. Example from human: database code CPSLHUMAN, 494 amino acids (55.82 kDa). steroidogenesis the biosynthesis of steroids, but often referring to the genesis of other steroids from cholesterol. sterol any of a group of steroids characterized by the presence of one or more hydroxyl groups and a hydrocarbon side-chain in the molecule. sterol D-acyltransferase EC 2.3.1.26; other names: cholesterol acyltransferase; sterol-ester synthase; an intracellular enzyme that catalyses the formation of cholesterol ester from acyl-CoA and cholesterol. It is involved in the storage of cholesterol esters in phagocytic cells, a process that plays a part in producing lipid-laden cells in arterial walls. Example from human: database code ACAT_HUMAN, 550 amino acids (64.77 kDa). steryl-sulfatase EC 3.1.6.2; other names: steroid sulfatase (sulfatase); steryl-sulfate sulfohydrolase; arylsulfatase C; an enzyme that catalyses the hydrolysis of 3-p-hydroxyandrost-5en-17-one 3-sulfate to 3-p-hydroxyandrost-5-en-17-one and sulfate. Example (precursor) from human: database code STS_HUMAN, 583 amino acids (65.42 kDa). stevioside 13-[(2- O-p-o- gl ucopyranosyl-t;r- 0- glucopyranosyl)oxy]kaur-16-en-18-oic acid p-o-glucopyranosyl ester; a glycoside extracted from the leaves of Stevia rebaudiana (yerba dulce). It is used liS a sweetening agent, being about 300 times as sweet as sucrose.

STH abbr. for somatotropic hormone; see somatotropin. STI abbr. for soybean trypsin inhibitor. sticky end see cohesive end. stigmasterol 3p-hydroxy-24-ethyl-Ll 5,22-cholestadiene; a phytosterol structurally related to p-sitosterol (see sitosterol) and

found in plant oils.

stilbestrol or (esp. Brit.) stilboestrol 4,4'-dihydroxystilbene; a

synthetic nonsteroid compound, first prepared in 1938, that proved to be the mother substance of a range of compounds with estrogenic activity, of which a,p-diethylstilbene (see diethylstilbestrol) is the most active. Stilbestrol was formerly used as a growth promoter in farm animals but is now banned in most countries. However, it is still sometimes used to treat hormonal disorders in small animals. It was formerly used to treat prostatic cancer but there is some evidence for its carcinogenicity.

OH

trans-stH bestrol still an apparatus for the distillation of liquids, including the preparation of distilled water. It consists of a heated vessel, a

condenser, and a receiver. A continuous apparatus incorporates an automatic feed for the liquid in question, a heating element, and a thermoregulator. stimulate (in physiology) to provide a stimulus to any tissue or cell leading to its excitation or to initiation of a sequence of events with some defined endpoint, involving an electrical event, activation of a metabolic pathway, or initiation of cell division or growth. -stimulation n.; stimulative ad}. stimulus (in physiology) any event or phenomenon, such as radiation, electrical potential, or addition of molecules that leads to excitation of a tissue or cell. stimulus-response coupling a molecular mechanism, often involving signal transduction, that transmits a stimulus from the exterior of a cell's plasma membrane, in many cases through second messenger pathways, to effector systems that bring about a response. For example, in stimulus-secretion coupling the effector system brings about a secretion event such as degranulation of mast cells or release of hormone (e.g. insulin) from storage granules to the cell exterior. stimulus-secretion coupling see stimulus-response coupling. stochastic arrived at by skilful conjecture; e.g. a stochastic model, a stochastic process. stock solution a solution of a reagent, at a stable or convenient concentration, from which appropriate dilutions can be made at the time of use. Stock system (in inorganic nomenclature) a system of designating the oxidation number of an element by placing a Roman numeral in parentheses immediately following the name of the element or, where symbols are used, in superscript to the right of the symbol; e.g. manganese(Iv) oxide, MnIV02' stoichiometry or (rarely) stoicheiometry the quantitative relationship of the reactants and products of a chemical reaction

620

stokes in the proportions that they appear in the chemical equation describing the reaction. -stoichiometric or stoicheiometric adj. stokes symbol: St; the cgs unit of kinematic viscosity; its use is now discouraged. In SI units, kinematic viscosity is measured in square metres per second; I St = 10-4 m 2 s I. [After (Sir) George Gabriel Stokes (1819-1903), British mathematician.] Stokes' law of fluorescence a law stating that the wavelength of the emitted fluorescent light, Aem , is greater than that of the light exciting the fluorescence, A. ex • This relationship is true for most fluorescent materials; those for which it does not hold are termed anti-Stokes. Stokes' law of viscosity a law stating that the frictional coefficient, f, of a spherical particle of radius r, moving through a liquid of viscosity 1/, is given byf= 67C1/r. Stokes' loss the loss of excitation energy available for fluorescence due to collision of molecules in the first excited state, Sj, with their neighbours, which results in a lower vibration level of St. Stokes' shift the difference in wavelength between the excitation and emission maxima for a particular fluorescent substance. In quantitative form, Stokes' shift is 10 7(I/A ex ~ I/A em ), where Aex and Aem are the corrected maximum wavelengths for excitation and emission expressed in nanometres. stoma (pl. stomata) any of the pores occurring in the epidermis of plants, particularly in leaves, through which gaseous exchange takes place. stop codon any of the trinucleotide codons, UGA, UAG, and UAA, that signal the termination of translation of a messenger RNA molecule and the release of the nascent polypeptide chain. See also termination codon. stopped-flow technique a method in which two solutions are caused to flow into a mixing chamber and then into an observation chamber, after which the flow is caused to stop abruptly and the time course of the chemical reaction can be followed, usually spectroscopically, as the mixture in the observation chamber ages. Critical features include the quality of mixing, the speed with which the mixed solution fills the observation volume, and the geometry of the observation volume in relation to the sensitivity of observation. See also rapid-reaction kinetics. STOP protein abbr. for stable tubule only polypeptide; a pro-

tein that blocks the endwise dissociation of microtubules. stop-transfer protein see signal peptide. storage granule any small organelle, bounded by a membrane having a single lipid bilayer, that contains stored material. For example, mast-cell storage granules contain histamine, while those of pancreatic B cells contain insulin; in both cases the stored material is destined for secretion. This involves a stimulus applied to the cell that causes fusion of the granule membrane with the plasma membrane, followed by release of the granule contents by exocytosis. storage polysaccharide any polysaccharide that serves as a form of stored energy in living organisms. Storage polysaccharides include starch, phytoglycogen (e.g. in maize), and fructosans (e.g. inulin) in plants, and glycogen in animals. stp or s.t.p. or STP abbr. for standard temperature and pressure. straight-chain describing any chain of carbon atoms in which none of the carbon atoms is directly bonded to more than two other carbon atoms. strain 1 a group of related individuals having certain characters that distinguish the members from other such groups within the same species or variety; a race. 2 a line of organisms descended or derived from a particular ancestral individual. 3 (in physics) the temporary or permanent deformation of a body resulting from an applied stress. streptavidin a tetrameric biotin-binding protein (subunit M r 14 500) produced by Streptomyces avidin ii, capable of binding up to four molecules of biotin per molecule. It is useful in techniques such as enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, immunocytochemistry, and protein blotting. It is also used with DNA probes as a detection reagent,

streptolydigin where biotin can be incorporated into the molecule under study; streptavidin can then be used to bind to the biotin. The streptavidin may be labelled with File, gold, peroxidase, or another agent directly as a detection reagent. Alternatively, a biotin-labelled detection system (such as alkaline phosphatase) can be bound to streptavidin through another of its biotin-binding sites. Streptavidin has the advantage over avidin (also used in such techniques) of having a near-neutral isoelectric point (7.25-7.45); consequently its use results in less nonspecific binding. See also biotinylation. streptidine 1,3-diguanido-2,4,5,6-cyclohexanetetrol; the noncarbohydrate component of streptomycin.

streptobiosamine 5-deoxy-2- O-[2-deoxy-2-(methylamino )-a-

L-glucopyranosyl]-3-C-formyl-L-Iyxose; a disaccharide component of streptomycin, containing streptose and N-methylglucosamine.

o

~;';-OH Hi:r----f

>?;"oJ ~ OH

R= NHCH3

Streptococcus a genus of Gram-positive, facultatively or obligately anaerobic cocci or coccoid bacteria, of biochemical significance for their production of streptokinase, streptolysin, and streptodornase. streptodornase any of the extracellular deoxyribonucleases produced by streptococci. At least four such serologically distinct nucleases are known. Some or all have the characteristics of deoxyribonuclease I (EC 3.1.21.1), bringing about endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products. [From streptococcal deoxyribonuclease.] streptokinase any of a number of extracellular proteins produced by certain streptococci; they exhibit no enzymic activity, despite the name. In human blood streptokinase forms a tight 1:1 complex with plasminogen that catalyses the activation of plasminogen to plasmin, and this in turn lyses fibrin clots. It has been used therapeutically after heart attacks and strokes. It is assumed that streptokinase assists the invasiveness of pathogenic streptococci. Example, streptokinase A precursor from Streptococcus pyogenes: database code STRP_ STRPY, 440 amino acids (49.84 kDa); residues 1-26 are the signal, 27-440 the protein. streptolydigin an antibiotic, derived from Streptomyces lydicus, that possesses potent antibacterial action, particularly against anaerobes and some Gram-positive aerobes. This is probably due to its inhibitory activity against bacterial RNA

621

striated muscle

streptolysin polymerase; it reduces the rate of transcription, slowing the rate of phosphodiester bond formation without affecting the fidelity of transcription. This contrasts with rifampicin, which inhibits initiation. Compare rifamycin.

bacterium Streptomyces griseus, having a relatively broad spectrum of activity against bacteria; it is particularly active against mycobacteria (especially against Mycobacterium tuberculosis), enterobacteria, and staphylococci. It acts at the 30S ribosomal subunit and distorts the A site (aminoacyl site), thereby causing miscoding or prevention of binding of aminoacyl-tRNA. The components of streptomycin are streptidine, streptose, and N-methyl-L-glucosamine. streptose L-streptose; 5-deoxy-3-C-formyl-L-lyxose; a component of streptomycin and streptobiosamine.

streptolysin either of two dissimilar hemolysins produced by certain streptococci (particularly of group A). Streptolysin-O (oxygen-sensitive) is produced by culture in serum-free medium. Its hemolytic activity is destroyed by oxygen (but restored by certain mild reducing agents, e.g. 2-mercaptoethanol) and inhibited by free cholesterol. It is immunogenic, the level of circulating antibody (antistreptolysin-O, ASO) being useful clinically in the diagnosis of streptococcal infections. Hemolysis by streptolysin-O is not complement-dependent. Streptolysin-O can also lyse lysosomes. Biochemically and serologically it resembles O-toxin of Clostridium perfringens. It can be used as an agent to permeabilize cells. Streptolysin-S (serum-dependent) is oxygen-insensitive and its production is promoted by serum proteins. Its hemolytic activity is inhibited by certain phosphatides, e.g. phosphatidyl ethanolamine, at low concentration. It is nonimmunogenic, and is also toxic to leukocytes. Streptomyces a genus of filamentous, spore-forming, Grampositive bacteria that are largely responsible for the 'earthy' smell of soil but are chiefly remarkable for the diversity of secondary metabolites that they produce, including clinically useful antibiotics, e.g. streptomycin. They are amenable to genetic manipulation with many plasmid and phage vectors; this provides a unique opportunity for overexpression and for the design and synthesis of novel and 'hybrid' antibiotics. See also streptomycete. streptomycete strictly, any member of the bacterial genus Streptomyces. However, the term may sometimes be extended to include certain related types, including Streptoverticillum spp. streptomycin an aminoglycoside antibiotic produced by the soil

streptovaricin anyone of a group of ansamycin antibiotics obtained from Streptomyces spectabilis. Compare rifamycin.

W~

Streptovariein

A

OH

X

y

OH OH OH OH

Ae Ae

Z

B

H

C

H

D E

H H H 0= H

G

OH

H

J K

OH

R

- - - - -

OH OH OH H OH OH OH OH

H

OH OAe OAe

H H H

COOCH3 COOCH3 COOCH 3 COOCH 3 COOCH3 COOCH 3 COOCH 3 COOCH 3

streptozocin 2-deoxy-2-(3-methyl-3-nitrosoureido)-D-glucopyranose; a broad-spectrum antibiotic, antineoplastic, and diabetogenic substance isolated from Streptomyces achromogenes. It has a rapid and specific cytotoxic effect on the B cells in pancreatic islets, and is used to induce experimental diabetes in animals and for chemotherapy of insulinoma or other islet-cell neoplasms in humans. It acts as a methylating agent for DNA.

H~OCH20 OH HO

OH

N=O

HNyN/

'CH3

o a-D-streptozocin striated muscle muscle in which the thick filaments and thin liIa-

strict aerobe

622

ments are arranged in microscopically visible bands producing a striped appearance. Such an arrangement is typical of skeletal muscle and cardiac muscle. Compare smooth muscle. See also sarcomere. strict aerobe see aerobe. strict anaerobe see anaerobe. stringency (in molecular biology) the rigour with which the ability of complementary DNA sequences to recognize each other (and thus to hybridize) is tested. As temperature is increased it becomes less likely that more distantly related sequences will hybridize; hence, high stringency is associated with high temperature. stringent very rigorous. See also stringency, stringent control, stringent plasmid, stringent response. stringent control a mechanism of control of plasmid replication whereby the plasmid is replicated only once for each time the chromosome is replicated, thus regulating the plasmid copy number. stringent factor a protein associated with ribosomes, and encoded by the gene felA, that is associated with the stringent response. The stringent factor is associated with enzyme activity that donates a pyrophosphate group to 3' of either 5'-GTP or GDP for the production of pppGpp and ppGpp, which probably act as allosteric modulators mediating the stringent response. See also relaxed mutant, spoT. stringent plasmid a plasmid that has a limited number of copies per cell. stringent response a response by bacteria to poor growth conditions (e.g. lack of amino acids) in which the cell shuts down protein synthesis and other metabolic activity. See also relaxed mutant, stringent factor. strip 1 to remove adherent, admixed, or combined substances or material from a fundamental, underlying, or required substance or structure. 2 (in molecular biology) a to remove polysomes from rough endoplasmic reticulum in vitro to produce stripped membranes (see degranulation (def. 2». b to remove ribosomal proteins from a ribosome to produce a core particle. c to remove the amino acid from an aminoacyl-transfer RNA molecule to produce stripped transfer RNA. d to remove hybridized probe (deL 3) from a transfer membrane prior to reprobing. 3 (in biochemistry) to remove endogenous 2,3-bisphosphoglycerate from a hemoglobin solution to produce stripped hemoglobin. 4 to remove liquid components from a gaseous mixture. stripped hemoglobin a hemoglobin solution from which endogenous 2,3-bisphosphoglycerate has been removed, e.g. by gel filtration or dialysis at high NaCI concentrations. stripped membrane rough endoplasmic reticulum from which polysomes have been removed in vitro. This technique has been applied mainly to membranes from dog pancreas, which lack ribonuclease; the ribosomes are removed by treatment with EDTA. stripped transfer RNA a molecule of aminoacyl-transfer RNA from which the amino acid has been hydrolytically removed. stroma (pl. stromata) 1 fibrous connective tissue or other intercellular material that forms the structural framework of an organ, as opposed to the functional tissue (parenchyma). 2 the spongy framework of protein strands within a red blood cell in which the hemoglobin is packed. 3 (in botany) the space enclosed by the double membrane of a chloroplast but excluding the thylakoid space. It contains DNA, ribosomes, and some temporary products of photosynthesis. 4 (in mycology) a mass of interwoven hyphae in which fruiting bodies (perithecia) develop. -stromal adj. stromelysin EC 3.4.24.17; other names: matrix metalloproteinase-3 (abbr.: MMP-3); transin-I; an enzyme that catalyses the degradation of fibronectin, laminin, and some (but not all) gelatins and collagens. Zn 2 + and Ca 2 + are cofactors. It is a glycoprotein of the extracellular matrix. Example, stromelysin I precursor from human: database code COG3_HUMAN, 477 amino acids (53.92 kDa).

sub+ strong acid an acid that remains ionized at all except the lowest pH values, i.e. one that has a large acid dissociation constant. strong base a base that remains ionized at all except the highest pH values, i.e. one that has a large basic dissociation constant. strophanthin a highly toxic glycoside mixture produced by Strophanthus kombe, with actions similar to those of digoxin and ouabain. structural gene any gene that carries the genetic information determining the structure, and therefore the specificity of function, of a protein. One or more structural genes may be contained in an operon. Compare regulator gene. structural polysaccharide any of several components of a plant cell wall that perform a structural function. They can be divided into three solubility classes: pectins, extractable with dilute acid; hemicelluloses, extractable with aqueous alkali; and microfibrillar polysaccharides. structure factor a parameter describing the scattering of electromagnetic radiation (e.g. X-rays) by an electron. It is the ratio of the radiation scattered by any real sample to that scattered by a single electron at the origin. Strutt, John William, Lord Rayleigh (3rd Baron Rayleigh) (1842-1919), British mathematician and physicist noted inter alia for his contributions to the theory of sound, for his investigations of physical optics, e.g. Rayleigh scattering, and for his discovery (with W. Ramsay) of argon; Nobel Laureate in Physics (1904) 'for his investigations of the densities of the most important gases and for his discovery of argon in connection with these studies'. strychnine a bitter alkaloid obtained from seeds of the Indian tree Strychnos nux-vomica. It is highly toxic, and is sometimes used to poison moles, rodents, and other vermin. Its lethal convulsant action is a result of antagonism of the inhibitory transmitter, glycine, in the spinal cord (see glycine receptor). See also brucine.

STS abbr. for sequence-tagged site. Stuart factor or Stuart-Prower factor an alternative name for factor X; see blood coagulation. [After a Mr Stuart, in whom the deficiency was first described.] Student's t test a statistical test, based on a distribution due to William Sealy Gosset (1876-1937) writing in 1908 under the pseudonym 'Student', that can be applied to small samples of data, x. In this distribution t depends only on the sample size, N, and not on the variance of the population; as N increases, the distribution curve of t approaches a normal distribution curve more closely. STX abbr. for saxitoxin. sU symbol for a residue of the ribonucleoside thiouridine (when the position of the thiol group in its thiouracil moiety is unspecified or unknown; alternative to S or Srd). S2U symbol for a residue of the ribonucleoside 2-thiouridine (alternative to 2S). S4U symbol for a residue of the ribonucleoside 4-thiouridine (alternative to 4S). sub jargon term for subculture (def. I). sub+ prefix 1 beneath, under, at the bottom (of). 2 immediately below in order, rank, or status; secondary. 3 less than, partial(ly), imperfect(ly). 4 in place of. 5 denoting a subordinate part or subdivision of a whole. 6 (in chemical nomenclature) designating a compound that contains less than the usual pro-

623

subtrahend

subcellular portion of a specified element; e.g. carbon suboxide, C Z0 3• Compare infra+, super+. subcellular describing organelles, functional units, or other components that are found within cells or derived from cells. subcellular organelle a pleonasm that is commonly used to describe organelles (which by definition are subcellular). subclone to clone into a new vector a subfragment of part of a larger cloned DNA, after excising the required fragment using restriction endonucleases. subculture 1 to prepare a fresh culture from a small sample of an existing culture. 2 a culture prepared in such a way. subcutaneous abbr.: s.c.; below the skin. suberin the polymeric substance that covers the epidermal cell layer in the underground parts of plants (e.g. roots and tubers). It is a polyester containing w-hydroxy fatty acids and aromatic fatty acids, e.g. ferulic acid. sublime to vaporize from the solid without passing through a liquid phase. -sublimation n. submaxillaris protease an endopeptidase isolated from the submaxillary gland of mice. It acts specifically at Arg-j-Xaa bonds. submaxillary relating to the region beneath the upper jaw (maxilla). submaximal below the maximal. submitochondrial particle any particle derived by disruption of mitochondria. See W-transporting ATPase, complex I, II. III. IV. submolecular describing any chemical or chemical component that exists or functions at a lower level of complexity than that of intact individual molecules. The term may be used in reference to electrons, ions, free radicals, or other molecular fragments. Compare supramolecular. subnatant 1 lying under. 2 a liquid lying under a supernatant or under solid material. Compare infranatant. suboptimal below or failing to reach the optimal condition. subsite a site, e.g. on a protein, that has a specific function within the overall function of a larger site. substance K see neurokinin A. substance K receptor or neurokinin A receptor or NK-2 receptor a membrane protein that binds substance K and mediates its intracellular effects. It is a G-protein-coupled, seven-transmembrane-domain protein that activates the phosphBtidylinositol cycle. Example from Bas taurus: database code NK2R_BOVIN, 384 amino acids (43.07 kDa). substance P abbr.: SP; an II-residue amide, H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH 2, found in most tissues of the mammalian body but at highest concentrations in nervous tissue (both central and peripheral) and in gut tissues. It also occurs in the central nervous system of many other vertebrtates. Derived from protachykinin 13 precursor, it is a tachykinin; its main pharmacological actions are to cause hypotension and vasodilatation, and to stimulate contraction of the intestine and secretion of saliva. However, its physiological function remains to be fully determined. See also tachykinin receptor. substituent group or substituent (in organic-chemical nomenclature) any atom or group (def. I) that has replaced or can be considered to have replaced (i.e. been substituted for) a hydrogen atom in a parent molecular entity, which may be either real or hypothetical; in the special cases of bivalent or tervalent groups there are corresponding replacements of two or three hydrogen atoms. substituted mechanism a mechanism of an enzyme reaction in which the first substrate reacts with the original enzyme to produce a modified enzyme and one product. The modified enzyme then reacts with the second substrate to produce the second product and regenerate the original enzyme, e.g.

E + SI """" E* + PI> then

where E is the enzyme, E * the modified enzyme, SI and S2 the substrates, and PI and P 2 the products. substitution reaction the replacement of a substituent (normally hydrogen), usually at a carbon atom, by any other group. substrate 1 a substance that is acted upon, especially by an enzyme; a molecule or structure whose transformation is catalysed by an enzyme. 2 or substratum a the base upon which an organism grows or lives, e.g. soil or rock. b the material upon which a microorganism grows or is placed to grow. substrate activation the increase of an enzyme's activity by its substrate by an allosteric mechanism. Compare substrate inhibition. substrate cycle interconversion of reactant and product by two enzymes, one of which (A) catalyses the reaction in one direction while the second enzyme (B) catalyses the reaction in the opposite direction, e.g.

+

fructose 1,6-bisphosphate. fructose 6-phosphate As flux (def. 3) (i.e. the rate of reaction catalysed by A minus rate of reaction catalysed by B) through a system varies, the rate of each enzyme reaction may vary independently with concomitant changes in cycling rate. The existence of a substrate cycle increases sensitivity of control, since even if rates of forward and reverse reaction are high, changes in one or both may make relatively larger changes to flux; e.g. if rate of A = 9 and rate of B = 8, then flux = I; if rate of A doubles to 18 and rate of B remains 8, then flux = 10 (i.e. increases tenfold). substrate dissociation constant or (formerly) substrate constant symbol K s; the parameter of an enzymatic reaction that is the equilibrium (dissociation) constant for the reaction ES = E + S; i.e. K s = [E][S]/[ES]. substrate inhibition the inhibition of an enzyme's activity by its substrate by an allosteric mechanism. Compare substrate activation. substrate-level phosphorylation the formation of ATP (or GTP) in a coupled reaction that is not linked to an electron transport system, e.g. coupled to the de acylation of succinyl coenzyme A or the conversion of 3-phosphoglyceroyl phosphate to 3-phosphoglycerate. substrate-site hypothesis a hypothesis for the control of insulin release from pancreatic islet B cells by glucose. It postulates that the glucoreceptor is either a carrier transporting glucose into the cell or an enzyme phosphorylating glucose, and the signal for insulin release is a metabolite in the pathway of metabolism of glucose in the B cell. Compare regulatorsite hypothesis. substratum (pl. substrata) 1 any layer (stratum) or structure that lies beneath another, or that forms a base or underlying support for something else. 2 an alternative term for substrate (def. 2). subtligase one of several engineered derivatives of subtilisin that efficiently ligate peptides. The two mutations converting the peptidase, subtilisin, to a ligase involve Ser 2Z ! to Cys and Pro 225 to Ala. subtilin or subtilin C an antibiotic produced by Bacillus subtitis and active against Gram-positive bacteria, Neisseria spp. (N. catarrhalis, N. gonorrhoeae), and some pathogenic fungi. subtilisin EC 3.4.21.62; a bacterial endopeptidase enzyme isolated from Bacillus subtitis and other Bacillus spp. (e.g. commercially from B. licheniformis). It is a serine endopeptidase that catalyses the hydrolysis of proteins with broad specificity for peptide bonds, with preference for a large uncharged residue at PI (see peptidase P-sites) and low activity for glutamyl residues; it hydrolyses peptide amides. Example from B. subtitis: database code NRL_ISBC, 274 amino acids (27.26 kDa); 3-D structure is known; the enzyme has similar active-site geometry to the trypsin family but otherwise no homology. See also Nagarse proteinase. subtrahend (in mathematics) the number to be subtracted from another number (the minuend).

subunit

624

subunit any polypeptide component within a protein or other

distinct biochemical entity, whether identical to or different from any other components, that is separable from such other components without rupture of covalent bonds. The term is sometimes used in a more restricted sense as referring to any chemically or physically identifiable submolecular entity within a protein, whether identical to, or different from, other components. subunit-exchange chromatography a form of chromatography in which protein subunits are immobilized on a solid matrix and allowed to interact with protein subunits in solution. Quantification of subunit exchange between the matrix and solution may be used in analysing the association-dissociation properties of the protein system. The method also provides a powerful, specific purification method. Sue- symbol for succinyl (def. 1). -Suc- or Suc< symbol for succinyl (def. 2). succinamic acid a trivial name for 3-carbamoylpropanoic acid, the monoamide of succinic acid. succinamide a trivial name for butanediamide, the diamide of succinic acid. succinate 1 a trivial name for butanedioate; ethanedicarboxylate; the dianion of succinic acid. It is an important intermediate in metabolism and a component of the tricarboxylic-acid cycle. 2 any mixture of free succinic acid and its mono- and dianions. 3 any salt or ester of succinic acid. succinate-CoA ligase (GOP-forming) EC 6.2.1.4; other name: succinyl-CoA synthetase (GDP-forming); an enzyme of the tricarboxylic-acid cycle that catalyses the formation of succinyl-CoA from GTP, succinate, and CoA with release of GDP and orthophosphate. Examples: a-chain precursor from rat: database code SUCA_RAT, 333 amino acids (34.99 kDa); ~ chain (from pig): database code A44529, 417 amino acids (45.10 kDa). succinate dehydrogenase EC 1.3.99.1; systematic name: succinate:(acceptor) oxidoreductase; other names: fumarate reductase/dehydrogenase; fumaric hydrogenase. A bacterial enzyme, or a degraded entity from succinate dehydrogenase (ubiquinonel, a major component of mitochondrial complex II (see respiratory complex). It catalyses the oxidation of succinate by an acceptor to form fumarate and a reduced acceptor; it does not react with ubiquinone. It is a flavoprotein (FAD) and plays an important role during anaerobic growth. Example from Escherichia coli; there are four subunits: (I) cytochrome bS56 ; (2) an iron-sulfur protein: database code DHSB_ECOLI, 238 amino acids (26.74 kDa); (3) a flavoprotein related to succinate dehydrogenase (ubiquinone): database code DHSA_ ECOLI, 588 amino acids (64.33 kDa); and (4) a hydrophobic anchor protein. succinate dehydrogenase (ubiquinone) EC 1.3.5.1; systematic name: succinate:ubiquinone oxidoreductase; other name: succinic dehydrogenase. An enzyme that catalyses the oxidation of succinate by ubiquinone to form fumarate and ubiquinol. It is an iron-sulfur flavoprotein (FAD), containing at least four different subunits: a flavoprotein, an iron-sulfur protein, and two hydrophobic anchor proteins. It is located in the mitochondrial inner membrane, where it is a major component of complex II (see complex I, II, III, IV) of the respiratory chain. Example, FAD, subunit (precursor) from bovine: database code DHSA_BOVIN, 664 amino acids (73.63 kDa). Two other examples (subunits, precursors, from yeast); flavoprotein subunit: database code DHSA_YEAST 640 amino acids (70.15 kDa); iron-sulfur protein subunit: database code DHSB_YEAST 266 amino acids (30.20 kDa). succinate-semialdehyde dehydrogenase EC 1.2.1.24; an enzyme that catalyses the reaction: succinate semialdehyde + NAD+ + H 2 0 = succinate + NADH. Succinate semialdehyde can undergo transamination to form y-aminobutyric acid. However, the transaminase primarily

sucrase functions to convert y-aminobutyrate to succinate-semialdehyde, which is then converted to succinate by succinate-semialdehyde dehydrogenase in the catabolism of y-aminobutyrate. See also 4-aminobutyrate transaminase. succinic dehydrogenase see succinate dehydrogenase (ubiquinone). succinimide a trivial name for butanimide; 2,5-pyrrolidinedione; the imide of succinic acid. For structure see +imide. succinoglycan an acidic exopolysaccharide needed for sym-

biosis between Rhizobium meliloti and alfalfa. Also synthesized by other bacteria, it is a polymer of octasaccharide subunits (one galactose and seven glucose residues) with acetyl, succinyl, and pyruvyl modifications. succinyl 1 (in biochemistry) symbol: Suc-; the univalent acyl group 3-carboxypropanoyl, HOOC-[CH 2h-CO-, derived from succinic acid by loss of one hydroxyl group. 2 (in chemistry) symbol: -Suc- or Suc neurokinin A (NKA) > neurokinin B (NKB); (2) NK 2 (398 amino acids, human), agonist potency: NKA > NKB» SP; and (3) NK 3 (452 amino acids, rat), agonist potency: NKB > NKA > SP. All are of the seven-transmembrane-domain type and share significant sequence similarity with G-protein-coupled receptors. The effector pathway in all cases is by activation of phosphoinositide-specific phospholipase C. Example of putative receptor from human: database code TXKR_HUMAN, 440 amino acids (49.43 kDa). tachyphylaxis a decline in the response to repeated applications of doses of agonists. See also desensitization, fade. tachyplesin any of a group of arthropodous peptide antibiotics, 17 or 18 amino acids long and with a C-terminal arginine a-amide. They are abundant in acid extracts of hemocyte debris of horseshoe crabs (Tachypleus spp.). They strongly inhibit the growth of Gram-positive and Gram-negative bacteria, and of fungi such as Candida albicans. Example from Tachypleus gigas: database code TAC3_T ACG1, 17 amino acids (2.24 kDa). tae promoter a hybrid promoter, constructed in vitro, that contains the -35 sequence of the trp promoter and the -10 sequence of the lacZ promoter. See minus 10 region. Tacrolimus see FK506. tactic polymer a regular polymer in whose molecules there is an ordered structure with respect to the configurations around at least one main-chain site of stereoisomerism per constitutional base unit. tactile capable of exciting the sense of touch; relating to the sense of touch (as a sense organ). tactoid a paracrystal-like aggregate; the term may be applied to the rodlike filaments of hemoglobin that form in sickle cells, or to assemblies of virus particles (e.g. of tobacco mosaic virus). tag 1 to identify by a marker; for example, a cell may be tagged by attachment of a (fluorescent or radiolabelled) antibody. 2 an identifier used in tagging. Tagamet see cimetidine. D-tagatose a nonsystematic name for o-lyxo-2-hexulose, a hydrolysis product of some plant gums.

a-o-pyranose form

Tagit a proprietary name for N-succinimidyl 3-(4-hydroxyphenyl) propionate; a substance used in the preparation of Bolton and Hunter reagent for tagging peptides and proteins with radioiodine.

tail 1 an extension growing or appending from a point of origin

633

tailing

tannin

or attachment. For example, the fatty-acyl groups of a phospholipid and the glycerol to which they are bonded are referred to as the tail. Compare headgroup. 2 (in chromatography) a region of more slowly moving or decomposed material extending back from a band towards the origin. See also poly(A) tail, tailing. tailing 1 the addition of a stretch of identical nuc1eotides to the ends of a restriction fragment using terminal deoxynucleotidyl transferase. 2 the spreading out of a band or spot in a chromatographic process. Tal symbol for a residue, or sometimes a molecule, of talose. talaric acid one of the hexaric acids; see also aldaric acid. talc a soft mineral composed of hydrated magnesium silicate, Mg 3Si4 0 lO (OHh, with small quantities of metal impurities. In its powdered form it is known as talcum powder, or French chalk, and in granular form as soapstone (steatite). Powdered talc is used as a lubricant, as a fiJIer in paper and other products, and in cosmetics, etc. talcum powder powdered talc. talin a protein involved in connections between the cytoskeleton and the plasma membrane. A phosphoprotein, it binds strongly to vinculin, and less strongly to integrins. It is a founder member of the TERM family. Example from mouse: database code TALI_MOUSE, 2541 amino acids (269.53 kDa). talo+ or (before a vowel) tal08+ comb. form of 18lose. tal~ prefix (in chemical nomenclature) indicating a particular configuration, a set of (usually four) contiguous CHOH groups as in the acyclic form of D- or L-talose. See also monosaccharide. talopeptin N-( 6-deoxy-a-L- talopyranosyl-oxyphospho)-Lleucyl-L-tryptophan; an inhibitor of several metallopeptidases, including thermolysin. Compare phosphoramidon. talosaminouronic acid a component of the peptidoglycan of Archaea.

CHO

I H2N- C- H I

HQ-C-H I HQ-C-H I H-C-OH I COOH

talose symbol: Tal; the trivial name for the aldohexose talo-hexose, which differs from glucose in the configuration of the groups at C-2 and C-4; there are two enantiomers. 2

~

HO

0 OH OH

OH

a-o-talose Tamm. Igor Yevgenyevich (1885-1971), Russian-born Soviet physicist; Nobel Laureate in Physics (1958) jointly with P. A. Cherenkov and I. M. Frank 'for the discovery and the interpretation of the Cherenkov effect'. Tamm-Horsfall glycoprotein or uTomodu)in the principal glycoprotein of human urine. It occurs in other species, e.g. the cow and rat. The molecule is filamentous with an M r of several miJIion and is composed of subunits of M r ~80 000; it contains about 25% carbohydrate and a small amount of lipid. An abnormally high M r is observed in cystic fibrosis. Example from human (precursor): database code UROM_HUMAN,

640 amino acids (69.76 kDa). See also proteinuria. [After Igor Tamm (1922-71), US virologist and Frank Lappin Horsfall (1906-71 ).1 Tamoxifen [Zl-2-[4-(1,2-diphenyl-l-butenyl)-phenoxy)-N,Ndimethylethanolamine; the proprietary name of an estrogen antagonist, used in the treatment of breast cancer and suggested for use as a prophylactic drug in women with a family history of breast cancer. The drug has complex pharmacological properties and can behave as a pure estrogen agonist, a partial agonist, or an antagonist, depending on the species of animal, the target organ examined, and the endpoint measured. It is a genutoxic carcinogen in the rat.

tan abbr. for tangent (def. I). tandem-crossed immunoelectrophoresis see crossed immunoelectrophoresis. tandem repeat 1 (of DNA sequences) an arrangement in which two or more copies of a particular base sequence are situated immediately one after the other. Tandem repeats are commonly found in telomeres, the repeated sequence being characteristic of species and source of DNA, and of relatively short length (up to about 10 bases). They also occur in highly repetitive DNA. 2 (of genes) a cluster of adjacent multiple copies of the same gene. The genes for ribosomal RNA (rRNA) are characteristically contained in tandem clusters, sometimes referred to as ribosomal DNA (rDNA). See also concatemer. Tanford-Kirkwood theory a theory of protein titration curves based on a model in which the charges are taken to be discrete unit charges located at fixed positions on the protein molecule. [After Charles Tanford (1921- ) and John Gamble Kirkwood (1907-59).) tangent 1 abbr.: tan; a function of an angle, being, in a rightangled triangle, the ratio of the side opposite the given angle (if acute) to that of the side opposite the other acute angle. The tangent of an obtuse angle is numerically equal to that of its supplement but of opposite sign. 2 a straight line that touches, but does not cut, a curve or a curved surface. tangential-flow filtration a convenient and rapid method of concentrating cells, cell organelles, or other particulate material, or for eliminating such material from solutions. Using a special apparatus, the suspension containing the material is caused to flow over ('tangential flow') a semipermeable membrane; only material smaller than the membrane pores wiJI pass through the membrane, forming the filtrate, leaving larger matter to be collected (retentate). Tangier disease a rare autosomal recessive condition in humans in which there is a deficiency or complete absence of high-density lipoprotein. Homozygotes have very low levels of apolipoprotein A-I. There is accumulation of cholesterol esters in cells of the mononuclear phagocyte system. The condition is relatively benign as organ function is not affected. [After Tangier Island, Chesapeake Bay; the disease was first found in inhabitants of this island.) tannic acid or tannin or gallotannin or gallotannic acid an imprecise term used for a mixture of hydrolysable tannins (def. I). tannin 1 any of a group of polyphenolic plant products that

634

tanning can be used to tan animal skins to produce leather. The term was introduced in 1796. Tannins are divided into hydrolysable tannins (the larger group) and condensed tannins. The former consist of a core of a polyhydric alcohol, usually glucose, esterified with either gallic acid or hexahydroxydiphenic acid. Condensed tannins are polymers of flavans and never contain sugar residues; they are often termed flavolans. Tannins form insoluble protein tannates with proteins, which, when the protein is a skin protein, forms the basis of tanning (def. I). The liberation of tannins during the extraction of plant enzymes can cause difficulties because they tan enzymes, i.e. form insoluble tannates. The addition of polyvinylpyrrolidone may help to avoid this problem. Good tanning agents should have an M r of between 500 and 3000 and contain sufficient phenolic hydroxyl groups (1-2% of M r ) to form effective cross-links with protein. 2 a common name for tannic acid. tanning 1 a technique of considerable antiquity, being known by the Egyptians around 3000 BC, for producing leather from animal skins by the use of tannin (def. I). Modern methods using chrome salts are faster, taking a few hours rather than weeks. 2 the treating of red blood cells with tannic acid. Such cells are used in a test for anti-thyroglobulin antibodies, after they have been treated with thyroglobulin. The tanning enhances sensitivity. T antigen 1 any of the several early gene products of a genetic locus of certain transforming DNA viruses, including adenovirus, simian virus 40 (SV40), and polyoma virus. The substance originally detected in nuclei of transformed cells by Immunofluorescence (hence the name antigen; the 'T' indicates tumour or transformation) led to the identification of several products, the genes of this locus encoding a number of essential early proteins that are needed for replication. Two products are formed by SV40, known as large T antigen (or T antigen) and small t antigen (or t antigen). Polyoma virus expresses three products from this locus, large T antigen, middle T antigen, and small t antigen. Large T antigen of SV40 alone is sufficient to immortalize primary rodent cells and transform established rodent cell lines. It is a multifunctional protein that is a potent transcriptional activator which promiscuously activates simple promoters containing a TATA box or initiator element and at least one upstream transcription-factorbinding site. Examples, large T antigen from SV40: database code TALA_SV40, 708 amino acids (81.58 kDa); large T antigen from polyoma virus: database code TALA_POVMK, 648 amino acids (74.71 kDa). Middle T antigen of polyoma virus is essential for polyoma-virus-mediated tumorigenesis and cell transformation. It associates with and activates cellular tyrosine kinases, including c-Src, c-Yes, and Fyn, and also binds phosphatidylinositol 3-kinase and protein phosphatase 2A. Example, middle T antigen of polyoma virus: database code TAMCPOVMA, 442 amino acids (48.62 kDa). Small t antigen of SV40 exercises a helper effect in SV40 transformation. It forms complexes with protein phosphatase 2A and regulates the phosphorylation and transcriptional transactivation of CREB protein. It stabilizes p53 in a manner that correlates with enhanced transformation efficiency of SV40. Example, small t antigen from polyoma virus: database code TASM POVMA 195 amino acids (22.81 kDa). 2 an antigen found ~n normai human erythrocytes that is unreactive unless the cells are first treated with neuraminidase. 3 one of the principal protein antigens in the cell wall of Streptococcus spp. 4 abbr. for transplantation antigen (i.e. a class I MHC antigen); see major histocompatibility complex. tapeworm any parasitic flatworm (phylum Platyhelminthes) belonging to the class Cestoda. Taps or TAPS abbr. for N-tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid; 3-{[2-hydroxy-l, l-bis(hydroxymethyl)ethyl]-amino }propanesulfonic acid; a Good buffer substance pKa (20°C) = 8.4. '

TATA-binding protein

Taps

TBq DNA polymerase a heat-stable DNA polymerase from Thermus aquaticus, a thermophilic bacterium. It is used in the

polymerase chain reaction. tare 1 to compensate for the weight of a container, etc. when weighing, by adjusting the balance to zero with the empty container in place before adding the material to be weighed. 2 the weight of the tared vessel or material. target the object at which an action or process is directed. For example, a target cell is the cell under attack by a cytolytic or killer cell or other cytolytic agent, and a target tissue is the tissue that is acted on by any hormone, growth factor, or other agonist. targeting subunits protein subunits that specify the location and catalytic and regulatory properties of protein phosphatases and kinases. target repeat see transposon. target site the site at which a restriction endonuclease cleaves a DNA molecule; usually the same as the recognition site (def. 2). target theory (in radiation chemistry) a theory stating that all single hits on biologically active macromolecules by particles or quanta of ionizing radiation result in damaged and inactive molecules, that no partially active molecules are formed, and that all unhit molecules retain full activity. tartaric acid 2,3-dihydroxybutanedioic acid; 2,3-dihydroxysuccinic acid; one of the aldaric acids formed by oxidation of a tetrose at Col and C-4. The Lg( +) (see OiL convention), or 2R,3R, enantiomer occurs widely in plants, especially grape juice, and in fungi and bacteria; the Dg(-) (or 2S,3S) enantiomer and meso form have limited distribution in plants. The racemic mixture, DL-tartaric acid, sometimes occurs during wine manufacture; it was originally known as paratartaric acid. The first determination of an absolute configuration by anomalous dispersion of X-rays was made on sodium rubidium L(+)-tartrate in 1951. The property of optical activity of some substances was first described by Pasteur in experiments with crystals of sodium ammonium tartrate.

yOOH H-e-OH I HQ-e-H I eOOH

Q,

~

HO

HO

""

,,'

o Her H

QH

L-form

yOOH H-e-OH I H-e-OH I eOOH

HO

Q,

H 0

Y5CHOH groups that occurs in o-threose (see threose for structure) or L-threose, e.g. o-threo-2-pentulose for o-xylulose. Compare erythro-. threoninate 1 threonine anion; the anion, CH 3-CH(OH)CH(NH2)-COO~, derived from threonine. 2 any salt containing threonine anion. 3 any ester of threonine. threonine the trivial name for a-amino-fJ-hydroxybutyric acid; (2R* ,3S*)-2-amino-3-hydroxybutanoic acid; CH 3-CH(OH)CH(NH 2)-COOH; an a-amino acid with two chiral centres.

645

threonine aldolase Because molecules of threonine possess a second chiral centre, at C-3, in addition to the chiral centre at C-2 common to all (;famino acids other than glycine, the enantiomers L-threonine, (2S,3R)-2-amino-3-hydroxybutanoic acid (symbol: T or Thr), and D-threonine, (2R,3S)-2-amino-3-hydroxybutanoic acid (symbol: D-Thr or DThr), are diastereoisomeric with those of allothreonine, (2R* ,3R*)-2-amino-3-hydroxybutanoic acid. [Note: The enantiomers of threonine may also be named semisystematically as derivatives of threose: L,-threonine in aminoacid nomenclature is synonymous with 2-amino-2,4dideoxy-Dg-threonic acid in carbohydrate nomenclature, and Ds-threonine with 2-amino-2,4-dideoxY-L g-threonic acid (the subscript letters d or g being added to the configurational prefixes where there might be uncertainty regarding the reference centre of chirality; see OiL convention).] L-Threonine is a coded amino acid found in peptide linkage in proteins; codon: ACA, ACC, ACG, or ACU. In mammals it is an essential dietary amino acid, is glucogenic, and its deficiency causes fatty liver. The fungal toxins phalloidin and phalloin contain one residue of D-threonine per molecule.

L-threonine

threonine aldolase see glycine hydroxymethyltransferase. threonine dehydratase EC 4.2.1.16; systematic name: L-threonine hydro-lyase (deaminating); other names: threonine deaminase; L-serine dehydratase; serine deaminase. A pyridoxal-phosphate enzyme that catalyses a reaction between Lthreonine and water to form 2-oxobutanoate, NH 3, and water; it acts also on L-serine. There are two types (examples from Escherichia coli): type I is responsible for the first step of isoleucine biosynthesis (serine is an alternative but poorer substrate): database code THDLECOLI, 514 amino acids (56.13 kDa); type 2 is a catabolic enzyme that acts on both serine and threonine, and is properly considered as a hydroxyamino-acid deaminase: database code THD2_ECOLI, 329 amino acids (35.19 kDa). threonine synthase EC 4.2.99.2; systematic name: O-phospho-L-homoserine phospho-lyase (adding water). A pyridoxalphosphate enzyme that catalyses the formation of L-threonine from O-phospho-L-homoserine and water with release of orthophosphate. Example from Escherichia coli: database code THRC_ECOLI, 428 amino acids (47.06 kDa); it shows sequence homology with the serine dehydratase/threonine dehydratase group. threoninium threonine cation; the cation, CHrCH(OH)CH(NH 3+)-COOH, derived from threonine. threonino the alkylamino group, CH 3-CH(OH)CH(COOH)-NH-, derived from threonine. threonin-O"-yl the alkyloxy group, HOOC-CH(NH 2)CH(CH 3)-O-, derived from threonine. threonyl the acyl group, CH 3-CH(OH)-CH(NH 2)-CO-, derived from threonine. threose the trivial name for the aldotetrose threo-tetrose; it has D and L enantiomers, which are respectively diastereoisomeric with those of erythrose. See also threo-.

CHO I HO-C-H I H-C-OH I CH2 0H

~O~

)--YbH OH

a-o-th reose

thromboxane

threshold the value that must be achieved or exceeded for an effect to become discernible. For example, the kidney threshold of excretion, for any substance, is the plasma concentration at which not all of the substance that appears in the filtrate can be reabsorbed, so that it appears in the urine. THRF abbr. for thyrotropic hormone releasing factor; i.e. thyrotropin-releasing hormone. THRH abbr. for thyrotropic hormone releasing hormone; I.e. thyrotropin-releasing hormone. thrombin EC 3.4.21.5; other name: fibrinogenase; a serine proteinase, M r 33 700-33 900, the natural coagulant of fibrinogen. Thrombin appears in the blood following activation of the coagulation system, as a result of proteolysis of prothrombin. It catalyses the preferential cleavage of Arg-I-Gly, activating fibrinogen to fibrin and releasing fibrinopeptides A and B. Its effects are mediated by the thrombin receptor. See also blood coagulation. thrombin receptor a protein of platelets and vascular endothelial cells that binds thrombin and mediates its intracellular effects. It is a G-protein-coupled receptor. Example from human (precursor): database code THRR_HUMAN, 425 amino acids (47.35 kDa); this is a glycoprotein; the signal peptide comprises amino acids 1-26, and amino acids 27-41 are removed by thrombin, after which the new N terminus functions as a tethered ligand and the receptor is thereby activated. thrombocyte an alternative name for platelet. thrombogenic 1 tending to promote the formation of a blood clot (i.e. a thrombus). 2 having a precursor function for, or tending to promote, the formation of thrombin. IJ-thromboglobulin a homotetramer of a peptide derived from platelet basic protein precursor by removal of the first four N-terminal residues from LA-PF4. It is released by activated platelets. It belongs to the intercrine a family (see chemokine) and mediates a number of actions in the inflammatory response, including chemotaxis of leukocytes. thrombokinase an alternative name for factor Xa; see blood coagulation. thrombolysis the degradation of a blood clot (i.e. thrombus) as a result of physiological or pharmacological action. thrombolytic 1 tending to promote thrombolysis. 2 a drug or other substance promoting thrombolysis. thrombomodulin abbr.: TM; other name: fetomodulin; a specific endothelial cell receptor that forms a I: I stoichiometric complex with thrombin, the complex being responsible for conversion of protein C to activated protein C. It is a type I membrane protein. Example (precursor) from human: database code TRBM_HUMAN, 575 amino acids (60.26 kDa). thromboplastin an alternative name for factor III; see blood coagulation. thrombospondin or glycoprotein G a thrombin-sensitive major glycoprotein located in the alpha granules of human platelets. It is secreted on thrombin activation and binds to the platelet membrane in the presence of Ca 2+. It is an adhesion molecule that mediates cell-cell and cell-matrix interactions and can bind to fibrinogen, fibronectin, laminin, and type V collagen. It is a trimeric disulfide-linked protein and contains three types of repeating amino-acid sequence; the first is 57 amino acids long and shows homology with circumsporozoite protein from a malarial parasite; the second is 50-60 amino acids long and shows homology with epidermal growth factor; the third occurs as a continuous eightfold repeat of a 38-residue sequence; structural homology with calmodulin indicates that these repeats constitute multiple calcium-binding sites. Example, human thrombospondin 1 precursor: database code TSP1_HUMAN, 1170 amino acids (129.27 kDa). There are at least three such related proteins in humans. thromboxane any of a class of prostanoids synthesized by thromboxane-A synthase (EC 5.3.99.5) from prostaglandin H (the product of prostaglandin-endoperoxide synthase) as thromboxane A (TXA). Depending on whether the substrate of the enzyme is dihomo-(6,9,12)-linolenate, arachidonate, or eicosa-

646

thromboxane-A synthase

thymidine 5'-phosphate

5,8,1 I, 14, I7-pentaenoate, the product is TXAJ, TXA2 , or TXA 3 respectively. TXA 2 is the major thromboxane in vivo. It is synthesized in platelets when these are activated by other aggregatory compounds and strongly reinforces the aggregatory reaction. Its biological lifetime is a few minutes, TXA 2 being converted to the inactive metabolite thromboxane B2 (TXB 2) by addition of water across the endoperoxide. Oxidation of the II-hydroxy group of TXB 2 to an oxo group yields II-dehydro-thromboxane A2, a major long-lived metabolite in human plasma, useful for measurement as an index of thromboxane production. Beta-oxidation of TXB 2 yields 2,3-dinorthromboxane B2, the major human urinary metabolite. Dideoxy-epoxymethanoprostaglandin F2<x is a stable analogue that mimics TXA 2 .

thymidine or deoxyribosylthymine symbol: dT or dThd; thymine 2'-deoxyriboside; 1-(2-deoxy-p-D-ribofuranosyl)-5methyl uracil; a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA. Compare ribothymidine. Because thymidine is absent from ribonucleic acid, the incorporation of radioisotope-labelled thymidine into cells has been made the basis of a procedure frequently used for measuring the rates of DNA synthesis and cell growth.

H

COOH CH3 H

thromboxane-A synthase EC 5.3.99.5; other names: thromboxane synthase; thromboxane synthetase (abbr.: TXS); an enzyme that catalyses the formation from (52,13E)(15S)-9a, Ila-epidioxy-15-hydroxyprosta-5, 13-dienoate of (52, 13E)-(15S)-9a, Ila-epoxy-15-hydroxythromba-5, 13dienoate (thromboxane A 2 ). It is a heme-thiolate protein. 1-(7Carboxyheptyl)imidazole and benzylimidazole inhibit thromboxane-A synthase, as does the drug U-63557A, sodium furegrelate. Example from human: database code THAS_ HUMAN, 533 amino acids (60.42 kDa). thrombus (pl. thrombi) a blood clot forming within a blood vessel. Thrombus formation may occur as a normal response during physiological blood coagulation. It may also occur pathologically, triggered by atheroma, and is the immediate cause of ischemia in a heart attack. Thrombi may also form, especially in veins, at other times, e.g. after surgery, and if they reach the lungs cause pulmonary embolism. Thunberg method an early method for detecting and estimating dehydrogenases depending on the rate and extent of decolorization of Methylene Blue in solution in the presence of dehydrogenase and substrate. The apparatus, known as a Thunberg tube, consists of a stoppered glass tube (sometimes with a side-arm for addition of reagents) that may be evacuated through the stopper, and then sealed by a twist of the stopper. [After Torsten Ludvig Thunberg (1873-1952), Swedish physiological chemisL] Thx symbol for a residue of the a-amino acid and thyroid hormone L-thyroxine (alternative to T 4). Thy symbol for a residue of the pyrimidine base thymine (alternative to T). Thy-1 an allelic variable molecule, encoded on mouse chromosome 9, that is present on all T lymphocytes and also occurs in brain. It is a GPI-anchored membrane glycoprotein of the immunoglobulin superfamily, with a simple structure homologous to the variable region of an immunoglobulin molecule. Example (precursor) from human: database code THY 1_ HUMAN, 161 amino acids (17.94 kDa). See also thymopoietin. thylakoid a saclike vesicle that bears the photosynthetic pigments in photosynthetic organisms. In prokaryotes the thylakoids are of various shapes and are attached to the plasma membrane. In eukaryotes they are flattened, membrane-bound disclike structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation. thymic hormones see thymopoietin, thymosin.

thymidine 5'-diphosphate symbol: dThd5'PP or ppdT; the recommended name for thymidine diphosphate (abbr.: dTDP), 5'-diphosphothymidine, 5'-thymidylyl phosphate, thymidine 5'-(trihydrogen diphosphate). It is an intermediate in the formation of thymidine 5'-triphosphate from thymidine 5'phosphate. Derived compounds are the rare nucleosidediphosphosugars thymidinediphosphorhamnose and its biosynthetic precursor thymidinediphosphoglucose. thymidine kinase EC 2.7.1.21; systematic name: ATP:thymidine 5'-phosphotransferase; an enzyme that catalyses the phosphorylation by ATP of thymidine to thymidine 5' -phosphate with release of ADP. It acts on thymidine taken into a cell, or on free thymidine released within a cell, as a first step in its further metabolism. Mitochondrial and cytosolic forms are known, the latter showing much greater activity in proliferating than in resting cells. Example from herpes simplex type 2: database code KITH_HSV23, 375 amino acids (40.32 kDa). thymidine monophosphate abbr.: dTMP; an alternative name for any thymidine phosphate, but in particular for thymidine 5'-phosphate, especially when its distinction from thymidine (5'-)diphosphate and thymidine (5'-)triphosphate requires emphasis. thymidine phosphate symbol: dThdP; thymidine monophosphate (abbr.: dTMP); any phosphoric monoester or diester of thymidine. There are two monoesters - thymidine 3'-phosphate and thymidine 5'-phosphate - and one diester - thymidine 3',5'-phosphate - although thymidine 5'-phosphate is the ester commonly denoted (the locant being omitted if no ambiguity may arise). Thymidine 3'-phosphate (symbol: dThd3'P), also named thymidine 3' -monophosphate (abbr.: 3'dTMP) or 3'thymidylic acid, is released from deoxyribonucleic acid by the action of certain endo- or exonucleases, e.g. deoxyribonuclease II (EC 3.1.22.1) or spleen exonuclease (EC 3.1.16.1). The monophosphoric diester thymidine 3',5'-phosphate (symbol: dThd-3',5'-P), also named thymidine 3',S'-(cyclic)phosphate or cyclic thymidine 3',5'-monophosphate (abbr.: 3',5'-cyclic dTMP or cyclic dTMP or cdTMP), has been isolated as an intermediate formed during the acid hydrolysis of deoxyribonucleic acid but is not known to be of significance otherwise. thymidine 3'-phosphate see thymidine phosphate. thymidine 3',5'-phosphate see thymidine phosphate. thymidine 5'-phosphate or 5'-thymidyIic acid or 5'-phosphothymidine or 5'-O-phosphonothymidine symbol: dThd5'P; alternative recommended names for thymidine monophosphate (abbr.: dTMP), thymidine 5'-(dihydrogen phosphate), thymine (mono)deoxynucleotide. (The locant is commonly omitted if there is no ambiguity as to the position of phosphorylation.) It

647

thymidine phosphorylase

thymus nucleic acid

is synthesized (very indirectly) from uridine 5' -phosphate, its immediate precursor being 2'-deoxyuridine 5'-phosphate - see thymidylate synthase. In addition, resynthesis of dTMP from free thymidine formed by degradation of DNA can be effected via a salvage pathway. thymidine phosphorylase see pyrimidine-nucleoside phosphorylase. thymidine 5'-triphosphate symbol: dThd5' PPP or pppdT; the recommended name for thymidine triphosphate (abbr.: dTTP), 5'-triphosphothymidine, 5'-thymidylyl diphosphate, thymidine 5'-(tetrahydrogen triphosphate); a substrate for DNA synthesis. It is formed from thymidine 5'-phosphate by the successive action of nucleoside-phosphate kinase (BC 2.7.4.4) and nucleoside-diphosphate kinase (EC 2.7.4.6), which transfer in turn the terminal phosphoric residues from two molecules of adenosine 5'-triphosphate.

~

~

~

H3C~

l ..N~O /NH

_ O-P-O-P-O-P-O-~O~

-b -b -b

)----I OH

thymidyl either of the chemical groups formed by the loss of a 3'- or a 5'-hydroxyl group from the deoxyribose moiety of thymidine. thymidylate 1 either the monoanion or the dianion of thymidylic acid. 2 any mixture of thymidylic acid and its anions. 3 any saIt or ester of thymidylic acid. thymidylate synthase BC 2.1.1.45; systematic name: 5,10methylenetetrahydrofolate:dUMP C-methyltransferase; an enzyme responsible for the formation of thymidylate, dTMP, by the de novo pathway. It catalyses reductive methylation of 2'deoxy-5'-uridylate, dUMP, by reaction with 5,10-methylenetetrahydrofolate to form dihydrofolate and dTMP. (The dihydrofolate thus formed is reduced again to tetrahydrofolate by dihydrofolate reductase.) Thymidylate synthase is important as a target for the antineoplastic agents fluorouracil and fluorodeoxyuridine. These drugs are metabolized to fluorodeoxyuridylate, which is a potent irreversible inhibitor of the enzyme. Example from Escherichia coli (homodimer): database code TYSY_ECOLI, 264 amino acids (30.44 kDa); 3-D structure known; five motifs. See also thymineless death. thymidylic acid the trivial name for any phosphoric monoester of thymidine. The position of the phosphoric residue on the deoxyribose moity of a given ester may be specified by a prefixed locant - see thymidine phosphate. However, 5'-thymidylic acid is the ester commonly denoted, its locant usually being omitted if no ambiguity may arise. 5'-Thymidylic acid is also an alternative recommended name for thymidine 5'-phosphate. thymidylyl the thymidine[mono]phospho group; the acyl group derived from thymidylic acid. thymin a former name for thymopoietin. thymine symbol: T or Thy; 5-methyluraciJ; 2,4-dihydroxy-5methylpyrimidine; one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base.

thymine dimer a pyrimidine dimer formed within a DNA strand from two adjacent thymine residues by photodimerization. It is most commonly of the cyclobutadipyrimidine type. thymineless death the death of an animal or bacterial cell following a period of thymine (or thymidylate) deprivation. Although such a deprived cell may continue to produce protein and RNA, it can no longer synthesize DNA in the absence of thymidylate, and it eventually loses its vitality and dies, perhaps because it is also unable to repair altered or damaged DNA. The phenomenon may be demonstrated with a thyminerequiring auxotrophic bacterial mutant by omitting thymine from the suspending medium, or with any cell by adding fluorouracil or its metabolite fluorodeoxyuridine, with consequent inhibition of thymidylate synthase. A rapidly metabolizing animal cell, such as a tumour cell, is particularly susceptible to thymineless death. thymine deoxyriboside an alternative name for thymidine. thymine riboside an alternative name for ribothymidine. thyminose a former name for 2-deoxY-D-ribose (see deoxyribose). thymo+ comb. form of, or pertaining to, the thymus. thymocyte (sometimes) any lymphocyte found in the thymus. thymocyte mitogenic factor abbr.: TMF; an alternative name for interleukin 2. thymocyte-stimulating factor abbr.: TSF; an alternative name for interleukin 2. thymoma a tumour of thymic tissue. thymonuclease another name for deoxyribonuclease I. thymonucleic acid an alternative term for thymus nucleic acid. thymopentin a synthetic pentapeptide that corresponds to residues 32-36 of thymopoietin. thymopoietin abbr.: TP; anyone of three polypeptide hormones that result from alternative splicing of the same gene, and originally isolated from bovine thymus. They have pleiotropic actions on prothymocytes, inducing expression of the differentiation antigens such as Thy-1, and are important in T-cell development and function. They were discovered in studies on myasthenia gravis and impair neuromuscular transmission after injection in mice, due to an effect on the nicotinic acetylcholine receptor. A synthetic pentapeptide corresponding to positions 32-36, named thymopentin and with the sequence Arg-Lys-Asp 34- Val-Tyr, has full activity. Splenin, a corresponding peptide in spleen, contains a similar pentapeptide, called splenopentin; bovine splenin has Glu in place of Asp 34, and human splenin has Ala in the corresponding position. These replacements affect the biological activity. Thymopoietin was formerly known as thymin. thymosin any of several related polypeptide hormones of thymic origin that are involved in differentiation of T lymphocytes in the thymus. They include Ul and ~4 thymosins, which are of known structure. Thymosin ~4 (human, bovine, rat) has the sequence SDKPDMAEIEKFDKSKLKKTETQEKNPLPSKETlEQEKQAGES. thymulin a zinc-requiring immunomodulatory thymic nonapeptide hormone known to induce intra- and extra-thymic Tcell differentiation. Its level is decreased in immunodeficiency and in autoimmune disease. thymus (gland) a bilobed glandular organ located in the posteroventral part of the neck. In mammals the thymus is encapsulated and divided into lobules, each lobule consisting of cortex and medulla; the cortex consists mainly of lymphocytes (thymocytes). The thymus is responsible for populating the blood, lymph, and thymus-dependent areas with T lymphocytes during the neonatal period. The thymus is large at birth but diminishes in size with increasing age and may be difficult to identify in adults. It is important in cell-mediated immunity. thymic ad). thymus nucleic acid a former name for deoxyribonucleic acid. It was so termed because the thymus gland was found to be a particularly rich source of nucleic acid of a type that was thought at the time to be characteristic of animal tissues and

thyro+

648

that was distinct from the type believed to be characteristic of plant tissues and known as yeast nucleic acid. thyro+ comb. form of, or pertaining to, the thyroid gland. thyrocalcitonin see calcitonin. thyroglobulin a protein in the thyroid gland, tyrosyl residues of which are modified to form the principal thyroid hormone, thyroxine, which is released by proteolysis. Thyroglobulin, a dimer of molecular mass about 660 kDa, is the main constituent of the so-called colloid of the thyroid follicles. Iodination of certain tyrosyl residues results in the formation of 3,5-iodotyrosyl residues; there is then transfer of the iodinated phenolic moiety of one of these tyrosyls (in the free form this would be a 2,6-iodophenyl group) to the phenolic oxygen of another iodinated tyrosyl to form a tetraiodo compound which, on release by proteolysis, is thyroxine (T4 ) (some triiodo forms are also produced). The proteolysis occurs as colloid migrates from the basal to the apical surfaces of the thyroid cell. Example (precursor) from human: database code THYG_HUMAN, 2767 amino acids (304.45 kDa). The colloid containing the modified thyroglobulin is taken into vesicles by phagocytosis to form periodic acid-Schiff positive (PAS) vesicles. Dense granules containing proteolytic enzymes then fuse with the vesicles to digest the thyroglobulin with the loss of PAS-positive material. The vesicles containing triodothyronine and thyroxine are then extruded. thyroidectomy the surgical removal of the thyroid gland. thyroid gland a ductless gland, located near the larynx in most species, that secretes the hormones thyroxine and triiodothyronine. Thyroid tissue is confined to vertebrates. The gland contains closely packed follicles, or acini, each consisting of a sac that has a peripheral single layer of cuboidal follicular cells forming an epithelium on an outer basement membrane; the centre of the follicle is occupied by a colloid of which the major component is thyroglobulin. This is synthesized and secreted into the colloid space by the follicular cells; microvilli extend from the apical surface of the follicular cells into the colloid. The thyroid also contains parafollicular cells, or C cells, that synthesize calcitonin. Enlargement of the thyroid in iodine deficiency is the basis of goitre. The thyroid concentrates iodide, a property that can be used for thyroid imaging, and for the treatment of cancer of the thyroid. thyroid hormone either of the compounds secreted by the thyroid gland, namely thyroxine and triiodothyronine. thyroid hormone receptor a nuclear receptor for triiodothyronine that mediates the effects of thyroid hormones on cells. These receptors bind triiodothyronine and directly regulate gene expression. The proteins belong to a superfamily of eukaryotic transcription factors and the steroid/thyroidlretinoic acid family of nuclear receptors for hormones. The ligandbinding domain is in the C-terminal region, the zinc-finger DNA-binding domain in a central region, and a functionmodulating domain in the N-terminal region. Binding of hormone induces changes in receptor conformation that control transcriptional activation and repression, and also regulates homo- or heterodimerization. In the absence of ligand, these receptors repress basal gene expression, probably through corepressor proteins. Example, (1-1 receptor from Mus musculus: database code THAI_MOUSE, 410 amino acids (46.79 kDa). thyroid hormone either of the compounds secreted by the thyroid gland, namely thyroxine and triiodothyronine. thyroid response element abbr.: TRE; see response element. thyroid-stimulating hormone abbr.: TSH; recommended name: thyrotropin; other name: thyrotropic hormone; a hormone, secreted by the adenohypophysis, that stimulates the activity of the thyroid gland. The bovine hormone is a glycoprotein, M r 28 300, and a heterodimer of two chains, (1 (Mr 13 600) and ~ (M r 14700). The a chain has an amino-acid sequence identical with that of the a chain of luteinizing hormone of the same species. TSH increases the uptake of iodide by the thyroid, increases the rate of conversion of diiodotyrosine to thyroxine, and increases the release of thyroid hormones from

thyroxine the thyroid. The release of TSH from the adenohypophysis is influenced by thyrotropin-releasing honnone. Examples, a chain (precursor) from human: database code GLHA_HUMAN, 116 amino acids (13.06 kDa); ~ chain (precursor) from human: database code TSHB_HUMAN, 138 amino acids (15.59 kDa). thyroliberin recommended name for thyrotropin-releasing hormone. thyronine 4-(4-hydroxyphenoxy)phenylalanine; the structure

from which thyroid hormones may be notionally derived by iodination. It is not naturally occurring, even in bound form, since in the synthesis of thyroid hormones the tyrosyl residues of thyroglobulin are iodinated before addition of the further phenolic group (see thyroglobulin).

thyrotoxicosis see hyperthyroidism. thyrotroph a thyrotropic cell. thyrotrophic having the effect of nourishing the thyroid gland,

stimulating its growth and maintaining its size. thyrotropic or (esp. Brit.) thyrotrophic having a modulating

effect on the thyroid gland, especially in stimulating the synthesis of thyroid hormones. See thyrotropin. thyrotropic hormone an alternative name for thyroid-stimulating hormone. thyrotropic hormone releasing factor (abbr.: THRF) or thyrotropic hormone releasing hormone (abbr.: THRH) an alternative name for thyrotropin-releasing hormone. thyrotropin the recommended name for thyroid-stimulating hormone. thyrotropin receptor an integral membrane protein that binds thyrotropin (i.e. thyroid-stimulating hormone) and mediates

its intracellular effects. It is a G-protein-linked receptor, with different forms produced by alternative splicing. Example from human (precursor): database code TSHR_HUMAN, 764 amino acids (86.70 kDa). Mutations are associated with hyperfunctioning thyroid adenomas. The hyperthyroidism of Graves' disease is thought to be due to the presence in the blood of these patients of autoantibodies that stimulate the thyroid through the thyrotropin receptor. thyrotropin-releasing factor abbr.: TRF; an alternative name for thyrotropin-releasing honnone. thyrotropin-releasing hormone abbr.: TRH; recommended name: thyroliberin; other names: thyrotropin-releasing factor (abbr.: TRF); thyrotropic hormone releasing factor (abbr.: THRF); thyrotropic hormone releasing hormone (abbr.: THRH); a hormone, released by the mammalian hypothalamus into the hypophyseal-portal circulation in response to neural and/or chemical stimuli, that regulates the secretion of thyroid-stimulating hormone (TSH) by the adenohypophysis. It has a wide distribution, being present not only in primitive vertebrates but also in Amphioxus (a provertebrate) and in nerve ganglia of snail. It is the tripeptide pyroGlu-His-ProNH 2 , the cyclized glutamate and intact prolylamide being essential for activity. It is synthesized as part of a large prohormone that has six repeats of the TRH sequence. TRH is present in many other parts of the brain, in pancreatic islets, and in the gastrointestinal tract; it probably serves widely as a neurotransmitter or neuromodulator, being known in mammals to alter sleep patterns, increase motor activity, increase blood pressure, and affect norepinephrine turnover, among many activities. Its regulation of TSH secretion is controlled by the pituitary-thyroid axis. thyroxine abbr.: Thx or T 4 ; 4-(4-hydroxy-3,5-diodophenoxy)3,5-diodophenylalanine; 3,3',5,5'-tetraiodothyronine; the main hormone secreted by the thyroid gland, although its ac-

649

thyroxine-binding globulin tivity is lower than that of triiodothyronine (T 3)' Its synthesis from L-tyrosyl residues of thyroglobulin means that the L-isomer is the naturally occurring form. Thyroxine is essential for normal metabolism and physical development. It stimulates the metabolic rate, causing increased oxygen consumption and heat production in tissues. Although in humans the plasma levels of T 4 are 20- to 50-fold higher than those of T 3 , T 4 is converted to T 3 in tissues and the effects are thought to be mediated by T 3 binding to receptors in the cell nucleus (chromatin fraction), leading to mRNA and protein synthesis. The normal range in human blood is 60-150 nmol VI (total of bound and free), 9-26 pmol L-1 (free). The chemical constitution of thyroxine was deduced by the British biochemist Sir Charles R. Harington (1897-1972), and confirmed by synthesis (1927).

I\NH,~I

HOOC~I ~OH I

thyroxine-binding globulin abbr.: TBG; a major thyroid hormone transport protein found in mammalian serum. It is synthesized in liver, and variations in its concentration in serum result in similar variations in the level of circulating thyroid hormones. Alterations in its affinity for thyroid hormone also affect circulating thyroid hormone levels, decreased affinity being accompanied by decreased serum concentration. In the human, this variation may result from non-thyroidal illness, the presence of drugs (salicylates and phenytoin block thyroid-binding sites), or genetic variation, many variants being known, and listed in the example from human: database code THBG_HUMAN, 415 amino acids (46.32 kDa). Ti symbol for titanium. tight coupling a term applied to mitochondrial function implying a high degree of efficiency in the yield of ATP (or other functional response) in relation to electron flow. The nearer the yield approaches the optimal value, the tighter the coupling is said to be. Tight coupling is obtained in isolated mitochondria only if gentle procedures, preserving membrane integrity, are employed during isolation. See also chemiosmotic coupling hypothesis, phosphorus:oxygen ratio. tight junction or zona occludens (in vertebrate tissues) a beltlike region of very close contact between the plasma membranes of adjacent cells, such that the intercellular space is completely occluded. Tight junctions occur in epithelia and brain endothelia, and are effective barriers to the passage of water and solutes. Compare gap junction. tight turn see beta turn. time symbol: t; one of the seven SI base physical quantities, usually indicating duration or a precise moment. The SI base unit of time is the second. time constant a characteristic time taken by a system or a process to respond to a perturbation. time course a graph plot of a parameter (that changes with time) scaled on the ordinate and time scaled on the abscissa. time-resolved fluorescence spectrometry a method in which a sample is irradiated using a laser delivering a short (sub-nanosecond) pulse of light, after which the exponential decay of fluorescence is measured using a photomultiplier. The sensitivity of detection must be at the single photon level ('single photon counting'), and fluorescence lifetimes as short as a few nanoseconds can be determined. However, a disadvantage of the technique is that many measurements over possibly several hours may be needed to obtain reliable and sufficient data. See also steady-state fluorescence anisotropy. TIMP abbr. for tissue inhibitor of metalloproteases; any of a

titrate

group of proteins that inhibit metalloproteinases. An example is TIMP-I, also known as EPA (erythroid potentiating activity), a protein that mediates erythropoiesis. It forms complexes with enzymes such as collagenases, bringing about irreversible inactivation. Example (precursor) from human: database code TIM I_HUMAN, 207 amino acids (23.14 kDa). See also matrix metalloproteinase. tintometer an apparatus formerly used for determining the colour of a solution by comparison with a graded colour scale. Ti plasmid abbr. for tumour-inducing plasmid; any of a class of large conjugative plasmids found in the soil bacterium Agrobacterium tumefaciens and responsible for crown-gall disease of broad-leaved plants ~ a segment of the Ti plasmid, the T-DNA, is found in the genome of the tumour tissue of affected plants. With appropriate modifications the Ti plasmid can carry foreign DNA sequences of any desired kind into the genome of a susceptible plant. Tiselius, Arne Wilhelm Kaurin (1902-71), Swedish protein chemist; Nobel Laureate in Chemistry (1948) 'for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins'. Tiselius apparatus an apparatus for performing moving boundaryelectrophoresisin which there is a U-tube with sliding joints. This enables the protein (or other) solution and the buffer to be placed in separate parts of the U-tube and sharp boundaries made between them when the parts are slid into position to complete the U-tube. tissue any collection of cells that is organized to perform one or more specific function. Compare organ. tissue culture 1 the technique or process of growing or maintaining tissue cells (cell culture), whole organs (organ culture), or parts of an organ, from an animal or plant, in artificial conditions. 2 any living material grown or maintained by such a technique. tissue extract an alternative name for factor III; see blood coagulation. tissue factor abbr.: TF; a transmembrane glycoprotein (eight motifs), also known as factor III, that initiates blood coagulation by forming a complex with factor VII or VIlA. The complex activates factors IX or X. Tissue factor plays a role in normal hemostasis by initiating cell-surface assembly and propagation of the coagulation protease cascade. Example from human (precursor): database code TF_HUMAN, 295 amino acids (33.03 kDa). tissue grinder any device for disrupting tissue by a crushing or shearing action. The term may embrace devices ranging from a meat grinder (mincer), mechanical pestle and mortar, or mill, to the more precise Potter-Elvehjem homogenizer or the Dounce homogenizer. tissue kallikrein see kallikrein. titer the US spelling of titre. titin or connectin a giant protein that forms a single molecule elastic filament extending from the M line to the Z line in the striated muscle sarcomere and is one of the largest polypeptides yet described. The sequence consists mainly of repeats of two types of approximately 100-amino-acid motifs, known as class I and class II that show homology to the fibronectin type-III domain and immunoglobulin superfamily C2 domain, respectively. There is also a domain characteristic of protein kinases near the C terminus. It is thought to play an important role in sarcomere alignment during muscle contraction. Example from human: database code HSTITIN, 4650 amino acids (521.48 kDa). See also twitchin. titratable acidity 1 a measure of the acidity of a urine sample, expressed as the volume of O.I-M NaOH required to neutralize, usually to a phenolphthalein endpoint, a 24-hour volume of urine. 2 a measure of the acidity of any solution, etc. titrate 1 to add acid of known concentration to base of unknown concentration (or vice versa) until the point of equivalence is reached, from which can be determined the con-

titration curve

650

centration of the unknown. -2 more generally, to add any standard solution to an unknown until some detectable equivalence point is reached, enabling the amount of the unknown to be determined. 3 (esp. in microbiology or immunology) to determine the maximum dilution at which activity can be detected. See titre (def. 2). -titratable adj.; titration n. titration curve originally, a curve relating pH to the equivalents of strong base added per equivalent of acid in the solution. Similar curves are obtained when the logarithm of ligand concentration is plotted against the degree of association (or dissociation) of a ligand to its acceptor, or when redox potential is plotted against the degree of oxidation (or reduction) of a redox system. titration pK symbol: pG; a kind of pK that characterizes the titration curve of a multibasic acid. If this acid has n hydrons that titrate over the pH range of interest, then its titration curve is identical to that of an equimolar mixture of n (hypothetical) monobasic acids. The pK values of these acids are the titration pK values of the multibasic acid. They differ little from the molecular pK values if the differences between sequential molecular values exceed unity. See also group pK. titre or (esp. US) titer 1 a value found by titration; see titrate (def. 1, 2). 2 (in microbiology and immunology) a measure of the concentration or activity of an active substance, e.g. an antibody, in a solution, usually expressed as the highest dilution of the solution in which the activity can be detected. By convention, if the highest dilution giving activity is 100-fold, the titre is said to be 100. titrimetry the technique of measurement by titration, particularly using instrumentation and automation. TI symbolfor thallium. TLC abbr. for thin-layer chromatography. tId a gene in Drosophila for Tolloid protein, which is required for normal dorsal development. Mutations in tid lead to a partial transformation of dorsal ectoderm into ventral ectoderm. T lymphocyte or T cell any of a class of lymphocytes that undergo maturation and differentiation in thymus. They are responsible for immune reactions involving cell-cell interaction, i.e. cell-mediated immunity. Subsets of T lymphocytes include: (I) cytotoxic T-lymphocytes, directly reponsible in vivo for the death of cells identified for elimination; they include nonspecific killer cells (NK cells) and specific cytotoxic T-lymphocytes primed by antigen activation; (2) helper cells, which collaborate with antigen-presenting cells in the initiation of an immune response; and (3) suppressor cells, which down-regulate the response of helper cells. Tm symbol for thulium. TMB-8 abbr. for (8-diethylamino)octyl-3,4,5-trimethoxybenzoate; a Ca 2 + antagonist that blocks intracellular Ca 2 + channels.

TMF abbr. for thymocyte mitogenic factor; i.e. interleukin 2. TMP abbr. for 1 ribosylthymine monophosphate or ribothymidine monophosphate, the common names for ribosylthymine 5'-phosphate, ribothymidine 5'-phosphate, 5'-ribothymidylyl phosphate, thymine riboside 5'-phosphate. 2 (sometimes) thymidine monophosphate. dTMP is recommended. TMR spectroscopy abbr. for topical magnetic resonance spectroscopy. TMS abbr. for 1 tetramethylsilane; a water-soluble reference

Toll substance used in nuclear magnetic resonance spectroscopy. 2 the trimethylsilyl group; the symbol Me3Si- is preferred. TMV abbr. for tobacco mosaic virus, an RNA plant virus. Tn abbr. for 1 troponin. 2 transposon. TNBS abbr. for 2,4,6-trinitrobenzenesulfonate; a reagent that combines readily with amino groups. It may be used either to protect these groups or to introduce a chromophore. It is removable using hydrazine. Tn-C abbr. for troponin C. TNF abbr. for tumour necrosis factor. Tn-I abbr. for troponin I. TNMR or tnmr abbr. for tritium nuclear magnetic resonance (spectroscopy) . TNS abbr. for 2-p-toluidylnaphthalene-6-sulfonate; a fluor used in extrinsic fluorescence studies of proteins. Tn-T abbr. for troponin T. tocopherol a generic term for di- and trimethyltocols; a-tocopherol is 5,7,8-trimethyltocol, and is active as vitamin E; p-tocopherol is 5,8-dimethyltocol; y-tocopherol is 7,8-dimethyltocol; and Ii-tocopherol is 8-methyltocol.

P1

s CHC H S Hsc q y '~ 10- 2 Pa; high (or hard) vacuum, 10-2_10-- 7 Pa; and ultrahigh vacuum, deuterium> protium. Racemates with a single chiral centre are labelled (RS); extensions of the sequence rule are used in the EIZ, pro-Rlpro-S, pro-Elpro-Z, and RelSi nomenclature systems. 64 36 48 21 10 43 44 37 49 65 13 60 41 50 75 42 5 16 19 38 74 17 52 51 34

acetoxy acetyl acetylamino acetylenyl allyl amino ammonio (+H 3N-) benzoyl benzoylamino benzoyloxy benzyl benzyloxy benzyloxycarbonyl benzyloxycarbonylamino bromo tert-butoxycarbonyl butyl sec-butyl tert-butyl carboxy chloro cyclohexyl diethylamino dimethylamino 2,4-dinitrophenyl

28 59 40 3 46 68 35 63 62 7 I 57 76 9 8 20 14 69 58 39 2 45 71 66 72 67

3,5-dinitrophenyl ethoxy ethoxycarbonyl ethyl ethylamino fluoro formyl formyloxy glycosyloxy hexyl hydrogen hydroxy iodo isobutyl isopentyl isopropenyl isopropyl mercapto (HS-) methoxy methoxycarbonyl methyl methylamino methylsulfinyl methylsulfinyloxy methylsulfonyl methylsulfonyloxy

70 II 56 27 33 24 55 6 61 22 47 54 18 4 29 12 73 25 30 23 53 32 15 31 26

methylthio (CH 3S-) neopentyl nitro m-nitrophenyl o-nitrophenyl p-nitrophenyl nitroso pentyl phenoxy phenyl phenylamino phenylazo propenyl propyl l-propynyl 2-propynyl sulfo (H03S~) m-tolyl o-tolyl p-tolyl trimethylammonio trityl vinyl 2,6-xylyl 3,5-xylyl

Appendix H Species names Below is a list of genera/species cited frequently in this Dictionary, together with their common names, where applicable. The asterisked names have their own entries in the Dictionary. *Agrobacterium Amanita a genus of toadstools; A. muscaria is fly

agaric, A. phalloides the 'death-cap' (deadly agaric) *Arabidops~thaliana

*Aspergillus *Bacillus Bos taurus cattle Brassica a genus of cruciferous plants; B. napus is the swede, B. oleracea includes the cabbage, cau-

liflower, etc. Caenorhabditis elegans a nematode Candida a genus of yeasts Canis familiaris the dog Chlamydomonas reinhardtii a unicellular green

alga

*Clostridium Corynebacterium a genus of coryneform (def. 2)

bacteria *Dictyostelium discoideum Digitalis the foxglove genus *Drosophila *Escherichia coli Euglena a unicellular, flagellate alga belonging to

the Euglenophyta Gallus gallus the domestic fowl Haemophilus influenzae an aerobic, nonmotile

Gram-negative rod Halobacterium halobium a halophilic archaebac-

terium Klebsiella a genus of Gram-negative rod non-

motile bacteria

Lactobacillus a genus of lactic-acid bacteria Lycopersicon esculentum the tomato Mus musculus the mouse *Mycobacterium *Neurospora Nocardia a genus of rod or filamentous Gram-

positive nonmotile bacteria *Paramecium Penicillium mould Pisum sativum the garden pea *Plasmodium Pseudomonas a genus of Gram-negative rod-

shaped motile bacteria Rattus norvegicus the rat *Rhizobium *Saccharomyces *Salmonella *Schizosaccharomyces pombe Shigella a genus of nonmotile Gram-negative rod coliform bacteria *Staphylococcus *Streptococcus *Streptomyces Sus scrofa the pig *Tetrahymena Thermus aquaticus a thermophilic archaebac-

terium Trypanosoma a genus of parasitic protozoans; see trypanosome *Xenopus laevis Zea mays maize (corn)