OXFORD DICTIONARY OF Biochemistry and Molecular Biology REVISED EDITION Managing Editor Professor R Cammack King's College London General Editors Professor T.K Attwood University of Manchester Professor P.N Campbell University College London Dr J.H Parish University of Leeds Dr A.D Smith University College London Dr J.L Stirling King's College London Professor F Vella University of Saskatchewan Editors Teresa K Attwood Professor of Bioinformatics, Faculty of Life Sciences & School of Computer Science, University of Manchester Richard Cammack (Managing Editor) Biochemistry, King's College London Professor of Peter N Campbell (deceased) Emeritus Professor of Biochemistry and Honorary Research Fellow, University College London J Howard Parish Life Fellow, University of Leeds Anthony D Smith Emeritus Reader in Biochemistry, University College London John L Stirling Senior Lecture in Molecular Genetics, King's College London Francis Vella Former Professor of Biochemistry, Faculty of Medicine, University of Saskatchewan, Saskatoon, Canada OXFORD DICTIONARY OF Biochemistry and Molecular Biology Great Clarendon Street, Oxford OX2 6DP 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 Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam 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, 2000, 2006 The moral rights of the authors have been asserted Database right Oxford University Press (maker) First edition published 1997 Revised edition 2000 Reprinted 2001, 2003 Second edition published 2006 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 the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Data available Typeset by Market House Books Ltd Printed on acid-free paper ISBN 0-19-852917-1 978–0–19–852917-0 10 In memory of Peter Nelson Campbell (1921–2005) Peter Campbell was the first person to synthesize a protein using components of the cell rather than complete cells He was one of the group who first showed the importance of autoimmunity in human disease Peter was Head of the Biochemistry Department in the University of Leeds from 1967 until 1975 He was a founder of the Federation of European Biochemical Societies (FEBS) and, among many international commitments, chaired the Education Committee of the International Union of Biochemistry and Molecular Biology (IUB) A great advocate of biochemistry teaching, he started the journal Biochemical Education His books included Biochemistry Illustrated, with Tony Smith He was also one of the main driving forces behind the creation of the first edition of the Oxford Dictionary of Biochemistry and Molecular Biology Preface Preface to this edition It is a decade since the first edition of the Oxford Dictionary of Biochemistry and Molecular Biology It was a remarkable work of scholarship, arising from the work of journal editors and scientific writers Since then the landscape of biochemistry has changed immeasurably The genome sequences have laid out the blueprints of whole organisms, especially Man They have revealed the diversity of gene expression, and the complex systems by which cellular molecules organize themselves The molecular basis of many diseases has been revealed, and vital cellular components discovered The literature is more diverse than ten years ago The identification of the genes has rushed ahead of the biochemical characterization of their functions Many protein and nucleic acid factors have been discovered While their functions are incompletely understood, they are referred to by laboratory shorthand abbreviations These are well understood by the investigators who work on them, but the mass of them becomes very confusing to the student, or to those viewing biochemistry from the outside New methods of bioinformatics have been developed to bridge the gap Meanwhile the ‘-omics’ projects have introduced new layers of complexity as we see the interactions between macromolecules leading to new emergent properties As predicted in the first edition, the influence of the Internet has expanded Instead of searching for information in libraries, students now usually go first to a search engine So, does such a dictionary have a role in the age of Google? In fact it has gained in sales and popularity Evidently it fills a need for a source of reliable information that is not always so easy to find A revised version of the dictionary, with some additions and corrections was printed in 2000 At that time, the need for a complete revision was apparent The work continued with a new team, recruited by the ever-enthusiastic Peter Campbell We deeply regret that he did not live to see the completion of this task, having died on February 8th 2005 from complications after an accident In order to keep the dictionary as a handy reference volume, we have endeavoured to avoid it becoming much heavier It is only by being selective that there are only about 20% more entries than the first edition Most of the appendices have been removed, or their useful parts transferred The listed Nobel prizewinners in biochemistry and molecular biology have been omitted except for eponymous entries, when they have lent their names to compounds or procedures There has been a judicious removal of some older terms, though we found that surprisingly few have disappeared from the literature to such an extent that they are obsolete The literature abounds with laboratory shorthand names, database identifiers; TLA's (three-letter abbreviations) and other acronyms are extremely common, and a notorious source of ambiguity We have cited these selectively, sometimes to indicate that a word or phrase has two meanings in different contexts In the printed form we can show the full range of printed characters – boldface, italic, sub- and superscripts, Greek letters – that make up the syntax of many of the names, and that are difficult to find with search engines The dictionary is not intended to be a nomenclature document, and the terms that are in the entries are generally those that are in common use We continue the practice of pointing the reader in the direction of recommended terminology and nomenclature Nomenclature rules are applied less prescriptively these days; ‘recommended’ chemical nomenclature has become ‘preferred’; ‘recommended names’ for enzymes have given way to ‘common names’ A great many of the new entries, on inherited diseases and much else besides are provided by Frank Vella, drawing on the eclectic collection of topical papers that he assembled for his columns in journals such as IUBMB Life The entries on bioinformatics and genetics, which have assumed greater importance in BMB over the past decade, have been bolstered by the work of Terri Attwood and John Stirling Finally it has been a pleasure to work with John Daintith and Robert Hine of Market House Books, whose expertise in chemistry and biology meant that their assembly of the book was an expert job The content of such a dictionary is necessarily selective We have tried to ensure that the entries in the dictionary reflect current usage in biochemistry and molecular biology As always, we are grateful to readers who point out errors in the present text Richard Cammack March 2006 Preface to the revised first edition 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 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 September 1999 A D S Preface to the first edition 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 turn 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 of meaning 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 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 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 of Biochemistry 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 viii 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 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 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) 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 ix Xx x symbol for amount-of-substance fraction (i.e mole fraction) or number fraction for condensed phases Compare y a cartesian space coordinate, complementary to y and z X symbol for a a residue of an unknown, unspecified, or (specified) unusual a-amino acid (alternative to Xaa) b a residue of the ribonucleoside xanthosine (alternative to Xao) X symbol for (electric) reactance X-537A an alternative name for lasaloacid Xaa symbol for a residue of an unknown, unspecified, or (specified) unusual a-amino acid (alternative to X) Xan symbol for a residue of the purine base xanthine xanthan gum a capsular complex heteropolysaccharide formed by strains of the pseudomonad bacterium Xanthomonas campestris and believed to promote adhesion of the organism to its plant host It is widely used in the cosmetic, food, and other industries as a crystallization inhibitor, emulsifier, gelling agent, etc xanthine symbol: Xan; 2,6-dihydroxypurine; 2,6-dioxopurine; 3,7dihydro-1H-purine-2,6-dione; a purine formed in the metabolic breakdown of guanine Compare hypoxenthine See also allopurinol O H N O NH N N xanthopterin xanthosine symbol: X or Xao; xanthine riboside; 9-b-D-ribofura- nosylxanthine; a nucleoside formed by the deamination of guanosine O N HN O HN H N OH O N H N N H O HOCH2 O NH2 OH N xanthine oxidase EC 1.1.3.22; the recommended name for hypox- anthine oxidase; systematic name: xanthine:oxygen oxidoreductase; former name: Schardinger enzyme A flavoprotein (FAD) enzyme containing two 2Fe–2S clusters and molybdenum cofactor, abundant in milk and liver, that catalyses the oxidation of xanthine to urate and superoxide (or hydrogen peroxide) and also the oxidation of hypoxanthine to xanthine The enzyme has two forms: (1) xanthine dehydrogenase, which has NAD as coenzyme, and urate and NADH as products; and (2) xanthine oxidase, which reacts with dioxygen and has urate and H2O2 as products The dehydrogenase is converted reversibly to the oxidase by oxidation of sulfhydryl groups or irreversibly by proteolysis xanthinuria the excretion of excessive amounts of xanthine in the urine It is sometimes due to a hereditary disease in which there is a gross deficiency of xanthine oxidase activity in the tissues See molybdoenzymes xantho+ or (before a vowel) xanth+ comb form denoting yellow xanthoma a yellow fatty deposit below the skin or associated with a tendon Usually multiple, xanthomas are due to extravascular phagocytosis of chylomicrons, LDL-derived cholesterol, or other sterols, by macrophages of skin or subcutaneous tissue They usually occur in a variety of hyperlipidemias and in cerebrotendinous xanthomatosis but may also occur with a normal plasma lipid profile –xanthomatous adj xanthophyll any carotenoid in which one or more oxygenated functions are present in the molecule xanthoproteic test a test for protein in which a yellow colour (or precipitate from solution) forms on addition of conc nitric acid; the colour turns orange when made alkaline xanthopterin a yellow pterin pigment of insect wings, e.g of the common sulfur butterfly Compare leukopterin xanthosine monophosphate abbr.: XMP; any xanthosine phos- phate, particularly xanthosine 5′-phosphate when its distinction from xanthosine (5′-)diphosphate and xanthosine (5′-)triphosphate requires emphasis xanthosine phosphate xanthosine monophosphate (abbr.: XMP); any phosphoric monoester or diester of xanthosine Of the three possible monoesters and the two possible diesters only xanthosine 5′phosphate occurs naturally (the locant being omitted if no ambiguity may arise) xanthosine 5′-phosphate or 5′-xanthylic acid or 5′-phosphoxanthosine or 5′-O-phosphonoxanthosine symbol: Xao5′P; alternative recommended names for xanthosine monophosphate (abbr.: XMP); xanthosine 5′-(dihydrogen phosphate); xanthine (mono)ribonucleotide (The locant is commonly omitted if there is no ambiguity as to the position of phosphorylation.) An intermediate in the biosynthesis of guanosine 5′-phosphate (i.e 5′-guanylic acid, or GMP), it is formed from inosine 5′-phosphate (i.e 5′-inosinic acid) by an NAD+-dependent dehydrogenase; a glutamine-requiring amidotransferase reaction (catalysed by GMP synthase) then converts XMP to GMP O N HN -O O O N H P O CH2 -O OH N O OH xanthylic acid the trivial name for any phosphoric monoester of xanthosine The position of the phosphoric residue on the ribose moiety of a given ester may be specified by a prefixed locant (see 708 Xao xanthosine phosphate) However, 5′-xanthylic acid is the ester commonly denoted, its locant usually being omitted if no ambiguity may arise Xao symbol for a residue of the ribonucleoside xanthosine (alternative to X) Xao5′P symbol for xanthosine 5′-phosphate Xao5′PP symbol for xanthosine 5′-diphosphate (alternative to ppX) Xao5′PPP symbol for xanthosine 5′-triphosphate (alternative to pppX) Xba I a type restriction endonuclease; recognition sequence: T↑CTAGA X box a small nucleotide sequence within the 150 bp response element of the promoter of all MHC class II genes It binds the RFX complex X cell see X-Y-Z cell theory X chromosome a sex chromosome It is often found paired in the homogametic sex, which in many species is the female, and single in the heterogametic sex, in many species the male The X chromosome carries a large number of genes that control many aspects of development and function A mutant gene so carried is called X linked Since males possess only one X chromosome an abnormal gene that it carries cannot be paired with a normal allele; the male is then said to be hemizygous for that gene The female with two identical members of a pair of X-linked genes is said to be homozygous for that gene; the female with one mutant gene is called a heterozygote or carrier for the abnormal allele One X chromosome is inactivated during early embryonic development Since the progeny of each cell have the same inactivated X chromosome, a proportion of cells have the paternal X chromosome in an active state while in the other cells the maternal X chromosome is active Hence the female who is heterozygous for an abnormal gene will have cells with the normal gene and cells with the mutant gene She is said to be a mosaic Compare Y chromosome See also sex determination X-chromosome inactivation or X inactivation the inactivation in female mammals of one of the two X chromosomes during early embryonic development This phenomenon occurs randomly in cells of the female embryo, which is thus a mosaic in respect to whether it the maternal or paternal X chromosome is functional X inactivation means that the dosage of genes in female cells is comparable with that of males, who inherit only one X chromosome See also Lyon hypothesis XDP abbr for xanthosine (5′-)diphosphate Xe symbol for xenon Xeloda another name for Capecitabine Xenical (Orlistat) A slimming drug that acts by inhibiting lipase in the gut so that fat is not absorbed As a result about 30% of the fat in a meal is indigested xenin a 25-residue peptide isolated from human gastric mucosa The six C-terminal amino acids are identical to those of the octapeptide, xenopsin, present in the skin of amphibians It stimulates exocrine pancreatic secretion, its concentration rising in plasma after a meal xeno+ or (before a vowel) xen+ comb form indicating something strange or foreign xenobiochemistry the biochemistry of organic compounds foreign to the organism xenobiotic any substance that does not occur naturally but interacts with the metabolism of any organism of, or relating to, substances that are foreign to living systems xenobiotic-response element abbr.: XRE; a DNA-regulatory sequence that binds transcription factors that activate gene expression for enzymes that detoxify xenobiotics, including halogenated and other aryl hydrocarbons See also Ah xenogeneic or xenogenic originating in a different species, especially of a tissue transplant See also xenograft xenograft a tissue graft between individuals of different species xenologue or (esp US) xenolog a gene acquired by horizontal transfer from another species (but not including gene transfer to eukaryotic cells from their endosymbionts, or hence from organelles to the nucleus) Compare synologue Xenopus laevis the South African clawed toad, the oocytes and embryos of which have been extensively exploited in molecular genetics and vertebrate embryology XPum xenotope an antigenic epitope that is foreign to an animal xenotransplantation the transfer of living cells, tissues, and/or or- gans from one species to another, especially from nonhuman animals into humans for medical purposes –xenotransplant n., vb xenotype a class or group of related xenotopes; i.e an antigenic epitype that is foreign to a particular animal xeroderma pigmentosum an autosomal recessive hereditary skin disease of humans in which homozygotes show a marked tendency to develop skin cancers following exposure to sunlight It is due to a reduced ability to excise UV-induced cyclobutane pyrimidine dimers from DNA xerophthalmia progressive drying and wrinkling of the conjunctiva of the eye One cause is vitamin A deficiency X-gal abbr for 5-bromo-4-chloro-3-indolyl-b-D-galactoside, a colourless substrate that is hydrolysed by b-galactosidase to galactose and a blue product It is used with cloning vectors containing part of the lacZ gene to select recombinants in molecular cloning: the peptide produced by the lacZ fragment complements the defective b-galactosidase enzyme in host cells Insertion of foreign DNA into the vector inactivates the lacZ gene, so host cells containing recombinant plasmids will grow as white colonies on medium containing X-gal, whereas host cells containing ‘empty’ vectors will have a functional b-galactosidase and thus produce blue colonies Xho I a type restriction endonuclease; recognition sequence: C↑TCGAG Xho II a type restriction endonuclease; recognition sequence: R↑GACTY xi symbol: n (lower case) or N (upper case); the fourteenth letter of the Greek alphabet For uses see Appendix A XIAP abbr for X-linked inhibitor of apoptosis XIC abbr for X inactivation centre See Xist X-inactive-specific transcript see Xist Xiphophorus a genus of fish, that includes the South American minnow, some species of which have been much used for the study of inherited characteristics involved in carcinogenesis Crossing of certain species, e.g backcrossing X maculatus (platyfish) with X helleri (swordtail: recurrent parent) leads to spontaneous development of melanoma Xis protein or excisionase the product of the xis gene in lambda phage It is essential in the excision of phage DNA from prophage See also integrase XIST or (in mouse) Xist abbr for X-inactive-specific transcript; the noncoding RNA(16 500 nt) transcript of the X inactivation centre (XIC) on the X chromosomes of female mammals It is confined to the nucleus and associated with the heterochromatin (or Barr body) in female interphase nuclei Xist accumulates before inactivation of the X chromosome XL1-Blue a proprietary strain of E coli allowing blue-white colour screening for recombinants and the single-stranded rescue of phagemid DNA XL1-Blue MRF′ a proprietary strain of E coli lacking K12 restriction systems and suitable for cloning methylated DNA such as that from eukaryotes Xma I a type restriction endonuclease; recognition sequence: C↑CCGG XML abbr for extensible markup language See markup language XMP abbr for xanthosine monophosphate; i.e xanthosine (5′-)phosphate XNU see sequence filter xotch a transmembrane protein in Xenopus that is similar in sequence, and presumably in role, to the product of notch It is uniformly expressed in early embryos It contains 36 EGF-like domains and three notch-type repeats X-Pro dipeptidase EC 3.4.13.9; other names: proline dipeptidase; imidodipeptidase; prolidase; peptidase D; c-peptidase A cytosolic homodimeric enzyme that catalyses the hydrolysis of Xaa-|-Pro dipeptides; it also acts on aminoacyl-hydroxyproline analogues, but has no action on Pro-|-Pro It requires manganese Enzyme deficiency leads to imidodipeptiduria XPS abbr for X-ray photoelectron spectroscopy; see photoelectron spectroscopy XPum a homologue of Pumilio, in Xenopus laevis 709 X-ray crystallography X-ray crystallography the study of the geometric forms of crystals by X-ray diffraction Myoglobin was the first protein for which the structure was solved by X-ray crystallography X-ray diffraction a method that uses the diffraction pattern obtained by passing X-rays through crystals, or other regular molecular arrays, to measure interatomic distances and to determine the three-dimensional arrangement of atoms (or molecules) in the structure studied For the pattern to be sharp, the wavelength of the radiation used must be shorter than the regular spacing between the elements of the structure X-rays typically have wavelengths of only a few tenths of a nanometre, making them suitable for biological samples X-ray diffraction is used extensively in the determination of structures of proteins, nucleic acids, and other natural products (an early landmark was the determination of the structure of penicillin) In order to resolve the phase differences, much use has been made of isomorphous replacement with heavy metal atoms X-ray photoelectron spectroscopy abbr.: XPS; see photoelectron spectroscopy X-rays or (sometimes, esp US) x-rays or (formerly) röntgen rays electromagnetic radiation emitted by atoms during extranuclear loss of energy of incident radiation (e.g high-energy electrons, gamma radiation) or by atoms of certain radionuclides during transformation by electron capture X-rays have wavelengths in the range pm–10 nm (frequencies PHz–3 EHz), which lies above that of gamma radiation and overlaps the wavelengths of the far ultraviolet Characteristic X-rays have specific wavelengths of a particular nuclide or target element See also bremsstrahlung, synchrotron XRE abbr for xenobiotic-response element XTP abbr for xanthosine (5′-)triphosphate Xul symbol for a residue (or a molecule) of the ketopentose xylulose xyl+ a variant (sometimes before a vowel) of xylo+ Xyl symbol for a residue (or a molecule) of the aldopentose xylose xylan any homopolysaccharide of xylose, consisting mainly of b-1,4linked xylopyranose units with various substituent groups, that occurs in the cell walls of higher plants, and in some marine algae Xylans form the major glycans of the hemicellulose in the fibrous parts of plants xylaric acid the aldaric acid derived from xylose xylE a gene in Escherichia coli encoding a xylose transport protein that contains 12 transmembrane segments and is an H+–xylose symporter The gene is induced by xylose See also sugar transporter xylem the vascular tissue that conducts water and mineral salts from the roots to the aerial parts of a plant and provides it with mechanical support xylene cyanol a dye used as a mobility marker in agarose gel electrophoresis L-xylitol reductase EC 1.1.1.10; an enzyme of the glucuronate pathway that catalyses the reaction: xylitol + NADP+ = L-xylulose + NADPH + H+ Deficiency of the enzyme results in essential pentosuria X-Y-Z-cell theory xylo+ or (sometimes before a vowel) xyl+ comb form indicating the trivial name for the aldopentose xylose xylo- prefix (in chemical nomenclature) indicating a particular configuration of a set of three contiguous >CHOH groups, as in the acyclic form of D- or L-xylose See monosaccharide xylose symbol: Xyl; xylo-pentose; a constituent of plant polysaccharides (see xylan); the naturally occurring enantiomer is always D-xylose In humans most ingested xylose is excreted unchanged in the urine This is the basis for the xylose absorption test, the most widely used test of carbohydrate absorption O OH OH HO OH f β b-D-pyranose form xylose isomerase EC 5.3.1.5; systematic name: D-xylose ketol-iso- merase; an enzyme that catalyses the reaction: D-xylose = D-xylulose; magnesium ions are a cofactor The 3-D structure is known, and it is a beta-barrel protein xylose-1-phosphate uridylyltransferase see UTP–xylose-1-phosphate uridylyltransferase xylulose symbol: Xul; the trivial name for the ketopentose threo-2pentulose; D-xylulose is the naturally occurring enantiomer Excessive excretion of xylulose in the urine is called essential pentosuria O CH2OH HO OH OH a-D-xylulose 5-phosphate the 5-phosphate ester of D-xylulose and a component of the pentose phosphate pathway It is formed from Dribulose 5-phosphate by ribulose-phosphate 3-epimerase (EC 5.1.3.1); D-xylulose 5-phosphate then reacts with D-ribose 5-phosphate, catalysed by transketolase, to give glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate X-Y-Z-cell theory a theory of immunocyte maturation that proposes that the first committed immunocyte, the X cell, is transformed by antigen into a memory cell, the Y cell, in the primary response, and is further stimulated in the secondary response to become an antibody producer, the Z cell D-xylulose 710 Yy y symbol for yocto+ (SI prefix denoting 10–24 times) y symbol for amount-of-substance fraction (i.e mole fraction) or number fraction for gases Compare x a Cartesian space coordi- nate, complementary to x and z Y symbol for yotta+ (SI prefix denoting 1024 times) a residue of the a-amino acid L-tyrosine (alternative to Tyr) a residue of an incompletely specified base in a nucleic-acid sequence that may be either cytosine or thymine a residue of an unspecified pyrimidine nucleoside (alternative to Pyd) a residue of the minor nucleoside wyosine (alternative to W) yield yttrium Y symbol for admittance (reciprocal of impedance) YAC abbr for yeast artificial chromosome Yang cycle see methionine salvage pathway Yb symbol for ytterbium Y cell see X-Y-Z-cell Y chromosome a sex chromosome found only in the heterogametic sex and usually different in size from the X chromosome In many animals it carries the testis-determining factor that triggers male embryonic development yeast any of a group of unicellular fungi that reproduce asexually – by budding or fission – and sexually – by the production of ascospores Yeast cells may occur singly or in short chains, and some species produce a mycelium The term ‘yeast’ is often used to mean members of the genus Saccharomyces, e.g S cerevisiae), which is an example of a budding yeast, or Schizosaccharomyces pombe, which is an example of a fission yeast yeast artificial chromosome abbr.: YAC; a specialized cloning vector that contains a centromere, an autonomously replicating sequence (ARS), a pair of telomeres, selectable marker genes, and the fragment of DNA to be cloned Usually, genomic DNA is digested to produce fragments containing the genes, which are separated by pulsed field gel electrophoresis; the large fragments are then ligated into YACs They are capable of propagation in yeasts, where they function as ‘artificial chromosomes’, being efficiently replicated YACs are essential in large mapping projects, such as the Human Genome Project (see HUGO), as they are stable and can carry vast DNA inserts of 100 to 1000 kbp yeast cloning any method of cloning using yeast as the host Expression of eukaryote genes by yeasts and other microbial eukaryotes is subject to eukaryotic regulatory systems, and the products undergo post-translational modification in contrast to when they are expressed in prokaryotes Thus, yeast clones are often used for the expression of glycoproteins yeast eluate factor a former term for vitamin B6 yeast filtrate factor a former term for pantothenic acid See pantothenate yeast nucleic acid a former term for ribonucleic acid yeast two-hybrid system a system that exploits two hybrid proteins, X, fused to the GAL4 DNA-binding domain, and Y, fused to the GAL4 activation domain Plasmids encoding each of the hybrid proteins are introduced together into yeast, which leads to the expression of both hybrids The system is used to test whether protein Y binds to protein X, for example in investigating the role of newly discovered proteins If the proteins bind, the resulting complex will be bound to the upstream activation sequence for the yeast GAL genes by the GAL4 DNA-binding domain, and the presence of the GAL4 activation domain will lead to transcriptional activation of the reporter gene, i.e b-galactosidase The system has the advantage over immunoprecipitation that if Y binds to X, the gene encoding it is already available as a clone The hybrid containing X is referred to as the bait yellow enzyme old yellow enzyme, EC 1.6.99.1; NADPH dehydrogenase; a flavoprotein (FMN in yeast, FAD in plants) new yellow enzyme an alternative name for D-amino-acid oxidase; see amino-acid oxidase yellow fever virus There are two kinds of fever; jungle which is a disease of monkeys which is spread by infected mosquitoes; rare in humans; and urban, a disease of humans caused by infected mosquitoes Aedes aegypti The virus is a member of the Flaviviridae with a sense plus RNA genome translated to a polyprotein of envelope, membrane and capsid proteins Vaccination is by live-attenuated 17D strain yellow marrow see bone marrow Yersinia murine toxin see murine toxin YES v-yes is the oncogene of the Yamaguchi sarcoma virus, and has a cellular counterpart, c-yes, the product of which is a member of the src family of non-receptor tyrosine kinases, having a myristoylation site, and SH2, SH3 and tyrosine kinase domains yield symbol: Y; a ratio expressing the efficiency of a mass conversion process The yield coefficient is defined as the amount of cell mass or product formed related to the consumed substrate or to the intracellular ATP production yin-yang hypothesis a model of biological regulation based on the opposing actions of certain cyclic nucleotides It arises from the observation that hormones or other biologically active substances that promote the cellular accumulation of cyclic GMP produce cellular responses that are antagonistic to ones occurring when the concentration of cyclic AMP is increased in the same tissues or cells Hence cyclic GMP and cyclic AMP may have opposing or antagonistic regulatory influences in certain biological systems, by analogy with the oriental concept of yin and yang symbolizing a dualism between opposing natural forces +yl suffix (in chemical nomenclature) denoting a free valence derived from the loss of a hydrogen atom from a parent hydride, e.g methyl, pentanyl It also applies to particular acyl groups, that are exceptions to the rule that acyl groups are named by changing the ‘-ic acid’ or ‘-oic acid’ ending to ‘-oyl’ These exceptions are acetyl, malonyl, succinyl, propionyl, butyryl, oxalyl, and glutaryl yocto+ symbol: y; SI prefix denoting 10–24 times yohimbine an indole alkaloid, C21H26N2O3, with a2-adrenoceptor antagonist activity It is produced by Corynanthe johimbe and Rauwolfia serpentina N N H H H3C O H H O OH Yop abbr for Yersinia outer protein; any of a number of proteins, known as virulence proteins, originally found on the surface of Gram-negative bacteria of the genus Yersinia; they are now known to be characteristic of plant-pathogenic proteins that are secreted by bacteria of genera as diverse as Pseudomonas, Xanthomonas, and Erwinia They are also produced by animal pathogens, such as Shigella flexneri, Salmonella typhimurium, and Escherichia coli They are secreted by the type III system Unlike other secreted proteins, they lack a signal sequence yotta+ symbol: Y; SI prefix denoting 1024 times Yphantis method an alternative name for meniscus depletion method (sedimentation equilibrium) 711 Zz z symbol for zepto+ (SI prefix denoting 10–21 times) z symbol for charge number of an ion a Cartesian space coordi- nate, complementary to x and y Z symbol for zetta+ (SI prefix denoting 1021 times) a residue of ei- ther of the a-amino acids L-glutamic acid or L-glutamine when the state of amidation is uncertain (alternative to Glx) It may also be used to represent a residue of any other substance, such as 4-carboxy-L-glutamic acid (as alternative to Gla) or 5-oxo-L-proline (as alternative to Glp), that yields glutamic acid on acid hydrolysis of peptides the benzyloxycarbonyl group (alternative to Cbz) Z symbol for proton number impedance (Z)- prefix (in chemical nomenclature) denoting a geometric isomer in which the highest priority substituent groups, determined according to the Cahn–Ingold–Prelog rules (see sequence rule), are located on the same side of a double bond See also E/Z convention zalcitabine or 2′,3′-dideoxycytidine (abbr.: ddC); an inhibitor of reverse transcriptase that is used in the treatment of HIV-1 infection Zantac see ranitidine ZAP abbr for zinc finger antiviral protein; a protein (776 amino acids) of rat that contains four zinc fingers (of C4H type) When expressed in fibroblasts in cell culture it confers specific antiviral activity ZAP-70 or zeta chain-associated tyrosine kinase a protein-tyrosine kinase (70 kDa) that associates with the f subunit that functions as part of the T-cell receptor and CD3 complex in lymphocytes It contains two SH2 domains, which interact with immunoglobulin tyrosine-based motifs on f or other subunits of these complexes Rare inactivating mutations in the f chain gene cause severe combined immunodeficiency (SCID) zaragozic acid any of a family of fungal metabolites that are potent inhibitors of squalene synthase O HO O OAc CH3 CH3 COO - O CH2 CH3 COO - O - OOC CH3 OH zaragozic acid A Z-average relative molecular mass see average relative molecular mass Z cell see X-Y-Z cell theory Z disk or Z line a platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached It is seen as a dark transverse line in micrographs Z-DNA abbr for Z form of DNA zeatin trans-zeatin; (E)-2-methyl-4-(1H-purin-6-ylamino)-2-buten1-ol; a plant hormone of the cytokinin class Its derivative, transzeatin riboside (N6-(trans-4-hydroxy-3-methyl-cis-2-buten-1-yl)ad- CH3 NH HOH2C N N N N H enosine) is also a cytokinin The cis form is a rare component in some RNA structures zebrafish Brachydanio rerio; a small, highly fertile species of characinoid teleost fish with a shiny blue body and four longitudinal yellowish stripes along its sides It is much used in studies on the molecular biology of differentiation and development in metazoan animals Zeeman effect the splitting of a single line in a spectrum, indicative of the degeneration of the excited state of a particular chromophore, into two or more components of slightly different wavelengths brought about by the application of an external magnetic field [After Pieter Zeeman (1865–1943), Dutch physicist.] zein the principal storage protein of maize (corn) seeds It is relatively deficient in the essential amino acids lysine and tryptophan; tryptophan deficiency can occur in human populations dependent on maize as the major protein source The zein genes are clustered Zellweger syndrome or cerebrohepatorenal syndrome a heterogeneous disorder of peroxisome biogenesis that results from mutations in at least 11 loci for PEX proteins (see peroxin), most commonly for PEX1 Typically patients have multiple congenital anomalies of the face and head, ongoing metabolic disturbances with accumulation of very-long-chain fatty acids, and usually die in infancy Infantile Refsum’s disease is one form of the syndrome [After Hans Ulrich Zellweger (1909–1990), US paediatrician.] zeolite any porous alkali metal- or alkaline earth-aluminium silicate that shows ion-exchange properties Zeolites may be used for water softening or as molecular sieves —zeolitic adj zepto+ symbol: z; SI prefix denoting 10–21 times zero-order kinetics kinetics shown by a zero-order reaction zero-order reaction a chemical reaction whose velocity is independent of the concentration of one or more of the reactants See order of reaction zeroth law of thermodynamics see thermodynamics, laws of zervamicin see peptaibophol zeta symbol: f (lower case) or F (upper case); the sixth letter of the Greek alphabet For uses see Appendix A zeta chain a transmembrane protein (16 kDa) of most T cells that contains three intracellular immunoreceptor tyrosine-based activation motifs (ITAMs) to which protein tyrosine kinases (e.g ZAP-70) bind It forms a dimer of disulfide-linked chains that are tightly associated with components of CD3 and T-cell receptors the a-globin-like globin that with c-globin forms Hb Portland I, and with eglobin forms Hb Gower I, in the first few weeks of human embryonic development See hemoglobin zeta chain-associated tyrosine kinase an alternative name for ZAP-70 zeta potential symbol: f; the potential at the surface of shear of a charged particle; for macromolecular ions it is the potential at the surface of the hydrodynamic particles formed by such ions zeta protein an alternative name for cellular fibronectin zetta+ symbol: Z; SI prefix denoting 1021 times zeugmatography a technique in which the addition of carefully controlled inhomogeneous magnetic fields enables measurements of nuclear magnetic resonance (NMR) to be made at selected regions of heterogeneous samples and hence the formation of two-dimensional maps of the distribution of almost any property measurable by NMR Zfn abbr for zinc finger nuclease; a synthetic chimeric protein that contains three C2H2 zinc fingers and a nonspecific DNA cleavage domain Z form of DNA abbr Z-DNA or DNA-Z; a form of DNA consisting of a left-handed double helix in which the pyrimidine residues are always in the anti orientation and the purine residues in the syn So-called because of the zig-zag appearance of its conformation See also A form (def 1), B form, C form Zfp abbr for zinc finger protein zidovudine 3′-azido-3′-deoxythymidine (abbr.: AZT); an analogue 712 Zimm–Crothers viscometer Z scheme of thymidine, the phosphorylated form of which is an inhibitor of reverse transcriptase in retroviruses; it also terminates DNA synthesis Zidovudine undergoes phosphorylation in human T cells to a nucleoside 5′-triphosphate, which competes with thymidine triphosphate (TTP) and serves as a chain-terminating inhibitor of HIV reverse transcriptase It is used clinically to treat patients with HIV infection and AIDS Proprietary name: Retrovir O H3C NH N O HOCH2 O N3 Zimm–Crothers viscometer a modified Couette viscometer in which the inner cylinder is a self-centring float containing a steel pellet The inner cylinder is rotated by an external rotating magnetic field, the speed of rotation being dependent, inter alia, on the viscosity of the fluid The instrument only measures the viscosity of a sample relative to a standard.[After Bruno H Zimm (1920– ) US chemist and Donald M Crothers (1937– ) US biophysical chemist.] Zimmermann reaction the reaction of m-nitrobenzene in strongly alkaline solution with the methylene group at position 16 in 17-ketosteroids to give a purple colour with an absorption maximum at 520 nm It may be used to estimate such steroids Zimm plot a graphical double extrapolation used to analyse most macromolecular light-scattering data Measurements are made of Kc/R h at various concentrations as a function of the scattering angle, 2h, where K is an optical constant, c is the concentration, and R h is the Rayleigh ratio A series of plots of Kc/R h against (sin2h + K′c) are made, where K′ is an arbitrary constant chosen to provide a convenient spread The data are then extrapolated separately to c = and h = The intersection of the two extrapolated curves yields the relative molecular mass zinc symbol Zn; a metal of group 12 of the IUPAC periodic table; relative atomic mass 65.38; atomic number 30 The principal ore is zincblende, ZnS Its oxidation state is Zn(II) Zinc oxide is used as an antiseptic Naturally occurring nuclides include (relative abun64 dance follows each) 30Zn (48%), 66 Zn (28%), 68 Zn (18%) Radionu30 30 clides include zinc-62, zinc-65, and zinc-72 Dietary deficiency in the rat is manifested by retarded growth, alopecia, and lesions in the skin, esophagus, and cornea Deficiency is rare in normal individuals, but can manifest itself in alcoholics and in patients with renal disease or malabsorption Zn2+ is an essential cofactor for many enzymes Recent work suggests zinc is bactericidal zinc-62 the artificial radioactive nuclide 62 Zn; it emits a positron (b+ 30 particle) (0.66 Mev), and c-radiation of four energies (0.041, 0.25, 0.51, and 0.60 Mev) It has a half-life of 9.26 h zinc-65 the artificial radioactive nuclide 65 Zn; it emits a positron (b+ 30 particle) (0.325 Mev) and c-radiation (1.12 Mev) It has a half-life of 244.1 days zinc-72 the artificial radioactive nuclide 72 Zn; it emits an electron 30 (b– particle) (0.3 Mev) and c-radiation of three energies (0.016, 0.145, and 0.192 Mev) It has a half-life of 1.938 days zinc finger a polypeptide motif present in many DNA-binding proteins, and having the consensus sequence -CX2–4CX3FX5LX2HX3H- The motif takes its name from its zinc-binding site, which forms a finger-like loop in the peptide, also described as the Cys2/His2 finger, the Cys and His residues coordinating a zinc ion Zinc fingers are most notably present in transcription factors (e.g., TFIIIA and SP1), which have several repeats of the motif; they are required for binding of the transcription factor to DNA ZIP abbr for the leucine zipper domain See also bZIP a family of membrane proteins involved in import of zinc into the cytoplasm in eukaryotes They are predicted to contain eight transmembrane segments, of which S4 and S8 are highly conserved and contain conserved histidine residues, which may be involved in metal binding Z line another name for Z disk Zn symbol for zinc ZNF9 a protein that contains seven zinc finger motifs, binds RNA, and is expressed in skeletal and heart muscle Expansion of a CCTG tetranucleotide repeat in intron of the gene causes myotonic dystrophy type Zollinger–Ellison syndrome a disease syndrome caused by excessive secretion of gastrin, either from (type 1) G-cell hyperplasia in the antrum of the stomach, or from (type 2) a benign or malignant pancreatic islet tumour (gastrinoma) The manifestations include multiple peptic ulcers, or peptic ulcers in unusual sites, with a marked tendency to bleeding, often associated with hyperparathyroidism [After Robert M Zollinger (1903– ) and Edwin H Ellison (1918–70).] zona adherens see desmosome zonadhesin a protein of spermatozoa, probably present in the acrosome, that binds to ZP3 of the zona pellucida of mammalian ova zona fasciculata see adrenal gland zona glomerulosa see adrenal gland zonal centrifugation an alternative name for density-gradient centrifugation zonal centrifuge a centrifuge designed to allow large-scale and continuous fractionation by density-gradient centrifugation zonal rotor any centrifuge rotor of high capacity used preparatively in a zonal centrifuge zona occludens an alternative name for tight junction zona pellucida a layer of glycoproteins that surrounds a mammalian ovum and disappears before implantation It is secreted by cells of the Graafian follicle See also ZP zona pellucida sperm-binding protein abbr.: ZP; any of the sulfated transmembrane glycoproteins (ZP1, ZP2, ZP3) that together form the zona pellucida of the oocyte ZP3 is a sperm receptor zona reticularis see adrenal gland zone electrophoresis a method of electrophoresis in which the protein (or other) solution is placed at the starting position as a thin band or spot in an inert supporting medium (paper, starch gel, polyacrylamide gel, etc.), containing buffer solution An electric potential is then applied to the supporting medium, causing the proteins (or other substances) to migrate to give distinct bands or zones These may be located in situ by staining, light absorption, etc., or by analysis after elution of discrete pieces of the supporting medium zone precipitation a technique in which protein is precipitated as a zone in a gel-filtration column by eluting with a gradient of a protein-precipitating agent See gel-permeation chromatography zone spreading the broadening of a zone in electrophoresis or chromatography due to eddy currents or other disturbances in the supporting medium zoo blot a method for detecting conservation of DNA sequence during evolution A segment of DNA being investigated is used as a probe to hybridize against a series of DNA samples from various species, and hence establish whether the DNA sequence has been conserved during evolution zoonosis (pl zoonoses) any disease that can be transmitted to humans from other animals in natural circumstances zooplankton see plankton zootoxin any poisonous substance formed by animal cells Zovirax a proproetary name for acyclovir ZP abbr for zona pellucida protein; any of three glycoproteins (ZP1, ZP2, and ZP3) present in the zona pellucida of mammalian ova ZP3 binds the sperm proteins p47, Sp56, and zonadhesin, which may be present in the acrosome Zr symbol for zirconium Z ring a contractile ring of proteins that forms in the mid-region of the inner side of the plasma membrane of bacteria as part of cell division, normally towards the end of replication Formation is initiated by FtsZ and depends on the presence of the Min system for correct localization Z scheme a term applied to two-system photosynthetic light reac713 zuotin tions, utilizing both photosystems I and II It describes the mode of photosynthesis used by higher plants and algae, and by cyanobacteria As it is normally plotted, with redox potential (on the ordinate) against time, it shows there is a sudden jump on excitation by a photon of a reaction centre, followed by a slow decline through electron transport components, and gives a (horizontal) Z-like appearance, hence the name zuotin a nuclear Z-DNA-binding protein of Saccharomyces cerevisiae zwischenferment an obsolete term for the enzyme–coenzyme complex of glucose-6-phosphate dehydrogenase Zwittergent the proprietary name for any of a group of zwitterionic detergents containing a betaine and a sulfonate group; such molecules retain their amphoteric (zwitterionic) properties over a very wide range of pH The formula is n-alkyl N,N-dimethyl-3-ammonio-1-propanesulfonate In Zwittergent 3-08, alkyl is octyl (CMC 330 mm); 3-10, decyl (aggregation number 41, CMC 25–40 mm); 312, dodecyl (aggregation number 55, CMC 2–4 mm); 3-14, tetradecyl (aggregation number 83, CMC 0.1–0.4 mm); 3-16, hexadecyl (aggregation number 155, CMC 0.01–0.06 mm) zwitterion an alternative name for dipolar ion zwitterionic buffer a buffer solution whose acid or base component is a zwitterion (i.e dipolar ion) The term is used especially of solutions of Good buffer substances and newer equivalents zygote any fertilized ovum before it has undergone cleavage —zygotic adj zygotene the second phase of prophase I in meiosis zymase the name originally given to the heat-labile, nondiffusible fraction of a crude extract of brewers’ yeast that, with the addition of the heat-stable, diffusible fraction (i.e cozymase), would enable the alcoholic fermentation of glucose to occur in a cell-free system It was later shown to consist of a mixture of enzymes, including those of the glycolytic pathway zyxin zymogen or proenzyme or (formerly) proferment the inactive pre- cursor of an enzyme, often convertible to the enzyme by partial proteolysis The term is applied especially to catalytically inactive forms of pancreatic enzymes such as trypsinogen, chymotrypsinogen, proelastase, and procarboxypeptidase; these are cleaved to release the active enzyme after their secretion from granules (zymogen granules) in the acinar cells of the pancreas zymogen granule a membrane-bound, cytoplasmic secretory granule visible by light microscopy Zymogen granules are formed in the Golgi apparatus of enzyme-secreting cells and serve to store a zymogen The term is used especially of a secretory granule containing the proenzyme of a digestive enzyme zymogram any record of a zone electrophoresis separation in which enzymes in a sample have been separated and their positions, and relative amounts, revealed by an activity stain any table showing the results of carbohydrate-fermentation tests carried out in the process of identifying a microorganism zymology the science dealing with fermentations —zymological adj.; zymologist n zymosan a crude preparation of yeast cell walls, consisting chiefly of polysaccharide, that activates the alternative pathway of the complement system in the presence of properdin zymosterol cholesta-8,24-dien-3b-ol; a sterol present in yeasts e.g Candida albicans, Saccharomyces cerevisiae zymurgy the branch of chemistry dealing with the applications of fermentation processes, especially to brewing and wine-making Zyvox another name for Linezolid zyxin a protein component of cell substratum and cell–cell adherens junctions It is a component of adhesion plaques and the termini of stress fibres near the point of association with the cytoplasmic face of the adhesive membrane; it interacts with a-actinin 714 Appendices Appendix A The Greek alphabet to a cyclic structure an anomeric configuration (of a sugar molecule or residue; see anomer) winding number (of a helical duplex DNA molecule) The Greek alphabet Name alpha beta gamma delta epsilon zeta eta theta iota kappa lambda mu nu xi omicron pi rho sigma Capital letter Lower-case letter A B C D E F G H I J K L M N O P Q R a b c d e f g h i j k l m n o p q r or y (at end S T U V W X s t u v w x English transliteration b (or b) beta particle (b– is used for an electron and b+ for a positron) b (or b) buffer value pressure coefficient plane angle (in organic chemical nomenclature) a locant for a substituent on the second atom from the atom carrying the principal function in an acyclic structure or in a side chain attached to a cyclic structure an anomeric configuration (of a sugar molecule or residue; see anomer) number of secondary turns (in an unconstrained helical duplex DNA molecule) c (or c) a heavy chain of immunoglobulin G a photon of gamma radiation (obsolete) microgram (lg now used) c (or c) activity coefficient (cc is used for activity coefficient when expressed on a concentration basis, cm when expressed on a molality basis, cx when expressed on a mole fraction basis, and c± is used for mean ionic activity coefficient) electrical conductivity (alternative to j or r) mass concentration or mass density (alternative to q) plane angle surface tension or interfacial tension (alternative to r) gyromagnetic ratio (in organic chemical nomenclature) a locant for a substituent on the third atom from the atom carrying the principal function in an acyclic structure or in a side chain attached to a cyclic structure … (or d) a heavy chain of immunoglobulin D (in mathematics) an infinitesimal change or difference ‡ (or d) chemical shift number fraction (in organic chemical nomenclature) a locant for a substituent on the fourth atom from the atom carrying the principal function in an acyclic structure or in a side chain attached to a cyclic structure kh D (or D) (in mathematics) a finite change or difference ps D (or D) (in older organic chemical nomenclature) a locant for a double bond (a right superscript number designates the lowernumbered carbon atom; see fatty-acid nomenclature); no longer recommended for denoting unsaturation in names of individual compounds although it may still be used in generic terms (e.g D5-steroid) and in symbols (e.g D2Ach) e (or e) a heavy chain of immunoglobulin E e (or e) molar (decadic) absorption coefficient permittivity (er is used for relative permittivity and e0 for permittivity of vacuum) (in organic chemical nomenclature) a locant for a substituent on the fifth atom from the atom carrying the principal function in an acyclic structure or in a side chain attached to a cyclic structure (in chemical nomenclature) hapticity of a ligand (less common alternative to g; see hapto) ea degree of activation (of an enzymic reaction) a b g d e z ē or e th i k l m n x o p r s of word) tau upsilon phi chi psi omega t u ph ō or o Single-character symbols „ ‘ (or a) a heavy chain of immunoglobulin A maximal agonist effect alpha particle (or a) angle of optical rotation (aobs is used for observed rotation and [a] for specific optical rotation or specific optical rotatory power; am is used for molar optical rotatory power) absorptance (linear) napierian absorption coefficient Bunsen coefficient partition coefficent plane angle (in organic chemical nomenclature) a locant for a substituent on the first atom from the atom carrying the principal function in an acyclic structure or in a side chain attached 717 Appendix A Appendix A rate of conversion ei degree of inhibition (of an enzymic reaction) n evs elasticity coefficient (of a specific enzymic step in a metabolic system) p (or p) a transcendental number that is the ratio of the circumference of a circle to its diameter (3.141 592 653 59 ) f (or f) electrokinetic potential or zeta potential p (or p) pros (or ps) surface pressure g (or g) viscosity (alternative to l) (in chemical nomenclature) hapticity (of a ligand; more common alternative to e; see hapto) P (or P) osmotic pressure (PD may be used to represent colloid osmotic pressure) binding potential (of a ligand) (or h) Bragg angle (see Bragg’s law) (in surface chemistry) contact angle plane angle torsion angle (in a linear sequence of four attached atoms; alternative to x) Celsius temperature (alternative to t) q h (or q) density or mass density (qA or qS is used for surface density) mass concentration or mass density (alternative to c) radiant energy density (alternative to w) charge density resistivity r (or r) surface tension or interfacial tension (alternative to c) electrical conductivity (alternative to c or j) wavenumber in a medium surface charge density (in surface chemistry) area per molecule (in nuclear magnetic resonance spectroscopy) shielding constant superhelix density (of a helical duplex DNA molecule) R (or R) (in mathematics) a summation sign s (or s) tele bond angle relaxation time or time constant (alternative to S) transmittance or transmission factor (alternative to S) mean life number of superhelical turns (in a helical duplex DNA molecule) u (or u) osmotic coefficient (um is used for osmotic coefficient when expressed on a molality basis and ux when expressed on a mole fraction basis) electric potential (alternative to V) fluidity plane angle phase difference volume fraction Dalziel coefficient torsion angle (from the anomeric carbon atom to the oxygen atom of a glycosidic bond) quantum yield (alternative to ) 10 winding angle (of intercalated helical DNA) (or K) molar conductivity (of an electrolyte) U l (or l) a heavy chain of immunoglobulin M micro+ (SI prefix denoting 10–6 times) (obsolete) micron (now called micrometre; symbol: lm) (or U) heat flow rate radiant power or radiant (energy) flux (alternative to P) magnetic flux potential energy (alternative to Ep or V) quantum yield (alternative to u) v l (or l) (in chemical nomenclature) a bridging ligand viscosity (alternative to g) chemical potential (lo or lŠ is used for standard chemical potential and l~ is used for electrochemical potential) electric mobility (alternative to u) (in magnetism) permeability (lr is used for relative permeability) magnetic dipole moment (bold italic) (alternative to m) electric dipole moment (bold italic) (alternative to p) (or v) electronegativity magnetic susceptibility (alternative to j; vm is sometimes used, but it should be reserved for molar magnetic susceptibility) surface electric potential exocyclic torsion angle (in a sugar residue) w (or w) replacement of the –CO–NH– group in a peptide by another (indicated) grouping torsion angle (from the oxygen atom of a glycosidic bond to the glycosylated molecule) wavefunction (alternative to W) W (or W) a residue of the ribonucleoside pseudouridine (alternative to Wrd) electric flux wave function (alternative to w) x (or x) angular frequency angular velocity solid angle torsion angle (in a linear assembly of four attached atoms; alternative to h) (in organic chemical nomenclature) a locant for the terminal atom or group in an acyclic organic compound (in notation for polyunsaturated fatty acids) x-x signifies that a double bond is located on the xth carbon; unlike standard chemical nomenclature it is counted from the distal (methyl carbon) atom X (or X) ohm X (or X) solid angle Hm melting temperature (alternative to Tm or tm) [H] molar ellipticity ] j (or j) one type of light chain of any class of immunoglobulin (the other being k) j (or j) electrical conductivity (alternative to c or r) electrolytic conductivity or (formerly) specific conductance molar napierian absorption coefficient magnetic susceptibility (alternative to v) (in inorganic chemical nomenclature) an affix in the name of a polydentate chelate complex indicating single attachments of a polydentate ligand to a coordination centre A right superscript numerical index indicates the number of such attachments k (or k) one type of light chain of any class of immunoglobulin (the other being j) (obsolete) microlitre (ll now used) k (or k) (in thermodynamics) absolute activity (see activity, def 4) disintegration constant or decay constant wavelength thermal conductivity (alternative to k) l0 permeability of vacuum (a fundamental physical constant) lB Bohr magneton (a fundamental physical constant) le electron magnetic moment (a fundamental physical constant) lN nuclear magneton (a fundamental physical constant) lp proton magnetic moment (a fundamental physical constant) m (or m) stoichiometric number (of a chemical reactant) frequency (alternative to f for electromagnetic radiation) kinematic viscosity endocyclic torsion angle (in a sugar residue) n (in organic chemical nomenclature) unknown configuration at a chiral centre extent of reaction 718 Appendix A Multi-character biochemical symbols commencing with a Greek character aLnn the linolenoyl or (9,12,15)-linolenoyl or (formerly) a-linolenoyl (i.e (all-Z)-octadeca-9,12,15-trienoyl) group (alternative to Lnn) bAad a residue of the b-amino acid L-b-aminoadipic acid (i.e L3-aminohexanedioic acid) bAla a residue of the b-amino acid b-alanine (i.e 3-aminopropanoic acid) cLnn the (6,9,12)-linolenoyl or (formerly) c-linolenoyl (i.e (allZ)-octadeca-6,9,12-trienoyl) group Appendix A D2Ach the (all-Z)-eicosa-8,11-dienoyl group D3Ach the (all-Z)-eicosa-5,8,11-trienoyl group D4Ach the arachidonoyl (i.e (all-Z)-eicosa-5,8,11,14-tetraenoyl) group DPam the palmitoleoyl (i.e (Z)-hexadec-9-enoyl) group eAcp see eAhx eAhx or (formerly) eAcp a residue of the e-amino acid 6-aminohexanoic acid (formerly known as e-aminocaproic acid) Wrd a residue of the ribonucleoside pseudouridine (alternative to W) 719 Appendix B Sequence-rule priorities The names of some common ligands are listed alphabetically below, the numbers preceding them indicating the relative priorities assigned to the ligands under the sequence rule A higher number denotes greater preference; for example, a hydroxy group (numbered 57) takes precedence over an amino group (numbered 43) It should be noted that any change to the structure of a listed ligand may alter the order of preference Where a ligand consists of or contains a heavy or radioactive isotope of hydrogen, the relative priorities are tritium > deuterium > protium Racemates with a single chiral centre are labelled (RS); extensions of the sequence rule are used in the E/Z, pro-R/pro-S, pro-E/pro-Z, and Re/Si nomenclature systems 64 36 48 21 10 43 44 37 49 65 13 60 41 50 75 42 15 16 19 38 74 17 52 51 34 28 acetoxy acetyl acetylamino acetylenyl allyl amino ammonio (+H3N–) benzoyl benzoylamino benzoyloxy benzyl benzyloxy benzyloxycarbonyl benzyloxycarbonylamino bromo tert-butoxycarbonyl butyl sec-butyl tert-butyl carboxy chloro cyclohexyl diethylamino dimethylamino 2,4-dinitrophenyl 3,5-dinitrophenyl 59 40 13 46 68 35 63 62 17 11 57 76 19 18 20 14 69 58 39 12 45 71 66 72 67 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 720 70 11 56 27 33 24 55 16 61 22 47 54 18 14 29 12 73 25 30 23 53 32 15 31 26 methylthio (CH3S–) neopentyl nitro m-nitrophenyl o-nitrophenyl p-nitrophenyl nitroso pentyl phenoxy phenyl phenylamino phenylazo propenyl propyl 1-propynyl 2-propynyl sulfo (HO3S–) m-tolyl o-tolyl p-tolyl trimethylammonio trityl vinyl 2,6-xylyl 3,5-xylyl The periodic table of the elements Group 1 Period 7 10 11 12 13 14 15 16 18 17 H He Li Be 11 B 12 Na 21 Ca 37 38 55 Cs La–Lu Ba 87 88 Fr Lanthanoids Ac–Lr Actinoids 57 La 89 Ac Ta 104 89–103 Ra Hf 58 Ce 90 Th 74 105 Rf 106 Db 59 Pr 91 Pa Re 107 Sg 60 92 Pm 93 U Np Ir 108 Bh 61 Nd Os 62 63 Sm 94 Pu Gd 96 Am Cm Tb 97 Bk 82 Tl 112 Rg 65 81 Hg 111 Ds 64 Eu 95 Au 110 Mt 80 Pb 113 114 Dy 98 Cf Xe 86 At 116 117 Uub 66 54 85 Po 115 Kr I 84 Bi 36 53 Te 83 Ar Br 52 Sb Sn 18 35 Se 51 Ne Cl 34 As 50 In Cd 79 Pt 109 Hs Ag 78 49 48 17 S 33 Ge 10 F 16 P 32 Ga O 15 Si 31 Zn 47 Pd 77 30 Cu 46 Rh 76 29 Ni 45 Ru 75 28 Co 44 Tc W 27 Fe 43 Mo 73 26 Mn 42 Nb 72 25 Cr 41 Zr 57–71 24 V 40 Y 56 23 Ti 39 Sr Rb 22 Sc N 14 Al 20 K C 13 Mg 19 Uut Uuq Uup Uuh 67 68 69 70 118 71 Ho 99 Es Er 100 Fm Tm 101 Md Yb 102 No Uus Rn Uuo Lu 103 Lr Correspondence of recommended group designations to other designations in recent use IUPAC 1990 recommendations Usual European convention Usual N American convention IA IIA IIIA IVA VA VIA VIIA IA IIA IIIB IVB VB VIB VIIB 10 11 12 13 14 15 16 17 18 VIII (or VIIIA) IB IIB IIIB IVB VB VIB VIIB (or VIIIB) VIII (or VIIIB) IB IIB IIIA IVA VA VIA VIIA VIIIA (or 0) SI base units SI derived units with special names Physical quantity Name of SI unit Symbol for SI unit Physical quantity Name of SI unit Length Mass Time Electric current Thermodynamic temperature Amount of substance Luminous intensity metre kilogram second ampere kelvin m kg s A K Absorbed dose (of radiation) Activity (radioactive) Catalytic activity Celsius temperature gray Gy J kg–1 becquerel katal degree Celsius sievert Bq kat °C s–1 mol s–1 K Sv J kg–1 = m2 s–2 mole candela mol cd farad coulomb siemens volt F C S V C V–1 As X–1 J C–1 = m–2 kg–1 s4 A2 ohm joule newton hertz lux henry lumen weber tesla radian watt pascal steradian X J N Hz lx H lm Wb T rad W Pa sr SI prefixes Submultiple Prefix Symbol Multiple Prefix Symbol 10–1 10 102 103 106 109 1012 1015 1018 1021 1024 10–2 10–3 10–6 10–9 10–12 10–15 10–18 10–21 10–24 deci centi milli micro nano pico femto atto zepto yocto d c m l n p f a z y deca hecto kilo mega giga tera peta exa zetta yotta da h k M G T P E Z Y Dose equivalent (dose equivalent index) Electric capacitance Electric charge Electric conductance Electric potential, electromotive force Electric resistance Energy, work, heat Force Frequency Illuminance Inductance Luminous flux Magnetic flux Magnetic flux density Plane angle* Power, radiant flux Pressure, stress Solid angle* Symbol for Expression in SI unit terms of SI base units = m2 s–2 = m–2 kg–1 s3 A2 = m2 kg s–3 A–1 V A–1 = m2 kg s–3 A–2 Nm = m2 kg s–2 m kg s–2 s–1 cd sr m–2 V A–1 s = m2 kg s–2 A–2 cd sr Vs = m2 kg s–2 A–1 V s m–2 = kg s–2 A–1 = m m–1 J s–1 = m2 kg s–3 N m–2 = m–1 kg s–2 = m2 m–2 Prefix symbols should be printed in roman type with no space between the prefix and the unit symbol Prefixes should not be combined into compound prefixes * The units radian and steradian are also known as ‘SI supplementary units’ Names of units, even those derived from proper names, should be printed with lower-case initial letters Symbols for units should be printed in roman type Single-letter and three-letter symbols for amino acids The genetic code Amino acid One letter ′ 5′ base Three letter Alanine A Ala Arginine R Arg Asparagine N D C Cys Glutamine Q Gln A G U UUU Phe UUC Phe UUA Leu UUG Leu UCU Ser UCC Ser UCA Ser UCG Ser UAU Tyr UAC Tyr UAA Ter* UAG Ter* UGU Cys UGC Cys UGA Ter*/Sec UGG Trp U C A G C CUU Leu CUC Leu CUA Leu CUG Leu CCU Pro CCC Pro CCA Pro CCG Pro CAU His CAC His CAA Gln CAG Gln CGU Arg CGC Arg CGA Arg CGG Arg U C A G A AUU Ile AUC Ile AUA Ile AUG Met† ACU Thr ACC Thr ACA Thr ACG Thr AAU Asn AAC Asn AAA Lys AAG Lys AGU Ser AGC Ser AGA Arg AGG Arg U C A G G GUU Val GUC Val GUA Val GUG Val GCU Ala GCC Ala GCA Ala GCG Ala GAU Asp GAC Asp GAA Glu GAG Glu GGU Gly GGC Gly GGA Gly GGG Gly U C A G Asp Cysteine C Asn Aspartic acid Glutamic acid E Glu Glycine G Gly Histidine H His Isoleucine I Ile ′ 3′ base Middle base U Leucine L Leu Lysine K Lys Methionine M Met Phenylalanine F Phe Proline P Pro Serine S Ser Threonine T Thr Tryptophan W Trp Tyrosine Y Tyr Valine V Val Unspecified or unknown X Xaa *Termination codons have no amino acids assigned to them, except that UGA can be the code for Sec; see selenocysteine insertion sequence †The AUG codon is the usual initiation codon as well as that for methionine residues elsewhere The code is almost universal but differences have been found in mitochondrial DNA from some organisms (see the genetic code entry) ... decade since the first edition of the Oxford Dictionary of Biochemistry and Molecular Biology It was a remarkable work of scholarship, arising from the work of journal editors and scientific writers... Smith He was also one of the main driving forces behind the creation of the first edition of the Oxford Dictionary of Biochemistry and Molecular Biology Preface Preface to this edition It is a decade... University of Saskatchewan, Saskatoon, Canada OXFORD DICTIONARY OF Biochemistry and Molecular Biology Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of