Biological Molecules PDF
Preview Biological Molecules
BioloJ(ical MOLECULES r-- MoleclAlar aVId Cell ---, BIOCHEMISTRY SMITH ANO WOOO Springer-Science+Business Media, B.V. Published by Chapman &-Hali, 2-6 Boundary Row, London SEI8HN Chapman &: Hali, 2-6 Boundary Row, London SEI8HN, UK 81adie Academic &-Professional. Wesler Oeddens Road, 8ishopbriggs. Glasgow G642NZ, UK Chapman&-HaU, 29 West J5th Street, New York NYIOOOI, USA Olaprnan& HaUJapan, Thomson PublilihingJapan, HirakawachoNemoto Building. 6F, 1-1-11 Hirakawa-cho, Chiyoda.ku. Tokyo 102, Japan Chapman &-HaU Australia, Thomas Nelson AuslraUa, 102 Dodds Street, South Melboume. Victoria 3205, Australia Chapman &-HaU India, R. 5eshadri, 32 Second Main Road, OT East, Madras 600035, India First edition 1991 © 1991 Springtr S("itllce+llusinf5S Media Oordrechl Originally published by ChMpm~n & 1IMllin 1')<)1 Typeset in 10011'hpt Palatino by EJS Chemical Composition, er Norton, Balh, Avon ISBN 978-0-412-40780-2 ISBN978-94-011-3126-1(eBook) DOI 10.1007/978-94-011-3126-1 Apart rrom any fair dealing for the pUrpose$ of research or private study. or critic:ism or review, as permitted under the UK Copyright Designs and Patents Act, 1988, this publication may not be reproduced, slored, ortr"ansmîtted. in any formorby any means, wilhout the prior permission in writing of the publishers, or in the case of reprographic reproduction only in accordance with the lerms of the licences issued by the Copyright Licensing Agency in the UK. or in acrordance with the tenns of licences issued by the appropriale Reproduction Rights Organization outside Ihe UK. Enquiries ronceming repruduction outside the lenns stated here should be senllo 1hC' publillhers allhe UK addT6S prinled an this page. The publisher makes no representation, express or implied with regard 10 the accuracy of the infonnalion contained in this book and cannot accept any legal responsibility or liability for any errors or omissions that maybemade. A cat.alogue record for this book is available from the Brirish Library. Library of Con~ u Woging-in-Public::ation Dab Smith, CA. (Chris A.) Biological moleculeslC.A. Smith and E. Wood. p. cm.-(Molecules and cell biochemistry) Indudes bibliographical references and index. 1. Biomolecules. 2. Biopolymer8. 3. Biochemistry. 1. wood, EdwardJ., 1941- . II. Title. III. Series. QP514.2.S575 1991 S14.19'2--dc2Q 91-10094 OP Copy Editors: Sara Firman and Judith Ockenden Sub-ed.îtor: Simon Armstrong Production ControUer: Marian SaviUe LayoutDesigner:GeoffreyWadsley(afteranoriginaldesignbyJuliaDenny) lUustrators: Capricom Graphics Contents Editors'foreword vii Contributors viii Preface ix Abbreviations x Greekalphabet xii 1 Basicprinciples 1 1.1 Introduction: Lifeisbasedoncarbon 1 1.2 Chemicalbonds 9 1.3 Thepropertiesofwater 11 1.4 Energy 13 1.5 Biologicalorganization 19 1.6 Interactionsbetweenproteinandothermolecules 25 1.7 Overview 28 Answerstoexercises 29 Questions 29 2 Globularproteins 32 2.1 Introduction 32 2.2 Generalfunctions ofproteins 33 2.3 Structureofproteins 35 2.4 Forcesthatstabilizeproteinmolecules 51 2.5 Proteinfolding 52 2.6 Molecularactivityofproteins: myoglobinandhaemoglobin 54 2.7 Proteindenaturation 60 2.8 Overview 62 Answers toexercises 63 Questions 63 3 Fibrousproteins 65 3.1 Introduction 65 3.2 Keratinsandsilks 67 3.3 Collagen 70 3.4 Elastin 77 3.5 Overview 79 Answerstoexercises 80 Questions 80 4 Enzymekinetics 83 4.1 Introduction 83 4.2 Theprinciplesofcatalysis 85 4.3 Kineticsofenzyme-catalysedreactions 87 4.4 Inhibitionofenzymeactivity 96 4.5 Controlofenzymeactivity 101 / 7 Contents v 4.6 Overview 102 Answers toexercises 103 Questions 103 5 Enzymemechanisms 105 5.1 Introduction 105 5.2 Enzymestructureandclassification 106 5.3 Theactivesite 108 5.4 Specificityofenzymes 111 5.5 Mechanismsofcatalysis 114 5.6 Generalcommentsaboutenzymemechanisms 120 5.7 Enzymefamilies 120 5.8 Overview 122 Answerstoexercises 122 Questions 123 6 Polysaccharides 124 6.1 Introduction 124 6.2 Distinguishingfeatures ofpolysaccharides 124 6.3 Specificpolysaccharides 136 6.4 Overview 143 Answerstoexercises 143 Questions 144 7 Lipids:structuresandfunctions 146 7.1 Introduction 146 7.2 Classificationoflipids 146 7.3 Simplelipids 147 7.4 Complexlipids 153 7.5 Polyprenyllipids 156 7.6 Overview 164 Answerstoexercises 164 Questions 165 8 Nucleicacids 166 8.1 Introduction 166 8.2 Discoveryofnucleicacids 166 8.3 Molecularcompositionofnucleicacids 167 8.4 Nucleicacids 171 8.5 StructureofDNA 172 8.6 AlternativestructuresofDNA 176 8.7 DynamicstructureofDNA 178 8.8 BasepairinginRNA 178 8.9 Biologicalfunctions ofnucleicacids 179 8.10 ReplicationofDNA 188 8.11 Enzymichydrolysisofnucleicacids 188 9.12 Overview 190 Answers toexercises 193 Questions 194 Answertoquestions 196 Glossary 200 Index 202 ~i Contents / / '---------~ Editors' foreword This book is one of a series of brief fundamental texts for junior under graduates and diploma students in biological science. The series, Molecular andCellBiochemistry,coversthewholeofmodernbiochemistry,integrating animal, plantand microbial topics. Theintentionisto give the seriesspecial appeal to the many students who read biochemistry for only part of their course and who are looking for an all-encompassing and stimulating approach. Althoughallbooksintheseriesbearadistinctfamilylikeness,each standsonitsownasanindependenttext. Many students, particularly those with less numerate backgrounds, find elements of their biochemistry courses daunting, and one of our principal concerns is to offer books which present the facts in a palatable style. Each chapterisprefacedbyalistoflearningobjectives, withshortsummariesand revision aids at the ends of chapters. The text itself is informal, and the incorporation of marginal notes and information boxes to accompany the main text give a tutorial flavour, complementing and supporting the main narrative. The marginal notes and boxesrelate facts in the text to applicable examplesineverydaylife, inindustry, inotherlifesciencesandinmedicine, and provide a variety of other educational devices to assist, support, and reinforce learning. References are annotated to guide students towards effectiveandrelevantadditionalreading. Althoughstudentsmuststartbylearningthebasicvocabularyofasubject, itismoreimportantsubsequentlytopromoteunderstandingandtheabilityto solve problemsthan to presentthefacts alone. Theprovisionofimaginative problems, examples, short-answer questions and other exercises are designed toencouragesuchaproblem-solvingattitude. A major challenge to both teacher and student is the pace at which biochemistryandmolecularbiologyareadvancingatthepresenttime.Forthe teacher and textbook writer the challenge is to select, distil, highlight and exemplify, tasks whichrequireabroadbaseofknowledgeand indefatigable reading of the literature. For the student the challenge is not to be over whelmed, tounderstandand ultimately topass theexamination!Itis hoped that the present serieswill help byofferingmajoraspectsofbiochemistryin digestible portions. Thisvastcorpusofaccumulated knowledgeisessentiallyvaluelessunless itcanbeused. Thusthesetextshavefrequent, simpleexercisesandproblems. Itisexpectedthatstudentswillbeableto testtheiracquisitionofknowledge butalsobeabletousethisknowledgetosolveproblems.Webelievethatonly in this way can students become familiar and comfortable with their knowledge. The fact that it is useful to them will mean that it is retained, beyondthelastexamination, intotheirfuture careers. Thepresentserieswaswrittenbylecturersinuniversitiesandpolytechnics who have many years of experience in teaching, and who are also familiar with current developments through their research interests. They are, in addition, familiar with the difficulties and pressures faced by present-day / Editors'foreword vii / students in the biological sciences area. The editors are grateful for the co-operation of all their authors in undergoing criticism and in meeting requests to re-write (and sometimes re-writeagain), shortenorextendwhat they originallywrote. Theyarealso happy to record theirgrateful thanks to those many individuals who very willingly supplied illustrative material promptly and generously. These include many colleagues as well as total strangers whose response was positiveand unstinting. Special thanks must go to the assessors who verycarefully read the chapters and made valuable suggestionswhichgaverisetoamorereadable text. Gratefulthanksarealso due to the teamatChapman& Hallwhosawtheprojectthrough withgood grace in spite, sometimes, of everything. These include Dominic Recaldin, CommissioningEditor, Jacqueline Curthoys, formerly DevelopmentEditor, SimonArmstrong, Sub-editor, andMarianSaville, ProductionController. Finally, though, it is the editors themselves who must take the responsibilityforerrorsandomissions, andforareaswherethetextisstillnot asclearasstudentsdeserve. Contributors DR B. CATLEY DepartmentofBiologicalSciences, Heriot-Watt University, Edinburgh, UK. Chapter6. DR P. GACESA DepartmentofBiochemistry, UniversityofWalesCollege ofCardiff, Cardiff, UK. Chapters4and5. DR J.J. GAFFNEY Department of Biological Sciences, The Manchester Metropolitan University, Manchester, UK. Chapters 7and8. DR J. HARLAND School of Health Sciences, The Liverpool John Moores University, Liverpool, UK. Chapter3. DR c.A. SMITH Department of Biological Sciences, The Manchester Metropolitan University, UK. Chapters2, 7and8. DR E.J. WOOD DepartmentofBiochemistryandMolecularBiology, University ofLeeds, Leeds, UK. Chapters1and2. Contributors viii / '/--- ---1 Preface This book looks at the basis of biological molecules largely from biological point of view. It aims to put biochemistry in its biological context with examplesfrom medicine, nutritionandagriculture. Inevitablythemolecules describedanddiscussedtendtobemacromolecules, ormoleculessuchasthe lipids, thatassociate non-covalently toform largeaggregates, becausethese arethetypesofmolecules thatcharacterizelivingorganisms. A background ofchemistry and some physics is required, although these aspectsareexplainedasgentlyaspossible,recognizingthatmanystudentsin thebiologicalsciencesregard theseasdifficultareas. Thisisnottoimplythat physicsandchemistryarenotimportant,fortheycertainlyare. Nevertheless, manyteachersinuniversitiesandpolytechnicsrecognisethatitisimpractical andunrealistictodemandarigorousstudyofchemistry, forexample,before students can be allowed to start on the study of biological chemistry. This state of affairs may not be the most desirable, but it exists. Therefore, the present text assumes some chemical knowledge and introduces additional chemistryinabiological, functionalcontextwhereappropriate.Thisishelped by the deliberate use of side-notes, glossaries and boxes of additional informationofrelevantinterest. The eightchapters in thisvolume examine aspects ofbiologicalmolecules that are features of, and are essential to, any biological science course, including proteins, polysaccharides, nucleic acids and lipids, with special emphasis on enzymes. It is hoped that the treatment will kindle students' interest and follow them to see the vital relevance ofmolecular structure to biologicalfunction. In the past many student have had difficulty in visualizing molecular structures, and this has to some extent inhibited their enjoyment and understanding ofbiochemistry. There is no excuse for this now. In the last 5-10years avastamountofresearch, coupledwithexplosive developments in computer-graphics technology, has enabled us to visualize clearly the structures of biological molecules, and especially of macromolecules, in atomic detail. Wherever appropriate such structural models have been included to enable readers to comprehend more easily how these macromoleculesfulfil theirbiologicalroles. / Preface ix / Abbreviations A adenine(alanine) ACP acylcarrierprotein ACTH adrenalcorticotrophichormone ADP adenosinediphosphate Ala,A alanine AMP adenosinemonophosphate cAMP adenosine3I,S'-cyclicmonophosphate Arg,R arginine Asn,N asparagine Asp,D asparticacid ATP adenosinetriphosphate ATPase adenosinetriphosphatase C cytosine(cysteine) CDP cytidinediphosphate CMP cytidinemonophosphate CTP cytidinetriphosphate CoA(CoASH) coenzymeA CoQ(Q) coenzymeQ,ubiquinone Cys,C cysteine d- 2-deoxy- D asparticacid d-Rib 2-deoxyribose DNA deoxyribonucleicacid eDNA complementaryDNA electron glutamicacid , oxidation-reductionpotential F phenylalanine F theFaraday(9.648 X 104coulombmol-i) FAD flavinadeninedinucleotide Fd ferredoxin fMet N-formylmethionine FMN flavinmononucleotide Fro fructose g gram g accelerationduetogravity G guanine(glycine) G freeenergy Gal galactose Glc glucose ~ Abbreviations / L/ - ---1 Gln,Q glutamine Glu,E glutamicacid Gly,G glycine GDP guanosinediphosphate GMP guanosinemonophosphate GTP guanosinetriphosphate H histidine H enthalpy Hb haemoglobin His,H histidine Hyp hydroxyproline(HOPro) I isoleucine IgG immunoglobulinG IgM immunoglobulinM lIe,I isoleucine ITP inosinetriphosphate J Joule K degreesabsolute(Kelvin) K lysine L leucine Leu,L leucine In x naturallogarithmofx = 2.3031og1ox Lys,K lysine M methionine M relativemolecularmass,molecularweight r Man mannose Mb myoglobin Met,M methionine N asparagine N Avogadro'snumber(6.022 X 1023) N anynucleotidebase(e.g.inNTPfornucleotide triphosphate) NAD+ nicotinamideadeninedinucleotide NADP+ nicotinamideadeninedinucleotidephosphate P proline Pi inorganicphosphate PPi inorganicpyrophosphate Phe,F phenylalanine Pro,P proline Q coenzymeQ,ubiquinone Q glutamine R arginine I R thegasconstant(8.314JK- mol-I) Rib ribose RNA ribonucleicacid mRNA messenl2.erRNA / Abbreviations xi /
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