Biological Molecules

216 Pages·1991·18.443 MB·English

by  Dr C. A. Smith, Dr E. J. Wood (auth.)

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.
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Chapman&-HaU, 29 West J5th Street, New York NYIOOOI, USA
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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.
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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 /
/
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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 /