molecular biology, third edition€¦ · physical chemistry psychology sub-series editor: hugh...

File Attachment
2001165ccoverv05bjpg

Molecular BiologyThird Edition

ii Section K ndash Lipid metabolism

BIOS INSTANT NOTES

Series Editor BD Hames School of Biochemistry and Microbiology Universityof Leeds Leeds UK

BiologyAnimal Biology Second EditionBiochemistry Third EditionBioinformaticsChemistry for Biologists Second EditionDevelopmental BiologyEcology Second EditionGenetics Second EditionImmunology Second EditionMathematics amp Statistics for Life ScientistsMedical MicrobiologyMicrobiology Second EditionMolecular Biology Third EditionNeuroscience Second EditionPlant Biology Second EditionSport amp Exercise BiomechanicsSport amp Exercise Physiology

ChemistryConsulting Editor Howard StanburyAnalytical ChemistryInorganic Chemistry Second EditionMedicinal ChemistryOrganic Chemistry Second EditionPhysical Chemistry

PsychologySub-series Editor Hugh Wagner Dept of Psychology University of CentralLancashire Preston UKCognitive PsychologyPhysiological PsychologyPsychologySport amp Exercise Psychology


Phil Turner Alexander McLennanAndy Bates amp Mike White

School of Biological Sciences University of Liverpool Liverpool UK

Published byTaylor amp Francis GroupIn US 270 Madison Avenue

New York NY 10016

In UK 4 Park Square Milton ParkAbingdon OX14 4RN

copy 2005 by Taylor amp Francis Group

First edition published in 1997Second edition published in 2000Third edition published in 2005

This book contains information obtained from authentic and highly regarded sources Reprinted material is quoted with permission and sources are indicated A wide variety of references are listed Reasonable efforts have been made to publish reliable data and information but the author and the publisher cannot assume responsibility for the validity of all materials or for the consequences of their use

All rights reserved No part of this book may be reprinted reproduced transmitted or utilized in any form by any electronic mechanical or other means now known or hereafter invented including photocopying microfilming and recording or in any information storage or retrieval system without written permission from the publishers

A catalogue record for this book is available from the British Library

Library of Congress Cataloging-in-Publication Data

Molecular biology Phil Turner hellip [et al] ndash ndash 3rd edp cm ndash ndash (BIOS instant notes)

Includes bibliographical references and indexISBN 0-415-35167-7 (alk paper)

1 Molecular biology ndash ndash Outlines syllabi etc [DNLM 1 Molecular Biology ndash ndash Outlines QH 506 M71902 2005] I Turner Philip C II SeriesQH506I4815 20055728 ndash ndash dc22

2005027956

Editor Elizabeth OwenEditorial Assistant Chris DixonProduction Editor Karin Henderson

Taylor amp Francis Groupis the Academic Division of TampF Informa plc Visit our web site at httpwwwgarlandsciencecom

This edition published in the Taylor amp Francis e-Library 2007

ldquoTo purchase your own copy of this or any of Taylor amp Francis or Routledgersquoscollection of thousands of eBooks please go to wwweBookstoretandfcoukrdquo

ISBN 0ndash203ndash96732ndash1 Master e-book ISBN

ISBN 0-415-35167-7 (Print Edition)

Abbreviations ixPreface to the third edition xiPreface to the second edition xiiPreface to the first edition xiii

Section A Cells and macromolecules 1A1 Cellular classification 1A2 Subcellular organelles 4A3 Macromolecules 7A4 Large macromolecular assemblies 11

Section B Protein structure 15B1 Amino acids 15B2 Protein structure and function 18B3 Protein analysis 25

Section C Properties of nucleic acids 33C1 Nucleic acid structure 33C2 Chemical and physical properties of nucleic acids 40C3 Spectroscopic and thermal properties of nucleic acids 44C4 DNA supercoiling 47

Section D Prokaryotic and eukaryotic chromosome structure 51D1 Prokaryotic chromosome structure 51D2 Chromatin structure 53D3 Eukaryotic chromosome structure 58D4 Genome complexity 63D5 The flow of genetic information 68

Section E DNA replication 73E1 DNA replication an overview 73E2 Bacterial DNA replication 78E3 The cell cycle 82E4 Eukaryotic DNA replication 86

Section F DNA damage repair and recombination 91F1 Mutagenesis 91F2 DNA damage 95F3 DNA repair 98F4 Recombination 101

Section G Gene manipulation 105G1 DNA cloning an overview 105G2 Preparation of plasmid DNA 110G3 Restriction enzymes and electrophoresis 113G4 Ligation transformation and analysis of recombinants 118

CONTENTS

Section H Cloning vectors 125H1 Design of plasmid vectors 125H2 Bacteriophage vectors 129H3 Cosmids YACs and BACs 134H4 Eukaryotic vectors 139

Section I Gene libraries and screening 145I1 Genomic libraries 145I2 cDNA libraries 148I3 Screening procedures 153

Section J Analysis and uses of cloned DNA 157J1 Characterization of clones 157J2 Nucleic acid sequencing 162J3 Polymerase chain reaction 167J4 Organization of cloned genes 172J5 Mutagenesis of cloned genes 176J6 Applications of cloning 180

Section K Transcription in prokaryotes 185K1 Basic principles of transcription 185K2 Escherichia coli RNA polymerase 188K3 The E coli 70 promoter 190K4 Transcription initiation elongation and termination 193

Section L Regulation of transcription in prokaryotes 199L1 The lac operon 199L2 The trp operon 203L3 Transcriptional regulation by alternative factors 207

Section M Transcription in eukaryotes 211M1 The three RNA polymerases characterization

and function 211M2 RNA Pol I genes the ribosomal repeat 213M3 RNA Pol III genes 5S and tRNA transcription 217M4 RNA Pol II genes promoters and enhancers 221M5 General transcription factors and RNA Pol II initiation 223

Section N Regulation of transcription in eukaryotes 227N1 Eukaryotic transcription factors 227N2 Examples of transcriptional regulation 233

Section O RNA processing and RNPs 239O1 rRNA processing and ribosomes 239O2 tRNA processing and other small RNAs 245O3 mRNA processing hnRNPs and snRNPs 249O4 Alternative mRNA processing 255

Section P The genetic code and tRNA 259P1 The genetic code 259P2 tRNA structure and function 263

Section Q Protein synthesis 269Q1 Aspects of protein synthesis 269Q2 Mechanism of protein synthesis 273

vi Contents

Contents vii

Q3 Initiation in eukaryotes 279Q4 Translational control and post-translational events 283

Section R Bacteriophages and eukaryotic virusesa 289R1 Introduction to viruses 289R2 Bacteriophages 293R3 DNA viruses 298R4 RNA viruses 302

Section S Tumor viruses and oncogenesb 307S1 Oncogenes found in tumor viruses 307S2 Categories of oncogenes 311S3 Tumor suppressor genes 314S4 Apoptosis 318

Section T Functional genomics and new technologies 323T1 Introduction to the rsquoomics 323T2 Global gene expression analysis 327T3 Proteomics 332T4 Cell and molecular imaging 337T5 Transgenics and stem cell technology 342

Section U Bioinformatics 347U1 Introduction to bioinformatics 347

Further reading 357

Index 362

a Contributed by Dr M Bennett Department of Veterinary PathologyUniversity of Liverpool Leahurst Neston South Wirral L64 7TE UKb Contributed by Dr C Green School of Biological Sciences University ofLiverpool PO Box 147 Liverpool L69 7ZB UK

ADP adenosine 5-diphosphateAIDS acquired immune deficiency

syndromeAMP adenosine 5-monophosphateARS autonomously replicating

sequenceATP adenosine 5-triphosphateBAC bacterial artificial chromosomeBER base excision repairBLAST basic local alignment search toolbp base pairsBRF TFIIB-related factorBUdR bromodeoxyuridinebZIP basic leucine zipperCDK cyclin-dependent kinasecDNA complementary DNACHEF contour clamped homogeneous

electric fieldCJD CreutzfeldndashJakob diseaseCRP cAMP receptor proteinCSF-1 colony-stimulating factor-1CTD carboxy-terminal domainDa DaltondNTP deoxynucleoside triphosphateddNTP dideoxynucleoside triphosphateDMS dimethyl sulfateDNA deoxyribonucleic acidDNase deoxyribonucleaseDOP-PCR degenerate oligonucleotide primer

PCRdsDNA double-stranded DNAEDTA ethylenediamine tetraacetic acidEF elongation factorELISA enzyme-linked immunosorbent

assayEMBL European Molecular Biology

LaboratoryENU ethylnitrosoureaER endoplasmic reticulumES embryonic stemESI electrospray ionizationEST expressed sequence tagETS external transcribed spacerFADH reduced flavin adenine

dinucleotideFIGE field inversion gel electrophoresisFISH fluorescent in situ hybridization

-gal -galactosidaseGFP green fluorescent proteinGMO genetically modified organismGST glutathione-S-transferaseGTP guanosine 5-triphosphateHIV human immunodeficiency virusHLH helixndashloopndashhelixhnRNA heterogeneous nuclear RNAhnRNP heterogeneous nuclear

ribonucleoproteinHSP heat-shock proteinHSV-1 herpes simplex virus-1ICAT isotope-coded affinity tagICC immunocytochemistryICE interleukin-1 β converting

enzymeIF initiation factorIg immunoglobulinIHC immunohistochemistryIHF integration host factorIP immunoprecipitationIPTG isopropyl--D-thiogalactopyra-

nosideIRE iron response elementIS insertion sequenceISH in situ hybridizationITS internal transcribed spacerJAK Janus activated kinasekb kilobase pairs in duplex nucleic

acid kilobases in single-strandednucleic acid

kDa kiloDaltonLAT latency-associated transcriptLC liquid chromatographyLINES long interspersed elementsLTR long terminal repeatMALDI matrix-assisted laser

desorptionionizationMCS multiple cloning sitemiRNA micro RNAMMS methylmethane sulfonateMMTV mouse mammary tumor virusmRNA messenger RNAMS mass spectrometryNAD+ nicotinamide adenine

dinucleotideNER nucleotide excision repair

ABBREVIATIONS

NLS nuclear localization signalNMN nicotinamide mononucleotideNMD nonsense mediated mRNA decayNMR nuclear magnetic resonancent nucleotideNTP nucleoside triphosphateORC origin recognition complexORF open reading framePAGE polyacrylamide gel

electrophoresisPAP poly(A) polymerasePCNA proliferating cell nuclear

antigenPCR polymerase chain reactionPDGF platelet-derived growth factorPFGE pulsed field gel electrophoresisPTH phenylthiohydantoinRACE rapid amplification of cDNA

endsRBS ribosome-binding siteRER rough endoplasmic reticulumRF replicative formRFLP restriction fragment length

polymorphismRISC RNA-induced silencing complexRNA ribonucleic acidRNAi RNA interferenceRNA Pol I RNA polymerase IRNA Pol II RNA polymerase IIRNA Pol III RNA polymerase IIIRNase A ribonuclease ARNase H ribonuclease HRNP ribonucleoproteinROS reactive oxygen speciesRP-A replication protein ArRNA ribosomal RNART reverse transcriptase

RTndashPCR reverse transcriptasendashpolymerasechain reaction

SAGE serial analysis of gene expressionSAM S-adenosylmethionineSDS sodium dodecyl sulfatesiRNA short interfering RNASINES short interspersed elementsSL1 selectivity factor 1snoRNP small nucleolar RNPSNP single nucleotide polymorphismsnRNA small nuclear RNAsnRNP small nuclear ribonucleoproteinSRP signal recognition particleSsb single-stranded binding proteinSSCP single stranded conformational

polymorphismssDNA single-stranded DNASTR simple tandem repeatSV40 simian virus 40TAF TBP-associated factorTBP TATA-binding protein-TIF -trans-inducing factortm RNA transfer-messenger RNATOF time-of-flightTris tris(hydroxymethyl)amino-

methanetRNA transfer RNAUBF upstream binding factorUCE upstream control elementURE upstream regulatory elementUV ultravioletVNTR variable number tandem repeatX-gal 5-bromo-4-chloro-3-indolyl--D-

galactopyranosideXP xeroderma pigmentosumYAC yeast artificial chromosomeYEp yeast episomal plasmid

x Abbreviations

It doesnrsquot seem like five years have passed since we were all involved in writing the second editionof Instant Notes in Molecular Biology However during that period there have been a number of eventsand discoveries that are worthy of comment We are impressed with how popular the text has becomewith students not only in the United Kingdom but all around the world The second edition hasbeen translated into Portuguese Turkish Polish French and Japanese We have received commentsand suggestions from as far afield as Katmandu and Istanbul as well as from much nearer home andwe would like to thank everyone who has taken the time to make their comments known as theyhave helped our improvements to the third edition Even though our text is a basic introduction toMolecular Biology there have been some dramatic developments in the field since the last editionwas written These include the whole area of small RNA molecules including micro RNAs and RNAinterference and we have updated the relevant sections to include this material Other importantdevelopments include the rapid growth in the areas of genomics proteomics cell imaging and bio-informatics and since we recognize that these areas will rapidly change in the future we havepragmatically included two new sections at the end of the book to deal with these fast moving topicsWe hope this will make changes to future editions less complex Several people who have helped usto keep on track with writing and production on the third edition deserve our thanks for their encour-agement and patience including Sarah Carlson Liz Owen and Alison Nick not to mention all ourfamilies who have tolerated our necessary preoccupations We sincerely hope that the third editioncontinues to help students to get to grips with this interesting area of biology

Phil Turner Sandy McLennan Andy Bates and Mike WhiteSeptember 2005

PREFACE TO THE THIRD EDITION

To assess how to improve Instant Notes in Molecular Biology for the second edition we studied thefirst edition readerrsquos comments carefully and were pleasantly surprised to discover how little wasdeemed to have been omitted and how few errors had been brought to our attention Thus theproblem facing us was how to add a number of fairly disparate items and topics without substan-tially affecting the existing structure of the book We therefore chose to fit new material into existingtopics as far as possible only creating new topics where absolutely necessary A superficial com-parison might therefore suggest that little has changed in the second edition but we have includedupdated or extended the following areas proteomics LINESSINES signal transduction BACs Z-DNA gene gun genomics DNA fingerprinting DNA chips microarrays RFLPs geneticpolymorphism genome sequencing projects SSCP automated DNA sequencing positional cloningchromosome jumping PFGE multiplex DNA amplification RT-PCR quantitative PCR PCR screeningPCR mutagenesis degenerate PCR and transgenic animals In addition three completely new topicshave been added Arguably no molecular biology text should omit a discussion of Crickrsquos centraldogma and it now forms the basis of Topic D5 ndash The flow of genetic information Two other rapidlyexpanding and essential subjects are The cell cycle and Apoptosis each of which we felt deservedits own topic These have been added to Section E on DNA replication and Section S on Tumorviruses and oncogenes respectively Finally in keeping with the ethos of the first edition that InstantNotes in Molecular Biology should be used as a study guide and revision aid we have added approx-imately 100 multiple choice questions grouped in section order This single improvement will wefeel greatly enhance the educational utility of the book

Phil Turner Sandy McLennan Andy Bates and Mike White

Acknowledgments

We thank all those readers of the first edition who took the trouble to return their comments andsuggestions without which the second edition would have been less improved Will Sansom AndreaBosher and Jonathan Ray at BIOS who kept encouraging us and finally our families who once againhad to suffer during the periods of (re)writing

PREFACE TO THE SECOND EDITION

The last 20 years have witnessed a revolution in our understanding of the processes responsible forthe maintenance transmission and expression of genetic information at the molecular level ndash thevery basis of life itself Of the many technical advances on which this explosion of knowledge hasbeen based the ability to remove a specific fragment of DNA from an organism manipulate it inthe test tube and return it to the same or a different organism must take pride of place It is aroundthis essence of recombinant DNA technology or genetic engineering to give it its more popular titlethat the subject of molecular biology has grown Molecular biology seeks to explain the relation-ships between the structure and function of biological molecules and how these relationshipscontribute to the operation and control of biochemical processes Of principal interest are the macro-molecules and macromolecular complexes of DNA RNA and protein and the processes of replicationtranscription and translation The new experimental technologies involved in manipulating thesemolecules are central to modern molecular biology Not only does it yield fundamental informationabout the molecules but it has tremendous practical applications in the development of new andsafe products such as therapeutics vaccines and foodstuffs and in the diagnosis of genetic diseaseand in gene therapy

An inevitable consequence of the proliferation of this knowledge is the concomitant proliferation ofcomprehensive glossy textbooks which while beautifully produced can prove somewhat over-whelming in both breadth and depth to first and second year undergraduate students With this inmind Instant Notes in Molecular Biology aims to deliver the core of the subject in a concise easily assim-ilated form designed to aid revision The book is divided into 19 sections containing 70 topics Eachtopic consists of a lsquoKey Notesrsquo panel with extremely concise statements of the key points coveredThese are then amplified in the main part of the topic which includes simple and clear black and whitefigures which may be easily understood and reproduced To get the best from this book materialshould first be learnt from the main part of the topic the Key Notes can then be used as a rapid revi-sion aid Whilst there is a reasonably logical order to the topics the book is designed to be lsquodippedintorsquo at any point For this reason numerous cross-references are provided to guide the reader torelated topics

The contents of the book have been chosen to reflect both the major techniques used and the conclu-sions reached through their application to the molecular analysis of biological processes They arebased largely on the molecular biology courses taught by the authors to first and second year under-graduates on a range of biological science degree courses at the University of Liverpool Section Aintroduces the classification of cells and macromolecules and outlines some of the methods used toanalyze them Section B considers the basic elements of protein structure and the relationship of struc-ture to function The structure and physico-chemical properties of DNA and RNA molecules arediscussed in Section C including the complex concepts involved in the supercoiling of DNA Theorganization of DNA into the intricate genomes of both prokaryotes and eukaryotes is covered inSection D The related subjects of mutagenesis DNA replication DNA recombination and the repairof DNA damage are considered in Sections E and F

Section G introduces the technology available for the manipulation of DNA sequences As describedabove this underpins much of our detailed understanding of the molecular mechanisms of cellularprocesses A simple DNA cloning scheme is used to introduce the basic methods Section H describesa number of the more sophisticated cloning vectors which are used for a variety of purposes SectionI considers the use of DNA libraries in the isolation of new gene sequences while Section J coversmore complex and detailed methods including DNA sequencing and the analysis of cloned sequencesThis section concludes with a discussion of some of the rapidly expanding applications of gene cloningtechniques

PREFACE TO THE FIRST EDITION

The basic principles of gene transcription in prokaryotes are described in Section K while SectionL gives examples of some of the sophisticated mechanisms employed by bacteria to control specificgene expression Sections M and N provide the equivalent but necessarily more complex story oftranscription in eukaryotic cells The processing of newly transcribed RNA into mature molecules isdetailed in Section O and the roles of these various RNA molecules in the translation of the geneticcode into protein sequences are described in Sections P and Q The contributions that prokaryoticand eukaryotic viruses have made to our understanding of molecular information processing aredetailed in Section R Finally Section S shows how the study of viruses combined with the knowl-edge accumulated from many other areas of molecular biology is now leading us to a detailedunderstanding of the processes involved in the development of a major human affliction ndash cancer

This book is not intended to be a replacement for the comprehensive mainstream textbooks ratherit should serve as a direct complement to your lecture notes to provide a sound grounding in thesubject The major texts some of which are listed in the Further Reading section at the end of thebook can then be consulted for more detail on topics specific to the particular course being studiedFor those of you whose fascination and enthusiasm for the subject has been sufficiently stimulatedthe reading list also directs you to some more detailed and advanced articles to take you beyond thescope of this book Inevitably there have had to be omissions from Instant Notes in Molecular Biologyand we are sure each reader will spot a different one However many of these will be covered inother titles in the Instant Notes series such as the companion volume Instant Notes in Biochemistry


Acknowledgments

We would like to acknowledge the support and understanding of our families for those many lostevenings and weekends when we could all have been in the pub instead of drafting and redraftingmanuscripts We are also indebted to our colleagues Malcolm Bennett and Chris Green for their contri-butions to the chapters on bacteriophages viruses and oncogenes Our thanks too go to the serieseditor David Hames and to Jonathan Ray Rachel Robinson and Lisa Mansell of BIOS ScientificPublishers for providing prompt and helpful advice when required and for keeping the pressure onus to finish the book on time

xiv Preface to the first edition

Section A ndash Cells and macromolecules

A1 CELLULAR CLASSIFICATION

Eubacteria The Eubacteria are one of two subdivisions of the prokaryotes Prokaryotes arethe simplest living cells typically 1ndash10 m in diameter and are found in all envi-ronmental niches from the guts of animals to acidic hot springs Classically theyare defined by their structural organization (Fig 1) They are bounded by a cell(plasma) membrane comprising a lipid bilayer in which are embedded proteinsthat allow the exit and entry of small molecules Most prokaryotes also have arigid cell wall outside the plasma membrane which prevents the cell fromswelling or shrinking in environments where the osmolarity differs significantlyfrom that inside the cell The cell interior (cytoplasm or cytosol) usually containsa single circular chromosome compacted into a nucleoid and attached to themembrane (see Topic D1) and often plasmids [small deoxyribonucleic acid(DNA) molecules with limited genetic information see Topic G2] ribonucleic acid(RNA) ribosomes (the sites of protein synthesis see Section Q) and most of theproteins which perform the metabolic reactions of the cell Some of these proteinsare attached to the plasma membrane but there are no distinct subcellular

Key Notes

Structurally defined as prokaryotes these cells have a plasma membraneusually enclosed in a rigid cell wall but no intracellular compartments Theyhave a single major circular chromosome They may be unicellular ormulticellular Escherichia coli is the best studied eubacterium

The Archaea are structurally defined as prokaryotes but probably branchedoff from the eukaryotes after their common ancestor diverged from theeubacteria They tend to inhabit extreme environments They arebiochemically closer to eubacteria in some ways but to eukaryotes in othersThey also have some biochemical peculiarities

Cells of plants animals fungi and protists possess well-defined subcellularcompartments bounded by lipid membranes (eg nuclei mitochondriaendoplasmic reticulum) These organelles are the sites of distinct biochemicalprocesses and define the eukaryotes

In most multicellular eukaryotes groups of cells differentiate duringdevelopment of the organism to provide specialized functions (eg as in liverbrain kidney) In most cases they contain the same DNA but transcribedifferent genes Like all other cellular processes differentiation is controlledby genes Co-ordination of the activities of different cell types requirescommunication between them

Related topics Subcellular organelles (A2) Bacteriophages and eukaryotic Prokaryotic and eukaryotic viruses (Section R)

chromosome structure (Section D)

Differentiation

Eubacteria

Archaea

Eukaryotes

organelles as in eukaryotes to compartmentalize different parts of the metabo-lism The surface of a prokaryote may carry pili which allow it to attach to othercells and surfaces and flagella whose rotating motion allows the cell to swimMost prokaryotes are unicellular some however have multicellular forms inwhich certain cells carry out specialized functions The Eubacteria differ from theArchaea mainly in their biochemistry The eubacterium Escherichia coli has agenome size (DNA content) of 4600 kilobase pairs (kb) which is sufficient geneticinformation for about 3000 proteins Its molecular biology has been studied exten-sively The genome of the simplest bacterium Mycoplasma genitalium has only 580kb of DNA and encodes just 470 proteins It has a very limited metabolic capacity

Archaea The Archaea or archaebacteria form the second subdivision of the prokary-otes and tend to inhabit extreme environments Structurally they are similar toeubacteria However on the basis of the evolution of their ribosomal RNA(rRNA) molecules (see Topic O1) they appear as different from the eubacteriaas both groups of prokaryotes are from the eukaryotes and display someunusual biochemical features for example ether in place of ester linkages inmembrane lipids (see Topic A3) The 1740 kb genome of the archaeonMethanococcus jannaschii encodes a maximum of 1738 proteins Comparisonsreveal that those involved in energy production and metabolism are most likethose of eubacteria while those involved in replication transcription and trans-lation are more similar to those of eukaryotes It appears that the Archaea andthe eukaryotes share a common evolutionary ancestor which diverged from theancestor of the Eubacteria

Eukaryotes Eukaryotes are classified taxonomically into four kingdoms comprising animalsplants fungi and protists (algae and protozoa) Structurally eukaryotes aredefined by their possession of membrane-enclosed organelles (Fig 2) withspecialized metabolic functions (see Topic A2) Eukaryotic cells tend to be largerthan prokaryotes 10ndash100 m in diameter They are surrounded by a plasmamembrane which can have a highly convoluted shape to increase its surfacearea Plants and many fungi and protists also have a rigid cell wall The cyto-plasm is a highly organized gel that contains in addition to the organelles andribosomes an array of protein fibers called the cytoskeleton which controls theshape and movement of the cell and which organizes many of its metabolicfunctions These fibers include microtubules made of tubulin and microfila-ments made of actin (see Topic A4) Many eukaryotes are multicellular withgroups of cells undergoing differentiation during development to form thespecialized tissues of the whole organism

2 Section A ndash Cells and macromolecules

Fig 1 Schematic diagram of a typical prokaryotic cell

Differentiation When a cell divides the daughter cells may be identical in every way or theymay change their patterns of gene expression to become functionally differentfrom the parent cell

Among prokaryotes and lower eukaryotes the formation of spores is anexample of such cellular differentiation (see Topic L3) Among complex multi-cellular eukaryotes embryonic cells differentiate into highly specialized cellsfor example muscle nerve liver and kidney In all but a few exceptional casesthe DNA content remains the same but the genes which are transcribed havechanged Differentiation is regulated by developmental control genes (see TopicN2) Mutations in these genes result in abnormal body plans such as legs inthe place of antennae in the fruit fly Drosophila Studying such gene mutationsallows the process of embryonic development to be understood In multicellularorganisms co-ordination of the activities of the various tissues and organs iscontrolled by communication between them This involves signaling moleculessuch as neurotransmitters hormones and growth factors which are secreted byone tissue and act upon another through specific cell-surface receptors

A1 ndash Cellular classification 3

Fig 2 Schematic diagram of a typical eukaryotic cell


A2 SUBCELLULAR ORGANELLES

Key Notes

The membrane-bound nucleus contains the bulk of the cellular DNA inmultiple chromosomes Transcription of this DNA and processing of the RNAoccurs here Nucleoli are contained within the nucleus

Mitochondria are the site of cellular respiration where nutrients are oxidizedto CO2 and water and adenosine 5-triphosphate (ATP) is generated They arederived from prokaryotic symbionts and retain some DNA RNA and proteinsynthetic machinery though most of their proteins are encoded in thenucleus Photosynthesis takes place in the chloroplasts of plants andeukaryotic algae Chloroplasts have a basically similar structure tomitochondria but with a thylakoid membrane system containing the light-harvesting pigment chlorophyll

The smooth endoplasmic reticulum is a cytoplasmic membrane system wheremany of the reactions of lipid biosynthesis and xenobiotic metabolism arecarried out The rough endoplasmic reticulum has attached ribosomesengaged in the synthesis of membrane-targeted and secreted proteins Theseproteins are carried in vesicles to the Golgi complex for further processingand sorting

The lysosomes contain degradative hydrolytic enzymes the peroxisomescontain enzymes which destroy certain potentially dangerous free radicalsand hydrogen peroxide the glyoxysomes of plants carry out the reactions ofthe glyoxylate cycle

After disruption of the plasma membrane the subcellular organelles can beseparated from each other and purified by a combination of differentialcentrifugation and density gradient centrifugation (both rate zonal andisopycnic) Purity can be assayed by measuring organelle-specific enzymes

Related topics Cellular classification (A1) Translational control and post-rRNA processing and translational events (Q4)

ribosomes (O1)

Nuclei

Microbodies

Organelle isolation

Mitochondriaand chloroplasts

Endoplasmicreticulum

Nuclei The eukaryotic nucleus carries the genetic information of the cell in multiplechromosomes each containing a single DNA molecule (see Topics D2 and D3)The nucleus is bounded by a lipid double membrane the nuclear envelopecontaining pores which allow passage of moderately large molecules (see TopicA1 Fig 2) Transcription of RNA takes place in the nucleus (see Section M) andthe processed RNA molecules (see Section O) pass into the cytoplasm wheretranslation takes place (see Section Q) Nucleoli are bodies within the nucleus

where rRNA is synthesized and ribosomes are partially assembled (see TopicsM2 and O1)

Mitochondria and Cellular respiration that is the oxidation of nutrients to generate energy in thechloroplasts form of adenosine 5prime-triphosphate (ATP) takes place in the mitochondria These

organelles are roughly 1ndash2 m in diameter and there may be 1000ndash2000 per cellThey have a smooth outer membrane and a convoluted inner membrane thatforms protrusions called cristae (see Topic A1 Fig 2) They contain a smallcircular DNA molecule mitochondrial-specific RNA and ribosomes on whichsome mitochondrial proteins are synthesized However the majority of mito-chondrial (and chloroplast) proteins are encoded by nuclear DNA and synthe-sized in the cytoplasm These latter proteins have specific signal sequences thattarget them to the mitochondria (see Topic Q4) The chloroplasts of plants are thesite of photosynthesis the light-dependent assimilation of CO2 and water to formcarbohydrates and oxygen Though larger than mitochondria they have a similarstructure except that in place of cristae they have a third membrane system (thethylakoids) in the inner membrane space These contain chlorophyll which trapsthe light energy for photosynthesis Chloroplasts are also partly genetically inde-pendent of the nucleus Both mitochondria and chloroplasts are believed to haveevolved from prokaryotes which had formed a symbiotic relationship with aprimitive nucleated eukaryote

Endoplasmic The endoplasmic reticulum is an extensive membrane system within the reticulum cytoplasm and is continuous with the nuclear envelope (see Topic A1 Fig 2) Two

forms are visible in most cells The smooth endoplasmic reticulum carries manymembrane-bound enzymes including those involved in the biosynthesis ofcertain lipids and the oxidation and detoxification of foreign compounds (xenobi-otics) such as drugs The rough endoplasmic reticulum (RER) is so-called becauseof the presence of many ribosomes These ribosomes specifically synthesize proteins intended for secretion by the cell such as plasma or milk proteins or those destined for the plasma membrane or certain organelles Apart from theplasma membrane proteins which are initially incorporated into the RER mem-brane these proteins are translocated into the interior space (lumen) of the RERwhere they are modified often by glycosylation (see Topic Q4) The lipids andproteins synthesized on the RER are transported in specialized transport vesiclesto the Golgi complex a stack of flattened membrane vesicles which further modifies sorts and directs them to their final destinations (see Topic A1 Fig 2)

Microbodies Lysosomes are small membrane-bound organelles which bud off from the Golgicomplex and which contain a variety of digestive enzymes capable of degradingproteins nucleic acids lipids and carbohydrates They act as recycling centersfor macromolecules brought in from outside the cell or from damagedorganelles Some metabolic reactions which generate highly reactive free radi-cals and hydrogen peroxide are confined within organelles called peroxisomesto prevent these species from damaging cellular components Peroxisomescontain the enzyme catalase which destroys hydrogen peroxide

2H2O2 rarr 2H2O + O2

Glyoxysomes are specialized plant peroxisomes which carry out the reactionsof the glyoxylate cycle Lysosomes peroxisomes and glyoxysomes are collec-tively known as microbodies

A2 ndash Subcellular organelles 5

Organelle The plasma membrane of eukaryotes can be disrupted by various meansisolation including osmotic shock controlled mechanical shear or by certain nonionic

detergents Organelles displaying large size and density differences for examplenuclei and mitochondria can be separated from each other and from otherorganelles by differential centrifugation according to the value of their sedi-mentation coefficients (see Topic A4) The cell lysate is centrifuged at a speedwhich is high enough to sediment only the heaviest organelles usually thenuclei The supernatant containing all the other organelles is removed thencentrifuged at a higher speed to sediment the mitochondria and so on (Fig 1a)This technique is also used to fractionate suspensions containing cell types ofdifferent sizes for example red cells white cells and platelets in blood Thesecrude preparations of cells nuclei and mitochondria usually require furtherpurification by density gradient centrifugation This is also used to separateorganelles of similar densities In rate zonal centrifugation the mixture islayered on top of a pre-formed concentration (and therefore density) gradientof a suitable medium in a centrifuge tube Upon centrifugation bands or zonesof the different components sediment at different rates depending on their sedimentation coefficients and separate (Fig 1b) The purpose of the densitygradient of the supporting medium is to prevent convective mixing of thecomponents after separation (ie to provide stability) and to ensure linear sedi-mentation rates of the components (it compensates for the acceleration of thecomponents as they move further down the tube) In equilibrium (isopycnic)centrifugation the density gradient extends to a density higher than that ofone or more components of the mixture so that these components come to equi-librium at a point equal to their own density and stop moving In this case the density gradient can either be pre-formed and the sample layered on topor self-forming in which case the sample may be mixed with the gradientmaterial (Fig 1c) Density gradients are made from substances such as sucroseFicoll (a synthetic polysaccharide) metrizamide (a synthetic iodinated heavycompound) or cesium chloride (CsCl) for separation of nucleic acids (see TopicsC2 and G2) Purity of the subcellular fraction can be determined using an electron microscope or by assaying enzyme activities known to be associatedspecifically with particular organelles for example succinate dehydrogenase inmitochondria


Fig 1 Centrifugation techniques (a) Differential (b) rate zonal and (c) isopycnic (equilibrium)

Proteins and Proteins are polymers of amino acids linked together by peptide bonds Thenucleic acids structures of the amino acids and of proteins are dealt with in detail in Section

B Proteins have both structural and functional roles The nucleic acids DNAand RNA are polymers of nucleotides which themselves consist of a nitroge-nous base a pentose sugar and phosphoric acid Their structures are detailedin Section C There are three main types of cellular RNA messenger RNA(mRNA) ribosomal RNA (rRNA) and transfer RNA (tRNA) Nucleic acids areinvolved in the storage and processing of genetic information (see Topic D5)but the expression of this information requires proteins


A3 MACROMOLECULES

Key Notes

Proteins are polymers of amino acids and the nucleic acids DNA and RNAare polymers of nucleotides They are both essential components of themachinery which stores and expresses genetic information Proteins havemany additional structural and functional roles

-Amylose and cellulose are polymers of glucose linked (1rarr4) and (1rarr4)respectively Starch a storage form of glucose found in plants contains -amylose together with the (1rarr6) branched polymer amylopectinCellulose forms strong structural fibers in plants Glucose is stored asglycogen in animals Chitin a polymer of N-acetylglucosamine is found infungal cell walls and arthropod exoskeletons Mucopolysaccharides areimportant components of connective tissue

Triglycerides containing saturated and unsaturated fatty acids are the majorstorage lipids of animals and plants respectively Structural differencesbetween the two types of fatty acid result in animal triglycerides being solidand plant triglycerides (oils) liquid Phospholipids and sphingolipids havepolar groups in addition to the fatty acid components and are importantconstituents of all cell membranes

Nucleoproteins contain both nucleic acid and protein as in the enzymestelomerase and ribonuclease P Glycoproteins and proteoglycans(mucoproteins) are proteins with covalently attached carbohydrate and aregenerally found on extracellular surfaces and in extracellular spaces Lipid-linked proteins and lipoproteins have lipid and protein components attachedcovalently or noncovalently respectively Glycolipids have both lipid andcarbohydrate parts Mixed macromolecular complexes such as these provide awider range of functions than the component parts

Related topics Large macromolecular assemblies (A4) Properties of nucleic acids Protein structure (Section B) (Section C)

Proteins andnucleic acids

Complexmacromolecules

Polysaccharides

Lipids

Polysaccharides Polysaccharides are polymers of simple sugars covalently linked by glycosidicbonds They function mainly as nutritional sugar stores and as structural materialsCellulose and starch are abundant components of plants Both are glucose poly-mers but differ in the way the glucose monomers are linked Cellulose is a linearpolymer with (1rarr4) linkages (Fig 1a) and is a major structural component of theplant cell wall About 40 parallel chains form horizontal sheets which stack verti-cally above one another The chains and sheets are held together by hydrogenbonds (see Topic A4) to produce tough insoluble fibers Starch is a sugar store andis found in large intracellular granules which can be hydrolyzed quickly to releaseglucose for metabolism It contains two components -amylose a linear polymerwith (1rarr4) linkages (Fig 1b) and amylopectin a branched polymer with addi-tional (1rarr6) linkages With up to 106 glucose residues amylopectins are amongthe largest molecules known The different linkages in starch produce a coiledconformation that cannot pack tightly hence starch is water-soluble Fungi andsome animal tissues (eg liver and muscle) store glucose as glycogen a branchedpolymer like amylopectin Chitin is found in fungal cell walls and in theexoskeleton of insects and crustacea It is similar to cellulose but the monomer unitis N-acetylglucosamine Mucopolysaccharides (glycosaminoglycans) form thegel-like solutions in which the fibrous proteins of connective tissue are embeddedDetermination of the structures of large polysaccharides is complicated becausethey are heterogeneous in size and composition and because they cannot be studiedgenetically like nucleic acids and proteins

Lipids While individual lipids are not strictly macromolecules many are built up fromsmaller monomeric units and they are involved in many macromolecular assem-blies (see Topic A4) Large lipid molecules are predominantly hydrocarbon innature and are poorly soluble in water Some are involved in the storage andtransport of energy while others are key components of membranes protectivecoats and other cell structures Glycerides have one two or three long-chainfatty acids esterified to a molecule of glycerol In animal triglycerides the fattyacids have no double bonds (saturated) so the chains are linear the moleculescan pack tightly and the resulting fats are solid Plant oils contain unsaturatedfatty acids with one or more double bonds The angled structures of these chainsprevent close packing so they tend to be liquids at room temperatureMembranes contain phospholipids which consist of glycerol esterified to twofatty acids and phosphoric acid The phosphate is also usually esterified to asmall molecule such as serine ethanolamine inositol or choline (Fig 2)Membranes also contain sphingolipids such as ceramide in which the long-chain amino alcohol sphingosine has a fatty acid linked by an amide bondAttachment of phosphocholine to a ceramide produces sphingomyelin


Fig 1 The structures of (a) cellulose with (1rarr4) linkages and (b) starch -amylose with (1rarr4) linkagesCarbon atoms 1 4 and 6 are labeled Additional (1rarr6) linkages produce branches in amylopectin and glycogen

Complex Many macromolecules contain covalent or noncovalent associations of moremacromolecules than one of the major classes of large biomolecules This can greatly increase

the functionality or structural capabilities of the resulting complex For examplenearly all enzymes are proteins but some have a noncovalently attached RNAcomponent which is essential for catalytic activity Associations of nucleic acidand protein are known as nucleoproteins Examples are telomerase which isresponsible for replicating the ends of eukaryotic chromosomes (see Topics D3and E3) and ribonuclease P an enzyme which matures transfer RNA (tRNA)In telomerase the RNA acts as a template for telomere DNA synthesis whilein ribonuclease P the RNA contains the catalytic site of the enzyme Ribo-nuclease P is an example of a ribozyme (see Topic O2)

Glycoproteins contain both protein and carbohydrate (between lt1 and gt 90 of the weight) components glycosylation is the commonest form of post-translational modification of proteins (see Topic Q4) The carbohydrate isalways covalently attached to the surface of the protein never the interior and is often variable in composition causing microheterogeneity (Fig 3) Thishas made glycoproteins difficult to study Glycoproteins have functions that span the entire range of protein activities and are usually found extracel-lularly They are important components of cell membranes and mediate cellndashcell recognition

Proteoglycans (mucoproteins) are large complexes (gt107 Da) of protein andmucopolysaccharide found in bacterial cell walls and in the extracellular spacein connective tissue Their sugar units often have sulfate groups which makes

A3 ndash Macromolecules 9

Fig 2 A typical phospholipid phosphatidylcholine containing esterified stearic and oleicacids

Fig 3 Glycoprotein structure The different symbols represent different monosaccharideunits (eg galactose N-acetylglucosamine)

them highly hydrated This coupled with their lengths (gt 1000 units) producessolutions of high viscosity Proteoglycans act as lubricants and shock absorbersin extracellular spaces

Lipid-linked proteins have a covalently attached lipid component This isusually a fatty acyl (eg myristoyl or palmitoyl) or isoprenoid (eg farnesyl orgeranylgeranyl) group These groups serve to anchor the proteins in membranesthrough hydrophobic interactions with the membrane lipids and also promoteproteinndashprotein associations (see Topic A4)

In lipoproteins the lipids and proteins are linked noncovalently Becauselipids are poorly soluble in water they are transported in the blood as lipopro-teins These are basically particles of triglycerides and cholesterol esters coatedwith a layer of phospholipids cholesterol and protein (the apolipoproteins)The structures of the apolipoproteins are such that their hydrophobic aminoacids face towards the lipid interior of the particles while the charged and polaramino acids (see Topic B1) face outwards into the aqueous environment Thisrenders the particles soluble

Glycolipids which include cerebrosides and gangliosides have covalentlylinked lipid and carbohydrate components and are especially abundant in themembranes of brain and nerve cells


Protein complexes Cellular architecture contains many large complexes of the different classes ofmacromolecules with themselves or with each other Many of the major struc-tural and locomotory elements of the cell consist of protein complexes Thecytoskeleton is an array of protein filaments which organizes the shape andmotion of cells and the intracellular distribution of subcellular organellesMicrotubules are long polymers of tubulin a 110 kiloDalton (kDa) globularprotein (Fig 1 see Topic B2) These are a major component of the cytoskeletonand of eukaryotic cilia and flagella the hair-like structures on the surface ofmany cells which whip to move the cell or to move fluid across the cell surfaceCilia also contain the proteins nexin and dynein


A4 LARGE MACROMOLECULARASSEMBLIES

Key Notes

The eukaryotic cytoskeleton consists of various protein complexesmicrotubules (made of tubulin) microfilaments (made of actin and myosin)and intermediate filaments (containing various proteins) These organize the shape and movement of cells and subcellular organelles Cilia and flagella are also composed of microtubules complexed with dynein and nexin

Bacterial 70S ribosomes comprise a large 50S subunit with 23S and 5S RNAmolecules and 31 proteins and a small 30S subunit with a 16S RNA moleculeand 21 proteins Eukaryotic 80S ribosomes have 60S (28S 58S and 5S RNAs)and 40S (18S RNA) subunits Chromatin contains DNA and the basic histoneproteins Viruses are also nucleoprotein complexes

Membrane phospholipids and sphingolipids form bilayers with the polargroups on the exterior surfaces and the hydrocarbon chains in the interiorMembrane proteins may be peripheral or integral and act as receptorsenzymes transporters or mediators of cellular interactions

A large number of weak interactions hold macromolecular assembliestogether Chargendashcharge chargendashdipole and dipolendashdipole interactionsinvolve attractions between fully or partially charged atoms Hydrogen bondsand hydrophobic interactions which exclude water are also important

Related topics Macromolecules (A3) Bacteriophages and eukaryotic Chromatin structure (D2) viruses (Section R)rRNA processing and

ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein

Noncovalentinteractions

Microfilaments consisting of the protein actin form contractile assemblies withthe protein myosin to cause cytoplasmic motion Actin and myosin are also majorcomponents of muscle fibers The intermediate filaments of the cytoskeletoncontain a variety of proteins including keratin and have various functionsincluding strengthening cell structures In all cases the energy for motion isprovided by the coupled hydrolysis of ATP or guanosine 5-triphosphate (GTP)

Nucleoprotein Nucleoproteins comprise both nucleic acid and protein Ribosomes are largecytoplasmic ribonucleoprotein complexes which are the sites of proteinsynthesis (see Section Q) Bacterial 70S ribosomes have large (50S) and small(30S) subunits with a total mass of 25 106 Da (The S value eg 50S is thenumerical value of the sedimentation coefficient s and describes the rate atwhich a macromolecule or particle sediments in a centrifugal field It is deter-mined by both the mass and shape of the molecule or particle hence S valuesare not additive) The 50S subunit contains 23S and 5S RNA molecules and 31different proteins while the 30S subunit contains a 16S RNA molecule and 21proteins Eukaryotic 80S ribosomes have 60S (with 28S 58S and 5S RNAs) and40S (with 18S RNA) subunits Under the correct conditions mixtures of therRNAs and proteins will self-assemble in a precise order into functional ribo-somes in vitro Thus all the information for ribosome structure is inherent inthe structures of the components The RNAs are not simply frameworks for theassembly of the ribosomal proteins but participate in both the binding of themessenger RNA and in the catalysis of peptide bond synthesis (see Topic Q2)

Chromatin is the material from which eukaryotic chromosomes are made Itis a deoxyribonucleoprotein complex made up of roughly equal amounts ofDNA and small basic proteins called histones (see Topic D2) These form arepeating unit called a nucleosome Correct assembly of nucleosomes and many


Fig 1 Schematic diagram showing the (a) cross-sectional and (b) surface pattern of tubulin and subunits in a microtubule (see Topic B2) From BIOCHEMISTRY 4E by Stryer copy1995 by Lubert Stryer Used with permission of WH Freeman and Company [After JASnyder and JR McIntosh (1976) Annu Rev Biochem 45 706 With permission from theAnnual Review of Biochemistry Volume 45 copy 1976 by Annual Reviews Inc]

(a)

(b)

other protein complexes requires assembly proteins or chaperones Histonesneutralize the repulsion between the negative charges of the DNA sugarndashphosphate backbone and allow the DNA to be tightly packaged within the chromosomes Viruses are another example of nucleoprotein complexes Theyare discussed in Section R

Membranes When placed in an aqueous environment phospholipids and sphingolipidsnaturally form a lipid bilayer with the polar groups on the outside and thenonpolar hydrocarbon chains on the inside This is the structural basis of allbiological membranes Such membranes form cellular and organellar bound-aries and are selectively permeable to uncharged molecules The precise lipidcomposition varies from cell to cell and from organelle to organelle Proteinsare also a major component of cell membranes (Fig 2) Peripheral membraneproteins are loosely bound to the outer surface or are anchored via a lipid orglycosyl phosphatidylinositol anchor and are relatively easy to removeIntegral membrane proteins are embedded in the membrane and cannot beremoved without destroying the membrane Some protrude from the outer orinner surface of the membrane while transmembrane proteins span the bilayercompletely and have both extracellular and intracellular domains (see TopicB2) The transmembrane regions of these proteins contain predominantlyhydrophobic amino acids Membrane proteins have a variety of functions forexample

receptors for signaling molecules such as hormones and neurotransmitters enzymes for degrading extracellular molecules before uptake of the products pores or channels for the selective transport of small polar ions and molecules mediators of cellndashcell interactions (mainly glycoproteins)

Noncovalent Most macromolecular assemblies are held together by a large number ofinteractions different noncovalent interactions Chargendashcharge interactions (salt bridges)

operate between ionizable groups of opposite charge at physiological pH forexample between the negative phosphates of DNA and the positive lysine andarginine side chains of DNA-binding proteins such as histones (see Topic D2)Chargendashdipole and dipolendashdipole interactions are weaker and form when eitheror both of the participants is a dipole due to the asymmetric distribution ofcharge in the molecule (Fig 3a) Even uncharged groups like methyl groups

A4 ndash Large macromolecular assemblies 13

Fig 2 Schematic diagram of a plasma membrane showing the major macromolecularcomponents

can attract each other weakly through transient dipoles arising from the motionof their electrons (dispersion forces)

Noncovalent associations between electrically neutral molecules are knowncollectively as van der Waals forces Hydrogen bonds are of great importanceThey form between a covalently bonded hydrogen atom on a donor group (egndashO-H or ndashN-H) and a pair of nonbonding electrons on an acceptor group (egO=Cndash or Nndash) (Fig 3b) Hydrogen bonds and other interactions involvingdipoles are directional in character and so help define macromolecular shapesand the specificity of molecular interactions The presence of uncharged andnonpolar substances for example lipids in an aqueous environment tends toforce a highly ordered structure on the surrounding water molecules This isenergetically unfavorable as it reduces the entropy of the system Hencenonpolar molecules tend to clump together reducing the overall surface areaexposed to water This attraction is termed a hydrophobic (water-hating) inter-action and is a major stabilizing force in proteinndashprotein and proteinndashlipidinteractions and in nucleic acids


Fig 3 Examples of (a) van der Waals forces and (b) a hydrogen bond

Section B ndash Protein structure

B1 AMINO ACIDS

Key Notes

The 20 common amino acids found in proteins have a chiral -carbon atomlinked to a proton amino and carboxyl groups and a specific side chainwhich confers different physical and chemical properties They behave aszwitterions in solution Nonstandard amino acids in proteins are formed bypost-translational modification

Glutamic acid and aspartic acid have additional carboxyl groups and usuallyimpart a negative charge to proteins Lysine has an -amino group arginine aguanidino group and histidine an imidazole group These three basic aminoacids generally impart a positive charge to proteins

Serine and threonine have hydroxyl groups asparagine and glutamine haveamide groups and cysteine has a thiol group

Glycine is the simplest amino acid with no side chain Proline is a secondaryamino acid (imino acid) Alanine valine leucine and isoleucine havehydrophobic alkyl groups Methionine has a thioether sulfur atom

Phenylalanine tyrosine and tryptophan have bulky aromatic side chainswhich absorb ultraviolet light

Related topics Protein structure and function (B2) Mechanism of protein synthesis (Q2)

Charged side chains

Nonpolar aliphaticside chains

Aromatic sidechains

Polar unchargedside chains

Structure

Structure Proteins are polymers of L-amino acids Apart from proline all of the 20 aminoacids found in proteins have a common structure in which a carbon atom (the-carbon) is linked to a carboxyl group a primary amino group a proton anda side chain (R) which is different in each amino acid (Fig 1) Except in glycinethe -carbon atom is asymmetric ndash it has four chemically different groupsattached Thus amino acids can exist as pairs of optically active stereoisomers(D- and L-) However only the L-isomers are found in proteins Amino acidsare dipolar ions (zwitterions) in aqueous solution and behave as both acids andbases (they are amphoteric) The side chains differ in size shape charge andchemical reactivity and are responsible for the differences in the properties ofdifferent proteins (Fig 2) A few proteins contain nonstandard amino acids suchas 4-hydroxyproline and 5-hydroxylysine in collagen These are formed by post-translational modification of the parent amino acids proline and lysine (seeTopic Q4)

Charged Taking pH 7 as a reference point several amino acids have ionizable groupsside chains in their side chains which provide an extra positive or negative charge at this

BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS




SECTION A ndash CELLS AND MACROMOLECULES



A3 MACROMOLECULES

A4 LARGE MACROMOLECULAR ASSEMBLIES

SECTION B ndash PROTEIN STRUCTURE

B1 AMINO ACIDS

B2 PROTEIN STRUCTURE AND FUNCTION

B3 PROTEIN ANALYSIS

SECTION C ndash PROPERTIES OF NUCLEIC ACIDS

C1 NUCLEIC ACID STRUCTURE

C2 CHEMICAL AND PHYSICAL PROPERTIES OF NUCLEIC ACIDS

C3 SPECTROSCOPIC AND THERMAL PROPERTIES OF NUCLEIC ACIDS

C4 DNA SUPERCOILING

SECTION D ndash PROKARYOTIC AND EUKARYOTIC CHROMOSOME STRUCTURE

D1 PROKARYOTIC CHROMOSOME STRUCTURE

D2 CHROMATIN STRUCTURE

D3 EUKARYOTIC CHROMOSOME STRUCTURE

D4 GENOME COMPLEXITY

D5 THE FLOW OF GENETIC INFORMATION

SECTION E ndash DNA REPLICATION

E1 DNA REPLICATION AN OVERVIEW

E2 BACTERIAL DNA REPLICATION

E3 THE CELL CYCLE

E4 EUKARYOTIC DNA REPLICATION

SECTION F ndash DNA DAMAGE REPAIR AND RECOMBINATION

F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION

SECTION G ndash GENE MANIPULATION

G1 DNA CLONING AN OVERVIEW

G2 PREPARATION OF PLASMID DNA

G3 RESTRICTION ENZYMES AND ELECTROPHORESIS

G4 LIGATION TRANSFORMATION AND ANALYSIS OF RECOMBINANTS

SECTION H ndash CLONING VECTORS

H1 DESIGN OF PLASMID VECTORS

H2 BACTERIOPHAGE VECTORS

H3 COSMIDS YACS AND BACS

H4 EUKARYOTIC VECTORS

SECTION I ndash GENE LIBRARIES AND SCREENING

I1 GENOMIC LIBRARIES

I2 CDNA LIBRARIES

I3 SCREENING PROCEDURES

SECTION J ndash ANALYSIS AND USES OF CLONED DNA

J1 CHARACTERIZATION OF CLONES

J2 NUCLEIC ACID SEQUENCING

J3 POLYMERASE CHAIN REACTION

J4 ORGANIZATION OF CLONED GENES

J5 MUTAGENESIS OF CLONED GENES

J6 APPLICATIONS OF CLONING

SECTION K ndash TRANSCRIPTION IN PROKARYOTES

K1 BASIC PRINCIPLES OF TRANSCRIPTION

K2 ESCHERICHIA COLI RNA POLYMERASE

K3 THE E COLI SIGMA 70 PROMOTER

K4 TRANSCRIPTION INITIATION ELONGATION AND TERMINATION

SECTION L ndash REGULATION OF TRANSCRIPTION IN PROKARYOTES

L1 THE LAC OPERON

L2 THE TRP OPERON

L3 TRANSCRIPTIONAL REGULATION BY ALTERNATIVE SIGMA FACTORS

SECTION M ndash TRANSCRIPTION IN EUKARYOTES

M1 THE THREE RNA POLYMERASES CHARACTERIZATION AND FUNCTION

M2 RNA POL I GENES THE RIBOSOMAL REPEAT

M3 RNA POL III GENES 5S AND tRNA TRANSCRIPTION

M4 RNA POL II GENES PROMOTERS AND ENHANCERS

M5 GENERAL TRANSCRIPTION FACTORS AND RNA POL II INITIATION

SECTION N ndash REGULATION OF TRANSCRIPTION IN EUKARYOTES

N1 EUKARYOTIC TRANSCRIPTION FACTORS

N2 EXAMPLES OF TRANSCRIPTIONAL REGULATION

SECTION O ndash RNA PROCESSING AND RNPs

O1 rRNA PROCESSING AND RIBOSOMES

O2 tRNA PROCESSING AND OTHER SMALL RNAS

O3 mRNA PROCESSING hnRNPS AND snRNPS

O4 ALTERNATIVE mRNA PROCESSING

SECTION P ndash THE GENETIC CODE AND tRNA

P1 THE GENETIC CODE

P2 tRNA STRUCTURE AND FUNCTION

SECTION Q ndash PROTEIN SYNTHESIS

Q1 ASPECTS OF PROTEIN SYNTHESIS

Q2 MECHANISM OF PROTEIN SYNTHESIS

Q3 INITIATION IN EUKARYOTES

Q4 TRANSLATIONAL CONTROL AND POST-TRANSLATIONAL EVENTS

SECTION R ndash BACTERIOPHAGES AND EUKARYOTIC VIRUSES

R1 INTRODUCTION TO VIRUSES

R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES

SECTION S ndash TURNOR VIRUSES AND ONCOGENES

S1 ONCOGENES FOUND IN TUMOR VIRUSES

S2 CATEGORIES OF ONCOGENES

S3 TUMOR SUPPRESSOR GENES

S4 APOPTOSIS

SECTION T ndash FUNCTIONAL GENOMICS AND NEW TECHNOLOGIES

T1 INTRODUCTION TO THE rsquoOMICS

T2 GLOBAL GENE EXPRESSION ANALYSIS

T3 PROTEOMICS

T4 CELL AND MOLECULAR IMAGING

T5 TRANSGENICS AND STEM CELL TECHNOLOGY

SECTION U ndash BIOFORMATICS

U1 INTRODUCTION TO BIOINFORMATICS

FURTHER READING

INDEX



BIOS INSTANT NOTES









New York NY 10016











2005027956















CONTENTS












vi Contents

Contents vii






Further reading 357

Index 362


















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX





New York NY 10016











2005027956















CONTENTS












vi Contents

Contents vii






Further reading 357

Index 362


















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX









CONTENTS












vi Contents

Contents vii






Further reading 357

Index 362


















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX












vi Contents

Contents vii






Further reading 357

Index 362


















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX

Contents vii






Further reading 357

Index 362


















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX

















ABBREVIATIONS











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX











x Abbreviations






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX






Acknowledgments











Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX









Acknowledgments






Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX




Key Notes







Differentiation

Eubacteria

Archaea

Eukaryotes












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX












Key Notes







ribosomes (O1)

Nuclei

Microbodies

Organelle isolation




















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX

















A3 MACROMOLECULES

Key Notes








Polysaccharides

Lipids




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX




















Key Notes






ribosomes (O1)

Protein complexes

Membranes

Nucleoprotein







(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX






(a)

(b)













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX













B1 AMINO ACIDS

Key Notes







Charged side chains


Aromatic sidechains


Structure



BOOK COVER

TITLE

COPYRIGHT

CONTENTS

ABBREVIATIONS







A3 MACROMOLECULES



B1 AMINO ACIDS


B3 PROTEIN ANALYSIS





C4 DNA SUPERCOILING










E3 THE CELL CYCLE



F1 MUTAGENESIS

F2 DNA DAMAGE

F3 DNA REPAIR

F4 RECOMBINATION













I2 CDNA LIBRARIES















L1 THE LAC OPERON

L2 THE TRP OPERON

















P1 THE GENETIC CODE









R2 BACTERIOPHAGES

R3 DNA VIRUSES

R4 RNA VIRUSES





S4 APOPTOSIS




T3 PROTEOMICS





FURTHER READING

INDEX

molecular biology, third edition€¦ · physical chemistry psychology sub-series editor: hugh...

Documents