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Molecular Biology, Third Edition Neuroscience, Second Edition Plant Biology, Second Edition Sport & Exercise Biomechanics Sport & Exercise Physiology Molecular Biology Third Edition ii Section K – Lipid metabolism BIOS INSTANT NOTES Series Editor: B.D. Hames, School of Biochemistry and Microbiology, University of Leeds, Leeds, UK Biology Animal Biology, Second Edition Biochemistry, Third Edition Bioinformatics Chemistry for Biologists, Second Edition Developmental Biology Ecology, Second Edition Genetics, Second Edition Immunology, Second Edition Mathematics & Statistics for Life Scientists Medical Microbiology Microbiology, Second Edition Molecular Biology, Third Edition Neuroscience, Second Edition Plant Biology, Second Edition Sport & Exercise Biomechanics Sport & Exercise Physiology Chemistry Consulting Editor: Howard Stanbury Analytical Chemistry Inorganic Chemistry, Second Edition Medicinal Chemistry Organic Chemistry, Second Edition Physical Chemistry Psychology Sub-series Editor: Hugh Wagner, Dept of Psychology, University of Central Lancashire, Preston, UK Cognitive Psychology Physiological Psychology Psychology Sport & Exercise Psychology Molecular Biology Third Edition Phil Turner, Alexander McLennan, Andy Bates & Mike White School of Biological Sciences, University of Liverpool, Liverpool, UK Published by: Taylor & Francis Group In US: 270 Madison Avenue New York, NY 10016 In UK: 4 Park Square, Milton Park Abingdon, OX14 4RN © 2005 by Taylor & Francis Group This edition published in the Taylor & Francis e-Library, 2007. “To purchase your own copy of this or any of Taylor & Francis or Routledge’s collection of thousands of eBooks please go to www.eBookstore.tandf.co.uk.” First edition published in 1997 Second edition published in 2000 Third edition published in 2005 ISBN 0–203–96732–1 Master e-book ISBN ISBN: 0-415-35167-7 (Print Edition) 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 … [et al.]. – – 3rd ed. p. ; cm. – – (BIOS instant notes) Includes bibliographical references and index. ISBN 0-415-35167-7 (alk. paper) 1. Molecular biology – – Outlines, syllabi, etc. [DNLM: 1. Molecular Biology – – Outlines. QH 506 M71902 2005] I. Turner, Philip C. II. Series. QH506.I4815 2005 572.8 – – dc22 2005027956 Editor: Elizabeth Owen Editorial Assistant: Chris Dixon Production Editor: Karin Henderson Taylor & Francis Group is the Academic Division of T&F Informa plc. Visit our web site at http://www.garlandscience.com CONTENTS Abbreviations ix Preface to the third edition xi Preface to the second edition xii Preface to the first edition xiii Section A Cells and macromolecules 1 A1 Cellular classification 1 A2 Subcellular organelles 4 A3 Macromolecules 7 A4 Large macromolecular assemblies 11 Section B Protein structure 15 B1 Amino acids 15 B2 Protein structure and function 18 B3 Protein analysis 25 Section C Properties of nucleic acids 33 C1 Nucleic acid structure 33 C2 Chemical and physical properties of nucleic acids 40 C3 Spectroscopic and thermal properties of nucleic acids 44 C4 DNA supercoiling 47 Section D Prokaryotic and eukaryotic chromosome structure 51 D1 Prokaryotic chromosome structure 51 D2 Chromatin structure 53 D3 Eukaryotic chromosome structure 58 D4 Genome complexity 63 D5 The flow of genetic information 68 Section E DNA replication 73 E1 DNA replication: an overview 73 E2 Bacterial DNA replication 78 E3 The cell cycle 82 E4 Eukaryotic DNA replication 86 Section F DNA damage, repair and recombination 91 F1 Mutagenesis 91 F2 DNA damage 95 F3 DNA repair 98 F4 Recombination 101 Section G Gene manipulation 105 G1 DNA cloning: an overview 105 G2 Preparation of plasmid DNA 110 G3 Restriction enzymes and electrophoresis 113 G4 Ligation, transformation and analysis of recombinants 118 vi Contents Section H Cloning vectors 125 H1 Design of plasmid vectors 125 H2 Bacteriophage vectors 129 H3 Cosmids, YACs and BACs 134 H4 Eukaryotic vectors 139 Section I Gene libraries and screening 145 I1 Genomic libraries 145 I2 cDNA libraries 148 I3 Screening procedures 153 Section J Analysis and uses of cloned DNA 157 J1 Characterization of clones 157 J2 Nucleic acid sequencing 162 J3 Polymerase chain reaction 167 J4 Organization of cloned genes 172 J5 Mutagenesis of cloned genes 176 J6 Applications of cloning 180 Section K Transcription in prokaryotes 185 K1 Basic principles of transcription 185 K2 Escherichia coli RNA polymerase 188 K3 The E. coli ␴70 promoter 190 K4 Transcription, initiation, elongation and termination 193 Section L Regulation of transcription in prokaryotes 199 L1 The lac operon 199 L2 The trp operon 203 L3 Transcriptional regulation by alternative ␴ factors 207 Section M Transcription in eukaryotes 211 M1 The three RNA polymerases: characterization and function 211 M2 RNA Pol I genes: the ribosomal repeat 213 M3 RNA Pol III genes: 5S and tRNA transcription 217 M4 RNA Pol II genes: promoters and enhancers 221 M5 General transcription factors and RNA Pol II initiation 223 Section N Regulation of transcription in eukaryotes 227 N1 Eukaryotic transcription factors 227 N2 Examples of transcriptional regulation 233 Section O RNA processing and RNPs 239 O1 rRNA processing and ribosomes 239 O2 tRNA processing and other small RNAs 245 O3 mRNA processing, hnRNPs and snRNPs 249 O4 Alternative mRNA processing 255 Section P The genetic code and tRNA 259 P1 The genetic code 259 P2 tRNA structure and function 263 Section Q Protein synthesis 269 Q1 Aspects of protein synthesis 269 Q2 Mechanism of protein synthesis 273 Contents vii Q3 Initiation in eukaryotes 279 Q4 Translational control and post-translational events 283 Section R Bacteriophages and eukaryotic virusesa 289 R1 Introduction to viruses 289 R2 Bacteriophages 293 R3 DNA viruses 298 R4 RNA viruses 302 Section S Tumor viruses and oncogenesb 307 S1 Oncogenes found in tumor viruses 307 S2 Categories of oncogenes 311 S3 Tumor suppressor genes 314 S4 Apoptosis 318 Section T Functional genomics and new technologies 323 T1 Introduction to the ’omics 323 T2 Global gene expression analysis 327 T3 Proteomics 332 T4 Cell and molecular imaging 337 T5 Transgenics and stem cell technology 342 Section U Bioinformatics 347 U1 Introduction to bioinformatics 347 Further reading 357 Index 362 a Contributed by Dr M. Bennett, Department of Veterinary Pathology, University of Liverpool, Leahurst, Neston, South Wirral L64 7TE, UK. b Contributed by Dr C. Green, School of Biological Sciences, University of Liverpool, PO Box 147, Liverpool L69 7ZB, UK. ABBREVIATIONS ADP adenosine 5Ј-diphosphate ␤-gal ␤-galactosidase AIDS acquired immune deficiency GFP green fluorescent protein syndrome GMO genetically modified organism AMP adenosine 5Ј-monophosphate GST glutathione-S-transferase ARS autonomously replicating GTP guanosine 5Ј-triphosphate sequence HIV human immunodeficiency virus ATP adenosine 5Ј-triphosphate HLH helix–loop–helix BAC bacterial artificial chromosome hnRNA heterogeneous nuclear RNA BER base excision repair hnRNP heterogeneous nuclear BLAST basic local alignment search tool ribonucleoprotein bp base pairs HSP heat-shock protein BRF TFIIB-related factor HSV-1 herpes simplex virus-1 BUdR bromodeoxyuridine ICAT isotope-coded affinity tag bZIP basic leucine zipper ICC immunocytochemistry CDK cyclin-dependent kinase ICE interleukin-1 β converting cDNA complementary DNA enzyme CHEF contour clamped homogeneous IF initiation factor electric field Ig immunoglobulin CJD Creutzfeld–Jakob disease IHC immunohistochemistry CRP cAMP receptor protein IHF integration host factor CSF-1 colony-stimulating factor-1 IP immunoprecipitation CTD carboxy-terminal domain IPTG isopropyl-␤-D-thiogalactopyra- Da Dalton noside dNTP deoxynucleoside triphosphate IRE iron response element ddNTP dideoxynucleoside triphosphate IS insertion sequence DMS dimethyl sulfate ISH in situ hybridization DNA deoxyribonucleic acid ITS internal transcribed spacer DNase deoxyribonuclease JAK Janus activated kinase DOP-PCR degenerate oligonucleotide primer kb kilobase pairs in duplex nucleic PCR acid, kilobases in single-stranded dsDNA double-stranded DNA nucleic acid EDTA ethylenediamine tetraacetic acid kDa kiloDalton EF elongation factor LAT latency-associated transcript ELISA enzyme-linked immunosorbent LC liquid chromatography assay LINES long interspersed elements EMBL European Molecular Biology LTR long terminal repeat Laboratory MALDI matrix-assisted laser ENU ethylnitrosourea desorption/ionization ER endoplasmic reticulum MCS multiple cloning site ES embryonic stem miRNA micro RNA ESI electrospray ionization MMS methylmethane sulfonate EST expressed sequence tag MMTV mouse mammary tumor virus ETS external transcribed spacer mRNA messenger RNA FADH reduced flavin adenine MS mass spectrometry dinucleotide NAD+ nicotinamide adenine FIGE field inversion gel electrophoresis dinucleotide FISH fluorescent in situ hybridization NER nucleotide
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