Advanced Molecular Biology - R. Twyman (Bios, 1998) WW PDF
Preview Advanced Molecular Biology - R. Twyman (Bios, 1998) WW
dva C e d A Concise Reference Molecular Biologq To my parents, Peter and Irene and to my children, Emily and Lucy Richard M. Twyman Neurobiology Division, MRC Laboratory of Molecular Biology, Hills Road, Cambridge?BZ 2QH, UK Consultant Editor BIOS 0 BIOS Scientific Publishers Limited, 1998 First published 1998 All rights reserved, No part of this book may be reproduced or transmitted, in any form or by any means, with- out permission. A CIP catalogue record for this book is available from the British Library. ISBN 1 85996 141 X BIOS Scientific Publishem Ltd 9 Newtec Place, Magdalen Road, Oxford OX4 lRE, UK Tel: +44 (011865 726286. Fax: +44 (011865 246823 World Wide Web home page: http://www.bios.co.uk/ DISTRIBUTORS Australia and New Zealand India Blackwell Science Asia Viva Books Private Limited 54 University Street 4325/3 Ansari Road, Daryaganj Carlton, South Victoria 3053 New Delhi 110002 Published in the United States of America, its dependent territories and Canada by Springer-Verlag New York Inc., 175 Fifth Avenue, New York, NY 10010-7858, in association with BIOS Scientific Publishers Ltd Published in Hong Kong, Taiwan, Singapore, Thailand, Cambodia, Korea, The Phillippines, Indonesia, The People's Republic of China, Brunei, Laos, Malaysia, Macau and Vietnam by Springer-Verlag Singapore Pte. Ltd, 1 Tannery Road, Singapore 347719, in association with BIOS Scientific Publishers Ltd Production Editor: Andrea Bosher. Typeset by Poole Typesetting (Wessex) Ltd, Bournemouth, UK. Printed by Redwood Books, Trowbridge, UK. Contents 1. 2. 3. 4. 5. 6. 7. 8. Abbreviations How to use this book Preface Biological Heredity and Variation Mendelian inheritance Segregation at one locus Segregation at two loci Quantitative inheritance The Cell Cycle The bacterial cell cycle The eukaryotic cell cycle The molecular basis of cell cycle regulation Progress through the cell cycle Special cell cycle systems in animals Chromatin Nucleosomes Higher order chromatin organization Chromatin and chromosome function Molecular structure of the bacterial nucleoid Chromosome Mutation Numerical chromosome mutations Structural chromosome mutations Chromosome Structure and Function Normal chromosomes - gross morphology Special chromosome structures Molecular aspects of chromosome structure Development, Molecular Aspects Differentiation Pattern formation and positional information The environment in development DNA Methylation and Epigenetic Regulation DNA methylation in prokaryotes DNA methylation in eukaryotes Epigenetic gene regulation by DNA methylation in mammals The Gene The concept of the gene ix xi xii 1 1 2 8 11 21 21 23 26 28 33 35 35 38 39 42 45 45 49 57 57 58 60 65 65 72 75 93 93 94 97 103 103 vi 9. 10. 11. 12. 13. 14. 15. Advanced Molecular Biology Units of genetic structure and genetic function Gene-cistron relationship in prokaryotes and eukaryotes Gene structure and architecture Gene Expression and Regulation Gene expression Gene regulation Gene expression in prokaryotes and eukaryotes Gene Transfer in Bacteria Conjugation Transformation Transduction The Genetic Code An overview of the genetic code Translation Special properties of the code Genomes and Mapping Genomes, ploidy and chromosome number Physico-chemical properties of the genome Genome size and sequence components Gene structure and higher-order genome organization Repetitive DNA Isochore organization of the mammalian genome Gene mapping Genetic mapping Physical mapping Mobile Genetic Elements Mechanisms of transposition Consequences of transposition Transposons Retroelements Mutagenesis and DNA Repair Mutagenesis and replication fidelity DNA damage: mutation and killing DNA repair Direct reversal repair Excision repair Mismatch repair Recombination repair The SOS response and mutagenic repair Mutation and Selection Structural and functional consequences of mutation Mutant alleles and the molecular basis of phenotype The distribution of mutations and molecular evolution Mutations in Genetic Analysis 104 104 106 111 112 113 115 117 117 119 120 127 127 127 129 133 134 134 135 13€ 139 143 144 146 151 165 166 172 175 180 183 183 185 187 187 191 194 197 197 201 201 209 211 213 Contents vii 16. 17. 18. 19. 20. 21. 22. 23. 24. Nucleic Acid Structure Nucleic acid primary structure Nucleic acid secondary structure Nucleic acid tertiary structure Nucleic Acid-Binding Properties Nucleic acid recognition by proteins DNA-binding motifs in proteins RNA-binding motifs in proteins Molecular aspects of protein-nucleic acid binding Sequence-specific binding Techniques for the study of protein-nucleic acid interactions Oncogenes and Cancer Oncogenes Tumor-suppressor genes Organelle Genomes Organelle genetics Organelle genomes Plasmids Plasmid classification Plasmid replication and maintenance The Polymerase Chain Reaction (PCR) Specificity of the PCR reaction Advances and extensions to basic PCR strategy Alternative methods for in vitro amplification Proteins: Structure, Function and Evolution Protein primary structure Higher order protein structure Protein modification Protein families Global analysis of protein function Protein Synthesis The components of protein synthesis The mechanism of protein synthesis The regulation of protein synthesis Recombinant DNA and Molecular Cloning Molecular cloning Strategies for gene isolation Characterization of cloned DNA Expression of cloned DNA Analysis of gene regulation Analysis of proteins and protein-protein interactions 223 223 226 231 235 236 237 243 244 246 249 253 254 258 263 263 264 271 271 273 279 279 283 284 287 288 289 295 297 304 313 313 315 318 323 324 331 336 339 342 345 viii Advanced Molecular Biology In vitro mutagenesis Transgenesis: gene transfer to animals and plants 25. Recombination Homologous recombination Homologous recombination and genetic mapping Random and programmed nonreciprocal recombination Site specific recombination Generation of immunoglobulin and T-cell receptor diversity Illegitimate recombination 26. Replication Replication strategy The cellular replisome and the enzymology of elongation Initiation of replication Primers and priming Termination of replication The regulation of replication 27. RNA Processing Maturation of untranslated RNAs End-modification and methylation of mRNA RNA splicing RNA editing Post-processing regulation 28. Signal Transduction Receptors and signaling pathways Intracellular enzyme cascades Second messengers Signal ddivery 29. Transcription Principles of transcription Transcriptional initiation in prokaryotes -basal and constitutive components Transcriptional initiation in eukaryotes -basal and constitutive components Transcriptional initiation - regulatory components Strategies for transcriptional regulation in bacteria and eukaryotes Transcriptional elongation and termination 30. Viruses and Subviral Agents Viral infection strategy Diversity of replication strategy Strategies for viral gene expression Subviral agents Index 346 348 369 369 373 376 378 379 382 389 389 392 400 404 404 406 411 411 412 414 421 421 425 425 431 434 440 443 443 445 447 450 456 458 467 468 469 475 477 489 A adenine (base), adenosine (nucleoside) AER apical ectodermal ridge AMP, ADP, ATP ANT-C AP site APC ARS ATPase b, bp BAC BCR BER bHLH BMP BX-C bZIP C CAK CaM CAM CAMP CAP CBI’ CDK cDNA CDR cf. cGMP C H CMV cpDNA CREB cRNA CTD adenosine monophosphate, diphosphate, triphosphate Antennapedia complex apurinic/apyrimidinic site anaphase-promoting complex autonomously replicating sequence adenosine triphosphatase base, base pair bacterial artificial chromosome B-cell receptor base excision repair basic helix-loop-helix bone morphogenetic protein Bithorax complex basic leucine zipper cytosine (base), cytidine (nucleoside) CDK-activating kinase calmodulin cell adhesion molecule catabolite activator protein CREB factor binding protein cyclin-dependent kinase complementary DNA complementarity determining region compare cyclic guanosine monophosphate cyclin-dependent kinase inhibitor cauliflower mosaic virus chlorplast DNA CAMP response element binding (factor) complementary RNA C-terminal domain cyclic AMP CTF CTP DAG Darn dATP Dcm DEAE DIF DMS DNase dNTP DSBR dsDNA/ RNA EGF(R) ER ES cell EST FGF(R) FISH G GABA GAP GMP, GDP, GTP GNRP GPCR GTF GTPase Hfr HLH HMG hnRNA, hRNP CAAT transcription factor cytidine triphosphate diacylglycerol DNA adenine methylase deoxyadenosine triphosphate DNA cytosine methylase diethylaminoethyl differentiation inducing factor dimethylsulfate deoxyribonuclease deoxynucleotide triphosphate double strand break repair double-stranded DNA/RNA epidermal growth factor (receptor) endoplasmic reticulum embryonic stem cell expressed sequence tag fibroblast growth factor (receptor) fluorescence in situ hybridisation guanine (base), guanosine (nucleoside) y-aminobutyric acid GTPase-activating protein guanosine monophosphate, diphosphate, triphosphate guanine nucleotide releasing protein G-protein-coupled receptor general transcription factor guanosine triphosphatase high frequency of recombination helix-loop-helix high mobility group heterogeneous nuclear RNA, RNP
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