Genes XI

969 Pages·2014·364.256 MB·English

by  Goldstein, Elliott S.;Kilpatrick, Stephen T.;Krebs, Jocelyn E.;Lewin, Benjamin M

Lewin’s GENES XI

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JOCELYN E. KREBS
UNIVERSITY OF ALASKA, ANCHORAGE
ELLIOTT S. GOLDSTEIN
ARIZONA STATE UNIVERSITY
STEPHEN T. KILPATRICK
UNIVERSITY OF PITTSBURGH AT JOHNSTOWN
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Library of Congress Cataloging-in-Publication Data
Krebs, Jocelyn E.
Lewin’s genes XI. — 11th ed. / Jocelyn Krebs, Stephen Kilpatrick, and Elliott Goldstein.
p. ; cm.
Genes XI
Lewin’s genes 11
Lewin’s genes eleven
Rev. ed. of: Lewin’s genes X. 10th ed. / [edited by] Jocelyn E. Krebs, Elliott S. Goldstein, Stephen T. Kilpatrick. c2011.
Includes bibliographical references and index.
ISBN 978-1-4496-5905-9 (alk. paper)
I. Lewin, Benjamin. II. Kilpatrick, Stephen T. III. Goldstein, Elliott S. IV. Lewin’s genes X. V. Title. VI. Title: Genes XI.
VII. Title: Lewin’s genes 11. VIII. Title: Lewin’s genes eleven.
[DNLM: 1. Genes. 2. DNA—genetics. 3. Genetic Processes. 4. Genome. 5. Proteins—genetics. 6. RNA—genetics. QU 470]
576.5—dc23
2012020620
6048
Printed in the United States of America
17 16 15 14 13 10 9 8 7 6 5 4 3 2 1
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Dedication
To Benjamin Lewin, for setting the bar high.
To my mother, Ellen Baker, for raising me with a love of science; to the memory of
my stepfather, Barry Kiefer, for convincing me science would stay fun; to my partner, Susannah Morgan,
for always pretending my biology jokes are funny; and to my sons, Rhys and Frey, who have each
gestated during the writing of two editions of this book. Finally, I would like to dedicate this edition to
the memory of my PhD mentor, Dr. Marietta Dunaway, a great inspiration who set my feet on
the exciting path of chromatin biology.
Jocelyn Krebs
To my family: my wife, Suzanne, whose patience, understanding, and confidence in me
are amazing; my children, Andy, Hyla, and Gary, who have taught me so much about
using the computer; and my grandchildren, Seth and Elena, whose smiles and giggles
inspire me. And to the memory of my mentor and dear friend, Lee A. Snyder, whose
professionalism, guidance, and insight demonstrated the skills necessary to be a scientist
and teacher. I have tried to live up to his expectations. This is for you, Doc.
Elliott Goldstein
To my wife, Lori, for our many years of love, support, and sometimes tolerance; to my
daughter, Jennifer, who will actually read this book; to my son, Andrew, who continually
renews my faith in humanity; and to my daughter, Sarah, who brings me joy daily.
Stephen Kilpatrick
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Brief Table of Contents
Contents vii Chapter 16. repair Systems 395
Preface xix Chapter 17. Transposable Elements and
retroviruses 424
About the Authors xxi
Edited by Damon Lisch
Part 1. GENES aND ChromoSomES 1
Chapter 18. Somatic recombination and
Chapter 1. Genes are DNa 2
hypermutation in the Immune System 459
Chapter 2. Genes Encode rNas and
Polypeptides 26 Part 3. TraNSCrIPTIoN
Chapter 3. methods in molecular Biology and aND PoSTTraNSCrIPTIoNaL
Genetic Engineering 42 mEChaNISmS 508
Chapter 4. The Interrupted Gene 81 Chapter 19. Prokaryotic Transcription 509
Edited by Donald Forsdyke Edited by Richard Gourse
Chapter 5. The Content of the Genome 100
Chapter 20. Eukaryotic Transcription 549
Chapter 6. Genome Sequences and Gene
Chapter 21. rNa Splicing and Processing 578
Numbers 120
Chapter 22. mrNa Stability and
Chapter 7. Clusters and repeats 141
Localization 622
Chapter 8. Genome Evolution 161 Edited by Ellen Baker
Chapter 9. Chromosomes 192 Chapter 23. Catalytic rNa 647
Edited by Hank W. Bass
Edited by Douglas J. Briant
Chapter 10. Chromatin 223
Chapter 24. Translation 671
Part 2. DNa rEPLICaTIoN Chapter 25. Using the Genetic Code 714
aND rEComBINaTIoN 265 Edited by John Perona
Chapter 11. replication Is Connected to
Part 4. GENE rEGULaTIoN 744
the Cell Cycle 266
Chapter 26. The operon 745
Edited by Barbara Funnell
Edited by Liskin Swint-Kruse
Chapter 12. The replicon: Initiation of
Chapter 27. Phage Strategies 777
replication 286
Edited by Stephen D. Bell Chapter 28. Eukaryotic Transcription
regulation 804
Chapter 13. DNa replication 304
Edited by Peter Burgers Chapter 29. Epigenetic Effects are
Inherited 838
Chapter 14. Extrachromosomal replicons 328
Edited by Trygve Tollefsbol
Edited by Søren Johannes Sørensen and
Lars Hestbjerg Hansen Chapter 30. regulatory rNa 872
Chapter 15. homologous and Site-Specific
recombination 354 Glossary 894
Edited by Hannah L. Klein and Samantha Hoot Index 920
vi
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Contents
Preface xix Chapter 2. Genes Encode RNAs
About the Authors xxi and Polypeptides 26
2.1 Introduction 27
ParT 1. GENES aND
2.2 Most Genes Encode Polypeptides 28
ChromoSomES 1
2.3 Mutations in the Same Gene Cannot
Chapter 1. Genes Are DNA 2 Complement 29
1.1 Introduction 3 2.4 Mutations May Cause Loss of Function or
Gain of Function 30
1.2 DNA Is the Genetic Material of Bacteria
and Viruses 5 2.5 A Locus May Have Many Different Mutant
Alleles 31
1.3 DNA Is the Genetic Material of Eukaryotic Cells 6
2.6 A Locus May Have More Than One Wild-Type
1.4 Polynucleotide Chains Have Nitrogenous Bases
Allele 31
Linked to a Sugar–Phosphate Backbone 7
2.7 Recombination Occurs by Physical Exchange
1.5 Supercoiling Affects the Structure of DNA 8
of DNA 32
1.6 DNA Is a Double Helix 10
2.8 The Genetic Code Is Triplet 34
1.7 DNA Replication Is Semiconservative 12
2.9 Every Coding Sequence Has Three Possible
1.8 Polymerases Act on Separated DNA Strands at Reading Frames 36
the Replication Fork 13
2.10 Bacterial Genes Are Colinear with Their
1.9 Genetic Information Can Be Provided by DNA Products 37
or RNA 14
2.11 Several Processes Are Required to Express
1.10 Nucleic Acids Hybridize by Base Pairing 15 the Product of a Gene 38
1.11 Mutations Change the Sequence of DNA 17 2.12 Proteins Are trans-Acting but Sites on
DNA Are cis-Acting 39
1.12 Mutations May Affect Single Base Pairs or
Longer Sequences 18 2.13 Summary 41
References 41
1.13 The Effects of Mutations Can Be Reversed 19
1.14 Mutations Are Concentrated at Hotspots 20 Chapter 3. Methods in Molecular Biology
1.15 Many Hotspots Result from Modified Bases 21 and Genetic Engineering 42
1.16 Some Hereditary Agents Are Extremely Small 22 3.1 Introduction 43
1.17 Summary 23 3.2 Nucleases 44
References 24
3.3 Cloning 46
vii
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3.4 Cloning Vectors Can Be Specialized for Chapter 5. The Content of the Genome 100
Different Purposes 49
5.1 Introduction 101
3.5 Nucleic Acid Detection 52
5.2 Genomes Can Be Mapped at Several Levels of
3.6 DNA Separation Techniques 54 Resolution 102
3.7 DNA Sequencing 58 5.3 Individual Genomes Show Extensive Variation 103
3.8 PCR and RT-PCR 59 5.4 RFLPs and SNPs Can Be Used for Genetic
Mapping 104
3.9 Blotting Methods 65
5.5 Eukaryotic Genomes Contain Nonrepetitive and
3.10 DNA Microarrays 69
Repetitive DNA Sequences 106
3.11 Chromatin Immunoprecipitation 72
5.6 Eukaryotic Protein-Coding Genes Can Be Identified
3.12 Gene Knockouts and Transgenics 74 by the Conservation of Exons 107
3.13 Summary 79 5.7 The Conservation of Genome Organization Helps to
Identify Genes 109
Chapter 4. The Interrupted Gene 81
5.8 Some Organelles Have DNA 111
Edited by Donald Forsdyke
5.9 Organelle Genomes Are Circular DNAs That Encode
4.1 Introduction 82 Organelle Proteins 113
4.2 An Interrupted Gene Consists of Exons 5.10 The Chloroplast Genome Encodes Many Proteins
and Introns 83 and RNAs 115
4.3 Exon and Intron Base Compositions Differ 84 5.11 Mitochondria and Chloroplasts Evolved
by Endosymbiosis 116
4.4 Organization of Interrupted Genes May Be
Conserved 84 5.12 Summary 117
4.5 Exon Sequences Under Negative Selection Are References 117
Conserved but Introns Vary 86
Chapter 6. Genome Sequences and
4.6 Exon Sequences Under Positive Selection Vary but
Introns Are Conserved 87 Gene Numbers 120
4.7 Genes Show a Wide Distribution of Sizes 6.1 Introduction 121
Due Primarily to Intron Size and Number
6.2 Prokaryotic Gene Numbers Range Over
Variation 88
an Order of Magnitude 122
4.8 Some DNA Sequences Encode More Than One
6.3 Total Gene Number Is Known for Several
Polypeptide 90
Eukaryotes 123
4.9 Some Exons Can Be Equated with Protein Functional
6.4 How Many Different Types of Genes Are There? 125
Domains 92
6.5 The Human Genome Has Fewer Genes Than Originally
4.10 Members of a Gene Family Have a Common
Expected 127
Organization 93
6.6 How Are Genes and Other Sequences Distributed in
4.11 There Are Many Forms of Information in DNA 95
the Genome? 129
4.12 Summary 97
6.7 The Y Chromosome Has Several Male-Specific
References 97 Genes 131
6.8 How Many Genes Are Essential? 132
viii Contents
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6.9 About 10,000 Genes Are Expressed at Widely 8.10 Globin Clusters Arise by Duplication and
Differing Levels in a Eukaryotic Cell 135 Divergence 181
6.10 Expressed Gene Number Can Be Measured 8.11 Pseudogenes Are Nonfunctional Gene Copies 183
En Masse 136
8.12 Genome Duplication Has Played a Role in Plant and
6.11 Summary 137 Vertebrate Evolution 185
References 138 8.13 What Is the Role of Transposable Elements in
Genome Evolution? 186
Chapter 7. Clusters and Repeats 141
8.14 There May Be Biases in Mutation, Gene Conversion,
7.1 Introduction 142 and Codon Usage 187
7.2 Unequal Crossing Over Rearranges Gene 8.15 Summary 188
Clusters 144 References 189
7.3 Genes for rRNA Form Tandem Repeats Including an
Invariant Transcription Unit 147 Chapter 9. Chromosomes 192
Edited by Hank W. Bass
7.4 Crossover Fixation Could Maintain Identical
Repeats 149 9.1 Introduction 193
7.5 Satellite DNAs Often Lie in Heterochromatin 152 9.2 Viral Genomes Are Packaged into Their Coats 194
7.6 Arthropod Satellites Have Very Short Identical 9.3 The Bacterial Genome Is a Nucleoid 197
Repeats 154
9.4 The Bacterial Genome Is Supercoiled 198
7.7 Mammalian Satellites Consist of Hierarchical
Repeats 154 9.5 Eukaryotic DNA Has Loops and Domains Attached to
a Scaffold 200
7.8 Minisatellites Are Useful for Genetic Mapping 158
9.6 Specific Sequences Attach DNA to an Interphase
7.9 Summary 159 Matrix 201
References 160 9.7 Chromatin Is Divided into Euchromatin and
Heterochromatin 202
Chapter 8. Genome Evolution 161
9.8 Chromosomes Have Banding Patterns 204
8.1 Introduction 162
9.9 Lampbrush Chromosomes Are Extended 205
8.2 DNA Sequences Evolve by Mutation and a Sorting
9.10 Polytene Chromosomes Form Bands 206
Mechanism 163
9.11 Polytene Chromosomes Expand at Sites of Gene
8.3 Selection Can Be Detected by Measuring Sequence
Expression 208
Variation 165
9.12 The Eukaryotic Chromosome Is a Segregation
8.4 A Constant Rate of Sequence Divergence Is a
Device 209
Molecular Clock 169
9.13 Regional Centromeres Contain a Centromeric Histone
8.5 The Rate of Neutral Substitution Can Be Measured
H3 Variant and Repetitive DNA 210
from Divergence of Repeated Sequences 173
9.14 Point Centromeres in S. cerevisiae Contain Short,
8.6 How Did Interrupted Genes Evolve? 174
Essential DNA Sequences 212
8.7 Why Are Some Genomes So Large? 177
9.15 The S. cerevisiae Centromere Binds a Protein
8.8 Morphological Complexity Evolves by Adding New Complex 213
Gene Functions 179
9.16 Telomeres Have Simple Repeating Sequences 213
8.9 Gene Duplication Contributes to Genome
9.17 Telomeres Seal the Chromosome Ends and Function
Evolution 180
in Meiotic Chromosome Pairing 214
Contents ix
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