Hartwell genetics from genes to genomes 4th

FOURTH EDITION Genetics From Genes to Genomes Leland H. Hartwell FRED HUTCHINSON CANCER RESEARCH CENTER Leroy Hood THE INSTITUTE FOR SYSTEMS BIOLOGY Michael L. Goldberg CORNELL UNIVERSITY Ann E. Reynolds FRED HUTCHINSON CANCER RESEARCH CENTER Lee M. Silver PRINCETON UNIVERSITY har2526x_fm_i-xxii.indd Page i 7/18/10 4:15:52 AM user-f500har2526x_fm_i-xxii.indd Page i 7/18/10 4:15:52 AM user-f500 /Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02/Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02 GENETICS: FROM GENES TO GENOMES, FOURTH EDITION Published by McGraw-Hill, a business unit of The McGraw-Hill Companies, Inc., 1221 Avenue of the Americas, New York, NY 10020. Copyright © 2011 by The McGraw-Hill Companies, Inc. All rights reserved. Previous editions © 2008, 2004, and 2000. No part of this publication may be reproduced or distributed in any form or by any means, or stored in a database or retrieval system, without the prior written consent of The McGraw-Hill Companies, Inc., including, but not limited to, in any network or other electronic storage or transmission, or broadcast for distance learning. Some ancillaries, including electronic and print components, may not be available to customers outside the United States. This book is printed on acid-free paper. 1 2 3 4 5 6 7 8 9 0 DOW/DOW 1 0 9 8 7 6 5 4 3 2 1 0 ISBN 978–0–07–352526–6 MHID 0–07–352526–X Vice President, Editor-in-Chief: Marty Lange Vice President, EDP: Kimberly Meriwether David Senior Director of Development: Kristine Tibbetts Publisher: Janice Roerig-Blong Developmental Editor: Fran Schreiber Senior Marketing Manager: Tamara Maury Lead Project Manager: Sheila M. Frank Project Coordinator: Mary Jane Lampe Buyer II: Sherry L. Kane Senior Media Project Manager: Jodi K. Banowetz Designer: Tara McDermott Cover Designer: Elise Lansdon Cover Image: Jim Dowdalls/Photo Researchers, Inc.(front cover); © Pixtal/age Fotostock/RF (Mendel); Courtesy of the National Library of Medicine (Darwin) Lead Photo Research Coordinator: Carrie K. Burger Photo Research: Jerry Marshall/pictureresearching.com Compositor: Aptara ® , Inc. Typeface: 10.5/12 Times Roman Printer: R. R. Donnelley All credits appearing on page or at the end of the book are considered to be an extension of the copyright page. Library of Congress Cataloging-in-Publication Data Genetics : from genes to genomes / Leland Hartwell . . . [et al.].—4th ed. p. cm. Includes index. ISBN 978–0–07–352526–6—ISBN 0–07–352526–X (hard copy : alk. paper) 1. Genetics. I. Hartwell, Leland. QH430.G458 2011 576.5—dc22 2009012742 www.mhhe.com har2526x_fm_i-xxii.indd Page ii 7/19/10 5:18:34 PM user-f499har2526x_fm_i-xxii.indd Page ii 7/19/10 5:18:34 PM user-f499 /Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell/Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell iii About the Authors Dr. Leland Hartwell is President and Director of Seattle’s Fred Hutchinson Cancer Research Center and Professor of Genome Sciences at the University of Washington. Dr. Hartwell’s primary research contributions were in identifying genes that control cell division in yeast includ- ing those necessary for the division process as well as those necessary for the  delity of genome reproduction. Subsequently, many of these same genes have been found to control cell division in humans and often to be the site of alteration in cancer cells. Dr. Hartwell is a member of the National Academy of Sciences and has received the Albert Lasker Basic Medical Research Award, the Gairdner Foundation International Award , the Genetics Society Medal, and the 2001 Nobel Prize in Physiology or Medicine. Dr. Lee Hood received an M.D. from the Johns Hopkins Medical School and a Ph.D. in biochemistry from the California Institute of Tech nology. His research interests include immunology, cancer biology, development, and the develop- ment of biological instrumentation (for example, the protein sequencer and the automated  uorescent DNA sequencer). His early research played a key role in unraveling the mysteries of antibody diversity. More recently he has pioneered systems approaches to biology and medicine. Dr. Hood has taught molecular evolution, immunology, molecular biology, genomics and biochemistry and has co- authored textbooks in biochemistry, molecular biology, and immunology, as well as The Code of Codes —a mono- graph about the Human Genome Project. He was one of the  rst advocates for the Human Genome Project and directed one of the federal genome centers that sequenced the human genome. Dr. Hood is currently the president (and co-founder) of the cross-disciplinary Institute for Systems Biology in Seattle, Washington. Dr. Hood has received a variety of awards, including the Albert Lasker Award for Medical Research (1987), the Dis- tinguished Service Award from the National Association of Teachers (1998) and the Lemelson/MIT Award for Invention (2003). He is the 2002 recipient of the Kyoto Prize in Advanced Biotechnology—an award recognizing his pioneering work in developing the protein and DNA synthesizers and sequenc- ers that provide the technical foundation of modern biology. He is deeply involved in K–12 science education. His hob- bies include running, mountain climbing, and reading. Dr. Michael Goldberg is a professor at Cornell University, where he teaches introductory genetics and human genet- ics. He was an undergraduate at Yale University and received his Ph.D. in biochemistry from Stanford University. Dr. Goldberg performed postdoctoral research at the Biozentrum of the Uni ver- sity of Basel (Switzerland) and at Harvard University, and he received an NIH Fogarty Senior International Fellowship for study at Imperial College (England) and fellowships from the Fondazione Cenci Bolognetti for sabbatical work at the University of Rome (Italy). His current research uses the tools of Drosophila genetics and the biochemical analysis of frog egg cell extracts to investigate the mech- anisms that ensure proper cell cycle progression and chro- mosome segregation during mitosis and meiosis. Dr. Ann Reynolds is an educator and author. She began teaching genetics and biology in 1990, and her research has included studies of gene regulation in E. coli, chromosome structure and DNA replication in yeast, and chloroplast gene expression in marine algae. She is a grad- uate of Mount Holyoke College and re- ceived her Ph.D. from Tufts University. Dr. Reynolds was a postdoctoral fellow in the Harvard University Department of Molecular Biology and Genome Sciences at the University of Washington. She was also an author and producer of the laser- disc and CD-ROM Genetics: Fundamentals to Frontiers . Dr. Lee M. Silver is a professor at Princeton Uni versity in the Department of Molecular Biology and the Woodrow Wilson School of Public and Inter- national Affairs. He has joint appoint- ments in Princeton’s Program in Science, Technology, and Environmental Policy, the Program in Law and Public Policy har2526x_fm_i-xxii.indd Page iii 7/18/10 4:16:05 AM user-f500har2526x_fm_i-xxii.indd Page iii 7/18/10 4:16:05 AM user-f500 /Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02/Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02 and the Princeton Environmental Institute. He received a Bachelor’s and Master’s degree in physics from the University of Pennsylvania, a doctorate in biophysics from Harvard University, postdoctoral training in mammalian genetics at the Sloan-Kettering Cancer Center, and training in molecular biology at Cold Spring Harbor Laboratory. Silver was elected a lifetime Fellow of the American Association for the Advancement of Science and was a recipient of an unsolicited National Institutes of Health MERIT award for outstanding research in genetics. He has been elected to the governing boards of the Genetics Society of America and the International Mammalian Genome Society, and is currently on the Board of Trustees of the American Council on Science and Health, the Advisory Board of The Reason Project, and the Scienti c Advisory Board of the Institute of Systems Biology in Seattle. Silver has published over 180 research articles in the  elds of developmental genetics, molecular evolution, popu- lation genetics, behavioral genetics, and computer model- ing. He is the lone author of three books: Mouse Genetics: Concepts and Applications (1995), Remaking Eden (1997) and Challenging Nature (2006). He has also published essays in The New York Times , Washington Post , Time , and Newsweek International and has appeared on numerous television and radio programs including the Charlie Rose Show, 20/20, 60 Minutes, PBS, NBC and ABC News, Nightline, NPR, and the Steven Colbert Report. Recently, Silver collaborated with the playwright Jeremy Kareken on the script of “Sweet, Sweet, Motherhood,” which won  rst prize in the 2007 Two-headed Challenge from the Guthrie Theater, awarded to the best play written by a playwright and a non-theater partner. Contributors Genetics research tends to proceed down highly specialized paths. A number of experts in speci c areas generously provided information in their areas of expertise. We thank them for their contributions to this edition of our text. Claudio Alonso, University of Sussex Jody Larson, Instructional Designer, Textbook Development Martha Hamblin, Cornell University Debra Nero, Cornell University iv About the Authors har2526x_fm_i-xxii.indd Page iv 7/18/10 4:16:10 AM user-f500har2526x_fm_i-xxii.indd Page iv 7/18/10 4:16:10 AM user-f500 /Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02/Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02 v Brief Contents 1 Genetics: The Study of Biological Information 1 PART I Basic Principles: How Traits Are Transmitted 13 2 Mendel’s Principles of Heredity 13 3 Extensions to Mendel’s Laws 43 4 The Chromosome Theory of Inheritance 79 5 Linkage, Recombination, and the Mapping of Genes on Chromosomes 118 PART II What Genes Are and What They Do 162 6 DNA Structure, Replication, and Recombination 162 7 Anatomy and Function of a Gene: Dissection Through Mutation 199 8 Gene Expression: The Flow of Information from DNA to RNA to Protein 246 PART III Analysis of Genetic Information 290 9 Digital Analysis of DNA 290 10 Genomes and Proteomes 334 11 Genome-Wide Variation and Trait Analysis 368 PART IV How Genes Travel on Chromosomes 405 12 The Eukaryotic Chromosome 405 13 Chromosomal Rearrangements and Changes in Chromosome Number 429 14 Prokaryotic and Organelle Genetics 477 PART V How Genes Are Regulated 519 15 Gene Regulation in Prokaryotes 519 16 Gene Regulation in Eukaryotes 552 17 Somatic Mutation and the Genetics of Cancer 586 18 Using Genetics to Study Development 617 PART VI Beyond the Individual Gene and Genome 655 19 Variation and Selection in Populations 655 20 Evolution at the Molecular Level 690 21 Systems Biology and the Future of Medicine 715 har2526x_fm_i-xxii.indd Page v 7/18/10 4:16:10 AM user-f500har2526x_fm_i-xxii.indd Page v 7/18/10 4:16:10 AM user-f500 /Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02/Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02 vi CHAPTER 3 Extensions to Mendel’s Laws 43 3.1 Extensions to Mendel for Single-Gene Inheritance 44 3.2 Extensions to Mendel for Multifactorial Inheritance 54 ■ Fast Forward: Gene Therapy for Sickle-Cell Disease in Mice 55 ■ Genetics and Society: Disease Prevention Versus the Right to Privacy 67 CHAPTER 4 The Chromosome Theory of Inheritance 79 4.1 Chromosomes: The Carriers of Genes 80 4.2 Mitosis: Cell Division That Preserves Chromosome Number 86 4.3 Meiosis: Cell Divisions That Halve Chromosome Number 92 4.4 Gametogenesis 100 4.5 Validation of the Chromosome Theory 101 ■ Genetics and Society: Prenatal Genetic Diagnosis 83 ■ Fast Forward: How Gene Mutations Cause Errors in Mitosis 91 CHAPTER 5 Linkage, Recombination, and the Mapping of Genes on Chromosomes 118 5.1 Gene Linkage and Recombination 119 5.2 The Chi-Square Test and Linkage Analysis 122 5.3 Recombination: A Result of Crossing-Over During Meiosis 125 5.4 Mapping: Locating Genes Along a Chromosome 129 5.5 Tetrad Analysis in Fungi 135 5.6 Mitotic Recombination and Genetic Mosaics 146 About the Authors iii Preface x Acknowledgements xxii Introduction to Genetics in the Twenty-First Century 1 CHAPTER 1 Genetics: The Study of Biological Information 1 1.1 DNA: The Fundamental Information Molecule of Life 1 1.2 Proteins: The Functional Molecules of Life Processes 3 1.3 Complex Systems and Molecular Interactions 4 1.4 Molecular Similarities of all Life-Forms 4 1.5 The Modular Construction of Genomes 6 1.6 Modern Genetic Techniques 7 1.7 Human Genetics 10 PART I Basic Principles: How Traits Are Transmitted 13 CHAPTER 2 Mendel’s Principles of Heredity 13 2.1 Background: The Historical Puzzle of Inheritance 14 2.2 Genetic Analysis According to Mendel 19 2.3 Mendelian Inheritance in Humans 30 ■ Fast Forward: Genes Encode Proteins 20 ■ Tools of Genetics: Plants as Living Chemical Factories 29 ■ Genetics and Society: Developing Guidelines for Genetic Screening 32 Contents har2526x_fm_i-xxii.indd Page vi 7/18/10 4:16:22 AM user-f500har2526x_fm_i-xxii.indd Page vi 7/18/10 4:16:22 AM user-f500 /Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02/Users/user-f500/Desktop/TEMPWORK/Don'tDelete_Jobs/MHDQ251:Beer:201/ch02 8.3 Translation: From mRNA to Protein 265 8.4 Differences in Gene Expression Between Prokaryotes and Eukaryotes 272 8.5 A Comprehensive Example: Computerized Analysis of Gene Expression in C. elegans 274 8.6 The Effect of Mutations on Gene Expression and Gene Function 276 ■ Genetics and Society: HIV and Reverse Transcription 260 PART III Analysis of Genetic Information 290 CHAPTER 9 Digital Analysis of DNA 290 9.1 Sequence-Specifi c DNA Fragmentation 291 9.2 Cloning Fragments of DNA 297 9.3 Hybridization 306 9.4 The Polymerase Chain Reaction 310 9.5 DNA Sequence Analysis 313 9.6 Bioinformatics: Information Technology and Genomes 317 9.7 The Hemoglobin Genes: A Comprehensive Example 322 ■ Tools of Genetics: Serendipity in Science: The Discovery of Restriction Enzymes 293 ■ Genetics and Society: The Use of Recombinant DNA Technology and Pest- Resistant Crops 304 CHAPTER 10 Genomes and Proteomes 334 10.1 Large-Scale Genome Mapping and Analysis 336 10.2 Major Insights from Human and Model Organism Genome Sequences 341 10.3 Global Analysis of Genes and Their mRNAs 348 10.4 Global Analysis of Proteomes 352 10.5 Repercussions of the Human Genome Project and High-Throughput Technology 359 ■ Genetics and Society: Patentability of DNA 360 ■ Tools of Genetics: The Chi-Square Test 124 ■ Fast Forward: Gene Mapping May Lead to a Cure for Cystic Fibrosis 137 ■ Genetics and Society: Mitotic Recombination and Cancer Formation 148 PART II What Genes Are and What They Do 162 CHAPTER 6 DNA: Structure, Replication, and Recombination 162 6.1 Experimental Evidence for DNA as the Genetic Material 163 6.2 The Watson and Crick Double Helix Model of DNA 168 6.3 Genetic Information in DNA Base Sequence 175 6.4 DNA Replication 179 6.5 Recombination at the DNA Level 186 ■ Tools of Genetics: Restriction Enzyme Recognition Sites 177 CHAPTER 7 Anatomy and Function of a Gene: Dissection Through Mutation 199 7.1 Mutations: Primary Tools of Genetic Analysis 200 7.2 What Mutations Tell Us About Gene Structure 216 7.3 What Mutations Tell Us About Gene Function 224 7.4 A Comprehensive Example: Mutations That Affect Vision 231 ■ Genetics and Society: Unstable Trinucleotide Repeats and Fragile X Syndrome 208 ■ Fast Forward: Using Mutagenesis to Look at Biological Processes 232 CHAPTER 8 Gene Expression: The Flow of Information from DNA to RNA to Protein 246 8.1 The Genetic Code 247 8.2 Transcription: From DNA to RNA 256 Contents vii har2526x_fm_i-xxii.indd Page vii 7/19/10 5:19:23 PM user-f499har2526x_fm_i-xxii.indd Page vii 7/19/10 5:19:23 PM user-f499 /Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell/Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell 14.3 Gene Transfer in Bacteria 486 14.4 Bacterial Genetic Analysis 496 14.5 The Genetics of Chloroplasts and Mitochondria 498 14.6 Non-Mendelian Inheritance of Chloroplasts and Mitochondria 503 14.7 mtDNA Mutations and Human Health 508 ■ Genetics and Society: Mitochondrial DNA Tests as Evidence of Kinship in Argentine Courts 507 PART V How Genes Are Regulated 519 CHAPTER 15 Gene Regulation in Prokaryotes 519 15.1 Overview of Prokaryotic Gene Regulation 520 15.2 The Regulation of Gene Transcription 521 15.3 Attenuation of Gene Expression: Termination of Transcription 535 15.4 Global Regulatory Mechanisms 537 15.5 A Comprehensive Example: The Regulation of Virulence Genes in V. cholerae 542 ■ Genetics and Society: Nitrogen Fixation and Gene Regulation 540 CHAPTER 16 Gene Regulation in Eukaryotes 552 16.1 Overview of Eukaryotic Gene Regulation 553 16.2 Control of Transcription Initiation 554 16.3 Chromatin Structure and Epigenetic Effects 562 16.4 Regulation After Transcription 568 16.5 A Comprehensive Example: Sex Determination in Drosophila 573 ■ Tools of Genetics: RNA Interference and Treatment of Disease 574 CHAPTER 17 Somatic Mutation and the Genetics of Cancer 586 17.1 Overview: Initiation of Division 587 17.2 Cancer: A Failure of Control Over Cell Division 589 17.3 The Normal Control of Cell Division 600 ■ Genetics and Society: The Uses of Genetic Testing in Predicting and Treating Cancer 609 viii Contents CHAPTER 11 Genome-Wide Variation and Trait Analysis 368 11.1 Genetic Variation Among Individual Genomes 370 11.2 (SNPs) and Small-Scale-Length Variations 371 11.3 Deletions or Duplications of a DNA Region 379 11.4 Positional Cloning: From DNA Markers to Disease-Causing Genes 384 11.5 Complex Traits 387 11.6 Genome-Wide Association Studies 390 ■ Genetics and Society: Social and Ethical Issues Surrounding Preimplantation Genetic Diagnosis 393 PART IV How Genes Travel on Chromosomes 405 CHAPTER 12 The Eukaryotic Chromosome 405 12.1 Chromosomal DNA and Proteins 406 12.2 Chromosome Structure and Compaction 408 12.3 Chromosomal Packaging and Function 413 12.4 Replication and Segregation of Chromosomes 417 CHAPTER 13 Chromosomal Rearrangements and Changes in Chromosome Number 429 13.1 Rearrangements of DNA Sequences 430 13.2 Transposable Genetic Elements 447 13.3 Rearrangements and Evolution: A Speculative Comprehensive Example 453 13.4 Changes in Chromosome Number 454 13.5 Emergent Technologies: Beyond the Karyotype 463 ■ Fast Forward: Programmed DNA Rearrangements and the Immune System 432 CHAPTER 14 Prokaryotic and Organelle Genetics 477 14.1 A General Overview of Bacteria 478 14.2 Bacterial Genomes 481 har2526x_fm_i-xxii.indd Page viii 7/19/10 5:19:56 PM user-f499har2526x_fm_i-xxii.indd Page viii 7/19/10 5:19:56 PM user-f499 /Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell/Users/user-f499/Desktop/Temp Work/Don't Delete Job/MHDQ122:Hertwell CHAPTER 18 Using Genetics to Study Development 617 18.1 Model Organisms: Prototypes for Developmental Genetics 619 18.2 Using Mutations to Dissect Development 620 18.3 Analysis of Developmental Pathways 628 18.4 A Comprehensive Example: Body-Plan Development in Drosophila 633 18.5 How Genes Help Control Development 645 ■ Genetics and Society: Stem Cells and Human Cloning 623 PART VI Beyond the Individual Gene and Genome 655 CHAPTER 19 Variation and Selection in Populations 655 19.1 The Hardy-Weinberg Law: Predicting Genetic Variation in Populations 656 19.2 Causes of Allele Frequency Changes 663 19.3 Analyzing Quantitative Variation 674 ■ Genetics and Society: DNA Analysis and 9/11 Victim Identifi cation 681 Contents ix CHAPTER 20 Evolution at the Molecular Level 690 20.1 The Origin of Life on Earth 691 20.2 The Evolution of Genomes 695 20.3 The Organization of Genomes 701 20.4 A Comprehensive Example: Rapid Evolution in the Immune Response and in HIV 709 ■ Genetics and Society: Evolution Versus Intelligent Design 699 CHAPTER 21 Systems Biology and the Future of Medicine 715 21.1 What Is Systems Biology? 716 21.2 Biology as an Informational Science 718 21.3 The Practice of Systems Biology 721 21.4 A Systems Approach to Disease 725 Guidelines for Gene Nomenclature A-1 Brief Answer Section B-1 Glossary G-1 Credits C-1 Index I-1 har2526x_fm_i-xxii.indd Page ix 7/23/10 6:55:46 AM user-f499har2526x_fm_i-xxii.indd Page ix 7/23/10 6:55:46 AM user-f499 /Users/user-f499/Desktop/Temp Work/JULY2010/23:07:10/Hartwell:MHDQ122/Users/user-f499/Desktop/Temp Work/JULY2010/23:07:10/Hartwell:MHDQ122 . of genetics moving forward. Our Focus—An Integrated Approach Genetics: From Genes to Genomes represents a new approach to an undergraduate course in genetics. . fourth edition of Genetics: From Genes to Genomes emphasizes both the core concepts of genetics and the cutting-edge discoveries, modern tools, and ana-