Genetics: Analysis & Principles (6th Ed.) PDF

GENE & T I ANALYSIS C SPRINCIPLES 6e Robert J. Brooker  Sixth Edition ROBERT J. BROOKER University of Minnesota GENETICS: ANALYSIS & PRINCIPLES, SIXTH EDITION Published by McGraw-Hill Education, 2 Penn Plaza, N...

GENE & T I ANALYSIS C SPRINCIPLES 6e Robert J. Brooker  Sixth Edition ROBERT J. BROOKER University of Minnesota GENETICS: ANALYSIS & PRINCIPLES, SIXTH EDITION Published by McGraw-Hill Education, 2 Penn Plaza, New York NY 10121. Copyright © 2018 by McGraw-Hill Education. All rights reserved. Printed in the United States of America. Previous editions © 2015, 2012, 2009, 2005, and 1999. 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 McGraw-Hill Educa- tion, 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 LWI/LWI 21 20 19 18 17 ISBN 978–1–259–61602-0 MHID 1–259–61602–9 Senior Vice President, Products & Markets: G. Scott Virkler Vice President, General Manager, Products & Markets: Marty Lange Vice President, Content Production & Technology Services: Betsy Whalen Director of Digital Content: Michael G. Koot, PhD Brand Manager: Justin K. Wyatt, PhD Director of Development, Biology: Elizabeth M. Sievers Digital Product Analyst: Christine Carlson Market Development Manager: Michelle Bradin Executive Marketing Manager: Patrick E. Reidy Project Manager: Angie FitzPatrick Content Project Managers: Jayne Klein/Christina Nelson Senior Buyer: Sandy Ludovissy Senior Designer: David W. Hash Cover Image: © Dr. Paul Andrews, University of Dundee/Science Photo Library/Getty Images Content Licensing Specialists: Carrie Burger/Shannon Manderscheid Compositor: Aptara, Inc. Typeface: STIX MathJax Main Printer: LSC Communications All credits appearing on page are considered to be an extension of the copyright page. Library of Congress Cataloging-in-Publication Data Names: Brooker, Robert J. Title: Genetics : analysis & principles / Robert J. Brooker, University of Minnesota. Description: Sixth edition. | New York NY : McGraw-Hill Education, | Includes index. Identifiers: LCCN 2016034541| ISBN 9781259616020 (alk. paper) | ISBN 1259616029 (alk. paper) Subjects: LCSH: Genetics. Classification: LCC QH430.B766 2018 | DDC 576.5--dc23 LC record available at https://lccn.loc.gov/2016034541 2013035482 The Internet addresses listed in the text were accurate at the time of publication. The inclusion of a website does not indicate an endorsement by the authors or McGraw-Hill Education, and McGraw-Hill Education does not guarantee the accuracy of the information presented at these sites. www.mhhe.com B R I E F C O N T E N T S P A R T I INTRODUCTION P A R T I V MOLECULAR PROPERTIES OF GENES 1 Overview of Genetics   1 12 Gene Transcription and RNA Modification   278 P A R T I I PATTERNS OF INHERITANCE 13 Translation of mRNA   306 2 Mendelian Inheritance  18 14 Gene Regulation in Bacteria   336 3 Chromosome Transmission During Cell 15 Gene Regulation in Eukaryotes I: Division and Sexual Reproduction   46 Transcriptional and Translation 4 Extensions of Mendelian Inheritance   76 Regulation  361 5 Non-Mendelian Inheritance  102 16 Gene Regulation in Eukaryotes II: Epigenetics  388 6 Genetic Linkage and Mapping in Eukaryotes  127 17 Non-coding RNAs  411 7 Genetic Transfer and Mapping in 18 Genetics of Viruses   433 Bacteria  155 19 Gene Mutation and DNA Repair   461 8 Variation in Chromosome Structure 20 Recombination, Immunogenetics, and and Number  177 Transposition  491 PA R T I I I M  OLECULAR STRUCTURE AND P A R T V GENETIC TECHNOLOGIES REPLICATION OF THE GENETIC MATERIAL 21 Molecular Technologies  511 9 Molecular Structure of DNA and RNA   208 22 Biotechnology  539 10 Chromosome Organization and Molecular 23 Genomics I: Analysis of DNA   563 Structure  229 24 Genomics II: Functional Genomics, Proteomics, 11 DNA Replication  252 and Bioinformatics  589 P A R T V I GENETIC ANALYSIS OF INDIVIDUALS AND POPULATIONS 25 Medical Genetics and Cancer   611 26 Developmental Genetics  643 27 Population Genetics  675 28 Complex and Quantitative Traits   707 29 Evolutionary Genetics  732 v T A B L E O F C O N T E N T S Preface  ix 4.2 4.3 Dominant and Recessive Alleles 78 Environmental Effects on Gene Expression 80 8 VARIATION IN CHROMOSOME STRUCTURE AND NUMBER 177 PA R T I 4.4 Incomplete Dominance, Overdominance, 8.1 Microscopic Examination of Eukaryotic and Codominance 81 Chromosomes 177 INTRODUCTION 1 4.5 X-Linked Inheritance 86 8.2 Changes in Chromosome Structure: 1 OVERVIEW OF GENETICS 1 4.6 4.7 Sex-Influenced and Sex-Limited Inheritance 88 Lethal Alleles 90 8.3 8.4 An Overview 180 Deletions and Duplications 181 Inversions and Translocations 187 1.1 The Molecular Expression of Genes   3 8.5 Changes in Chromosome Number: 4.8 Pleiotropy 91 1.2 The Relationship Between Genes and An Overview 192 4.9 Gene Interactions 92 Traits  6 8.6 Variation in the Number of 1.3 Fields of Genetics 11 Chromosomes Within a Set: 1.4 The Science of Genetics 13 5 NON-MENDELIAN INHERITANCE 102 8.7 Aneuploidy 193 Variation in the Number of Sets of Chromosomes 195 5.1 Maternal Effect 103 5.2 Epigenetic Inheritance: Dosage 8.8 Natural and Experimental Mechanisms PA R T I I Compensation 106 That Produce Variation in Chromosome Number 198 PATTERNS OF INHERITANCE 18 5.3 Epigenetic Inheritance: Genomic Imprinting 112 2 MENDELIAN INHERITANCE 18 5.4 Extranuclear Inheritance 116 PA R T I I I MOLECULAR STRUCTURE AND 2.1 2.2 2.3 Mendel’s Study of Pea Plants 19 Law of Segregation 22 Law of Independent Assortment 26 6 GENETIC LINKAGE AND MAPPING IN EUKARYOTES 127 REPLICATION OF THE GENETIC MATERIAL  208 9 6.1 Overview of Linkage 127 2.4 Studying Inheritance Patterns in MOLECULAR STRUCTURE OF DNA 6.2 Relationship Between Linkage and Humans 32 AND RNA 208 Crossing Over 129 2.5 Probability and Statistics 34 6.3 Genetic Mapping in Plants and 9.1 Identification of DNA as the Genetic Animals 135 Material 208 3 CHROMOSOME TRANSMISSION DURING CELL DIVISION AND SEXUAL REPRODUCTION 46 6.4 6.5 Genetic Mapping in Haploid Eukaryotes 142 Mitotic Recombination 145 9.2 9.3 Overview of DNA and RNA Structure 211 Nucleotide Structure 212 3.1 General Features of Chromosomes 46 9.4 Structure of a DNA Strand 214 7 3.2 Cell Division 50 GENETIC TRANSFER AND 9.5 Discovery of the Double Helix 215 3.3 Mitosis and Cytokinesis 53 MAPPING IN BACTERIA 155 9.6 Structure of the DNA Double Helix 218 3.4 Meiosis 57 9.7 RNA Structure 222 7.1 Overview of Genetic Transfer in 3.5 Sexual Reproduction 61 10 Bacteria 156 CHROMOSOME 3.6 The Chromosome Theory of Inheritance 7.2 Bacterial Conjugation 157 ORGANIZATION AND and Sex Chromosomes 64 MOLECULAR STRUCTURE 229 7.3 Conjugation and Mapping via Hfr 4 Strains 161 EXTENSIONS OF MENDELIAN 10.1 Organization of Sites Along Bacterial 7.4 Bacterial Transduction 166 Chromosomes 229 INHERITANCE 76 7.5 Bacterial Transformation 168 10.2 Structure of Bacterial Chromosomes 230 4.1 Overview of Simple Inheritance 7.6 Medical Relevance of Bacterial Genetic 10.3 Organization of Sites Along Eukaryotic Patterns 77 Transfer 170 Chromosomes 234 vi  TABLE OF CONTENTS vii 10.4 Sizes of Eukaryotic Genomes and 14.3 Regulation of the trp Operon 349 18.3 Bacteriophage λ Reproductive Repetitive Sequences 235 14.4 Translational and Posttranslational Cycle 444 10.5 Structure of Eukaryotic Chromosomes in Regulation 353 18.4 HIV Reproductive Cycle 450 Nondividing Cells 237 14.5 Riboswitches 354 10.6 Structure of Eukaryotic Chromosomes During Cell Division 243 19 GENE MUTATION AND DNA 15 REPAIR 461 GENE REGULATION IN 11 EUKARYOTES I: 19.1 Effects of Mutations on Gene Structure TRANSCRIPTIONAL AND DNA REPLICATION 252 TRANSLATION and Function 462 REGULATION 361 19.2 Random Nature of Mutations 468 11.1 Structural Overview of DNA 19.3 Spontaneous Mutations 470 Replication 252 15.1 Regulatory Transcription Factors 362 19.4 Induced Mutations 475 11.2 Bacterial DNA Replication: The 15.2 Chromatin Remodeling, Histone 19.5 DNA Repair 479 Formation of Two Replication Forks at Variants, and Histone the Origin of Replication 256 Modification 369 11.3 Bacterial DNA Replication: Synthesis of New DNA Strands 259 11.4 Bacterial DNA Replication: Chemistry 15.3 DNA Methylation 376 15.4 Insulators 378 20 RECOMBINATION, IMMUNOGENETICS, AND TRANSPOSITION 491 15.5 The ENCODE Project 379 and Accuracy 266 20.1 Homologous Recombination 491 15.6 Regulation of Translation 380 11.5 Eukaryotic DNA Replication 268 20.2 Immunogenetics 497 20.3 Transposition 499 PA R T I V MOLECULAR PROPERTIES 16 GENE REGULATION IN EUKARYOTES II: EPIGENETICS 388 PA R T V OF GENES 278 16.1 Overview of Epigenetics 388 GENETIC TECHNOLOGIES 511 12 GENE TRANSCRIPTION AND RNA MODIFICATION 278 16.2 16.3 Epigenetics and Development 393 Paramutation 398 12.1 12.2 Overview of Transcription 278 Transcription in Bacteria 281 16.4 Epigenetics and Environmental Agents 400 16.5 Role of Epigenetics in Cancer 405 21 MOLECULAR TECHNOLOGIES 511 12.3 Transcription in Eukaryotes 286 21.1 Gene Cloning Using Vectors 512 21.2 Polymerase Chain Reaction 519 12.4 12.5 RNA Modification 291 A Comparison of Transcription and RNA Modification in Bacteria 17 NON-CODING RNAs 411 21.3 21.4 DNA Sequencing 524 Gene Mutagenesis 526 and Eukaryotes 300 17.1 Overview of Non-coding RNAs 412 21.5 Blotting Methods to Detect Gene 17.2 Non-coding RNAs: Effects on Chromatin Products 529 13 TRANSLATION OF mRNA 306 Structure and Transcription 416 17.3 Non-coding RNAs: Effects on Translation, mRNA Degradation, and 21.6 Methods for Analyzing DNA- and RNA- Binding Proteins 531 13.1 The Genetic Basis for Protein Synthesis 306 13.2 The Relationship Between the Genetic RNA Modifications 417 17.4 Non-coding RNAs and Protein Targeting 422 22 BIOTECHNOLOGY 539 Code and Protein Synthesis 309 22.1 Uses of Microorganisms in 13.3 Experimental Determination of the 17.5 Non-coding RNAs and Genome Biotechnology 539 Genetic Code 315 Defense 423 22.2 Genetically Modified Animals 542 13.4 Structure and Function of tRNA 319 17.6 Role of Non-coding RNAs in Human 22.3 Reproductive Cloning and Stem Disease 427 Cells 546 13.5 Ribosome Structure and Assembly 322 13.6 Stages of Translation 324 22.4 Genetically Modified Plants 551 14 GENE REGULATION IN 18 GENETICS OF VIRUSES 433 22.5 Human Gene Therapy 555 BACTERIA 336 14.1 Overview of Transcriptional Regulation 337 18.1 Virus Structure and Genetic Composition 433 23 GENOMICS I: ANALYSIS OF DNA 563 18.2 Overview of Viral Reproductive 23.1 Overview of Chromosome 14.2 Regulation of the lac Operon 339 Cycles 438 Mapping 564 viii TABLE OF CONTENTS 23.2 Cytogenetic Mapping via Microscopy 564 23.3 Linkage Mapping via Crosses 567 25.3 25.4 25.5 Genetic Testing and Screening 621 Prions 623 Genetic Basis of Cancer 624 28 COMPLEX AND QUANTITATIVE TRAITS 707 23.4 Physical Mapping via Cloning and DNA 25.6 Personalized Medicine 634 28.1 Overview of Complex and Quantitative Sequencing 570 Traits 707 23.5 Genome-Sequencing Projects 574 23.6 Metagenomics 582 26 DEVELOPMENTAL GENETICS 643 28.2 Statistical Methods for Evaluating Quantitative Traits 709 28.3 Polygenic Inheritance 712 24 26.1 Overview of Animal Development 643 28.4 Identification of Genes that Control GENOMICS II: FUNCTIONAL GENOMICS, PROTEOMICS, AND 26.2 Invertebrate Development 647 Quantitative Traits 715 BIOINFORMATICS 589 26.3 Vertebrate Development 659 28.5 Heritability 717 26.4 Plant Development 662 28.6 Selective Breeding 722 24.1 Functional Genomics 590 29 26.5 Sex Determination in Animals 666 24.2 Proteomics 595 27 24.3 Bioinformatics 600 EVOLUTIONARY GENETICS 732 POPULATION GENETICS 675 29.1 Origin of Species 733 PA R T V I 29.2 Phylogenetic Trees 738 27.1 Genes in Populations and the Hardy- Weinberg Equation 675 29.3 Molecular Evolution 746 GENETIC ANALYSIS OF INDIVIDUALS AND 27.2 Overview of Microevolution 680 *Appendix A: Experimental Techniques POPULATIONS 611 27.3 Natural Selection 681 can be found on the website for this textbook: www.mhhe.com/ 27.4 Genetic Drift 689 25 brookergenetics6e MEDICAL GENETICS AND 27.5 Migration 692 CANCER 611 Appendix B 27.6 Nonrandom Mating 692 Solutions to Even-Numbered 25.1 Inheritance Patterns of Genetic 27.7 Sources of New Genetic Variation 694 Problems and All Comprehension Diseases 612 and Concept Check Questions B-1 25.2 Detection of Disease-Causing Alleles via Glossary G-1 Haplotypes 618 Index I-1 ABOUT THE AUTHOR Robert J. Brooker is a professor in the Department of Genetics, Cell Biology, and Development and the Department of Biology Teaching and Learning at the University of Minnesota– Minneapolis. He received his B.A. in biology from Wittenberg University in 1978 and his Ph.D. in genetics from Yale University in 1983. At Harvard, he conducted postdoctoral studies on the lactose permease, which is the product of the lacY gene of the lac operon. He continued to work on transporters at the University of Minnesota with an emphasis on the structure, function, and regulation of iron transporters found in bacteria and C. elegans. At the University of Minnesota, he teaches undergraduate courses in biology and genetics. DEDICATION To my wife, Deborah, and our children, Daniel, Nathan, and Sarah P R E FAC E I students may be provided with online lectures, “flipping the class- room” typically gives students more responsibility for understanding the textbook material on their own. Along these lines, Genetics: Analysis & Principles, Sixth Edition, is intended to provide students n the sixth edition of Genetics: Analysis & Principles, the with a resource that can be effectively used outside of the classroom. content has been updated to reflect current trends in the field. In Here are several of the key pedagogical features: addition, the presentation of the content has been improved in a ∙  NEW! A new feature called Genetic TIPS provides a way that fosters active learning. As an author, researcher, and teacher, I want a textbook that gets students actively involved in consistent approach to help students solve problems in learning genetics. To achieve this goal, I have worked with a genetics. This approach has three components. First, the ­talented team of editors, illustrators, and media specialists who student is made aware of the Topic at hand. Second, the have helped me to make the sixth edition of Genetics: Analysis & question is evaluated with regard to the Informaiton that is Principles a fun learning tool. available to the student. Finally, the student is guided Overall, an effective textbook needs to accomplish four through one or more Problem-Solving Strategies to tackle goals.14 First, it needsCHAP toT provide E R 1 :: comprehensive, OVERVIEW OF GENETICS accurate, and up- the question. to-date content in its field. Second, it needs to expose students to the techniques and skills they will need to become successful in that field. words, Third, what an effective scientifictextbook question should was thehave pedagogical researcher trying features, such to answer? as formative assessment, that foster student learn- GENETIC TIPS THE QUESTION: All of the Genetic TIPS begin with a question. As an example, let’s consider the following ing. And 3. finally, Next, the figure follows it should inspirethe experimental students so theysteps wantthe to scientist pursue question: that field as took to test the a career. Thehypothesis. hard workEach thatfeatured has gone experiment con- into the sixth The coding strand of DNA in a segment of a gene is as follows: edition oftains two parallel Genetics: Analysisillustrations labeled has & Principles Experimental been aimed Levelat ATG GGC CTT AGC. This strand carries the information to make a achieving and Conceptual all four of theseLevel. goals!The Experimental Level helps you region of a polypeptide with the amino acid sequence, methionine- to understand the techniques followed. The Conceptual glycine-leucine-serine. What would be the consequences if a mutation Level helps you to understand what is actually happening changed the second cytosine (C) in this sequence to an adenine (A)? at each step in the procedure. FLIPPING 4. The raw data THE for eachCLASSROOM experiment are then presented. T OPIC: What topic in genetics does this question address? The 5. Last, an interpretation of the data is offered within the text. topic is gene expression. More specifically, the question is about A recent trend in science education is the phenomenon that is some- the relationship between a gene sequence and the genetic code. The rationale behind this approach is that it enables you to see the timesexperimental called “flipping the classroom.” This phrase refers to the idea process from beginning to end. As you read through that some of the activities that usedwillto be done I NFORMATION: What information do you know based on the the chapters, the experiments help youintoclass see theare relationship now done question and your understanding of the topic? In the question, outside of class, and vice versa. between science and scientific theories. For example, instead of spending the entire As class time lecturing over textbook and other materials, you are given the base sequence of a short segment of a gene and a student of genetics, you will be given the opportunity told that one of the bases has been changed. From your understanding sometoofinvolve the classyourtimemind is in spent engaging students the experimental process. in various As you are activi- read- of the topic, you may remember that a polypeptide sequence is ties, ing such anas problem solving, experiment, you mayworking through find yourself case about thinking studies, and different determined by reading the mRNA (transcribed from a gene) in designing experiments. approaches This approach and alternative is called hypotheses. activepeople Different learning.can For view groups of three bases called codons. manytheinstructors, same datathe and classroom arrive at hasverybecome differentmore learner centered conclusions. As you rather teacherthrough progress centered. theAexperiments learner-centeredin thisclassroom book, youprovides will enjoy a P ROBLEM-SOLVING S TRATEGY: Compare and contrast. rich genetics environment far morein which if youstudents can interact try to develop your own withskills eachatother and formulat- One strategy to solve this problem is to compare the mRNA withingtheirhypotheses, instructors.designingInstructorsexperiments, and fellow students often provide and interpreting data. sequence (transcribed from this gene) before and after the mutation: Also, some formative of the questions in the assessment—immediate problem feedback thatsets are aimed helps at refin- each student Original: AUG GGC CUU AGC ing these understand skills. if his or her learning is on the right track. Mutant: AUG GGC AUU AGC Finally, What are some it is worthwhile advantages to of point activeoutlearning? that science is a social Educational discipline. As you develop your skills at scrutinizing studies reveal that active learning usually promotes greater learning experiments, ANSWER: The mutation has changed the sequence of bases in the gains.it In is fun to discuss addition, activeyour ideasoften learning with focuses other people, on skillincluding developmentfellow mRNA so that the third codon has changed from CUU to AUU. students and faculty members. Keep in mind that you do not need Because codons specify amino acids, this may change the third rather than on the memorization of facts that are easily forgotten. to “know all the answers” before you enter into a scientific discus- amino acid to something else. Note: If you look ahead to Chapter 13 Students become trained to “think like scientists” and to develop a (see Table 13.1), you will see that CUU specifies leucine, whereas skill sion. Instead, set that enables it isthem moretorewarding to view apply scientific science asAan reasoning. ongoing common AUU specifies isoleucine. Therefore, you would predict that the mu- and never-ending dialogue. concern among instructors who are beginning to try out active learn- tation would change the third amino acid from leucine to isoleucine. ing is that they think they will have less time to teach and therefore will cover Genetic less material. TIPS Will However, HelpthisYou maytonot be the case. Improve Although Your Problem-Solving Skills Throughout Chapters 2 through 29, each chapter will contain sev- ix As your progress through this textbook, your learning will involve eral Genetic TIPS. Some of these will be within the chapter itself two general goals: and some will precede the problem sets that are at the end of each x PREFACE ∙  Genes → Traits: Because genetics is such a broad discipline, ranging from the molecular level to populations, many SIGNIFICANT CONTENT CHANGES instructors have told us that it is a challenge for students to IN THE SIXTH EDITION see both “the forest and the trees.” It is commonly mentioned that students often have trouble connecting the concepts they ∙  NEW! A new problem-solving feature called Genetic TIPS have learned in molecular genetics with the traits that occur has been added to the sixth edition. The Genetic TIPS are at the level of a whole organism (i.e., What does found within each chapter and three or four are found at the transcription have to do with blue eyes?). To try to make this end of each chapter. connection more meaningful, certain figure legends in each ∙  NEW! The topic of Epigenetics has been expanded to a chapter, designated Genes → Traits, remind students that whole chapter, which is now Chapter 16. molecular and cellular phenomena ultimately lead to the ∙  NEW! A new chapter on non-coding RNA has been added, traits that are observed in each species (see Figure 14.8). which is Chapter 17. This long-overdue chapter is in ∙  Learning Outcomes: Each section of every chapter begins response to a remarkable explosion in our appreciation for with a set of learning outcomes. These outcomes help the roles of non-coding RNAs in many aspects of molecular students understand what they should be able to do once they biology. Note: Although two new chapters have been added have mastered the material in that section. to this edition, the overall page length of the sixth edition is ∙  Formative Assessment: When students are expected to learn not longer than the fifth edition. textbook material on their own, it is imperative that they are ∙  NEW! CRISPR-Cas systems: The role of the CRISPR-Cas regularly given formative assessment so they can gauge system in providing prokaryotes with a genome defense whether they are mastering the material. Formative mechanism is described in Chapter 17, and its use by assessment is a major feature of this textbook and is bolstered researchers to mutate genes is described in Chapter 21. by Connect—a state-of-the art digital assignment and assessment platform. In Genetics: Analysis & Principles, Sixth Examples of Specific Content Changes Edition, formative assessment is provided in multiple ways. to Individual Chapters 1. As mentioned, a new feature called Genetic TIPS is ∙  Chapter 2. Mendelian Inheritance: Several Genetic TIPS aimed at helping students refine their problem solving have been added to help students work through problem- skills. solving strategies involving Mendelian inheritance. 2. Each section of every chapter ends with multiple-choice ∙  Chapter 3. Chromosome Transmission During Cell Division questions. Also, compared with the previous edition, many and Sexual Reproduction: The discussion of the random chapters in the sixth edition are divided into more sections alignment of homologs during metaphase of meiosis I was that are shorter in length. Formative assessment at the end expanded. of each section allows students to evaluate their mastery of ∙  Chapter 4. Extensions of Mendelian Inheritance: The topic the material before moving on to the next section. of gene interaction was streamlined to focus primarily on 3. Most figures have Concept Check questions so students examples in which the underlying molecular mechanisms are can determine if they understand the key points in the known. figure. ∙  Chapter 5. Non-Mendelian Inheritance:A common 4. Extensive end-of chapter questions continue to provide misconception among students is that you can use a Punnett students with feedback regarding their mastery of the square to deduce nonMendelian inheritance patterns. material. Throughout the chapter, this misconception has been laid to 5. The textbook material is supported by digital learning rest, and students are given effective strategies to predict tools found in Connect. Questions and activities are offspring genotypes and phenotypes. assignable in Connect, and students also have access to ∙  Chapter 6. Genetic and Linkage Mapping in Eukaryotes: our valuable adaptive study tool, SmartBook. With this When looking at experiments involving linkage, student tool, students are repeatedly given questions regarding often find it very difficult to identify the recombinant the textbook material, and depending on their answers, offspring. In various parts of the chapter, a strong effort has they may advance ahead in their reading, or they are been made to make it clear that recombinant offspring have given specific advice on what textbook material to go inherited a chromosome that is the product of a crossover. back and review. Along these same lines, a new figure (see Figure 6.6) has Overall, the pedagogy of Genetics: Analysis & Principles, been added involving the experiments of Curt Stern showing sixth edition, has been designed to foster student learning. Instead of that recombinant offspring carry chromosomes that are the being a collection of facts and figures, Genetics: Analysis & Prin- product of a crossover. Also, Figure 6.8 has been revised to ciples, Sixth Edition, by Rob Brooker, is intended to be an engaging emphasis this point. and motivating textbook in which formative assessment allows stu- ∙  Chapter 7. Genetic Transfer and Mapping in Bacteria: dents to move ahead and learn the material in a productive way. We Figure 7.13 is a new figure showing the increase in methicillin welcome your feedback so we can make future editions even better! resistance in certain Staphylococcus aureus strains.  PREFACE xi ∙  Chapter 8. Variation in Chromosome Structure and Number: ∙  Chapter 21. DNA Technologies: A new subsection has Several Genetic TIPS have been added to help students solve been added on gene mutagenesis, which includes a problems that involve changes in chromosome structure and description of the Crispr-Cas system for inactivating chromosome number. and mutating genes. ∙  Chapter 9. Molecular Structure of DNA and RNA: The ∙  Chapter 22. Biotechnology: Several Genetic TIPS have been section on the discovery of the DNA double helix has been added to help students appreciate the uses of molecular streamlined to focus on the key experiments. techniques in biotechnology. ∙  Chapter 10. Chromosome Organization and Molecular ∙  Chapter 23. Genomics I: Analysis of DNA: The information Structure: The topic of bacterial chromosome structure has has been updated regarding completed genome sequences been updated, which includes a new figure (see Figure 10.3) and other aspects of genomics. and a discussion of microdomains. ∙  Chapter 24. Genomics II: Functional Genomics, Proteomics, ∙  Chapter 11. DNA Replication: A new figure has been added and Bioinformatics: A new subsection has been added on the initiation of DNA replication in eukaryotes (see on the method called RNA-Seq (see Figure 24.3). The Figure 11.20). Bioinformatics section has been reorganized with an emphasis ∙  Chapter 12. Gene Transcription and RNA Modification: The on gene prediction and homology. information on alternative splicing has been moved to this ∙  Chapter 25. Medical Genetics and Cancer: Several chapter. Genetic TIPS have been added to help students ∙  Chapter 13. Translation of mRNA: Several Genetic TIPS understand how mutations play a role in certain have been added to help students understand the relationship diseases, including cancer. between the genetic code and the synthesis of polypeptides. ∙  Chapter 26. Developmental Genetics: The information on ∙  Chapter 14. Gene Regulation in Bacteria: The information Hox genes in development, and the role of the SRY gene is on catabolite activator protein has been updated. human sex determination, have been updated. ∙  Chapter 15. Gene Regulation in Eukaryotes I: Transcriptional ∙  Chapter 27. Population Genetics: The topic of inbreeding and Translation Regulation: The material on eukaryotic gene has been expanded. regulation is now divided into two chapters. Chapter 15 ∙  Chapter 28. Complex and Quantitative Traits: The topic of focuses on transcriptional and translational regulation. the identification of QTLs is now found in its own ∙  Chapter 16. Gene Regulation in Eukaryotes II: Epigenetics: subsection. This topic has now been expanded to an entire chapter. A ∙  Chapter 29. Evolutionary Genetics: The cladistics method new subsection has been added on the role of epigenetics in for constructing a phylogenetic tree is compared with the vernalization, which is the process in which some plant UPGMA method. species require an exposure to cold in order to flower the following spring. Also, a new section has been added on the Suggestions Welcome! intriguing topic of paramutation. It seems very appropriate to use the word evolution to describe the ∙  Chapter 17. Non-coding RNA: This new chapter begins continued development of this textbook. I welcome any and all with an overview of the general functions of non-coding comments. The refinement of any science textbook requires input RNAs, and then the subsequent sections explore certain from instructors and their students. These include comments re- topics in greater detail, such as their role in chromatin garding writing, illustrations, supplements, factual content, and modification, transcription, translation, protein targeting, and topics that may need greater or less emphasis. You are invited to genome defense (e.g., the CRISPR-Cas system). contact me at: ∙  Chapter 18. Genetics of Viruses: The material on the integration of phage λ has been added to this chapter, along Dr. Rob Brooker with a brief discussion of Zika virus. Also, information on Dept. of Genetics, Cell Biology, and Development the origin of HIV and the occurrence of HIV infection University of Minnesota worldwide and in the US has been updated. 6-160 Jackson Hall ∙  Chapter 19. Gene Mutation and DNA Repair: The information 321 Church St. on the mismatch repair system has been updated. Minneapolis, MN 55455 ∙  Chapter 20. Recombination, Immunogenetics, and [email protected] Transposition: Section 20.2 has been revised to focus on 612-624-3053 immunogenetics.  ® Required=Results ©Getty Images/iStockphoto McGraw-Hill Connect® Learn Without Limits Connect is a teaching and learning platform that is proven to deliver better results for students and instructors. Connect empowers students by continually adapting to deliver precisely what they need, when they need it, and how they need it, so your class time is more engaging and effective. 73% of instructors who use Connect require it; instructor Using Connect improves retention rates by 19.8%, passing rates by satisfaction increases by 28% when 12.7%, and exam scores by 9.1%. Connect is required. Analytics Connect Insight® Connect Insight is Connect’s new one- of-a-kind visual analytics dashboard that provides at-a-glance information regarding student performance, which is immediately actionable. By presenting assignment, assessment, and topical performance results together with a time metric that is easily visible for aggregate or individual results, Connect Insight gives the user the ability to take a just-in-time approach to teaching and learning, which was never before available. Connect Insight presents data that helps instructors improve class performance in a way that is efficient and effective. Adaptive THE ADAPTIVE READING EXPERIENCE DESIGNED TO TRANSFORM THE WAY STUDENTS READ More students earn A’s and B’s when they use McGraw-Hill Education Adaptive products. SmartBook® Proven to help students improve grades and study more efficiently, SmartBook contains the same content within the print book, but actively tailors that content to the needs of the individual. SmartBook’s adaptive technology provides precise, personalized instruction on what the student should do next, guiding the student to master and remember key concepts, targeting gaps in knowledge and offering customized feedback, and driving the student toward comprehension and retention of the subject matter. Available on tablets, SmartBook puts learning at the student’s fingertips—anywhere, anytime. Over 8 billion questions have been answered, making McGraw-Hill Education products more intelligent, reliable, and precise. www.mheducation.com xiv PREFACE components that need to be assembled to produce a book. I would ACKNOWLEDGMENTS also like to thank Carrie Burger (Content Licensing Specialist), who acted as an interface between me and the photo company. In The production of a textbook is truly a collaborative effort, and I addition, my gratitude goes to David Hash (Designer), who pro- am deeply indebted to many people. All six editions of this text- vided much input into the internal design of the book as well as book went through multiple rounds of rigorous revision that in- created an awesome cover. Finally, I would like to thank Patrick volved the input of faculty, students, editors, and educational and Reidy (Executive Marketing Manager), whose major efforts begin media specialists. Their collective contributions are reflected in when the sixth edition comes out! the final outcome. I would also like to extend my thanks to everyone at Aptara Deborah Brooker (Freelance Developmental Editor) metic- who worked with great care in the paging of the book, making sure ulously read the new material, analyzed every figure, and offered that the figures and relevant text are as close to each other as pos- extensive feedback. Her attention to detail in this edition and pre- sible. Likewise, the people at Photo Affairs, Inc. have done a great vious editions has profoundly contributed to the accuracy and job of locating many of the photographs that have been used in the clarity of this textbook. I would also like to thank Jane Hoover sixth edition. (Freelance Copy Editor) for understanding the material and work- Finally, I want to thank the many scientists who reviewed ing extremely hard to improve the text’s clarity. Her efforts are the chapters of this textbook with special attention to the new truly appreciated. Chapter 17, Non-coding RNAs. Their broad insights and construc- I would particularly like to acknowledge the many people at tive suggestions were an overriding factor that shaped its final McGraw-Hill Education whose skills and insights are amazing. content and organization. I am truly grateful for their time and My highest praise goes to Elizabeth Sievers (Lead Product Devel- compassion. oper), who carefully checks all aspects of textbook development and makes sure that all of the pieces of the puzzle are in place. ∙  Susan Carpenter University of California, Santa Cruz I am also grateful to Justin Wyatt (Brand Manager) for overseeing ∙  Johnny El-Rady University of South Florida this project. I would like to thank other people at McGraw-Hill ∙  Terri McElhinny Michigan State University who have played key roles in producing an actual book and the ∙  Douglas Wendell Oakland University supplements that go along with it. 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Deborah Overath, Texas A&M Madhusudan Choudhary, Sam Houston University–Corpus Christi State University  PA RT I I N T RO D U C T I O N CHAPTER OUTLINE 1.1 The Molecular Expression of Genes 1.2 The Relationship Between Genes and Traits 1.3 Fields of Genetics 1.4 The Science of Genetics 1 CC (for “carbon copy” or “copy cat”), the first cloned pet. In 2002, the cat shown here was ­produced by cloning, a procedure described in Chapter 22. © Corbis OVERVIEW OF GENETICS Hardly a week goes by without a major news story involving a Studying the human genome allows us to explore fundamen- genetic breakthrough. The increasing pace of genetic discoveries tal details about ourselves at the molecular level. The results of the has become staggering. The Human Genome Project is a case in Human Genome Project and the 1000 Genomes Project have shed point. This project began in the United States in 1990, when the considerable light on basic questions, like how many genes we National Institutes of Health and the Department of Energy have, how genes direct the activities of living cells, how species joined forces with international partners to decipher the massive evolve, how single cells develop into complex tissues, and how amount of information contained in our genome—the DNA defective genes cause disease. Furthermore, such understanding found within all of our chromosomes (Figure 1.1). Remarkably, may lend itself to improvements in modern medicine by leading to in only a decade, they determined the DNA sequence (the order better diagnoses of diseases and the development of new treat- of the bases A, T, G, and C) of over 90% of the human genome. ments for them. The completed sequence, published in 2003, has an accuracy The journey to unravel the mysteries within our genes has greater than 99.99%; less than one mistake was made in every ­involved the invention of many new technologies. For example, re- 10,000 base pairs! searchers have developed genetic techniques to produce medicines, In 2008, a more massive undertaking, called the 1000 Ge- such as human insulin, that would otherwise be difficult or impos- nomes Project, was launched to establish a detailed understand- sible to make. Human insulin is synthesized in strains of Esche- ing of human genetic variation. In this international project, richia coli bacteria that have been genetically altered by the addition researchers set out to determine the DNA sequence of at least of genes that encode the polypeptides that form this hormone. The 1000 anonymous participants from around the globe. In 2015, bacteria are grown in a laboratory and make large amounts of hu- the sequencing of over 2500 genomes was described in the jour- man insulin. As discussed in Chapter 22, the insulin is purified and nal Nature. administered to many people with insulin-dependent diabetes. 1 2 C H A P T E R 1 :: OVERVIEW OF GENETICS Chromosomes DNA, the molecule of life Cell The adult human body is composed of trillions of cells. Most human cells contain the following: Gene 46 human chromosomes, found in 23 pairs C G T A T A 2 meters of DNA G C G T A T A Approximately 22,000 T A genes coding for A T C G proteins that perform A T most life functions DNA Approximately 3 billion DNA base pairs per set mRNA of chromosomes, containing the bases A, T, G, and C Amino acid Protein (composed of amino acids) FI G U RE 1.1 The human genome. The human genome is a complete set of human chromosomes. People have two sets of chromosomes—one set from each parent—which are found in the cell nucleus. The Human Genome Project revealed that each set of chromosomes is composed of a DNA sequence that is approximately 3 billion nucleotide base pairs long. Estimates suggest that each set contains about 22,000 different genes that encode ­proteins. As discussed later, most genes are first transcribed into mRNA and then the mRNA is used to make proteins. This figure emphasizes the DNA found in the cell nucleus. Humans also have a small amount of DNA in their mitochondria, which has also been sequenced. CONCEPT CHECK: How might a better understanding of our genes be used in the field of medicine? New genetic technologies are often met with skepticism and sometimes even with disdain. An example is mammalian cloning. In 1997, Ian Wilmut and his colleagues created clones of sheep, using mammary cells from an adult animal (Figure 1.2). More recently, such cloning has been achieved in several mammalian species, including cows, mice, goats, pigs, and cats. In 2002, the first pet was cloned, a cat named CC (for “carbon copy” or “copy cat”; see photo at the beginning of the chapter). The cloning of mammals provides the potential for many practical applications. With regard to livestock, cloning would enable farmers to use cells from their best individuals to create genetically homoge- neous herds. This could be advantageous in terms of agricultural yield, although such a genetically homogeneous herd may be more susceptible to certain diseases. However, people have be- come greatly concerned with the possibility of human cloning. This prospect has raised serious ethical questions. Within the past F I G URE 1. 2 The cloning of a mammal. The lamb in the front few years, legislation has been introduced that involves bans on is Dolly, the first mammal to be cloned. She was cloned from the cells human cloning. of a Finn Dorset (a white-faced sheep). The sheep in the back is Dolly’s Finally, genetic technologies provide the means to modify surrogate mother, a Blackface ewe. A description of how Dolly was the traits of animals and plants in ways that would have been ­produced is presented in Chapter 22. ­unimaginable just a few decades ago. Figure 1.3a illustrates © Roslin Institute/Phototake a striking example in which scientists introduced a gene from CONCEPT CHECK: What ethical issues may be associated with human cloning?  1.1 THE MOLECULAR EXPRESSION OF GENES 3 For example, Andrea Crisanti and colleagues have altered mosqui- toes to express GFP only in the gonads of males (Figure 1.3b). This enables the researchers to identify and sort males from fe- males. Why is this useful? Researchers can produce a population of mosquitoes and then sterilize the males. The ability to rapidly sort males and females makes it possible to release the sterile males without the risk of releasing additional females. The release of sterile males may be an effective means of controlling mosquito populations because females mate only once before they die. ­Mating with a sterile male prevents a female from producing off- spring. In 2008, Osamu Shimomura, Martin Chalfie, and Roger Tsien received the Nobel Prize in chemistry for the discovery and the development of GFP, which has become a widely used tool in biology. Overall, as we move forward in the twenty-first century, the excitement level in the field of genetics is high, perhaps higher than it has ever been. Nevertheless, new genetic knowledge and (a) GFP expressed in mice technologies will also create many ethical and societal challenges. In this chapter, we begin with an overview of genetics and then explore the various fields of genetics and their experimental GFP ­approaches. 1.1 THE MOLECULAR EXPRESSION OF GENES Learning Outcomes: (b) GFP expressed in the gonads of a male mosquito 1. Describe the biochemical composition of cells. 2. Explain how proteins are largely responsible for cell struc- FI GURE 1.3 The introduction of a jellyfish gene into ture and function. ­laboratory mice and mosquitoes. (a) A gene that naturally occurs 3. Outline how DNA stores the information to make proteins. in jellyfish encodes a protein called green fluorescent protein (GFP). The GFP gene was cloned and introduced into mice. When these mice Genetics is the branch of biology that deals with heredity and are exposed to UV light, GFP emits a bright green color. These mice variation. It stands as the unifying discipline in biology by glow green, just like the jellyfish! (b) The GFP gene was introduced next to a gene sequence that causes the expression of GFP only in the ­allowing us to understand how life can exist at all levels of gonads of male mosquitoes. This allows researchers to identify and ­complexity, ranging from the molecular to the population level. sort males from females. Genetic variation is the root of the natural diversity that we (a): © Advanced Cell Technology, Inc., Worcester, Massachusetts; (b): Photo taken by Flaminia ­observe among members of the same species and among differ- Catteruccia, Jason Benton and Andrea Crisanti, and assembled by www.luciariccidesign.com ent species. CONCEPT CHECK: Why is it useful to sort male mosquitoes from females? Genetics is centered on the study of genes. A gene is classi- cally defined as a unit of heredity. At the molecular level, a gene is a segment of DNA that produces a functional product. The func- jellyfish into mice. Certain species of jellyfish emit a “green tional product of most genes is a polypeptide, which is a linear glow” produced by a gene that encodes a bioluminescent protein sequence of amino acids that folds into units that constitute pro- called green fluorescent protein (GFP). When exposed to blue or teins. In addition, genes are commonly described according to the ultraviolet (UV) light, the protein emits a striking green-colored way they affect traits, which are the characteristics of an organ- light. Scientists were able to clone the GFP gene from a sample ism. In humans, for example, we speak of traits such as eye color, of jellyfish cells and then introduce this gene into laboratory hair texture, and height. The ongoing theme of this textbook is the mice. The green fluorescent protein is made throughout the cells relationship between genes and traits. As an organism grows and of their bodies. As a result, their skin, eyes, and organs give off develops, its collection of genes provides a blueprint that deter- an eerie green glow when exposed to UV light. Only their fur mines its traits. does not glow. In this section, we examine the general features of life, The expression of green fluorescent protein allows research- beginning with the molecular level and ending with popula- ers to identify particular proteins in cells or specific body parts. tions of organisms. As will become apparent, genetics is the 4 C H A P T E R 1 :: OVERVIEW OF GENETICS Plant cell common thread that explains the existence of life and its conti- nuity from generation to generation. For most students, this chapter should serve as an overview of topics they have learned in other introductory courses such as General Biology. Even so, it is usually helpful to see the “big picture” of genetics before delving into the finer details that are covered in Chapters 2 through 29. Nucleus Living Cells Are Composed of Biochemicals To fully understand the relationship between genes and traits, we need to begin with an examination of the composition of living organisms. Every cell is constructed from intricately organized chemical substances. Small organic molecules such as glucose and amino acids are produced from the linkage of atoms via chemical bonds. The chemical properties of organic molecules are essential for cell vitality in two key ways. First, the breaking of chemical bonds during the degradation of small molecules pro- Chromosome vides energy to drive cellular processes. A second important function of these small organic molecules is their role as the Proteins building blocks for the synthesis of larger molecules. Four impor- tant categories of larger molecules are nucleic acids (i.e., DNA and RNA), proteins, carbohydrates, and lipids. Three of these— nucleic acids, proteins, and carbohydrates—form macromolecules that are composed of many repeating units of smaller building blocks. RNA, proteins, and some carbohydrates are made from DNA hundreds or even thousands of repeating building blocks. DNA is the largest macromolecule found in living cells. A single DNA molecule can be composed of a linear sequence of hundreds of millions of building blocks called nucleotides! The formation of cellular structures relies on the interac- tions of molecules and macromolecules. For example, nucleo- tides are connected together to make DNA, which is a constituent of chromosomes (Figure 1.4). In addition, DNA is associated with many proteins that provide organization to the structure of chromosomes. Within a eukaryotic cell, the chromosomes are Nucleotides contained in a compartment called the cell nucleus. The nucleus is bounded by a double membrane composed of lipids and pro- teins that shields the chromosomes from the rest of the cell. The NH2 organization of chromosomes within a cell nucleus protects the Cytosine N H Guanine chromosomes from mechanical damage and provides a single O O– H compartment for genetic activities such as gene transcription. As O N H N N O P O CH2 H a general theme, the formation of large cellular structures arises O– O O– H2 N N N from interactions among different molecules and macromole- H H H H O P O CH2 O cules. These cellular structures, in turn, are organized to make a OH H O– H H H H complete living cell. OH H Each Cell Contains Many Different F I G URE 1. 4 Molecular organization of a living cell. Cellular Proteins That Determine Cell Structure structures are constructed from smaller building blocks. In this example, DNA is formed from the linkage of nucleotides to produce a very long and Function macromolecule. The DNA associates with proteins to form a chromosome. To a great extent, the characteristics of a cell depend on the types The chromosomes are located within a membrane-bound organelle called of proteins that it makes. The entire collection of proteins that a the nucleus, which, along with many different types of organelles, is cell makes at a given time is called its proteome. The range of found within a complete cell. functions among different types of proteins is truly remarkable. photo: © Biophoto Associates/Science Source Some proteins help determine the shape and structure of a given CONCEPT CHECK: Is DNA a small molecule, a macromolecule, or an organelle?  1.1 THE MOLECULAR EXPRESSION OF GENES 5 cell. For example, the protein known as tubulin assembles into large structures known as microtubules, which provide the cell with internal structure and organization. Other proteins are in- serted into cell membranes and aid in the transport of ions and small molecules across the membrane. Enzymes, which acceler- ate chemical reactions, are a particularly important category of proteins. Some enzymes play a role in the breakdown of molecules or macromolecules into smaller units. These are known as cata- bolic enzymes and are important in the utilization of energy. ­Alternatively, anabolic enzymes and accessory proteins function in the synthesis of molecules and macromolecules throughout the cell. The construction of a cell greatly depends on its proteins that are involved in anabolism because these are required to synthesize all cellular macromolecules. Molecular biologists have come to realize that the functions of proteins underlie the cellular characteristics of every organism. At the molecular level, proteins can be viewed as the active par- ticipants in the enterprise of life. DNA Stores the Information for Protein Synthesis The genetic material of living organisms is composed of a sub- stance called deoxyribonucleic acid, abbreviated DNA. The DNA stores the information needed for the synthesis of all cellular proteins. In other words, the main function of the genetic blueprint is to code for the production of proteins in the correct cell, at the proper time, and in suitable amounts. This is an extremely compli- cated task because living cells make thousands of different pro- teins. Genetic analyses have shown that a typical bacterium can make a few thousand different proteins, and estimates for the ­numbers produced by complex eukaryotic species range in the tens of thousands. DNA’s ability to store information is based on its structure. DNA is composed of a linear sequence of nucleotides. Each nucleotide contains one of four nitrogen-containing bases: ade- F I G URE 1. 5 A micrograph of the 46 chromosomes found in a nine (A), thymine (T), guanine (G), or cytosine (C). The linear cell from a ­human male. order of these bases along a DNA molecule contains information © CNRI/Science Source similar to the way that groups of letters of the alphabet represent CONCEPT CHECK: Which types of macromolecules are found in chromosomes? words. For example, the “meaning” of the sequence of bases ATGGGCCTTAGC differs from that of TTTAAGCTTGCC. DNA sequences within most genes contain the information to as a karyotype. The DNA of an average human chromosome is an direct the order of amino acids within polypeptides according to extraordinarily long, linear, double-stranded structure that con- the genetic code. In the code, a three-base sequence specifies tains well over a hundred million nucleotides. Along the immense one particular amino acid among the 20 possible choices. One length of a chromosome, the genetic information is parceled into or more polypeptides form a functional protein. In this way, the functional units known as genes. An average-sized human chro- DNA can store the information to specify the proteins made by mosome is expected to contain about 1000 different protein-­ an organism. encoding genes. DNA Sequence Amino Acid Sequence ATG GGC CTT AGC Methionine Glycine Leucine Serine The Information in DNA Is Accessed During TTT AAG CTT GCC Phenylalanine Lysine Leucine Alanine the Process of Gene Expression To synthesize its proteins, a cell must be able to access the informa- In living cells, the DNA is found within large structures known as tion that is stored within its DNA. The process of using a gene se- chromosomes. Figure 1.5 is a micrograph of the 46 chromosomes quence to affect the characteristics of cells and organisms is referred contained in a cell from a human male; this type of image is known to as gene expression. At the molecular level, the information 6 C H A P T E R 1 :: OVERVIEW OF GENETICS DNA 2. A gene is a segment of DNA that has the information to produce a functional product. The functional product of most genes is Gene a. DNA. b. mRNA. Transcription c. a polypeptide. d. all of the above. RNA (messenger RNA) 3. The function of the genetic code is to a. promote transcription. b. specify the amino acids within a polypeptide. Translation c. alter the sequence of DNA. d. none of the above. 4. The process of transcription directly results in the synthesis of Protein a. DNA. (sequence of amino acids) b. RNA. c. a polypeptide. d. all of the above. Functioning of proteins within living cells influences an organism’s traits. 1.2 THE RELATIONSHIP BETWEEN GENES AND TRAITS FI GURE 1.6 Gene expression at the molecular level. The ­expression of a gene is a multistep process. Learning Outcomes: During transcription, one of the DNA strands is used as a 1. Outline how the expression of genes leads to an o