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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.
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
All credits appearing on page are considered to be an extension of the copyright page.
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 PA R T I V M
OLECULAR 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
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
PA R T V I G
ENETIC ANALYSIS
OF INDIVIDUALS AND
POPULATIONS
26 Developmental Genetics 643
27 Population Genetics 675
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
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
12.1
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
BACTERIA 336
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
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
DEDICATION
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 brook005@umn.edu
Transposition: Section 20.2 has been revised to focus on 612-624-3053
immunogenetics.
®
Required=Results
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Adaptive
THE ADAPTIVE
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SmartBook’s adaptive technology provides precise,
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should do next, guiding the student to master
and remember key concepts, targeting gaps in
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xiv PREFACE
REVIEWERS Reggie Cobb, Nash Community College Thomas Peavy, California State University–
Dan Choffnes, Carthage College Sacramento
Previous editions Laurie Cotroneo, Southern Utah University Rongsun Pu, Kean University
Robert S. Dotson, Tulane University Robert Rutledge, DeSales University
Amy Abdulovic-Cui, Augusta State
Robert Hinrichsen, Indiana University of Julian Shull, Appalachian State University
University
Pennsylvania Jeffry Shultz, Louisiana Tech University
Steve Alas, California State Polytechnic
Margaret Hollingsworth, University at Ronald Wagner, Central Washington
University, Pomona
Buffalo University
Harvey Babich, Stern College for Women
Mitrick Johns, Illinois University Carey Waldburger, William Paterson
Laura Hill Bermingham, University of
Ekaterina Kaverina, East Tennessee State University
Vermont
University Gary L. Walker, Appalachian State
Hector Biliran Jr., Xavier University of
Jesse Mager, University of Massachusetts University
Louisiana
Norah R. McCabe, Washington State Jessica Wooten, The University of Findlay
Mirjana Milosevic Brockett, Georgia
University
Institute of Technology
R. 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.
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
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?
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
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
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
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
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pieces far more evident than it is in the ‘Well-Tempered Clavichord’
or even the ‘Inventions’ of Bach. He undoubtedly offers the player
enormous opportunity to exercise his arms and his fingers in the
production of brilliant, astonishing effects.
Of these effects two will always be associated with his name: the
one obtained by the crossing of the hands, the other by the rapid
repetition of one note. Both devices will be found freely used in the
works of his father, and it is absurd to suppose that the son invented
them. Yet it is hardly an exaggeration to say that he made more use
of them than any man down to the time of Liszt. The crossing of the
hands is not employed to interweave two qualities of sound, as it
oftenest is in music for the organ or for the German and French
harpsichords which have two or more manuals that work
independently of each other. The Italian harpsichords had but one
bank of keys, and Scarlatti’s crossing of the hands, if it be not
intended merely for display, succeeds in making notes wide apart
sound relatively simultaneous, and thus produces qualities of
resonance which hitherto had rested silent in the instrument.
Of his life little need be said. He was born in Paris on November 10,
1668, the son of Charles Couperin, himself a musician and brother to
Louis and François Couperin, disciples of the great Chambonnières.
The father died about a year after his son was born, and the musical
education of the young François seems to have been undertaken by
his uncle, François, and later by Jacques Thomelin, organist in the
king’s private chapel in Versailles. Practically nothing is known of his
youth, and, though it is certain that he was for many years organist
at the church of St. Gervais in Paris, as his uncle and even his
grandfather had been before him, the time at which he took up his
duties there has not been exactly determined. There is on record,
however, the account of a meeting held on the twenty-sixth of
December, 1693, at Versailles, at which Louis XIV heard Couperin
play and chose him from other competitors to succeed Thomelin as
his private organist. Thenceforth he passed his life in service of the
king and later of the regent. He died in Paris in 1733, after several
years of ill health.
The great François was, no doubt, an unusually skillful organist, but
his fame rests upon his work for the clavecin, the French
harpsichord, and his book of instruction for that instrument. His
duties at court were various. He says himself that for twenty years he
had the honor to be with the king, and to teach, almost at the same
time, Monseigneur le Dauphin, the Duke of Burgundy, and six
princes or princesses of the royal house.
The original editions being now rare and priceless, and hardly
serviceable to the average student on account of the confusing
obsolete clef signs, it is to be hoped that before long Chrysander’s
plan will be carried out and the almost forgotten treasures of
Couperin’s clavecin music be revealed in their great beauty to the
lover of music.
Another type of portrait fits its title a little more tangibly. There is La
Mylordine, in the style of an English jig; La Diane, which is built up
on the fanfare figure always associated with the hunt; La Diligente,
full of bustling finger work. Les Nonnettes are blonde and dark, the
blondes, oddly enough, in minor, the dark in major.
Many others are so purely music, delicate and tender, that the titles
seem more to be a gallant tribute to so and so, rather than the
names of prototypes in the flesh. La Manon, La Babet, La fleurie, ou
la tendre Nanette, L’Enchanteresse, La tendre Fanchon, and many
others are in no way program music; nor can they ever be
interpreted as such, since no man can say what charming girl, two
centuries dead, may have suggested their illusive features.
Between these and the few pieces which are frankly almost wholly
dependent upon a program are a great number of others lightly
suggestive of their titles. Sometimes it is only in general character.
Les vendangeuses and Les moissoneurs do not seem so particularly
related to wine-gathering or harvesting that the titles might not be
interchanged; but both have something of a peasant character. In
Les abeilles and in Le moucheron the characterization is finer. The
pleasant humming of the bees is reproduced in one, the monotonous
whirring of the gnat in the other. Les bergeries is simply pastoral, Les
matelots Provençales is a lively march, followed by a horn-pipe. Les
papillons is not unlike the little piece so named in the Schumann
Carnaval, though here it means but butterflies. There are some
imitative pieces which are in themselves charming music, such as
Les petits moulins à vent, Le réveille-matin, Le carillon de Cythère,
and Les ondes, with its undulating figures and fluid ornamentation.
III
The last of these compositions are in no way representative of
Couperin the artist. They might have been written by any one who
had a love for nonsense, and they are not meant to be taken
seriously. The quality of Couperin’s contribution to music must be
tested in such pieces as Le bavolet-flottant, La fleurie, Les
moissoneurs, Le carillon de Cythère, and La lugubre. His harmony is
delicate, suggesting that of Mozart and even Chopin, to whom he is
in many ways akin. He does not, like Scarlatti, wander far in the
harmonic field; but in a relatively small compass glides about by
semi-tones. There is, of course, a great deal of tonic and dominant,
such as will always be associated with a certain clear-cut style of
French dance music; but the grace of his melody and his style is too
subtle to permit monotony. The harmonies of the sarabande La
lugubre are profound.
This is not only because the peculiarities of the pianoforte call for a
different kind of ornamentation, but also because the playing of
harpsichord flourishes is practically a lost art. Couperin and Emanuel
Bach left minute directions and explanations in regard to them; but in
their treatises we have only the letter of the law, not the spirit which
inspired it. Even in their day, in spite of all laws, the agrémens were
subject to the caprice of the player; and they remained so down to
the time of Chopin.
IV
A glance over the many pieces of Scarlatti and Couperin discovers a
vast field of unfamiliar music. If one looks deep enough to perceive
the charm, the beauty, the perfection of these forgotten
masterpieces, one cannot but wonder what more than a trick of time
has condemned them to oblivion. For no astonished enthusiasm of
student or amateur whose eye can hear, renders back glory to music
that lies year after year silent on dusty shelves. The general ear has
not heard it. The general eye cannot hear it as it can scan the
ancient picture, the drama, the poetry of a time a thousand or two
thousand years ago. Music that is silent is music quite forgotten if not
dead.
And, what is more, the few pieces of Couperin which are still heard
seem almost to live on sufferance, as if the life they have were not of
their own, but lent them by the listener disposed to imagine a
courtier’s life long ago washed out in blood. ‘Sweet and delicate,’
one hears of the music of Couperin, as one hears of some bit of old
lace or old brocade, that has lain long in a chest of lavender. Yet the
music of Couperin is far more than a matter of fashion. It is by all
tokens great art. The lack is in the race of musicians and of men who
have lost the art of playing it and the simplicity of attentive listening.
In the first place, the style of its texture is solid. Instead of being
crushed, as Couperin’s music is, by the heavy, rich tone of the
modern pianoforte, it seems to grow stronger by speaking through
the stronger instrument. Bach’s style is nearly always an organ style,
whether he is writing for clavichord, for chorus, for bands or strings.
It is very possible that a certain mystical, intimate sentiment which is
innate in most of his clavichord music cannot find expression through
the heavy strings of the pianoforte. This may be far dearer than the
added depth and richness which the pianoforte has, as it were,
hauled up from the great reservoirs of music he has left us. But it is
none the less true that the high-tensioned heavy strings on their
gaunt frame of cast iron need not call in vain on the music of Bach to
set the heart of them vibrating.
Bach was a lovable man, but a stern and somewhat bellicose one as
well. He was shrewd enough to respect social rank quite in the
manner of his day, as the dedication of the Brandenburg concertos
plainly shows; but the records of his various quarrels with the
municipal authorities of Leipzig prove how quick he was to
unrestrained wrath whenever his rights either as man or artist were
infringed upon. A great deal of independence marked him. The same
can hardly be said either of Scarlatti or of Couperin, the one of whom
was lazy and good-natured, the other gently romantic and extremely
polite. Scarlatti rather enjoyed his indifference to accepted rules of
composition; and there was nothing either of self-abasement or of
self-depreciation in Couperin; but both lacked the stalwart vigor of
Bach. Scarlatti aimed, confessedly, to startle and to amuse by his
harpsichord pieces. He cautioned his friends not to look for anything
particularly serious in them. It is hard to dissociate an ideal of pure
and only faintly colored beauty from Couperin. But in the music of
Bach one seldom misses the ring of a strong and even an impetuous
need of self-expression. In the mighty organ works, and in the vocal
works, one may believe with him that he sang his soul out to the
glory of his Maker; but in the smaller keyboard pieces sheer delight
in expressing himself is unmistakable.
It is this that makes Bach a romanticist, while Couperin, with all his
fanciful titles, is classic. It is this that made Bach write in nearly the
same style for all instruments, drawing upon his personal inspiration
without consideration of the instrument for which he wrote; while
Couperin, exquisitely sensitive to all external impressions, forced his
fine art to conformity with the special and limited qualities of the
instrument for which he wrote the great part of his music. And, finally,
it is this which produced utterance of so many varied moods and
emotions in the music of Bach; while in the music of Couperin we
find all moods and emotions tempered to one distinctly normal cast
of thought.
Bach has been the subject of so much profound and special study
that there is little to be added to the explanation of his character or of
his works. In considering him as a composer for the harpsichord or
clavichord, one has to bear two facts in mind: that he was a great
player and a great teacher.
There is much evidence from his son and from prominent musicians
who knew him, that the technical dexterity of his fingers was
amazing. He played with great spirit and, when the music called for
it, at a great speed. Perhaps the oft-repeated story of his triumph
over the famous French player, Marchand, who, it will be
remembered, defaulted at the appointed hour of contest, has been
given undue significance. As we have had occasion to remark, in
speaking of the contest between Handel and D. Scarlatti, such
tourneys at the harpsichord were tests of wits, not of fingers. Bach
was first of all an organist and it may be suggested, with no
disloyalty to the great man among musicians, that he played the
harpsichord with more warmth than glitter. We find little evidence in
his harpsichord music of the sort of virtuosity which makes D.
Scarlatti’s music astonish even today; or, it may be added, of the
special flexible charm which gives Couperin’s its inimitable grace.
His system passed on through the facile hands of his son Emanuel,
the greatest teacher of the next generation; and if it is not the crest of
the wave of new styles of playing which was to break over Europe
and flood a new and special pianoforte literature, is at any rate a
considerable part of its force. Yet it must be borne in mind that
Scarlatti founded by his own peculiar gifts a tradition of playing the
piano and composing for it, in which Clementi was to grow up; and
that, influential as Emanuel Bach was, Clementi was the teacher of
the great virtuosi who paved the way to Chopin, the composer for the
piano par excellence.
The foundation of all Bach’s music is the organ. Even in his works for
violin alone, or in those for double chorus and instruments, the
conjunct, contrapuntal style of organ music is unmistakable. His
general technique was acquired by study of the organ works of his
great predecessors, Frescobaldi, Sweelinck, Pachelbel, Buxtehude,
Bohm, and others. He was first and always an organist. So it is not
surprising to find by far the greater part of his harpsichord and
clavichord music shaped to a polyphonic ideal; and, what is more,
written in the close, smooth style which is primarily fitting to the
organ.
His intelligence, however, was no less alert than it was acute. There
is evidence in abundance that he not only knew well the work of
most of his contemporaries, but that he appropriated what he found
best in their style. He seems to have found the violin concertos of
Vivaldi particularly worthy of study. He was indebted to him for the
form of his own concertos; and, furthermore, he adapted certain
features of Vivaldi’s technique of writing for the violin to the
harpsichord. Of the influence of Couperin there is far less than was
once supposed. The ‘French Suites’ were not so named by Bach
and are, moreover, far more in his own contrapuntal style than in the
tender style of Couperin. Kuhnau’s Bible sonatas are always cited as
the model for Bach’s little Capriccio on the departure of his brother;
but elsewhere it is hard to find evidence of indebtedness to Kuhnau.
So, for the most part, the forms which had evolved during the
seventeenth century were the forms in which he chose to express
himself. Of these, two will be for ever associated with him, because