Contents

Letter from the Author

Preface

1. Introduction to Genetics

Albinism among the Hopis

1.1 Genetics Is Important to Us Individually, to Society, and to the Study of Biology

The Role of Genetics in Biology

Genetic Diversity and Evolution

Divisions of Genetics

Model Genetic Organisms

1.2 Humans Have Been Using Genetics for Thousands of Years

The Early Use and Understanding of Heredity

The Rise of the Science of Genetics

The Future of Genetics

1.3 A Few Fundamental Concepts Are Important for the Start of Our Journey into Genetics

2. Chromosomes and Cellular Reproduction

The Blind Men’s Riddle

2.1 Prokaryotic and Eukaryotic Cells Differ in a Number of Genetic Characteristics

2.2 Cell Reproduction Requires the Copying of the Genetic Material, Separation of the Copies, and Cell Division

Prokaryotic Cell Reproduction

Eukaryotic Cell Reproduction

The Cell Cycle and Mitosis

Genetic Consequences of the Cell Cycle

CONNECTING CONCEPTS Counting Chromosomes and DNA Molecules

2.3 Sexual Reproduction Produces Genetic Variation Through the Process of Meiosis

Meiosis

Sources of Genetic Variation in Meiosis

CONNECTING CONCEPTS Mitosis and Meiosis Compared

The Separation of Sister Chromatids and Homologous Chromosomes

Meiosis in the Life Cycles of Animals and Plants

3. Basic Principles of Heredity

The Genetics of Red Hair

3.1 Gregor Mendel Discovered the Basic Principles of Heredity

Mendel’s Success

Genetic Terminology

3.2 Monohybrid Crosses Reveal the Principle of Segregation and the Concept of Dominance

What Monohybrid Crosses Reveal

CONNECTING CONCEPTS Relating Genetic Crosses to Meiosis

The Molecular Nature of Alleles

Predicting the Outcomes of Genetic Crosses

The Testcross

Genetic Symbols

CONNECTING CONCEPTS Ratios in Simple Crosses

3.3 Dihybrid Crosses Reveal the Principle of Independent Assortment

Dihybrid Crosses

The Principle of Independent Assortment

Relating the Principle of Independent Assortment to Meiosis

Applying Probability and the Branch Diagram to Dihybrid Crosses

The Dihybrid Testcross

3.4 Observed Ratios of Progeny May Deviate from Expected Ratios by Chance

The Chi-Square Goodness-of-Fit Test

3.5 Geneticists Often Use Pedigrees to Study the Inheritance of Human Characteristics

Symbols Used in Pedigrees

Analysis of Pedigrees

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4. Extensions and Modifications of Basic Principles

The Odd Genetics of Left-Handed Snails

4.1 Sex Is Determined by a Number of Different Mechanisms

Chromosomal Sex-Determining Systems

Genic Sex Determination

Environmental Sex Determination

Sex Determination in Drosophila melanogaster

Sex Determination in Humans

4.2 Sex-Linked Characteristics Are Determined by Genes on the Sex Chromosomes

X-Linked White Eyes in Drosophila

MODEL GENETIC ORGANISM? The Fruit Fly Drosophila melanogaster

X-Linked Color Blindness in Humans

Symbols for X-Linked Genes

Dosage Compensation

Y-Linked Characteristics

CONNECTING CONCEPTS Recognizing Sex-Linked Inheritance

4.3 Additional Factors at a Single Locus Can Affect the Results of Genetic Crosses

Types of Dominance

Penetrance and Expressivity

Lethal Alleles

Multiple Alleles

4.4 Gene Interaction Takes Place When Genes at Multiple Loci Determine a Single Phenotype

Gene Interaction That Produces Novel Phenotypes

Gene Interaction with Epistasis

CONNECTING CONCEPTS Interpreting Phenotypic Ratios Produced by Gene Interaction

Complementation: Determining Whether Mutations Are at the Same Locus or at Different Loci

4.5 Sex Influences the Inheritance and Expression of Genes in a Variety of Ways

Sex-Influenced and Sex-Limited Characteristics

Cytoplasmic Inheritance

Genetic Maternal Effects

Genomic Imprinting

4.6 The Expression of a Genotype May Be Influenced by Environmental Effects

Environmental Effects on the Phenotype

The Inheritance of Continuous Characteristics

5. Linkage, Recombination, and Eukaryotic Gene Mapping

Linked Genes and Bald Heads

5.1 Linked Genes Do Not Assort Independently

5.2 Linked Genes Segregate Together, While Crossing Over Produces Recombination Between Them

Notation for Crosses with Linkage

Complete Linkage Compared with Independent Assortment

Crossing Over Between Linked Genes

Calculating Recombination Frequency

Coupling and Repulsion

CONNECTING CONCEPTS Relating Independent Assortment, Linkage, and Crossing Over

Predicting the Outcomes of Crosses with Linked Genes

Testing for Independent Assortment

Gene Mapping with Recombination Frequencies

Constructing a Genetic Map with Two-Point Testcrosses

5.3 A Three-Point Testcross Can Be Used to Map Three Linked Genes

Constructing a Genetic Map with a Three-Point Testcross

CONNECTING CONCEPTS Stepping Through the Three-Point Cross

Effects of Multiple Crossovers

Mapping with Molecular Markers

5.4 Genes Can Be Located with Genome-Wide Association Studies

6. Chromosome Variation

Building a Better Banana

6.1 Chromosome Mutations Include Rearrangements, Aneuploidy, and Polyploidy

Chromosome Morphology

Types of Chromosome Mutations

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6.2 Chromosome Rearrangements Alter Chromosome Structure

Duplications

Deletions

Inversions

Translocations

Fragile Sites

Copy-Number Variations

6.3 Aneuploidy Is an Increase or Decrease in the Number of Individual Chromosomes

Types of Aneuploidy

Effects of Aneuploidy

Aneuploidy in Humans

6.4 Polyploidy Is the Presence of More Than Two Sets of Chromosomes

Autopolyploidy

Allopolyploidy

The Significance of Polyploidy

The Importance of Polyploidy in Evolution

7. Bacterial and Viral Genetic Systems

Life in a Bacterial World

7.1 The Genetic Analysis of Bacteria Requires Special Methods

Bacterial Diversity

Techniques for Studying Bacteria

The Bacterial Genome

Plasmids

7.2 Bacteria Exchange Genes through Conjugation, Transformation, and Transduction

Conjugation

Natural Gene Transfer and Antibiotic Resistance

Transformation

Bacterial Genome Sequences

MODEL GENETIC ORGANISM? The Bacterium Escherichia coli

7.3 Viruses Are Simple Replicating Systems Amenable to Genetic Analysis

Techniques for the Study of Bacteriophages

Transduction: Using Phages to Map Bacterial Genes

CONNECTING CONCEPTS Three Methods for Mapping Bacterial Genes

Gene Mapping in Phages

RNA Viruses

Human Immunodeficiency Virus and AIDS

Influenza

8. DNA: The Chemical Nature of the Gene

Arctic Treks and Ancient DNA

8.1 Genetic Material Possesses Several Key Characteristics

8.2 All Genetic Information Is Encoded in the Structure of DNA

Early Studies of DNA

DNA as the Source of Genetic Information

Watson and Crick’s Discovery of the Three-Dimensional Structure of DNA

8.3 DNA Consists of Two Complementary and Antiparallel Nucleotide Strands That Form a Double Helix

The Primary Structure of DNA

Secondary Structures of DNA

Genetic Implications of DNA Structure

8.4 Large Amounts of DNA Are Packed into a Cell

Supercoiling

The Bacterial Chromosome

Eukaryotic Chromosomes

8.5 Eukaryotic Chromosomes Possess Centromeres and Telomeres

Centromere Structure

Telomere Structure

8.6 Eukaryotic DNA Contains Several Classes of Sequence Variation

Types of DNA Sequences in Eukaryotes

Organization of Genetic Information in Eukaryotes

9. DNA Replication and Recombination

Topoisomerase, Replication, and Cancer

9.1 Genetic Information Must Be Accurately Copied Every Time a Cell Divides

9.2 All DNA Replication Takes Place in a Semiconservative Manner

Meselson and Stahl’s Experiment

Modes of Replication

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Requirements of Replication

Direction of Replication

9.3 Bacterial Replication Requires a Large Number of Enzymes and Proteins

Initiation

Unwinding

Elongation

Termination

The Fidelity of DNA Replication

CONNECTING CONCEPTS The Basic Rules of Replication

9.4 Eukaryotic DNA Replication Is Similar to Bacterial Replication but Differs in Several Aspects

Eukaryotic Origins of Replication

The Licensing of DNA Replication

Unwinding

Eukaryotic DNA Polymerases

Replication at the Ends of Chromosomes

Replication in Archaea

9.5 Recombination Takes Place Through the Alignment, Breakage, and Repair of DNA Strands

10. From DNA to Proteins: Transcription and RNA Processing

Death Cap Poisoning

10.1 RNA, a Single Strand of Ribonucleotides, Participates in a Variety of Cellular Functions

An Early RNA World

The Structure of RNA

Classes of RNA

10.2 Transcription Is the Synthesis of an RNA Molecule from a DNA Template

The Template

The Substrate for Transcription

The Transcription Apparatus

10.3 Bacterial Transcription Consists of Initiation, Elongation, and Termination

Initiation

Elongation

Termination

CONNECTING CONCEPTS The Basic Rules of Transcription

10.4 Many Genes Have Complex Structures

Gene Organization

Introns

The Concept of the Gene Revisited

10.5 Many RNA Molecules Are Modified after Transcription in Eukaryotes

Messenger RNA Processing

CONNECTING CONCEPTS Eukaryotic Gene Structure and Pre-mRNA Processing

The Structure and Processing of Transfer RNA

The Structure and Processing of Ribosomal RNA

Small RNA Molecules and RNA Interference

Long Noncoding RNAs Regulate Gene Expression

MODEL GENETIC ORGANISM? The Nematode Worm Caenorhabditis elegans

11. From DNA to Proteins: Translation

Hutterites, Ribosomes, and Bowen–Conradi Syndrome

11.1 The Genetic Code Determines How the Nucleotide Sequence Specifies the Amino Acid Sequence of a Protein

The Structure and Function of Proteins

Breaking the Genetic Code

Characteristics of the Genetic Code

CONNECTING CONCEPTS Characteristics of the Genetic Code

11.2 Amino Acids Are Assembled into a Protein Through Translation

The Binding of Amino Acids to Transfer RNAs

The Initiation of Translation

Elongation

Termination

CONNECTING CONCEPTS A Comparison of Bacterial and Eukaryotic Translation

11.3 Additional Properties of Translation and Proteins

Polyribosomes

Folding and Posttranslational Modifications of Proteins

Translation and Antibiotics

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12. Control of Gene Expression

Operons and the Noisy Cell

12.1 The Regulation of Gene Expression Is Critical for All Organisms

Genes and Regulatory Elements

Levels of Gene Regulation

12.2 Operons Control Transcription in Bacterial Cells

Operon Structure

Negative and Positive Control: Inducible and Repressible Operons

The lac Operon of Escherichia coli

Mutations Affecting the lac Operon

Positive Control and Catabolite Repression

The trp Operon of E. coli

12.3 Gene Regulation in Eukaryotic Cells Takes Place at Multiple Levels

Changes in Chromatin Structure

Transcription Factors and Transcriptional Regulator Proteins

Gene Regulation by RNA Processing and Degradation

RNA Interference and Gene Regulation

Gene Regulation in the Course of Translation and Afterward

CONNECTING CONCEPTS A Comparison of Bacterial and Eukaryotic Gene Control

MODEL GENETIC ORGANISM? The Plant Arabidopsis thaliana

12.4 Epigenetic Effects Influence Gene Expression

Molecular Mechanisms of Epigenetic Changes

Epigenetic Effects

The Epigenome

13. Gene Mutations, Transposable Elements, and DNA Repair

A Fly Without a Heart

13.1 Mutations Are Inherited Alterations in the DNA Sequence

The Importance of Mutations

Categories of Mutations

Types of Gene Mutations

Phenotypic Effects of Mutations

Suppressor Mutations

Mutation Rates

13.2 Mutations May Be Caused by a Number of Different Factors

Spontaneous Replication Errors

Spontaneous Chemical Changes

Chemically Induced Mutations

Radiation

Detecting Mutations with the Ames Test

13.3 Transposable Elements Are Mobile DNA Sequences Capable of Inducing Mutations

General Characteristics of Transposable Elements

Transposition

The Mutagenic Effects of Transposition

Evolutionary Significance of Transposable Elements

13.4 A Number of Pathways Repair DNA

Types of DNA Repair

Genetic Diseases and Faulty DNA Repair

14. Molecular Genetic Analysis and Biotechnology

Helping the Blind to See

14.1 Molecular Techniques Are Used to Isolate, Recombine, and Amplify Genes

The Molecular Genetics Revolution

Working at the Molecular Level

Cutting and Joining DNA Fragments

Viewing DNA Fragments

Locating DNA Fragments with Southern Blotting and Probes

Cloning Genes

Amplifying DNA Fragments by Using the Polymerase Chain Reaction

14.2 Molecular Techniques Can Be Used to Find Genes of Interest

DNA Libraries

Positional Cloning

14.3 DNA Sequences Can Be Determined and Analyzed

Restriction Fragment Length Polymorphisms

DNA Sequencing

Next-Generation Sequencing Technologies

DNA Fingerprinting

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14.4 Molecular Techniques Are Increasingly Used to Analyze Gene Function

Forward and Reverse Genetics

Transgenic Techniques

Knockout Mice

MODEL GENETIC ORGANISM? The Mouse Mus musculus

Silencing Genes by Using RNA Interference

14.5 Biotechnology Harnesses the Power of Molecular Genetics

Pharmaceutical Products

Specialized Bacteria

Agricultural Products

Genetic Testing

Gene Therapy

15. Genomics and Proteomics

Decoding the Waggle Dance: The Genome of the Honeybee

15.1 Structural Genomics Determines the DNA Sequences of Entire Genomes

Genetic Maps

Physical Maps

Sequencing an Entire Genome

The Human Genome Project

Single-Nucleotide Polymorphisms

Bioinformatics

Metagenomics

Synthetic Biology

15.2 Functional Genomics Determines the Function of Genes by Using Genome-Based Approaches

Predicting Function from Sequence

Gene Expression and Microarrays

15.3 Comparative Genomics Studies How Genomes Evolve

Prokaryotic Genomes

Eukaryotic Genomes

Comparative Drosophila Genomics

The Human Genome

15.4 Proteomics Analyzes the Complete Set of Proteins Found in a Cell

The Determination of Cellular Proteins

Protein Microarrays

Structural Proteomics

16. Cancer Genetics

Palladin and the Spread of Cancer

16.1 Cancer Is a Group of Diseases Characterized by Cell Proliferation

Tumor Formation

Cancer as a Genetic Disease

The Role of Environmental Factors in Cancer

16.2 Mutations in Several Types of Genes Contribute to Cancer

Oncogenes and Tumor-Suppressor Genes

Genes That Control the Cell Cycle

DNA-Repair Genes

Genes That Regulate Telomerase

Genes That Promote Vascularization and the Spread of Tumors

Epigenetic Changes Associated with Cancer

16.3 Colorectal Cancer Arises Through the Sequential Mutation of a Number of Genes

16.4 Changes in Chromosome Number and Structure Are Often Associated with Cancer

16.5 Viruses Are Associated with Some Cancers

17. Quantitative Genetics

Corn Oil and Quantitative Genetics

17.1 Many Quantitative Characteristics Are Influenced by Alleles at Multiple Loci

The Relation Between Genotype and Phenotype

Types of Quantitative Characteristics

Polygenic Inheritance

Kernel Color in Wheat

17.2 Statistical Methods Are Required for Analyzing Quantitative Characteristics

Distributions

The Mean

The Variance

Applying Statistics to the Study of a Polygenic Characteristic

17.3 Heritability Is Used to Estimate the Proportion of Variation in a Trait That Is Genetic

Phenotypic Variance

Types of Heritability

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Calculating Heritability

The Limitations of Heritability

Locating Genes That Affect Quantitative Characteristics

17.4 Genetically Variable Traits Change in Response to Selection

Predicting the Response to Selection

Limits to Selection Response

18. Population and Evolutionary Genetics

Genetic Rescue of Bighorn Sheep

18.1 Genotypic and Allelic Frequencies Are Used to Describe the Gene Pool of a Population

Calculating Genotypic Frequencies

Calculating Allelic Frequencies

Models in Population Genetics

18.2 The Hardy–Weinberg Law Describes the Effect of Reproduction on Genotypic and Allelic Frequencies

Genotypic Frequencies at Hardy–Weinberg Equilibrium

Closer Examination of the Hardy–Weinberg Law

Implications of the Hardy–Weinberg Law

Testing for Hardy–Weinberg Proportions

Estimating Allelic Frequencies by Using the Hardy–Weinberg Law

Nonrandom Mating Alters Genotype Frequencies

18.3 Several Evolutionary Forces Can Cause Changes in Allelic Frequencies

Mutation

Migration

Genetic Drift

Natural Selection

CONNECTING CONCEPTS The General Effects of Forces That Change Allelic Frequencies

18.4 Evolution Occurs Through Genetic Change Within Populations

Biological Evolution

Evolution as a Two-Step Process

Types of Evolution

18.5 New Species Arise Through the Evolution of Reproductive Isolation

The Biological Species Concept

Reproductive Isolating Mechanisms

Modes of Speciation

18.6 The Evolutionary History of a Group of Organisms Can Be Reconstructed by Studying Changes in Homologous Characteristics

The Construction of Phylogenetic Trees

18.7 Patterns of Evolution Are Revealed by Changes at the Molecular Level

Rates of Molecular Evolution

The Molecular Clock

Evolution Through Changes in Gene Regulation

Genome Evolution

Glossary

Answers to Selected Questions and Problems

Index