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1 Introduction to Genetics1

2 Mitosis and Meiosis17

3 Mendelian Genetics37

4 Modification of Mendelian Ratios60

5 Sex Determination and Sex Chromosomes92

6 Chromosome Mutations:Variation in Number and Arrangement111

7 Linkage and Chromosome Mapping in Eukaryotes132

8 Genetic Analysis and Mapping in Bacteria and B acteriophages159

9 DNA Structure and Analysis181

10 DNA Replication and Recombination203

11 Chromosome Structure and DNA Sequence Organization224

12 The Genetic Code and Transcription240

13 Translation and Proteins261

14 Gene Mutation,Transposition,and DNA Repair284

15 Regulation of Gene Expression308

16 Cancer and Regulation of the Cell Cycle334

17 Recombinant DNA Technology and Gene Cloning351

18 Genomics,Bioinformatics,and Proteomics375

19 Applications and Ethics of Genetic Engineering and Biotechnology407

20 Developmental Genetics433

21 Genetics and Behavior450

22 Quantitative Genetics and Multifactorial Traits465

23 Population and Evolutionary Genetics483

24 Conservation Genetics507

CHAPTER 1 Introduction to Genetics1

1.1 Genetics Has a Rich and Interesting History2

1.2 Genetics Progressed from Mendel to DNA in Less Than a Century4

1.3 Discovery of the Double Helix Launched the Era of Molecular Genetics6

1.4 Development of Recombinant DNA Technology Began the Era of DNA Cloning8

1.5 The Impact of Biotechnology Is Continually Expanding9

1.6 Genomics,Proteomics,and Bioinformatics Are New and Expanding Fields12

1.7 Genetic Studies Rely on the Use of Model Organisms12

1.8 We Live in the Age of Genetics14

GENETICS,TECHNOLOGY,AND SOCIETY15

Genetics and Society:The Application and Impact of Science and Technology15

EXPLORING GENOMICS15

Internet Resources for Learning about Genomics,Bioinformatics,and Proteomics15

Case Study:Extending essential ideas of genetics beyond the classroom16

Problems and Discussion Questions16

CHAPTER 2 Mitosis and Meiosis17

2.1 Cell Structure Is Closely Tied to Genetic Function18

2.2 Chromosomes Exist in Homologous Pairs in Diploid Organisms20

2.3 Mitosis Partitions Chromosomes into Dividing Cells22

2.4 Meiosis Reduces the Chromosome Number from Diploid to Haploid in Germ Cells and Spores26

2.5 The Development of Gametes Varies during Spermatogenesis and Oogenesis30

2.6 Meiosis Is Critical to the Sexual Reproduction Cycle of All Diploid Organisms32

2.7 Electron Microscopy Has Revealed the Cytological Nature of Mitotic and Meiotic Chromosomes33

EXPLORING GENOMICS34

PubMed:Exploring and Retrieving Biomedical Literature34

Case Study:Timing is everything35

Insights and Solutions35

Problems and Discussion Questions36

CHAPTER 3 Mendelian Genetics37

3.1 Mendel Used a Model Experimental Approach to Study Patterns of Inheritance38

3.2 The Monohybrid Cross Reveals How One Trait Is Transmitted from Generation to Generation39

3.3 Mendel's Dihybrid Cross Generated a Unique F2 Ratio42

How Mendel's Peas Become Wrinkled:A Molecular Explanation43

3.4 The Trihybrid Cross Demonstrates That Mendel's Principles Apply to Inheritance of Multiple Traits44

3.5 Mendel's Work Was Rediscovered in the Early Twentieth Century46

3.6 Independent Assortment Leads to Extensive Genetic Variation48

Tay-Sachs Disease:The Molecular Basis of a Recessive Disorder in Humans48

3.7 Laws of Probability Help to Explain Genetic Events49

3.8 Chi-Square Analysis Evaluates the Influence of Chance on Genetic Data49

3.9 Pedigrees Reveal Patterns of Inheritance of Human Traits52

EXPLORING GENOMICS54

Online Mendelian Inheritance in Man54

Case Study:To test or not to test55

Insights and Solutions55

Problems and Discussion Questions57

CHAPTER 4 Modification of Mendelian Ratios60

4.1 Alleles Alter Phenotypes in Different Ways61

4.2 Geneticists Use a Variety of Symbols for Alleles62

4.3 Neither Allele Is Dominant in Incomplete,or Partial,Dominance62

4.4 In Codominance,the Influence of Both Alleles in a Heterozygote Is Clearly Evident63

4.5 Multiple Alleles of a Gene May Exist in a Population64

4.6 Lethal Alleles Represent Essential Genes65

Thc Molecular Basis of Dominance and Recessiverness:The Agouti Gene66

4.7 Combinations of Two Gene Pairs with Two Modes of Inheritance Modify the 9:3:3:1 Ratio66

4.8 Phenotypes Are Often Affected by More Than One Gene67

4.9 Complementation Analysis Can Determine If Two Mutations Causing a Similar Phenotype Are Alleles of the Same Gene72

4.10 Expression of a Single Gene May Have Multiple Effects73

4.11 X-Linkage Describes Genes on the X Chromosome73

4.12 In Sex-Limited and Sex-Influenced Inheritance,an Individual's Sex Influences the Phenotype76

4.13 Genetic Background and the Environment Affect Phenotypic Expression77

4.14 Extranuclear Inheritance Modifies Mendelian Patterns80

GENETICS,TECHNOLOGY,AND SOCIETY84

Improving the Genetic Fate of Purebred Dogs84

Case Study:A twin difference85

Insights and Solutions85

Problems and Discussion Questions87

CHAPTER 5 Sex Determination and Sex Chromosomes92

5.1 Life Cycles Depend on Sexual Differentiation93

5.2 X and Y Chromosomes Were First Linked to Sex Determination Early in the Twentieth Century96

5.3 The Y Chromosome Determines Maleness in Humans97

5.4 The Ratio of Males to Females in Humans Is Not 1.0101

5.5 Dosage Compensation Prevents Excessive Expression of X-Linked Genes in Humans and Other Mammals102

5.6 The Ratio of X Chromosomes to Sets of Autosomes Determines Sex in Drosophila104

5.7 Temperature Variation Controls Sex Determination in Reptiles106

GENETICS,TECHNOGY,AND SOCIETY107

A Question of Gender:Sex Selection in Humans107

Case Study:Doggone it!108

Insights and Solutions108

Problems and Discussion Questions109

CHAPTER 6 Chromosome Mutations:Variation in Number and Arrangement111

6.1 Variation in Chromosome Number:Terminology and Origin112

6.2 Monosomy and Trisomy Result in a Variety of Phenotypic Effects113

6.3 Polyploidy,in Which More Than Two Haploid Sets of Chromosomes Are Present,Is Prevalent in Plants116

6.4 Variation Occurs in the Composition and Arrangement of Chromosomes119

6.5 A Deletion Is a Missing Region of a Chromosome119

6.6 A Duplication Is a Repeated Segment of a Chromosome121

6.7 Inversions Rearrange the Linear Gene Sequence123

Copy Number Variants(CNVs)—Duplications and Deletions at the Molecular Level123

6.8 Translocations Alter the Location of Chromosomal Segments in the Genome125

6.9 Fragile Sites in Human Chromosomes Are Susceptible to Breakage127

GENETICS,TECHNOLOGY,AND SOCIETY128

Down Syndrome,Prenatal Testing,and the New Eugenics128

Case study:Fish tales129

Insights and Solutions129

Problems and Discussion Questions130

CHAPTER 7 Linkage and Chromosome Mapping in Eukaryotes132

7.1 Genes Linked on the Same Chromosome Segregate Together133

7.2 Crossing Over Serves as the Basis of Determining the Distance between Genes during Mapping136

7.3 Determining the Gene Sequence during Mapping Requires the Analysis of Multiple Crossovers139

7.4 As the Distance between Two Genes Increases,Mapping Estimates Become More Inaccurate145

7.5 Lod Score Analysis and Somatic Cell Hybridization Were Historically Important in Creating Human Chromosome Maps147

7.6 Chromosome Mapping Is Now Possible Using DNA Markers and Annotated Computer Databases148

7.7 Linkage and Mapping Studies Can Be Performed in Haploid Organisms149

7.8 Other Aspects of Genetic Exchange150

7.9 Did Mendel Encounter Linkage?152

Why Didn't Gregor Mendel Find Linkag?152

EXPLORING GENOMICS153

Human Chromosome Maps on the Internet153

Case Study:Links to autism153

Insights and Solutions154

Problems and Discussion Questions155

CHAPTER 8 Genetic Analysis and Mapping in Bacteria and Bacteriophages159

8.1 Bacteria Mutate Spontaneously and Grow at an Exponential Rate160

8.2 Conjugation Is One Means of Genetic Recombination in Bacteria161

8.3 Rec Proteins Are Essential to Bacterial Recombination168

8.4 The F Factor Is an Example of a Plasmid168

8.5 Transformation Is Another Process Leading to Genetic Recombination in Bacteria169

8.6 Bacteriophages Are Bacterial Viruses170

8.7 Transduction Is Virus-Mediated Bacterial DNA Transfer173

8.8 Bacteriophages Undergo Intergenic Recombination175

GENETICS TECHNOLOGY,AND SOCIETY177

From Cholera Genes to Edible Vaccines177

Case Study:To treat or not to treat178

Insights and Solutions178

Problems and Discussion Questions179

DNA Structure and Analysis181

9.1 The Genetic Material Must Exhibit Four Characteristics182

9.2 Until 1944,Observations Favored Protein as the Genetic Material183

9.3 Evidence Favoring DNA as the Genetic Material Was First Obtained during the Study of Bacteria and Bacteriophages183

9.4 Indirect and Direct Evidence Supports the Concept that DNA Is the Genetic Materia in Eukaryotes188

9.5 RNA Serves as the Genetic Material in Some Viruses189

9.6 The Structure of DNA Holds the Key to Understanding Its Function190

Molecular Structure of Nucleic Acids:A Structure for Deoxyribose Nucleic Acid195

9.7 Alternative Forms of DNA Exist196

9.8 The Structure of RNA Is Chemically Similar to DNA,but Single-Stranded197

9.9 Many Analytical Techniques Have Been Useful during the Investigation of DNA and RNA197

EXPLORING GENOMICS200

Introduction to Bioinformatics:BLAST200

Case Study:Zigs and zags of the smallpox virus201

Insights and Solutions201

Problems and Discussion Questions201

CHAPTER 10 DNA Replication and Recombination203

10.1 DNA Is Reproduced by Semiconservative Replication204

10.2 DNA Synthesis in Bacteria Involves Five Polymerases,as Well as Other Enzymes208

10.3 Many Complex Issues Must Be Resolved during DNA Replication211

10.4 A Coherent Model Summarizes DNA Replication214

10.5 Replication Is Controlled by a Variety of Genes214

10.6 Eukaryotic DNA Replication Is Similar to Replication in Prokaryotes,but Is More Complex215

10.7 The Ends of Linear Chromosomes Are Problematic during Replication217

10.8 DNA Recombination,Like DNA Replication,Is Directed by Specific Enzymes219

GENETICS,TECHNOLOGY,AND SOCIETY Telomeres:The Key to Immortality?221

Case Study:At loose ends222

Insights and Solutions222

Problems and Discussion Questions222

CHAPTER 11 Chromosome Structure and DNA Sequence Organization224

11.1 Viral and Bacterial Chromosomes Are Relatively Simple DNA Molecules225

11.2 Mitochondria and Chloroplasts Contain DNA Similar to Bacteria and Viruses226

11.3 Specialized Chromosomes Reveal Variations in the Organization of DNA229

11.4 DNA Is Organized into Chromatin in Eukaryotes231

11.5 Eukaryotic Genomes Demonstrate Complex Sequence Organization Characterized by Repetitive DNA234

11.6 The Vast Majority of a Eukaryotic Genome Does Not Encode Functional Genes236

EXPLORING GENOMICS237

Database of Genomic Variants:Structural Variations in the Human Genome237

Case Study:Art inspires learning238

Insights and Solutions238

Problems and Discussion Questions238

CHAPTER 12 The Genetic Code and Transcription240

12.1 The Genetic Code Exhibits a Number of Characteristics241

12.2 Early Studies Established the Basic Operational Patterns of the Code242

12.3 Studies by Nirenberg,Matthaei,and Others Deciphered the Code242

12.4 The Coding Dictionary Reveals the Function of the 64 Triplets246

12.5 The Genetic Code Has Been Confirmed in Studies of Bacteriophage MS2248

12.6 The Genetic Code Is Nearly Universal248

12.7 Different Initiation Points Create Overlapping Genes249

12.8 Transcription Synthesizes RNA on a DNA Template249

12.9 RNA Polymerase Directs RNA Synthesis250

12.10 Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several Ways252

12.11 The Coding Regions of Eukaryotic Genes Are Interrupted by Intervening Sequences Called Introns254

12.12 Transcription Has Been Visualized by Electron Microscopy257

GENETICS,TECHNOLOGY,AND SOCIETY257

Nucleic Acid-Based Gene Silencing:Attacking the Messenger257

Case Study:A drug that sometimes works258

Insights and Solutions258

Problems and Discussion Questions259

CHAPTER 13 Translation and Proteins261

13.1 Translation of mRNA Depends on Ribosomes and TransferRNAs262

13.2 Translation of mRNA Can Be Divided into Three Steps265

13.3 Crystallographic Analysis Has Revealed Many Details about the Functional Prokaryotic Ribosome269

13.4 Translation Is More Complex in Eukaryotes269

13.5 The Initial Insight that Proteins Are Important in Heredity Was Provided by the Study of Inborn Errors of Metabolism270

13.6 Studies of Neurospora Led to the One-Gene:One-Enzyme Hypothesis271

13.7 Studies of Human Hemoglobin Established that One Gene Encodes One Polypeptide273

13.8 Variation in Protein Structure Is the Basis of Biological Diversity276

13.9 Proteins Function in Many Diverse Roles279

EXPLORING GENOMICS280

Translation Tools and Swiss-Prot for Studying Protein Sequences280

Case Study:Lost in translation281

Insights and Solutions281

Problems and Discussion Questions282

CHAPTER 14 Gene Mutation,Transposition,and DNA Repair284

14.1 Gene Mutations Are Classified in Various Ways285

14.2 Spontaneous Mutations Arise from Replication Errors and Base Modifications287

14.3 Induced Mutations Arise from DNA Damage Caused by Chemicals and Radiation289

14.4 Organisms Use DNA Repair Systems to Counteract Mutations292

14.5 The Ames Test Is Used to Assess the Mutagenicity of Compounds296

14.6 DNA Sequencing Has Enhanced Our Understanding of Mutations in Humans297

14.7 Geneticists Use Mutations to Identify Genes and Study Gene Function298

14.8 Transposable Elements Move within the Genome and May Create Mutations299

EXPLORING GENOMICS303

Sequence Alignment to Identify a Mutation303

Case Study:Genetic dwarfism304

Insights and Solutions305

Problems and Discussion Questions305

CHAPTER 15 Regulation of Gene Expression308

15.1 Prokaryotes Regulate Gene Expression in Response to Both External and Internal Conditions309

15.2 Lactose Metabolism in E.coli Is Regulated by an Inducible System309

15.3 The Catabolite-Activating Protein(CAP)Exerts Positive Contol over the lac Operon314

15.4 TheTryptophan(trp)Operon in E.coli Is a Repressible Gene System315

15.5 Attenuation Is a Regulatory Mechanism in Some Prokaryotic Operons317

15.6 Eukaryotic Gene Regulation Differs from That in Prokaryotes317

15.7 Eukaryotic Gene Expression Is Influenced by Chromosome Organization and Chromatin Modifications318

15.8 Eukaryotic Transcription Is Regulated at Specific Cis-Acting Sites320

15.9 Eukaryotic Transcription Is Regulated by Transcription Factors that Bind to Cis-Acting Sites323

15.10 Transcription Factors Bind to Cis-Acting sites and Interact with Basal Transcription Factors and Other Regulatory Proteins324

15.11 Posttranscriptional Gene Regulation Occurs at All the Steps from RNA Processing to Protein Modification325

15.12 RNA-induced Gene Silencing Controls Gene Expression in Several Ways328

EXPLORING GENOMICS330

Tissue-Specific Gene Expression330

Case Study:A mysterious muscular dystrophy330

Insights and Solutions331

Problems and Discussion Questions331

CHAPTER 16 Cancer and Regulation of the Cell Cycle334

16.1 Cancer Is a Genetic Disease at the Level of Somatic Cells335

16.2 Cancer Cells Contain Genetic Defects Affecting Genomic Stability,DNA Repair,and Chromatin Modifications337

16.3 Cancer Cells Contain Genetic Defects Affecting Cell-Cycle Regulation338

16.4 Proto-oncogenes and Tumor-suppressor Genes Are Altered in Cancer Cells340

16.5 Cancer Cells Metastasize,Invading Other Tissues343

16.6 Predisposition to Some Cancers Can Be Inherited344

16.7 Viruses Contribute to Cancer in Both Humans and Animals345

16.8 Environmental Agents Contribute to Human Cancers346

GENETICS,TECHNOLOGY,AND SOCIETY347

Breast Cancer:The Double-Edged Sword of Genetic Testing347

Case Study:I thought it was safe348

Insights and Solutions348

Problems and Discussion Questions349

CHAPTER 17 Recombinant DNA Technology and Gene Cloning351

17.1 An Overview of Recombinant DNA Technology352

17.2 Constructing Recombinant DNA Molecules Requires Several Steps352

17.3 Cloning DNA in Host Cells356

17.4 The Polymerase Chain Reaction Makes DNA Copies without Host Cells357

17.5 Recombinant Libraries Are Collections of Cloned Sequences359

17.6 Specific Clones Can Be Recovered from a Library361

17.7 Cloned Sequences Can Be Analyzed in Several Ways362

17.8 DNA Sequencing Is the Ultimate Way to Characterize a Clone366

EXPLORING GENOMICS369

Manipulating Recombinant DNA:Restriction Mapping and Designing a Recombinant DNA Experiment369

Case Study:Should we worry about recombinant DNA technology?370

Insights and Solutions371

Problems and Discussion Questions371

CHAPTER 18 Genomics,Bioinformatics,and Proteomics375

18.1 Whole-Genome Shotgun Sequencing Is a Widely Used Method for Sequencing and Assembling Entire Genomes376

18.2 DNA Sequence Analysis Relies on Bioinformatics Applications and Genome Databases380

18.3 Functional Genomics Attempts to Identify Potential Functions of Genes and Other Elements in a Genome383

18.4 The Human Genome Project Reveals Many Important Aspects of Genome Organization in Humans384

18.5 The"Omics"Revolution Has Created a New Era of Biological Research Methods386

18.6 Prokaryotic and Eukaryotic Genomes Display Common Structural and Functional Features and Important Differences387

18.7 Comparative Genomics Analyzes and Compares Genomes from Different Organisms390

18.8 Metagenomics Applies Genomics Techniques to Environmental Samples394

18.9 Transcriptome Analysis Reveals Profiles of Expressed Genes in Cells and Tissues396

18.10 Proteomics Identifies and Analyzes the Protein Composition of Cells398

EXPLORING GENOMICS403

Contigs and Shotgun Sequencing403

Case Study:Bioprospecting in Darwin's wake404

Insights and Solutions404

Problems and Discussion Questions405

CHAPTER 19 Appl ications and Ethics of Genetic Engineering and Biotechnology407

19.1 Genetically Engineered Organisms Synthesize a Wide Range of Biological and Pharmaceutical Products408

19.2 Genetic Engineering of Plants Has Revolutionized Agriculture411

19.3 Transgenic Animals with Genetically Enhanced Characteristics Have the Potential to Serve Important Roles in Agriculture and Biotechnology414

19.4 Genetic Engineering and Genomics Are Transforming Medical Diagnosis415

19.5 Genetic Engineering and Genomics Promise New,More Targeted Medical Therapies421

19.6 DNA Profiles Identify Individuals424

19.7 Genetic Engineering,Genomics,and Biotechnology Create Ethical,Social,and Legal Questions427

GENETICS,TECHNOLOGY,AND SOCIETY429

Personal Genome Projects and the Race for the$1000 Genome429

Case Study:A first for gene therapy430

Insights and Solutions430

Problems and Discussion Questions431

CHAPTER 20 Developmental Genetics433

20.1 Evolutionary Conservation of Developmental Mechanisms Can Be Studied Using Model Organisms434

20.2 Genetic Analysis of Embryonic Development in Drosophila Reveals How the Body Axis of Animals Is Specified434

20.3 Zygotic Genes Program Segment Formation in Drosophila437

20.4 Homeotic Selector Genes Specify Parts of the Adult Body439

20.5 Plants Have Evolved Developmental Systems That Parallel Those of Animals442

20.6 Cell-Cell Interactions in Development Are Modeled in C.elegans444

20.7 Transcriptional Networks Control Gene Expression in Development446

GENETICS,TECHNOLOGY,AND SOCIETY446

Stem Cell Wars446

Case Study:One foot or another447

Insights and Solutions448

Problems and Discussion Questions448

CHAPTER 21 Genetics and Behavior450

21.1 Behavioral Differences between Genetic Strains Can Be Identified451

21.2 The Behavior-First Approach Can Establish Genetic Strains with Behavioral Differences453

21.3 The Gene-First Approach Uses Analysis of Mutant Alleles to Study Molecular Mechanisms That Underlie Behavior455

21.4 Human Behavior Has Genetic Components459

EXPLORING GENOMICS462

HomoloGene:Searching for Behavioral Genes462

Case Study:Primate models for human disorders462

Insights and Solutions463

Problems and Discussion Questions463

CHAPTER 22 Quantitative Genetics and Multifactorial Traits465

22.1 Not All Polygenic Traits Show Continuous Variation466

22.2 Quantitative Traits Can Be Explained in Mendelian Terms467

22.3 The Study of Polygenic Traits Relies on Statistical Analysis469

22.4 Heritability Values Estimate the Genetic Contribution to Phenotypic Variability471

22.5 Twin Studies Allow an Estimation of Heritability in Humans475

22.6 Quantitative Trait Loci Can Be Mapped476

GENETICS,TECHNOLOGY,AND SOCIETY477

The Green Revolution Revisited:Genetic Research with Rice477

Case Study:A flip of the genetic coin478

Insights and Solutions478

Problems and Discussion Questions480

CHAPTER 23 Population and Evolutionary Genetics483

23.1 Genetic Variation Is Present in Most Populations and Species484

23.2 The Hardy-Weinberg Law Describes Allele Frequencies and Genotype Frequencies in Populations486

23.3 The Hardy-Weinberg Law Can Be Applied to Human Populations488

23.4 Natural Selection Is a Major Force Driving Allele Frequency Change491

23.5 Mutation Creates New Alleles in a Gene Pool493

23.6 Migration and Gene Flow Can Alter Allele Frequencies494

23.7 Genetic Drift Causes Random Changes in Allele Frequency in Small Populations494

23.8 Nonrandom Mating Changes Genotype Frequency but Not Allele Frequency496

23.9 Reduced Gene Flow,Selection,and Genetic Drift Can Lead to Speciation497

23.10 Genetic Differences Can Be Used to Reconstruct Evolutionary History499

EXPLORING GENOMICS503

The Y Chromosome Haplotype Reference Database(YHRD)503

Case Study:An unexpected outcome504

Insights and Solutions504

Problems and Discussion Questions504

CHAPTER 24 Conservation Genetics507

24.1 Genetic Diversity Is the Goal of Conservation Genetics509

24.2 Population Size Has a Major Impact on Species Survival511

24.3 Genetic Effects Are More Pronounced in Small,Isolated Populations512

24.4 Genetic Erosion Threatens Species'Survival515

24.5 Conservation of Genetic Diversity Is Essential to Species Survival516

GENETICS,TECHNOLOGY,AND SOCIETY519

Gene Pools and Endangered Species:The Plight of the Florida Panther519

Case Study:The flip side of the green revolution520

Insights and Solutions520

Problems and Discussion Questions521