Genetic Analysis - Pearson

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Genetic AnalysisAN INTEGRATED APPROACHThird EditionMark F. SandersUniversity of California at DavisJohn L. BowmanMonash University,Melbourne, AustraliaUniversity of California at Davis330 Hudson Street, NY NY 10013A01 SAND5173 03 SE FM.indd 111/15/17 10:46 PM

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Table of Contents1The Molecular Basis ofHeredity, Variation, andEvolution 11.12Transmission Genetics2.1The Development of Modern Genetics2Five Critical Experimental Innovations2.2The Four Phases of Modern Genetics 3Genetics—Central to Modern Biology 51.2Segregation of Alleles7DNA Replication 91.3102.3Hypothesis Testing by Test-Cross Analysis37Hypothesis Testing by F2 Self-Fertilization3839Dihybrid and Trihybrid Crosses Reveal theIndependent Assortment of Alleles 40DNA Transcription and MessengerRNA Translation Express Genes 11Dihybrid-Cross Analysis of Two GenesTranscription 12Testing Independent Assortment by Test-CrossAnalysis 43Experimental Insight 2.1Translation 13Genetic Analysis 1.21.43436Genetic Analysis 2.110Experimental Insight 1.1Monohybrid Crosses Reveal the Segregation of Alleles 34Evidence of Particulate Inheritance and Rejection of theBlending Theory 36The Discovery of DNA Structure 6Genetic Analysis 1.13133Identifying Dominant and Recessive TraitsThe Structure of DNA Suggestsa Mechanism for Replication 6DNA NucleotidesGregor Mendel Discovered the Basic Principles of Genetic Transmission 31Mendel’s Modern Experimental ApproachModern Genetics Is in Its SecondCentury 230Genetic Analysis 2.214404144Testing Independent Assortment by Trihybrid-CrossAnalysis 45Genetic Variation Can Be Detectedby Examining DNA, RNA, and Proteins 15The Rediscovery of Mendel’s WorkExperimental Insight 2.2Gel Electrophoresis 154646Stains, Blots, and Probes 162.4DNA Sequencing and Genomics 18Proteomics and Other “-omic” Analyses18Probability Theory Predicts MendelianRatios 47The Product Rule1.5The Sum RuleEvolution Has a Genetic Basis 19Binomial Probability 48Four Evolutionary Processes 20Genetic Analysis 1.324Case Study Ancient DNA: Genetics Looks intothe Past 24Summary 26 Preparing for ProblemSolving 27 Problems 2747Conditional Probability 47Darwin’s Theory of Evolution 19Tracing Evolutionary Relationships 21472.5Chi-Square Analysis Tests the Fitbetween Observed Values and ExpectedOutcomes 49Chi-Square Analysis50Chi-Square Analysis of Mendel’s Data50iiiA01 SAND5173 03 SE FM.indd 311/15/17 10:46 PM

iv    CONTENTS2.6Autosomal Inheritance and MolecularGenetics Parallel the Predictions of Mendel’s Hereditary Principles 513.5Expression of X-Linked Recessive TraitsAutosomal Dominant Inheritance 52X-Linked Dominant Trait TransmissionAutosomal Recessive Inheritance 53Y-Linked InheritanceProspective and Retrospective Predictions inHuman Genetics 53Genetic Analysis 3.3Molecular Genetics of Mendel’s Traits 54Genetic Analysis 2.33.655Cell Division and Chromosome Heredity674.1Dosage Compensation Equalizes theExpression of Sex-Linked Genes 96Interactions between Alleles Produce Dominance Relationships 106Functional Effects of Mutation106107Notational Systems for Genes and AlleleRelationships 109Chromosome Movement and Distribution 72Incomplete DominanceCompletion of Cell Division 73CodominanceCell Cycle Checkpoints 74110110Dominance Relationships of ABO AllelesGenetic Analysis 4.1Meiosis Produces Cells for SexualReproduction 75Allelic Series113Meiosis Features Two Cell Divisions 75Lethal Alleles116Meiosis IDelayed Age of Onset76Meiosis II 79Meiosis Generates Mendelian Ratios 804.2113118Some Genes Produce VariablePhenotypes 118Sex-Influenced Traits 119Incomplete PenetranceVariable Expressivity84120120Gene–Environment InteractionsX-Linked Inheritance 85Pleiotropic GenesTesting the Chromosome Theory of Heredity 864.3Sex Determination Is Chromosomaland Genetic 87121122Gene Interaction Modifies MendelianRatios 122Gene Interaction in Pathways122Sex Determination in Drosophila 87The One Gene–One Enzyme HypothesisGenetic Analysis 3.2Experimental Insight 4.188Mammalian Sex Determination 89Genetic Analysis 4.2Experimental Insight 3.1Epistasis and Its ResultsA01 SAND5173 03 SE FM.indd 4124125Genetic Dissection to Investigate Gene ActionDiversity of Sex Determination 8990110Sex-Limited Traits 119The Chromosome Theory of HeredityProposes That Genes Are Carried onChromosomes 82Genetic Analysis 3.1105The Molecular Basis of DominanceMitosis Divides Somatic Cells 68Substages of M Phase 693.495Gene InteractionThe Cell Cycle 683.39393433.292Case Study The (Degenerative) Evolutionof the Mammalian Y Chromosome 97Summary 99 Preparing for ProblemSolving 99 Problems 100Case Study OMIM, Gene Mutations, and HumanHereditary Disease 57Summary 59 Preparing for ProblemSolving 60 Problems 603.1Human Sex-Linked Transmission FollowsDistinct Patterns 9112712812911/15/17 10:46 PM

CONTENTS     v4.4Complementation Analysis DistinguishesMutations in the Same Gene from Mutations in Different Genes 133Allelic PhaseGenetic Analysis 4.3Genetic Analysis 5.3Lod Score AnalysisGenetic Analysis andMapping in Bacteria andBacteriophages 185Linked Genes Do Not AssortIndependently 1466.1Detecting Autosomal Genetic Linkage through Test-CrossAnalysis 150Characteristics of Bacterial GenomesGenetic Analysis 5.1Plasmids in Bacterial Cells1546.2The First Genetic Linkage Map 155Conjugation Identified 193Transfer of the F Factor 194Formation of an Hfr Chromosome 196Hfr Gene TransferThree-Point Test-Cross Analysis MapsGenes 156196Interrupted Mating and Time-of-Entry MappingTime-of-Entry Mapping Experiments198198Genetic Analysis 6.1199Constructing a Three-Point Recombination Map 158Consolidation of Hfr Maps200Determining Gamete Frequencies from Genetic Maps 161Conjugation with F′ Strains Produces Partial Diploids 201Correction of Genetic Map Distances 162Plasmids and Conjugation in ArchaeaGenetic Analysis 5.21636.3Multiple Factors Cause Recombinationto Vary 164Genetic Analysis 6.2204Steps in Transformation 205Recombination Is Dominated by Hotspots 165Mapping by Transformation 2056.4Bacterial Transduction Is Mediatedby Bacteriophages 205Human Genes Are Mapped Using Specialized Methods 166Bacteriophage Life CyclesMapping with Genetic MarkersCotransduction166The Inheritance of Disease-Causing Genes Linked toGenetic Markers 167A01 SAND5173 03 SE FM.indd 5203Bacterial Transformation Produces GeneticRecombination 203Sex Affects Recombination 164Genome Sequence Analysis Reveals RecombinationHotspot Distribution 1665.5189Bacteria Transfer Genes byConjugation 191Map Units156188189Research Technique 6.1Identifying Parental, Single-Crossover, and Double- Crossover Gametes in Three-Point Mapping 1575.4186Bacterial Culture and Growth AnalysisChi-Square Analysis of Genetic Linkage Data 1565.3Specialized Methods Are Used for GeneticAnalysis of Bacteria 186Cytological Evidence of Recombination 153Genetic Linkage Mapping Is Based on Recombination Frequency betweenGenes 1551746Detecting Genetic Linkage 1475.2172Case Study Mapping the Gene for CysticFibrosis 175Summary 176 Preparing for ProblemSolving 177 Problems 177145149172Linkage Disequilibrium and Evolutionary Analysis5The Discovery of Genetic Linkage171Genome-Wide Association StudiesCase Study Complementation Groups in a HumanCancer-Prone Disorder 136Summary 137 Preparing for ProblemSolving 138 Problems 1385.1169Experimental Insight 5.1134Genetic Linkage and Mapping in Eukaryotes168Generalized Transduction205208209Cotransduction Mapping209Specialized Transduction21111/15/17 10:46 PM

vi    CONTENTS6.5Bacteriophage Chromosomes Are Mappedby Fine-Structure Analysis 211Genetic Analysis 6.37.3Three Competing Models of Replication212The Meselson–Stahl Experiment 245Intragenic Recombination Analysis 213Origin and Directionality of Replication inBacterial DNA 247Lateral Gene Transfer Alters Genomes 214Lateral Gene Transfer and Genome Evolution 215Multiple Replication Origins in Eukaryotes7.4Identifying Lateral Gene Transfer in Genomes 216APPLICATIONATypes of Hereditary Disease 225DNA Proofreading 256Supercoiling and Topoisomerases7.5262263New Generations of DNA Sequencing TechnologyGenetic Analysis 7.3Genetic Counseling and Ethical Issues 232266267Case Study DNA Helicase Gene Mutations andHuman Progeroid Syndrome 269Summary 270 Preparing for ProblemSolving 271 Problems 27123323478DNA Structure andReplication 235Molecular Biology ofTranscription and RNAProcessing 275DNA Is the Hereditary Molecule of Life 236Chromosomes Contain DNA236A Transformation Factor Responsible for Heredity 236DNA Is the Transformation Factor 2388.1DNA Is the Hereditary Molecule 238The DNA Double Helix Consists ofTwo Complementary and AntiparallelStrands 240DNA Nucleotides 240241Genetic Analysis 7.1A01 SAND5173 03 SE FM.indd 6261Dideoxynucleotide DNA SequencingEthical Issues in Genetic Medicine 231The DNA DuplexMethods of Molecular Genetic Analysis Make Use of DNA ReplicationProcesses 260Separation of PCR ProductsAssessing and Communicating Risks and Options 228257258The Polymerase Chain ReactionGenetic Counseling 227Indicators and Goals of Genetic Counseling 2277.2257Replication at the Ends of Linear ChromosomesGenetic Testing and Diagnosis 2267.1253RNA Primer Removal and Okazaki FragmentLigation 254Synthesis of Leading and Lagging Strands at the Replication Fork 255Hereditary Disease and Disease Genes 225Problems253Continuous and Discontinuous Strand ReplicationGenetic Analysis 7.2In Closing249Molecular Biology of Replication InitiationHuman Hereditary Diseaseand Genetic CounselingA.2248DNA Replication Precisely Duplicates theGenetic Material 249DNA Sequences at Replication OriginsCase Study The Evolution of Antibiotic Resistanceand Its Impact on Medical Practice 217Summary 218 Preparing for ProblemSolving 219 Problems 219A.1245Genetic Complementation Analysis 213Deletion-Mapping Analysis 2146.6DNA Replication Is Semiconservativeand Bidirectional 244RNA Transcripts Carry the Messages ofGenes 276RNA Nucleotides and StructureCategories of RNA8.2277278Bacterial Transcription Is a Four-StageProcess 279Bacterial RNA Polymerase244276Experimental Discovery of Messenger RNABacterial Promoters28028011/15/17 10:46 PM

CONTENTS     viiTranscription Initiation 281Ribosome StructuresGenetic Analysis 8.1A Three-Dimensional View of the Ribosome283Research Technique 9.1Transcription Elongation and Termination 284Transcription Termination Mechanisms 2848.3Eukaryotic Transcription Is More Diversified and Complex than BacterialTranscription 2869.2Pol II Promoter Recognition 289Detecting Promoter Consensus Elements 290Translation Termination9.3Archaeal Promoters and Transcription292The Genetic Code Translates MessengerRNA into Polypeptide 329Genetic Analysis 9.2332Charging tRNA Molecules333The Signal HypothesisThe Torpedo Model of Transcription Termination 2969.5Splicing Signal Sequences 298334Experiments Deciphered the GeneticCode 334A Triplet Genetic Code336Alternative Patterns of RNA Transcription and AlternativeRNA Splicing 301No Gaps in the Genetic CodeSelf-Splicing Introns 302Genetic Analysis 9.3303307Case Study Sexy Splicing: Alternative mRNA Splicingand Sex Determination in Drosophila 307Summary 308 Preparing for ProblemSolving 309 Problems 309APPLICATION339BHuman Genetic ScreeningB.1The Molecular Biologyof Translation 314Polypeptides Are Amino Acid Chains ThatAre Assembled at Ribosomes 315337Case Study Antibiotics and TranslationInterference 340Summary 340 Preparing for ProblemSolving 341 Problems 342Transfer RNA Processing 3049336Deciphering the Genetic CodeRibosomal RNA Processing 304RNA Editing335No Overlap in the Genetic CodeA Gene Expression Machine Couples Transcription andPre-mRNA Processing 298Genetic Analysis 8.2Presymptomatic Diagnosis of Huntington’sDisease 348Trinucleotide Repeat ExpansionDetecting the Number of RepeatsB.2348348Newborn Genetic Screening 349Phenylketonuria and the First Newborn Genetic TestAmino Acid Structure 315Living with PKUPolypeptide and Transcript Structure 315The Recommended Uniform Screening PanelA01 SAND5173 03 SE FM.indd 7330331Protein Folding and Posttranslational PolypeptideProcessing 333Polyadenylation of 3′ Pre-mRNA 2959.1327The Genetic Code Displays Third-Base WobbleCapping 5′ Pre-mRNA 294Introns 296Translation Is Fast and Efficient 327The (Almost) Universal Genetic CodePosttranscriptional Processing ModifiesRNA Molecules 294Pre-mRNA Splicing 297327Translation of Polycistronic mRNA 329The Evolutionary Implications of ComparativeTranscription 2938.4326The Translational Complex9.4RNA Polymerase III Promoters 292324Genetic Analysis 9.1Other Regulatory Sequences and Chromatin-BasedRegulation of RNA Pol II Transcription 291RNA Polymerase I Promoters 292320Polypeptide Elongation288319319Translation Occurs in Three Phases 320Translation InitiationPolymerase II Transcription of mRNA in Eukaryotes 287Research Technique 8.131734935035111/15/17 10:46 PM

viii    CONTENTSB.3Genetic Testing to Identify Carriers 353Testing Blood Proteins 353DNA-Based Carrier Screening and DiagnosticVerification 35310.4 Chromosome Breakage Causes Mutationby Loss, Gain, and Rearrangement ofChromosomes 375Partial Chromosome DeletionUnequal Crossover 376Pharmacogenetic Screening 354Detecting Duplication and DeletionDeletion MappingB.4375Carrier Screening Criteria 353377377Prenatal Genetic Testing 354Invasive Screening Using Amniocentesis or Chorionic Villus Sampling 354Noninvasive Prenatal Testing 356Maternal Serum Screening 356Preimplantation Genetic Screening 356B.5Direct-to-Consumer Genetic Testing 357B.6Opportunities and Choices 359Problems 3591010.5 Chromosome Breakage Leadsto Inversion and Translocationof Chromosomes 378Chromosome InversionGenetic Analysis 10.310.1 Chromosome Number and Shape Varyamong Organisms 362Chromosomes in Nuclei 362Chromosome Visualization 363379Experimental Insight 10.1Chromosome Translocation38238310.6 Eukaryotic Chromosomes Are Organizedinto Chromatin 385Chromatin CompactionEukaryotic C hromosomeAbnormalities and Molecular Organization 361378386Histone Proteins and Nucleosomes386Higher Order Chromatin Organization and ChromosomeStructure 389Nucleosome Disassembly, Synthesis, and Reassemblyduring Replication 389Position Effect Variegation: Effect of Chromatin State onTranscription 390Case Study Human Chromosome EvolutionSummary 393 Preparing for ProblemSolving 394 Problems 394392Chromosome Banding 364Heterochromatin and Euchromatin 36510.2 Nondisjunction Leads to Changes in Chromosome Number 366Chromosome Nondisjunction 366Gene Dosage Alteration 366Genetic Analysis 10.111Gene Mutation, DNARepair, and HomologousRecombination 39936811.1 Mutations Are Rare and Random and AlterDNA Sequence 400Aneuploidy in Humans 368Mosaicism 370Proof of the Random Mutation HypothesisUniparental Disomy 371400Germ-Line and Somatic Mutations 40110.3 Changes in Euploid Content Leadto Polyploidy 371Point Mutations401Base-Pair Substitution MutationsCauses of Autopolyploidy and Allopolyploidy 371Frameshift Mutations402Genetic Analysis 10.2Regulatory Mutations402372Consequences of Polyploidy 373Polyploidy and EvolutionA01 SAND5173 03 SE FM.indd 8374401Experimental Insight 11.1404Forward Mutation and Reversion40511/15/17 10:46 PM

CONTENTS     ix1211.2 Gene Mutations May Arise from Spontaneous Events 405Regulation of GeneExpression in Bacteria andBacteriophage 439Spontaneous DNA Replication Errors 405Genetic Analysis 11.1407Spontaneous Nucleotide Base Changes 40911.3 Mutations May Be Caused by Chemicalsor Ionizing Radiation 410Chemical Mutagens 41012.1 Transcriptional Control of Gene Expression Requires DNA–ProteinInteraction 440Radiation-Induced DNA Damage 412Negative and Positive Control of TranscriptionThe Ames TestRegulatory DNA-Binding Proteins41312.2 The lac Operon Is an Inducible OperonSystem under Negative and PositiveControl 44311.4 Repair Systems Correct Some DNADamage 415Direct Repair of DNA Damage 415Genetic Analysis 11.2Lactose Metabolism416DNA Damage-Signaling Systems 41911.5 Proteins Control Translesion DNA Synthesis and the Repair of Double-StrandBreaks 420443lac Operon Structure444lac Operon Function44412.3 Mutational Analysis Deciphers Genetic Regulation of the lac Operon 447Translesion DNA Synthesis 420Double-Strand Break Repair 420Molecular Analysis of the lac OperonGenetic Analysis 12.111.6 DNA Double-Strand Breaks Initiate Homologous Recombination 422The Holliday Model 422The Bacterial RecBCD Pathway 422The Double-Stranded Break Model of HomologousRecombination 42244845312.4 Transcription from the Tryptophan OperonIs Repressible and Attenuated 454Feedback Inhibition of Tryptophan SynthesisAttenuation of the trp OperonThe Characteristics and Classification of TransposableElements 425The Mutagenic Effect of Transposition 426Transposable Elements in Bacterial Genomes 426459Alternative Sigma Factors and Stress ResponseThe Discovery of Ds and Ac Elements in MaizeTranslational Regulation in BacteriaCase Study Mendel’s Peas Are Shaped byTransposition 431Summary 432 Preparing for ProblemSolving 434 Problems 434A01 SAND5173 03 SE FM.indd 9459460Genetic Analysis 12.242745912.5 Bacteria Regulate the Transcriptionof Stress Response Gen

The Molecular Basis of Heredity, Variation, and Evolution 1 1.1 Modern Genetics Is in Its Second Century 2 The Development of Modern Genetics 2 The Four Phases of Modern Genetics 3 Genetics—Central to Modern Biology 5 1.2 The Structure of DNA Suggests a Mechanism for Replication 6 The Discovery of DNA Structure 6 DNA Nucleotides 7

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