Efnisyfirlit

• About this Book
  • Cover Page
  • Half Title Page
  • About the Authors
  • Title Page
  • Copyright Page
  • Contents in Brief
  • Contents
  • The Evolution of a Classic
  • Problem-Solving Skills for Success
  • Powerful Pedagogy
  • Acknowledgments
• Chapter 1: The Genetics Revolution
  • 1.1 The Birth of Genetics
    • Gregor Mendel—A monk in the garden
    • Mendel rediscovered
    • The central dogma of molecular biology
  • 1.2 After Cracking the Code
    • Model organisms
    • Tools for genetic analysis
  • 1.3 Genetics Today
    • From classical genetics to medical genomics
    • Investigating mutation and disease risk
    • When rice gets its feet a little too wet
    • Recent evolution in humans
    • The complex genetics of color blindness
  • Summary
  • Key Terms
  • Problems
• Part 1: Core Principles in Transmission Genetics
  • Chapter 2: Single-Gene Inheritance
    • 2.1 Single-Gene Inheritance Patterns
      • Mendel’s pioneering experiments
      • Mendel’s law of equal segregation
    • 2.2 Genes and Chromosomes
      • Single-gene inheritance in diploids
      • Single-gene inheritance in haploids
    • 2.3 The Molecular Basis of Mendelian Inheritance Patterns
      • Structural differences between alleles at the molecular level
      • Molecular aspects of gene transmission
      • Alleles at the molecular level
    • 2.4 Some Genes Discovered by Observing Segregation Ratios
      • A gene active in the development of flower color
      • A gene for wing development
      • A gene for hyphal branching
      • Predicting progeny proportions or parental genotypes by applying the principles of single-gene inheritance
    • 2.5 Sex-Linked Single-Gene Inheritance Patterns
      • Sex chromosomes
      • Sex-linked patterns of inheritance
      • X-linked inheritance
    • 2.6 Human Pedigree Analysis
      • Autosomal recessive disorders
      • Autosomal dominant disorders
      • Autosomal polymorphisms
      • X-linked recessive disorders
      • X-linked dominant disorders
      • Y-linked inheritance
      • Calculating risks in pedigree analysis
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
    • Appendix 2-1 Stages of Mitosis
    • Appendix 2-2 Stages of Meiosis
  • Chapter 3: Independent Assortment of Genes
    • 3.1 Mendel’s Law of Independent Assortment
    • 3.2 Working with Independent Assortment
      • Predicting progeny ratios
      • Using the chi-square test on monohybrid and dihybrid ratios
      • Synthesizing pure lines
      • Hybrid vigor
    • 3.3 The Chromosomal Basis of Independent Assortment
      • Independent assortment in diploid organisms
      • Independent assortment in haploid organisms
      • Recombination
    • 3.4 Polygenic Inheritance
    • 3.5 Organelle Genes: Inheritance Independent of The Nucleus
      • Patterns of inheritance in organelles
      • Cytoplasmic segregation
      • Cytoplasmic mutations in humans
      • mtDNA in evolutionary studies
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 4: Mapping Eukaryote Chromosomes by Recombination
    • 4.1 Diagnostics Of Linkage
      • Using recombinant frequency to recognize linkage
      • How crossovers produce recombinants for linked genes
      • Linkage symbolism and terminology
      • Evidence that crossing over is a breakage-and-rejoining process
      • Evidence that crossing over takes place at the four-chromatid stage
      • Multiple crossovers can include two or more than two chromatids
    • 4.2 Mapping By Recombinant Frequency
      • Map units
      • Three-point testcross
      • Deducing gene order by inspection
      • Interference
      • Using ratios as diagnostics
    • 4.3 Mapping with Molecular Markers
    • 4.4 Using the Chi-Square Test to Infer Linkage
    • 4.5 The Molecular Mechanism of Crossing Over
    • 4.6 Using Recombination-Based Maps in Conjunction with Physical Maps
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 5: Gene Interaction
    • 5.1 Interactions Between the Alleles of a Single Gene: Variations on Dominance
      • Complete dominance and recessiveness
      • Incomplete dominance
      • Codominance
      • Recessive lethal alleles
      • Penetrance and expressivity
    • 5.2 Interaction of Genes in Pathways
      • Biosynthetic pathways in Neurospora
      • Gene interaction in other types of pathways
    • 5.3 Inferring Gene Interactions
      • Sorting mutants using the complementation test
      • Analyzing double mutants of random mutations
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 6: The Genetics of Bacteria and Their Viruses
    • 6.1 Working with Microorganisms
    • 6.2 Bacterial Conjugation
      • Discovery of conjugation
      • Discovery of the fertility factor
      • Strains
        • Linear transmission of the genes from a fixed point
        • Inferring integration sites of and chromosome circularity
      • Mapping of bacterial chromosomes
        • Broad-scale chromosome mapping by using time of entry
        • Fine-scale chromosome mapping by using recombinant frequency
      • F plasmids that carry genomic fragments
      • Plasmids
    • 6.3 Bacterial Transformation
      • The nature of transformation
      • Chromosome mapping using transformation
    • 6.4 Bacteriophage Genetics
      • Infection of bacteria by phages
      • Mapping phage chromosomes by using phage crosses
    • 6.5 Transduction
      • Discovery of transduction
      • Generalized transduction
      • Specialized transduction
        • Behavior of the prophage
        • Insertion
      • Mechanism of specialized transduction
    • 6.6 Physical Maps and Linkage MAPS Compared
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
• Part 2: Core Principles in Molecular and Developmental Genetics
  • Chapter 7: DNA: Structure and Replication
    • 7.1 DNA is the Genetic Material
      • The discovery of bacterial transformation: The Griffith experiment
      • Evidence DNA that is the genetic material in bacteria: The Avery, MacLeod, and McCarty experiments
      • Evidence DNA that is the genetic material in phage: The Hershey–Chase experiment
    • 7.2 DNA Structure
      • DNA Structure before Watson and Crick
        • The building blocks of
        • Chargaff’s rules of base composition
        • Diffraction analysis of : Rosalind Franklin
      • The DNA double helix structure: Watson and Crick
    • 7.3 DNA Replication is Semiconservative
      • Evidence that DNA replication is semiconservative: The Meselson–Stahl experiment
      • Evidence for a replication fork: The Cairns experiment
    • 7.4 Replication in Bacteria
      • Unwinding the DNA double helix
      • Assembling the replisome: replication initiation
      • DNA Polymerases catalyze chain elongation
      • DNA Replication is semidiscontinuous
      • DNA Replication is accurate and rapid
    • 7.5 DNA Replication in Eukaryotes
      • Eukaryotic origins of replication
      • DNA Replication and the yeast cell cycle
      • Replication origins in higher eukaryotes
      • Telomeres and telomerase: Replication termination
    • Summary
    • Key Terms
    • Problems
  • Chapter 8: RNA: Transcription, Processing, and Decay
    • 8.1 RNA Structure
      • RNA is the information-carrying intermediate between DNA and proteins
      • Consequences of the distinct chemical properties of RNA
      • Classes of RNA
    • 8.2 Transcription and Decay of mRNA in Bacteria
      • Overview: DNA as transcription template
      • Stages of transcription
        • Transcription initiation in bacteria
        • Transcription elongation in bacteria
        • Transcription termination in bacteria
        • mRNA decay in bacteria
    • 8.3 Transcription in Eukaryotes
      • Transcription initiation in eukaryotes
        • RNA polymerase I promoters and GTFs
        • RNA polymerase II promoters and GTFs
        • RNA polymerase III promoters and GTFs
      • RNA polymerase II transcription elongation
      • Transcription termination in eukaryotes
    • 8.4 Processing of mRNA in Eukaryotes
      • Capping
      • Polyadenylation
      • The discovery of splicing
      • The splicing mechanism
      • snRNAs in the spliceosome may carry out the catalytic steps of splicing
      • Alternative splicing can expand the proteome
      • RNA editing
      • RNA nucleotide modification
      • RNA export from the nucleus
    • 8.5 Decay of mRNA in Eukaryotes
      • mRNA decay mechanisms
      • The discovery of RNA interference (RNAi)
      • siRNA-mediated RNA decay and transcriptional silencing
      • RNAi protects the genome from foreign DNA
    • Summary
    • Key Terms
    • Problems
  • Chapter 9: Proteins and Their Synthesis
    • 9.1 Protein Structure
    • 9.2 The Genetic Code
      • A degenerate three-letter genetic code specifies the 20 amino acids
      • The genetic code is nonoverlapping and continuous
      • Cracking the code
      • Stop codons
      • Degeneracy of the genetic code limits the effects of point mutations
    • 9.3 tRNAs and Ribosomes
      • tRNAs are adaptors
      • Wobble base pairing allows tRNAs to recognize more than one codon
      • Ribosome structure and function
    • 9.4 Translation
      • Translation initiation
      • Translation elongation
      • Translation termination
      • Nonsense suppressor mutations
    • 9.5 Translational and Post-Translational Regulation
      • Protein folding
      • Post-translational modification of amino acid side chains
        • Phosphorylation
        • Ubiquitination
      • Protein targeting
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 10: Gene Isolation and Manipulation
    • 10.1 Detecting and Quantifying DNA, RNA, and Protein
      • Detecting and quantifying molecules by Southern, Northern, and Western blot analysis
      • Detecting and amplifying DNA by the polymerase chain reaction
    • 10.2 Generating Recombinant DNA
      • DNA cloning
      • DNA libraries
      • Identifying a clone of interest from a genomic or cDNA library
      • Genomic and cDNA clones are used in different ways
      • Cloning by PCR
    • 10.3 Sequencing DNA
    • 10.4 Engineering Genomes
      • Genetic engineering in Saccharomyces cerevisiae
      • Genetic engineering in plants
      • Genetic engineering in animals
      • CRISPR-Cas9 genome engineering
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 11: Regulation of Gene Expression in Bacteria and Their Viruses
    • 11.1 Gene Regulation
      • The Basics of Bacterial Transcriptional Regulation: Genetic Switches
      • A First Look at the Lac Regulatory Circuit
    • 11.2 Discovery of the Lac System: Negative Regulation
      • Genes Controlled Together
      • Genetic Evidence for the Operator and Repressor
      • Genetic Evidence for Allostery
      • Genetic Analysis of the Lac Promoter
      • Molecular Characterization of the Lac Repressor and the Lac Operator
    • 11.3 Catabolite Repression of the Lac Operon: Positive Regulation
      • The Basics of Lac Catabolite Repression: Choosing the Best Sugar to Metabolize
      • The Structures of Target DNA Sites
      • A Summary of the Lac Operon
    • 11.4 Dual Positive and Negative Regulation: The Arabinose Operon
    • 11.5 Metabolic Pathways and Additional Levels of Regulation: Attenuation
    • 11.6 Bacteriophage life Cycles: More Regulators, Complex Operons
      • Regulation of the Bacteriophage λ life Cycle
      • Molecular Anatomy of the Genetic Switch
      • Sequence-Specific Binding of Regulatory Proteins to DNA
    • 11.7 Alternative Sigma Factors Regulate Large Sets of Genes
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 12 Regulation of Transcription in Eukaryotes
    • 12.1 Transcription Factors Regulate Transcription
      • Transcription factors bind distal and proximal enhancers
      • Transcription factors: lessons from the yeast GAL system
        • Gal4 binds enhancers called upstream activation sequences
      • Gal4 domains function independently of one another
      • Regulation of Gal4
      • Combinatorial control of transcription: lessons from yeast mating type
    • 12.2 Chromatin Structure
      • Histones
      • Nucleosomes
      • Chromatin folding
    • 12.3 Chromatin Regulates Transcription
      • Histone modification: a type of chromatin modification
      • The histone code hypothesis
      • DNA modification: another type of chromatin modification
      • Chromatin remodeling
      • Connecting chromatin structure to transcription: lessons from the interferon‐β gene
    • 12.4 Chromatin in Epigenetic Regulation
      • Cellular memory
      • Position-effect variegation
      • Genomic imprinting
      • X-chromosome inactivation
    • Summary
    • Key Terms
    • Problems
  • Chapter 13: The Genetic Control of Development
    • 13.1 The Genetic Approach to Development
    • 13.2 The Genetic Toolkit for Drosophila Development
      • Classification of genes by developmental function
      • Homeotic genes and segmental identity
      • Organization and expression of Hox genes
      • The homeobox
      • Clusters of Hox genes control development in most animals
    • 13.3 Defining the Entire Toolkit
      • The anteroposterior axis
      • Expression of toolkit genes
    • 13.4 Spatial Regulation of Gene Expression in Development
      • Maternal gradients and gene activation
      • Drawing stripes: Integration of gap-protein inputs
      • Making segments different: integration of inputs
    • 13.5 Post-Transcriptional Regulation of Gene Expression in Development
      • RNA splicing and sex determination in Drosophila
      • Regulation of mRNA translation and cell lineage in C. elegans
      • Translational control in the early embryo
      • miRNA control of developmental timing in C. elegans and other species
    • 13.6 From Flies to Fingers, Feathers, and Floor Plates: The Many Roles of Individual Toolkit Genes
    • 13.7 Development and Disease
      • Polydactyly
      • Holoprosencephaly
      • Cancer as a developmental disease
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 14: Genomes and Genomics
    • 14.1 The Genomics Revolution
    • 14.2 Obtaining the Sequence of a Genome
      • Turning sequence reads into an assembled sequence
      • Whole-genome sequencing
      • Traditional WGS sequencing
      • Next-generation WGS sequencing
      • Whole-genome-sequence assembly
    • 14.3 Bioinformatics: Meaning from Genomic Sequence
      • The nature of the information content of DNA
      • Deducing the protein-encoding genes from genomic sequence
    • 14.4 The Structure of the Human Genome
      • Noncoding functional elements in the genome
    • 14.5 The Comparative Genomics of Humans with other Species
      • Phylogenetic inference
      • Of mice and humans
      • Comparative genomics of chimpanzees and humans
    • 14.6 Comparative Genomics and Human Medicine
      • The evolutionary history of human disease genes
      • The exome and personalized genomics
      • Comparative genomics of nonpathogenic and pathogenic E. coli
    • 14.7 Functional Genomics and Reverse Genetics
      • “ ’Omics”
      • Reverse genetics
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
• Part 3: Core Principles in Mutation, Variation, and Evolution
  • Chapter 15: DNA Damage, Repair, and Mutation
    • 15.1 Molecular Consequences of Point Mutations
      • The types of point mutations
      • The molecular consequences of a point mutation in an open reading frame
      • The molecular consequences of a point mutation in a noncoding region
    • 15.2 Molecular Basis of Spontaneous Mutations
      • Evidence for spontaneous mutations: The Luria and Delbrück fluctuation test
      • Mechanisms of spontaneous mutations
    • 15.3 Molecular Basis of Induced Mutations
      • Mechanisms of induced mutagenesis
      • Identifying mutagens in the environment: The Ames test
    • 15.4 DNA Repair Mechanisms
      • Direct repair of damaged DNA
      • Base excision repair
      • Nucleotide excision repair
      • Mismatch repair
      • Translesion synthesis
      • Repair of double-strand breaks
    • Summary
    • Key Terms
    • Problems
  • Chapter 16: The Dynamic Genome: Transposable Elements
    • 16.1 Discovery of Transposable Elements in Maize
      • McClintock’s experiments: the Ds element
      • Ac (Activator) and Ds (Dissociation) today
      • Transposable elements: Only in maize?
    • 16.2 Transposable Elements in Bacteria
      • Evidence for transposable elements in bacteria
      • Simple and composite transposons
      • Mechanism of transposition
    • 16.3 Transposable Elements in Eukaryotes
      • Class 1: retrotransposons
      • Class 2: DNA transposons
      • Utility of DNA transposons as tools for genetic research
    • 16.4 The Dynamic Genome: More Transposable Elements Than Ever Imagined
      • Large genomes are largely transposable elements
      • Transposable elements in the human genome
      • Plants: LTR-retrotransposons thrive in large genomes
      • Safe havens
    • 16.5 Regulation of Transposable Element Movement by the Host
      • RNAi silencing of transposable elements
      • Genome surveillance
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 17: Large-Scale Chromosomal Changes
    • 17.1 Changes in Chromosome Number
      • Aberrant euploidy
      • Aneuploidy
      • The concept of gene balance
    • 17.2 Changes in Chromosome Structure
      • Deletions
      • Duplications
      • Inversions
      • Reciprocal translocations
      • Robertsonian translocations
      • Applications of inversions and translocations
    • 17.3 Phenotypic Consequences of Chromosomal Changes
      • Chromosome rearrangements and evolution
      • Chromosome rearrangements and cancer
      • Overall incidence of human chromosome mutations
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 18: Population Genetics
    • 18.1 Detecting Genetic Variation
      • Single nucleotide polymorphisms (SNPs)
      • Microsatellites
      • Haplotypes
      • Other sources and forms of variation
    • 18.2 The Gene-Pool Concept and the Hardy–Weinberg Law
    • 18.3 Mating Systems
      • Assortative mating
      • Isolation by distance
      • Inbreeding
      • The inbreeding coefficient
      • Population size and inbreeding
    • 18.4 Genetic Variation and its Measurement
    • 18.5 The Modulation of Genetic Variation
      • New alleles enter the population: mutation and migration
      • Recombination and linkage disequilibrium
      • Genetic drift and population size
      • Selection
      • Forms of selection
      • Balance between mutation and drift
      • Balance between mutation and selection
    • 18.6 Biological and Social Applications
      • Conservation genetics
      • Calculating disease risks
      • DNA forensics
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 19: The Inheritance of Complex Traits
    • 19.1 Measuring Quantitative Variation
      • Types of traits and inheritance
      • The mean
      • The variance
      • The normal distribution
    • 19.2 A Simple Genetic Model for Quantitative Traits
      • Genetic and environmental deviations
      • Genetic and environmental variances
      • Correlation between variables
    • 19.3 Broad-Sense Heritability: Nature Versus Nurture
      • Measuring heritability in humans using twin studies
    • 19.4 Narrow-Sense Heritability: Predicting Phenotypes
      • Gene action and the transmission of genetic variation
      • The additive and dominance effects
      • A model with additivity and dominance
      • Narrow-sense heritability
      • Predicting offspring phenotypes
      • Selection on complex traits
    • 19.5 Mapping QTL in Populations With Known Pedigrees
      • The basic method for QTL mapping
      • From QTL to gene
    • 19.6 Association Mapping in Random-Mating Populations
      • The basic method for GWAS
      • GWA, genes, disease, and heritability
    • Summary
    • Key Terms
    • Solved Problems
    • Problems
  • Chapter 20: Evolution of Genes, Traits, and Species
    • 20.1 Evolution by Natural Selection
    • 20.2 Natural Selection in Action: An Exemplary Case
      • The Selective Advantage of HbS
      • The Molecular Origins of HbS
    • 20.3 Molecular Evolution
      • The Development of the Neutral Theory of Evolution
      • The Rate of Neutral Substitutions
      • The Signature of Purifying Selection on DNA Sequences
      • The Signature of Positive Selection on DNA Sequences
    • 20.4 Evolution of Genes and Genomes
      • Expanding Gene Number
      • The Fate of Duplicated Genes
      • The Fate of Duplicated Genomes
    • 20.5 Evolution of Traits
      • Adaptive Changes in a Pigment-Regulating Protein
      • Gene Inactivation
      • Regulatory-Sequence Evolution
      • Loss of Characters Through Regulatory-Sequence Evolution
      • Regulatory Evolution in Humans
    • 20.6 Evolution of Species
      • Species Concepts
      • Mechanisms of Reproductive Isolation
      • Genetics of Reproductive Isolation
    • Summary
    • Key Terms
    • Problems
• A Brief Guide to Model Organisms
  • Escherichia Coli
  • Saccharomyces Cerevisiae
  • Neurospora Crassa
  • Arabidopsis Thaliana
  • Caenorhabditis Elegans
  • Drosophila Melanogaster
  • Mus Musculus
  • Beyond Model Organisms
• Appendix A: Genetic Nomenclature
• Appendix B: Bioinformatic Resources for Genetics and Genomics
• Glossary
• Answers to Selected Problems
• Notes
• Index
• Back Cover

UM RAFBÆKUR Á HEIMKAUP.IS

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