دانلود کتاب iGenetics. A Molecular Approach

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Cover
Copyright Page
Title Page
Brief Contents
Detailed Contents
Preface
Acknowledgments
CHAPTER 1. Genetics: An Introduction
Classical and Modern Genetics
Geneticists and Genetic Research
The Subdisciplines of Genetics
Basic and Applied Research
Genetic Databases and Maps
Organisms for Genetics Research
Summary
CHAPTER 2. DNA: The Genetic Material
The Search for the Genetic Material
Griffith’s Transformation Experiment
Avery’s Transformation Experiment
Hershey and Chase’s Bacteriophage Experiment
RNA as Viral Genetic Material
The Composition and Structure of DNA and RNA
The DNA Double Helix
Different DNA Structures
DNA in the Cell
RNA Structure
The Organization of DNA in Chromosomes
Viral Chromosomes
Prokaryotic Chromosomes
Eukaryotic Chromosomes
Focus on Genomics: Genome Size and Repetitive DNA Content
Unique-Sequence and Repetitive-Sequence DNA
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 3. DNA Replication
Semiconservative DNA Replication
The Meselson–Stahl Experiment
DNA Polymerases, the DNA Replicating Enzymes
DNA Polymerase I
Roles of DNA Polymerases
Molecular Model of DNA Replication
Initiation of Replication
Semidiscontinuous DNA Replication
Rolling Circle Replication
DNA Replication in Eukaryotes
Replicons
Initiation of Replication
Eukaryotic Replication Enzymes
Replicating the Ends of Chromosomes
Assembling Newly Replicated DNA into Nucleosomes
Focus on Genomics: Replication Origins in Yeast
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 4. Gene Function
Gene Control of Enzyme Structure
Garrod’s Hypothesis of Inborn Errors of Metabolism
The One-Gene–One-Enzyme Hypothesis
Genetically Based Enzyme Deficiencies in Humans
Focus on Genomics: Metabolomics in the Gut
Phenylketonuria
Albinism
Kartagener Syndrome
Tay–Sachs Disease
Gene Control of Protein Structure
Sickle-Cell Anemia
Other Hemoglobin Mutants
Cystic Fibrosis
Genetic Counseling
Carrier Detection
Fetal Analysis
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 5. Gene Expression: Transcription
Gene Expression—The Central Dogma: An Overview
The Transcription Process
Transcription in Bacteria
Initiation of Transcription at Promoters
Elongation of an RNA Chain
Termination of an RNA Chain
Transcription in Eukaryotes
Eukaryotic RNA Polymerases
Transcription of Protein-Coding Genes by RNA Polymerase II
Focus on Genomics: Finding Promoters
The Structure and Production of Eukaryotic mRNAs
Self-Splicing Introns
RNA Editing
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 6. Gene Expression: Translation
Proteins
Chemical Structure of Proteins
Molecular Structure of Proteins
The Nature of the Genetic Code
The Genetic Code Is a Triplet Code
Deciphering the Genetic Code
Characteristics of the Genetic Code
Focus on Genomics: Other Genetic Codes
Translation: The Process of Protein Synthesis
Transfer RNA
Ribosomes
Initiation of Translation
Elongation of the Polypeptide Chain
Termination of Translation
Protein Sorting in the Cell
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 7. DNA Mutation, DNA Repair, and Transposable Elements
DNA Mutation
Adaptation versus Mutation
Mutations Defined
Spontaneous and Induced Mutations
Focus on Genomics: Radiation Resistance in the Archaea–Conan the Bacterium
Detecting Mutations
Repair of DNA Damage
Direct Reversal of DNA Damage
Excision Repair of DNA Damage
Human Genetic Diseases Resulting from DNA Replication and Repair Mutations
Transposable Elements
General Features of Transposable Elements
Transposable Elements in Bacteria
Transposable Elements in Eukaryotes
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 8. Genomics: The Mapping and Sequencing of Genomes
The Human Genome Project
Converting Genomes into Clones, and Clones into Genomes
DNA Cloning
Cloning Vectors and DNA Cloning
Genomic Libraries
Chromosome Libraries
DNA Sequencing and Analysis of DNA Sequences
Dideoxy Sequencing
Pyrosequencing
Analysis of DNA Sequences
Assembling and Annotating Genome Sequences
Genome Sequencing Using a Whole-Genome Shotgun Approach
Assembling and Finishing Genome Sequences
Annotation of Variation in Genome Sequences
Identification and Annotation of Gene Sequences
Focus on Genomics: The Real Old Blue Eyes
Insights from Genome Analysis: Genome Sizes and Gene Densities
Genomes of Bacteria
Genomes of Archaea
Genomes of Eukarya
Selected Examples of Genomes Sequenced
Genomes of Bacteria
Genomes of Archaea
Genomes of Eukarya
Future Directions in Genomics
Ethical, Legal, and Social Implications of the Human Genome
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 9. Functional and Comparative Genomics
Functional Genomics
Sequence Similarity Searches to Assign Gene Function
Assigning Gene Function Experimentally
Organization of the Genome
Describing Patterns of Gene Expression
Comparative Genomics
Examples of Comparative Genomics Studies and Uses
Focus on Genomics: The Neanderthal Genome Project
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 10. Recombinant DNA Technology
Versatile Vectors for More Than Simple Cloning
Shuttle Vectors
Expression Vectors
PCR Cloning Vectors
Transcribable Vectors
Non-Plasmid Vectors
Cloning a Specific Gene
Finding a Specific Clone Using a DNA Library
Focus on Genomics: Finding a New Gene Linked to Type 1 Diabetes
Identifying Genes in Libraries by Complementation of Mutations
Identifying Specific DNA Sequences in Libraries Using Heterologous Probes
Identifying Genes or cDNAs in Libraries Using Oligonucleotide Probes
Molecular Analysis of Cloned DNA
Southern Blot Analysis of Sequences in the Genome
Northern Blot Analysis of RNA
The Wide Range of Uses of the Polymerase Chain Reaction (PCR)
Advantages of Limitations of PCR
Applications of PCR
RT-PCR and mRNA Qualification
Applications of Molecular Techniques
Site-Specific Mutagenesis of DNA
Analysis of Expression of Individual Genes
Analysis of Protein–Protein Interactions
Uses of DNA Polymorphisms in Genetic Analysis
Classes of DNA Polymorphisms
DNA Molecular Testing for Human Genetic Disease Mutations
DNA Typing
Gene Therapy
Biotechnology: Commercial Products
Genetic Engineering of Plants
Transformation of Plant Cells
Applications for Plant Genetic Engineering
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 11. Mendelian Genetics
Genotype and Phenotype
Mendel’s Experimental Design
Monohybrid Crosses and Mendel’s Principle of Segregation
The Principle of Segregation
Representing Crosses with a Branch Diagram
Confirming the Principle of Segregation: The Use of Testcrosses
The Wrinkled-Pea Phenotype
Dihybrid Crosses and Mendel’s Principle of Independent Assortment
The Principle of Independent Assortment
Branch Diagram of Dihybrid Crosses
Trihybrid Crosses
The “Rediscovery” of Mendel’s Principles
Statistical Analysis of Genetic Data: The Chi-Square Test
Mendelian Genetics in Humans
Pedigree Analysis
Focus on Genomics: Sometimes Identical Just Isn’t That Similar
Examples of Human Genetic Traits
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 12. Chromosomal Basis of Inheritance
Chromosomes and Cellular Reproduction
Eukaryotic Chromosomes
Mitosis
Meiosis
Focus on Genomics: Genes Involved in Meiotic Chromosome Segregation
Chromosome Theory of Inheritance
Sex Chromosomes
Sex Linkage
Nondisjunction of X Chromosomes
Sex Chromosomes and Sex Determination
Genotypic Sex Determination
Genic Sex Determination
Analysis of Sex-Linked Traits in Humans
X-Linked Recessive Inheritance
X-Linked Dominant Inheritance
Y-Linked Inheritance
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 13. Extensions of and Deviations from Mendelian Genetic Principles
Multiple Alleles
ABO Blood Groups
Drosophila Eye Color
Relating Multiple Alleles to Molecular Genetics
Modifications of Dominance Relationships
Incomplete Dominance
Codominance
Molecular Explanations of Incomplete Dominance and Codominance
Essential Genes and Lethal Alleles
Gene Expression and the Environment
Penetrance and Expressivity
Effects of the Environment
Nature versus Nurture
Maternal Effect
Determining the Number of Genes Involved in a Set of Mutations with the Same Phenotype
Gene Interactions and Modified Mendelian Ratios
Gene Interactions That Produce New Phenotypes
Epistasis
Focus on Genomics: Redheads of the Past
Gene Interactions Involving Modifier Genes
Extranuclear Inheritance
Extranuclear Genomes
Rules of Extranuclear Inheritance
Examples of Extranuclear Inheritance
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 14. Genetic Mapping in Eukaryotes
Early Studies of Genetic Linkage: Morgan’s Experiments with Drosophila
Gene Recombination and the Role of Chromosomal Exchange
Constructing Genetic Maps
Detecting Linkage through Testcrosses
Gene Mapping with Two-Point Testcrosses
Generating a Genetic Map
Gene Mapping with Three-Point Testcrosses
Calculating Accurate Map Distances
Genetic Maps and Physical Maps Compared
Constructing Genetic Linkage Maps of the Human Genome
The lod Score Method for Analyzing Linkage of Human Genes
Human Genetic Maps
Focus on Genomics: Genome-Wide Screens for Genes Involved in Multiple Sclerosis
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 15. Genetics of Bacteria and Bacteriophages
Genetics Analysis of Bacteria
Gene Mapping in Bacteria by Conjugation
Discovery of Conjugation in E. coli
The Sex Factor F
High-Frequency Recombination Strains of E. coli
F\' Factors
Using Conjugation to Map Bacterial Genes
Circularity of the E. coli Map
Genetic Mapping in Bacteria by Transformation
Focus on Genomics: Artificial Life–Artificial Genomes and Genome Transfer
Genetic Mapping in Bacteria by Transduction
Bacteriophages
Transduction Mapping of Bacterial Chromosomes
Mapping Bacteriophage Genes
Fine-Structure Analysis of a Bacteriophage Gene
Recombination Analysis of rII Mutants
Deletion Mapping
Defining Genes by Complementation (Cis-Trans) Tests
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 16. Variations in Chromosome Structure and Number
Types of Chromosomal Mutations
Variations in Chromosome Structure
Deletion
Duplication
Inversion
Focus on Genomics: Gene Duplications and Deletions in the Androgen-Binding Protein Family
Translocation
Chromosomal Mutations and Human Tumors
Position Effect
Fragile Sites and Fragile X Syndrome
Variations in Chromosome Number
Changes in One or a Few Chromosomes
Changes in Complete Sets of Chromosomes
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 17. Regulation of Gene Expression in Bacteria and Bacteriophages
Focus on Genomics: Models of Gene Expression
The lac Operon of E. coli
Lactose as a Carbon Source for E. coli
Experimental Evidence for the Regulation of lac Genes
Jacob and Monod’s Operon Model for the Regulation of lac Genes
Positive Control of the lac Operon
Molecular Details of lac Operon Regulation
The trp Operon of E. coli
Gene Organization of the Tryptophan Biosynthesis Genes
Regulation of the trp Operon
The ara Operon of E. coli: Positive and Negative Control
Regulation of Gene Expression in Phage Lambda
Early Transcription Events
The Lysogenic Pathway
The Lytic Pathway
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 18. Regulation of Gene Expression in Eukaryotes
Levels of Control of Gene Expression in Eukaryotes
Control of Transcription Initiation by Regulatory Proteins
Regulation of Transcription Initiation by Activators
Inhibiting Transcription Initiation by Repressors
Case Study: Positive and Negative Regulation of Transcription of the Yeast Galactose Utilization Genes
Case Study: Regulation of Transcription in Animals by Steroid Hormones
Combinatorial Gene Regulation: The Control of Transcription by Combinations of Activators and Repressors
The Role of Chromatin in Regulating Gene Transcription
Repression of Gene Activity by Histones
Facilitation of Transcription Activation by Remodeling of Chromatin
Gene Silencing and Genomic Imprinting
Gene Silencing at a Telomere
Gene Silencing by DNA Methylation
Focus on Genomics: ChIP on Chip
Genomic Imprinting
RNA Processing Control: Alternative Polyadenylation and Alternative Splicing
mRNA Translation Control by Ribosome Selection
RNA Interference: Silencing of Gene Expression at the Posttranscriptional Level by Small Regulatory RNAs
The Roles of Small Regulatory RNAs in Posttranscriptional Gene Silencing
Regulation of Gene Expression Posttranscriptionally by Controlling mRNA Degradation and Protein Degradation
Control of mRNA Degradation
Control of Protein Degradation
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 19. Genetic Analysis of Development
Basic Events of Development
Model Organisms for the Genetic Analysis of Development
Developmental Results from Differential Gene Expression
Constancy of DNA in the Genome during Development
Examples of Differential Gene Activity during Development
Exception to the Constancy of Genomic DNA during Development: DNA Loss in Antibody-Producing Cells
Case Study: Sex Determination and Dosage Compensation in Mammals and Drosophila
Sex Determination in Mammals
Focus on Genomics: The Platypus–An Odd Mammal with a Very Odd Genome
Dosage Compensation Mechanism for X-Linked Genes in Mammals
Sex Determination in Drosophila
Dosage Compensation in Drosophila
Case Study: Genetic Regulation of the Development of the Drosophila Body Plan
Drosophila Developmental Stages
Embryonic Development
Microarray Analysis of Drosophila Development
The Roles of miRNAs in Development
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 20. Genetics of Cancer
Relationship of the Cell Cycle to Cancer
Molecular Control of the Cell Cycle
Regulation of Cell Division in Normal Cells
Cancers Are Genetic Diseases
Genes and Cancer
Oncogenes
Tumor Suppressor Genes
MicroRNA Genes
Mutator Genes
Telomere Shortening, Telomerase, and Human Cancer
The Multistep Nature of Cancer
Chemicals and Radiation as Carcinogens
Chemical Carcinogens
Focus on Genomics: The Cancer Methylome
Radiation
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 21. Population Genetics
Genetic Structure of Populations
Genotype Frequencies
Allele Frequencies
The Hardy–Weinberg Law
Assumptions of the Hardy–Weinberg Law
Predictions of the Hardy–Weinberg Law
Derivation of the Hardy–Weinberg Law
Extensions of the Hardy–Weinberg Law to Loci with More than Two Alleles
Extensions of the Hardy–Weinberg Law to X-Linked Alleles
Testing for Hardy–Weinberg Proportions
Using the Hardy–Weinberg Law to Estimate Allele Frequencies
Genetic Variation in Space and Time
Genetic Variation in Natural Populations
Measuring Genetic Variation at the Protein Level
Measuring Genetic Variation at the DNA Level
Focus on Genomics: The 1,000 Genome Project
Forces That Change Gene Frequencies in Populations
Mutation
Random Genetic Drift
Migration
Natural Selection
Balance between Mutation and Selection
Assortative Mating
Inbreeding
Summary of the Effects of Evolutionary Forces on the Genetic Structure of a Population
Changes in Allele Frequency Within a Population
Increases and Decreases in Genetic Variation Within Populations
The Effects of Crossing Over on Genetic Variation
The Role of Genetics in Conservation Biology
Speciation
Barriers to Gene Flow
Genetic Basis for Speciation
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 22. Quantitative Genetics
The Nature of Continuous Traits
Questions Studied in Quantitative Genetics
The Inheritance of Continuous Traits
Polygene Hypothesis for Quantitative Inheritance
Polygene Hypothesis for Wheat Kernel Color
Statistical Tools
Samples and Populations
Distributions
The Mean
The Variance and the Standard Deviation
Correlation
Regression
Analysis of Variance
Quantitative Genetic Analysis
Inheritance of Ear Length in Corn
Heritability
Components of the Phenotypic Variance
Broad-Sense and Narrow-Sense Heritability
Understanding Heritability
How Heritability is Calculated
Response to Selection
Estimating the Response to Selection
Genetic Correlations
Quantitative Trait Loci
Focus on Genomics: QTL Analysis of Aggression in Drosophila melanogaster
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
CHAPTER 23. Molecular Evolution
Patterns and Modes of Substitutions
Nucleotide Substitutions in DNA Sequences
Rates of Nucleotide Substitutions
Variation in Evolutionary Rates between Genes
Rates of Evolution in Mitochondrial DNA
Molecular Clocks
Molecular Phylogeny
Phylogenetic Trees
Focus on Genomics: Horizontal Gene Transfer
Reconstruction Methods
Phylogenetic Trees on a Grand Scale
Acquisition and Origins of New Functions
Multigene Families
Gene Duplication and Gene Conversion
Arabidopsis Genome
Summary
Analytical Approaches to Solving Genetics Problems
Questions and Problems
Glossary
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Suggested Readings
Solutions to Selected Questions and Problems
Credits
Index
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