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Cover of An Introduction to Genetic Analysis

An Introduction to Genetic Analysis, 7th edition

, , , , and .

Author Information
New York: W. H. Freeman; .
ISBN-10: 0-7167-3520-2

Excerpt

True to its title, the theme of this book is genetic analysis. This theme emphasizes our belief that the best way to understand genetics is by learning how genetic inference is made. On almost every page, we recreate the landmark experiments in genetics and have the students analyze the data and draw conclusions as if they had done the research themselves. This proactive process teaches students how to think like scientists. The modes of inference and the techniques of analysis are the keys to future exploration.

Similarly, quantitative analysis is central to the book because many of the new ideas in genetics, from the original conception of the gene to such modern techniques as SSLP mapping, are based on quantitative analysis. The problems at the end of each chapter provide students with the opportunity to test their understanding in quantitative analyses that effectively simulate the act of doing genetics.

Contents

  • Preface
  • Chapter 1. Genetics and the Organism
    • Introduction
    • Genes as determinants of the inherent properties of species
      • DNA and its replication
      • Generation of form
    • Genetic variation
      • Types of variation
      • Molecular basis of allelic variation
    • Methodologies used in genetics
      • Detecting specific molecules of DNA, RNA, and protein
    • Genes, the environment, and the organism
      • Genetic determination
      • Environmental determination
      • The use of genotype and phenotype
      • Norm of reaction
      • Developmental noise
      • Three levels of development
    • Summary
    • Concept Map
    • Problems
  • Chapter 2. Patterns of Inheritance
    • Introduction
    • Mendel’s experiments
      • Plants differing in one character
      • Molecular basis of Mendelian genetics
      • Plants differing in two characters
    • Using genetic ratios
    • Sex chromosomes and sex-linked inheritance
    • Human genetics
      • Medical genetics
      • X-chromosome inactivation
      • Y-linked inheritance
      • Human autosomal polymorphisms
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 3. Chromosomal Basis of Heredity
    • Introduction
    • Historical development of the chromosome theory
      • Evidence from nuclear division
      • Evidence from sex linkage
      • An aside on genetic symbols
      • A critical test of the chromosome theory
    • Mendelian genetics in eukaryotic life cycles
      • Diploids
      • Haploids
      • Alternating haploid and diploid
      • The molecular basis of mitosis and meiosis
    • Topography of the chromosome set
      • Chromosome number
      • Chromosome size
      • Centromeres
      • Position of nucleolar organizers
      • Chromomere patterns
      • Heterochromatin patterns
      • Banding patterns
    • Three-dimensional structure of chromosomes
      • One DNA molecule per chromosome
      • Role of histone proteins in packaging DNA
      • High-order coiling
      • Nature of heterochromatin and euchromatin
    • Sequence organization
      • Functional repetitive sequences
      • Sequences with no known function
      • Spacer DNA
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 4. Gene Interaction
    • Introduction
    • From genes to phenotypes
    • A diagnostic test for alleles
    • Interactions between the alleles of one gene
      • Incomplete dominance
      • Codominance
      • Lethal alleles
    • Gene interaction and modified dihybrid ratios
      • Interacting genes in different pathways
      • Interacting genes in the same pathway
    • Gene interaction in petal color of foxgloves
    • Gene interaction in coat color of mammals
      • A gene
      • B gene
      • C gene
      • D gene
      • S gene
    • Penetrance and expressivity
    • Chi-square test
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 5. Basic Eukaryotic Chromosome Mapping
    • Introduction
    • The discovery of linkage
    • Recombination
      • Recombination by independent assortment
      • Recombination by crossing-over
    • Linkage symbolism
    • Linkage of genes on the X chromosome
    • Linkage maps
    • Three-point testcross
    • Interference
    • Calculating recombinant frequencies from selfed dihybrids
    • Examples of linkage maps
    • Chi-square test for linkage
    • Mapping with molecular markers
      • Use of restriction fragment length polymorphisms in mapping
      • Use of polymorphism of VNTRs in mapping
    • Linkage mapping by recombination in humans
      • Mapping the X chromosome
      • Lod score for linkage testing by pedigrees
    • Nature of crossing-over
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 6. Specialized Eukaryotic Chromosome Mapping Techniques
    • Introduction
    • Accurate calculation of large map distances
      • Poisson distribution
      • Derivation of a mapping function
    • Analysis of single meioses
      • Advantages of haploids for genetic analysis
      • Benefits of analyzing individual meioses in genetics
      • Using linear tetrads to map centromeres
      • Using tetrad analysis to correct map distance for double crossovers
    • Mapping genes by mitotic segregation and recombination
      • Mitotic segregation
      • Mitotic crossing-over
      • Mitotic recombination in fungi
    • Mapping by in situ hybridization
    • Mapping human genes by using human–rodent somatic cell hybrids
      • Assigning genes to chromosomes
      • Chromosome mapping
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 7. Gene Transfer in Bacteria and Their Viruses
    • Introduction
    • Working with microorganisms
    • Bacterial conjugation
      • Discovery of conjugation
      • Requirement for physical contact
      • Discovery of the fertility factor (F)
      • Hfr strains
      • Determining linkage from interrupted-mating experiments
      • Chromosome circularity and integration of F
      • R factors
      • Mechanics of transfer
      • E. coli conjugation cycle
      • Recombination between marker genes after transfer
      • Gradient of transfer
      • Determining gene order from gradient of transfer
      • Higher-resolution mapping by recombinant frequency in bacterial crosses
      • Sample cross
      • Infectious marker-gene transfer by episomes
    • Bacterial transformation
      • Linkage information from transformation
    • Bacteriophage genetics
      • Infection of bacteria by phages
      • Phage cross
      • rII system
      • Selection in genetic crosses of bacteriophages
    • Transduction
      • Discovery of transduction
      • Transducing phages and generalized transduction
      • Linkage data from transduction
      • Lysogeny
      • Genetic basis of lysogeny
      • Prophage attachment
      • Specialized transduction
    • Chromosome mapping
    • Bacterial gene transfer in review
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 8. The Structure and Replication of DNA
    • Introduction
    • DNA: The genetic material
      • Discovery of transformation
      • Hershey-Chase experiment
    • Structure of DNA
      • Double helix
      • Three-dimensional view of the double helix
      • Implications of DNA structure
      • Alternative structures
    • Replication of DNA
      • Semiconservative replication
      • Meselson-Stahl experiment
      • Autoradiography
      • Harlequin chromosomes
      • Chromosome structure
      • Replication fork
      • Rolling-circle replication
    • Mechanism of DNA replication
      • DNA polymerases
      • Prokaryotic origins of replication
      • Eukaryotic origins of replication
      • Priming DNA synthesis
      • Leading strand and lagging strand
      • Replication at chromosome tips
      • Helicases and topoisomerases
      • Exonuclease editing
      • Eukaryotic DNA polymerases
      • Experimental applications of base-sequence complementarity
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 9. Genetics of DNA Function
    • Introduction
    • How genes work
      • One-gene–one-enzyme hypothesis
      • Experiments of Beadle and Tatum
    • Gene-protein relations
      • Protein structure
      • Protein motifs
      • Determining protein sequence
      • Relation between gene mutations and altered proteins
      • Colinearity of gene and protein
      • X-ray determination of threedimensional structure of proteins
      • Enzyme function
      • Genes and cellular metabolism: genetic diseases
      • Genetic observations explained by enzyme structure
    • Genetic fine structure
      • Intragenic recombination
    • Mutational sites
      • Using deletions in mapping mutational sites
      • Deletion mapping of the rII region
      • Analysis of mutational sites
      • Destruction of the bead theory
    • Complementation
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 10. Molecular Biology of Gene Function
    • Introduction
    • Properties of RNA
    • Transcription
      • Early experiments suggesting RNA intermediate
      • Complementarity and asymmetry in RNA synthesis
    • Transcription and RNA polymerase
      • RNA polymerase
      • Initiation
      • Elongation
      • Termination
    • Eukaryotic RNA
      • RNA synthesis
      • RNA processing
      • Split genes
      • Alternative splicing
      • Mechanism of gene splicing
      • Self-splicing RNA
    • Translation
      • Application of sucrose gradients
    • Genetic code
      • Overlapping versus nonoverlapping codes
      • Number of letters in the code
      • Use of suppressors to demonstrate a triplet code
      • Degeneracy of the genetic code
      • Cracking the code
      • tRNA recognition of the codon
      • The complete code
      • Multiple codons for a single amino acid
      • Stop codons
    • Protein synthesis
      • Ribosomes
      • Initiation
      • Elongation
      • Termination
      • Overview of protein synthesis
      • Protein processing
      • Protein splicing
    • Universality of genetic information transfer
    • Functional division of labor in the gene set
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 11. Regulation of Gene Transcription
    • Introduction
    • Basic control circuits
    • Discovery of the lac system: negative control
      • Genes controlled together
      • The I gene
      • The repressor
      • The operator and the operon
      • The lac promoter
      • Characterization of the lac repressor and the lac operator
    • Catabolite repression of the lac operon: positive control
    • Positive and negative control
    • Dual positive and negative control: the arabinose operon
    • Metabolic pathways
    • Additional examples of control: attenuation
    • Lambda phage: a complex of operons
    • Transcription: an overview of gene regulation in eukaryotes
      • Cis-acting sequences in transcriptional regulation
      • Core promoter and promoter-proximal elements
      • Distance-independent cis-acting elements
      • Mechanisms for action at a distance
      • Trans control of transcription
      • Tissue-specific regulation of transcription
      • Properties of tissue-specific enhancers
      • Dissecting eukaryotic regulatory elements
      • Using reporter genes to find enhancers
      • Regulatory elements and dominant mutations
    • Regulation of transcription factors
      • Steroid hormones: linking enhancers to the physiology of the organism
      • Structure of regulatory proteins
    • Epigenetic inheritance
      • Paramutation
      • Parental imprinting
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 12. Recombinant DNA Technology
    • Introduction
    • Making recombinant DNA
      • Isolating DNA
      • Cutting DNA
      • Joining DNA
      • Amplifying recombinant DNA
    • Cloning a specific gene
      • Choosing a cloning vector
      • Making a DNA library
      • Finding specific clones by using probes
      • Finding specific clones by functional complementation
      • Positional cloning
      • Cloning a gene by tagging
    • Using cloned DNA
      • Cloned DNA used as a probe
      • Probing to find a specific nucleic acid in a mixture
      • DNA sequence determination
      • Detecting and amplifying sequences by the polymerase chain reaction
      • Locating genes on restriction maps
      • A century of genetic research on alkaptonuria
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problem
    • Problems
  • Chapter 13. Applications of Recombinant DNA Technology
    • Introduction
    • In vitro mutagenesis
    • RFLP mapping
    • Reverse genetics
    • Expressing eukaryotic genes in bacteria
    • Recombinant DNA technology in eukaryotes
      • Transgenic eukaryotes
      • Genetic engineering in baker’s yeast
      • Genetic engineering in plants
      • Transgenic crop plants
      • Genetic engineering in animals
    • Gene therapy
      • Human gene therapy
    • Using recombinant DNA to detect disease alleles directly
      • Alteration of restriction site by mutation
      • Probing for altered sequences
      • PCR tests
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 14. Genomics
    • Introduction
    • Genomics: an overview
    • Genome projects: practical considerations
    • Structural genomics
      • Assigning loci to specific chromosomes
      • High-resolution chromosome maps
      • Physical mapping of genomes
      • Genome sequencing
      • Using genome maps for genetic analysis
    • Functional genomics
      • Characterize the proteome by ORF analysis
      • Gene disruption knockouts
      • The study of gene interactions by the yeast two-hybrid system
      • The study of developmental regulation by using DNA chips
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 15. Gene Mutation
    • Introduction
    • How DNA changes affect phenotype
    • Somatic versus germinal mutation
      • Somatic mutation
      • Germinal mutation
    • Mutant types
      • Morphological mutations
      • Lethal mutations
      • Conditional mutations
      • Biochemical mutations
      • Loss-of-function mutations
      • Gain-of-function mutations
    • Occurrence of mutations
      • Mutation detection systems
      • How common are mutations?
    • Selective systems
      • Reversion of auxotrophs
      • Filtration enrichment
      • Penicillin enrichment
      • Resistance
      • Measuring mutation rate
      • Isolating mutations from cultures of plant and animal cells
    • Mutation induction
    • Mutation and cancer
    • Mutagens in genetic dissection
    • Mutation breeding
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 16. Mechanisms of Gene Mutation
    • Introduction
    • Molecular basis of gene mutations
    • Spontaneous mutations
      • Errors in DNA replication
      • Spontaneous lesions
      • Spontaneous mutations and human diseases
    • Induced mutations
      • Mutational specificity
      • Mechanisms of mutagenesis
      • Ionizing radiation
    • Reversion analysis
    • Relation between mutagens and carcinogens
      • Induced mutations and human cancer
      • Ames test
    • Biological repair mechanisms
      • Prevention of errors before they happen
      • Direct reversal of damage
      • Excision-repair pathways
      • Postreplication repair
      • Strategy for repair
      • Mutators
    • Repair defects and human diseases
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problem
    • Problems
  • Chapter 17. Chromosome Mutation I: Changes in Chromosome Structure
    • Introduction
    • Origin of changes in chromosome structure
      • Types of changes
      • Mechanisms of change
    • Deletions
    • Duplications
    • Inversions
    • Translocations
      • Use of translocations in producing duplications and deletions
      • Position-effect variegation
    • Diagnosis of rearrangements by tetrad analysis
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 18. Chromosome Mutation II: Changes in Chromosome Number
    • Introduction
    • Aberrant euploidy
      • Monoploids
      • Polyploids
      • Triploids
      • Autotetraploids
      • Allopolyploids
      • Somatic allopolyploids from cell hybridization
      • Polyploidy in animals
    • Aneuploidy
      • Nullisomics (2n − 2)
      • Monosomics (2n − 1)
      • Trisomics (2n + 1)
      • Disomics (n + 1)
      • Somatic aneuploids
    • Mechanisms of gene imbalance
    • Chromosome mechanics in plant breeding
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 19. Mechanisms of Recombination
    • Introduction
    • Breakage and reunion of DNA molecules
    • Chiasmata: the crossover points
    • Genetic results leading to recombination models
    • Holliday model
      • Enzymatic cleavage and the creation of heteroduplex DNA
      • Branch migration
      • Resolution of the Holliday structure
      • Application of the Holliday model to genetic crosses
      • Meselson-Radding model
      • Double-strand break-repair model for recombination
      • Visualization of recombination intermediates
    • Enzymatic mechanism of recombination
      • Production of single-stranded DNA
      • RecA-protein-mediated single-strand exchange
      • Branch migration
      • Resolution of Holliday junctions
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 20. Transposable Genetic Elements
    • Introduction
    • Controlling elements in maize
      • McClintock’s experiments: the Ds element
      • The wx (waxy) locus
      • General characteristics of controlling elements
    • Bacterial insertion sequences
      • Physical demonstration of DNA insertion
      • Direct visualization of inserted DNA
      • Identification of discrete IS elements
      • Orientation of IS elements
    • Prokaryotic transposons
      • Physical structure of transposons
      • Movement of transposons
      • Phage mu
    • Mechanism of transposition in prokaryotes
      • Replicative transposition
      • Conservative transposition
      • Molecular consequences of transposition
      • Rearrangements mediated by transposable elements
    • Review of transposable elements in prokaryotes
    • Molecular nature of transposable elements in eukaryotes
      • Retroviruses
      • Retrotransposons
      • Nonviral retrotransposons: LINES and SINES
      • Function of transposable elements
      • Uses of transposable elements
      • P elements
      • Using P elements to insert genes
    • Review of transposable elements in eukaryotes
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problem
    • Problems
  • Chapter 21. Extranuclear Genes
    • Introduction
    • Origin of extranuclear genes
    • Structure of organelle chromosomes
      • Overall organization
      • How many copies?
      • Mitochondrial genomes
      • Chloroplast genomes
    • Organelle mutations
    • Inheritance of organelle genes and mutations
      • Expression of organelle mutations
      • Cytoplasmic segregation
      • Maternal inheritance
    • Recombination of extranuclear DNA
    • Cytoplasmic male sterility
    • Mitochondria and aging
    • Summary
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 22. Cancer as a Genetic Disease
    • Introduction
    • Cancer and the control of cell number: an overview
      • Machinery of cell proliferation
      • Machinery of cell death
      • Linking cell proliferation and death to the environment
    • Cell proliferation machinery
      • Cell cycle
      • Cyclins and cyclin-dependent protein kinases
      • CDK targets
      • Yeasts: genetic models for the cell cycle
    • Machinery for programmed cell death
      • Apoptosis pathway
      • Caspases
      • The nematode Caenorhabditis elegans: a genetic model for programmed cell death
    • Controlling the cell-proliferation and death machinery
      • Intracellular signals
      • Extracellular signals
      • An integrated view of the control of cell numbers
    • Cancer: the genetics of aberrant cell control
      • How cancer cells differ from normal cells
      • Evidence for the genetic origin of cancers
      • Mutations in cancer cells
      • Classes of oncogenes
      • Types of oncogene mutations
      • Classes of tumor-suppressor genes
      • Inheritance of the tumor phenotype
      • p53 tumor-suppressor gene: a link between the cell cycle and apoptosis
      • Complexities of cancer
    • Cancer research in the genomic analysis era
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 23. Developmental Genetics
    • Introduction
    • Central themes of developmental genetics
      • Logic of building the body plan
      • Major decisions in building the embryo
      • Applying regulatory mechanisms to developmental decisions
    • Gene regulation at levels other than transcription initiation: examples
      • Tissue-specific regulation at the level of DNA structure
      • Transcript processing and tissue-specific regulation
      • Posttranscriptional regulation
      • Posttranslational regulation
    • Binary fate decisions: pathways of sex determination
    • Drosophila sex determination: every cell for itself
      • Phenotypic consequences of different X-chromosome-to-autosome ratios
      • Basics of the regulatory pathway
      • Regulatory switch
      • Mutational analysis of Drosophila sex determination
    • Sex determination in mammals: coordinated control by the endocrine system
      • Mammalian reproductive development and endocrine organ control
      • Setting the switch in the “on” or “off” position
      • Mutational analysis of mammalian sex determination
    • Binary fate decisions: the germ line versus the soma
      • Cytoskeleton of the cell
      • Intrinsic asymmetry of cytoskeletal filaments
      • Localizing determinants through cytoskeletal asymmetries: the germ line
    • Forming complex pattern: establishing positional information
      • Mutational analysis of early Drosophila development
      • Cytoskeletal asymmetries and the Drosophila anterior–posterior axis
      • Studying the BCD gradient
      • Cell–cell signaling and the Drosophila dorsal–ventral axis
      • The two classes of positional information
    • Forming complex pattern: utilizing positional information to establish cell fates
      • Initial interpretation of positional information
      • Refining fate assignments through transcription-factor interactions
      • A cascade of regulatory events
    • Additional aspects of pattern formation
      • Memory systems for remembering cell fate
      • Ensuring that all fates are allocated: decisions by committee
      • Developmental pathways are composed of plug and play modules
    • The many parallels in vertebrate and insect pattern formation
    • Do the lessons of animal development apply to plants?
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 24. Population Genetics
    • Introduction
    • Variation and its modulation
      • Observations of variation
      • DNA sequence polymorphism
      • Quantitative variation
    • Effect of sexual reproduction on variation
    • Sources of variation
      • Variation from mutations
      • Variation from recombination
      • Variation from migration
      • Inbreeding and assortative mating
      • Balance between inbreeding and new variation
    • Selection
      • Two forms of selection
      • Measuring fitness differences
      • How selection works
      • Rate of change in gene frequency
    • Balanced polymorphism
    • Artificial selection
    • Random events
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 25. Quantitative Genetics
    • Introduction
    • Some basic statistical notions
      • Distributions
      • Statistical measures
    • Genotypes and phenotypic distribution
    • Norm of reaction and phenotypic distribution
    • Determining norms of reaction
      • In domesticated plants and animals
      • In natural populations
      • Results of norm of reaction studies
    • Heritability of a trait
      • Familiality and heritability
      • Phenotypic similarity between relatives
    • Quantifying heritability
      • Methods of estimating H2
      • Meaning of H2
    • Locating the genes
      • Marker-gene segregation
      • Linkage analysis
    • More on analyzing variance
      • Additive and dominance variance
      • Estimating genetic variance components
      • Use of h2 in breeding
    • Summary
    • Concept Map
    • Statistical Appendix
      • Measures of central tendency
      • Measures of dispersion: the variance
      • Measures of relation
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Chapter 26. Evolutionary Genetics
    • Introduction
    • A synthesis of forces: variation and divergence of populations
    • Multiple adaptive peaks
      • Exploration of adaptive peaks
    • Heritability of variation
    • Observed variation within and between populations
    • Process of speciation
      • Genetics of species isolation
    • Origin of new genes
      • Polyploidy
      • Duplications
      • Imported DNA
      • Relation of genetic to functional change
    • Rate of molecular evolution
    • Summary
    • Concept Map
    • Chapter Integration Problem
    • Solved Problems
    • Problems
  • Appendices
    • Genetic nomenclature
    • Further Readings
  • Glossary

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2000, W. H. Freeman and Company.
Bookshelf ID: NBK21766

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