Download An Introduction to Genetic Analysis

An Introduction to
Genetic Analysis
FiMnEetitioitm'
Anthony J. F. Griffiths
University of British Columbia
j
Jeffrey H. Miller
University of California, Los Angeles
David T. Suzuki
University of British Columbia
Richard C. Lewontin
Harvard University
William M. Gelbart
Harvard University
IS
W. H. Freeman and Company / New York
Contents in Brief
1 Genetics and the Organism
2 Mendelian Analysis
3 Chromosome Theory of
Inheritance
4 Extensions of Mendelian
Analysis
5 Linkage I: Basic Eukaryotic
Chromosome Mapping
6 Linkage II: Special Eukaryotic
Chromosome Mapping
Techniques
7 Gene Mutation
8 Chromosome Mutation I:
Changes in Chromosome
Structure
9 Chromosome Mutation II:
Changes in Number
10 Recombination in Bacteria
and Their Viruses
11 The Structure of DNA
12 The Nature of the Gene
13 DNA Function
1
19
50
87
118
149
178
205
241
265
304
333
374
14 Recombinant DNA
15 Applications of Recombinant
DNA
16 The Structure and Function of
Eukaryotic Chromosomes
17 Control of Gene Expression
18 Mechanisms of Genetic
Change I: Gene Mutation
19 Mechanisms of Genetic
Change II: Recombination
20 Mechanisms of Genetic
Change III: Transposable
Genetic Elements
21 The Extranuclear Genome
22 Developmental Genetics: Cell
Fate and Pattern Formation
23 Developmental Genetics:
Topics in Gene Regulation
and Differentiation
24 Quantitative Genetics
25 Population Genetics
415
440
467
491
529
561
579
605
636
671
703
737
Contents
Preface
XII
GENETICS AND THE ORGANISM
Genetics and Human Affairs
Genetics and Biology
Genes and Environment I
Techniques of Genetic Analysis
Summary
Concept Maps
1
2
6
8
15
17
18
MENDELIAN ANALYSIS
19
Mendel's Experiments
Simple Mendelian Genetics in
Humans
Simple Mendelian Genetics in
Agriculture
Variants and Genetic Dissection
Summary
20
30
38
41
42
Concept Map 42 • Chapter Integration
Problem 42 ' Solved Problems 43 •
Problems 45
Mendelian Genetics and Life Cycles
Summary
74
79
Concept Map 80 • Chapter Integration
Problem 80 • Solved Problems 81 •
Problems 82
EXTENSIONS OF
MENDELIAN ANALYSIS
87
Variations on Dominance
Multiple Alleles
Lethal Alleles
Several Genes Affecting the Same
Character
Penetrance and Expressivity
Summary
Concept Map 105 • Chapter Integration
Problem 106 • Solved Problems 107 •
Problems 109
88
89
91
94
103
104
LINKAGE I: BASIC EUKARYOTIC
CHROMOSOME THEORY
OF INHERITANCE
50
Mitosis and Meiosis
The Chromosome Theory of
Heredity
Sex Chromosomes and Sex Linkage
The Parallel Behavior of Autosomal
Genes and Chromosomes
51
58
66
72
CHROMOSOME MAPPING
118
The Discovery of Linkage
Recombination
Linkage Symbolism
Linkage of Genes on the X
Chromosome
Linkage Maps
Three-Point Testcross
119
121
123
124
124
128
Contents
VIII
Interference
T h e / 2 Test
Early Thoughts on the Nature of
Crossing-Over
Linkage Mapping by Recombination in Humans
Summary
130
132
Duplications
Summary
Concept Map 229 • Chapter Integration
Problem 229 • Solved Problems 230 •
Problems 233
135
137
138
CHROMOSOME M U T A T I O N II:
CHANGES IN NUMBER
Concept Map 139 • Chapter Integration
Problem 139 Solved Problems 140
Problems 142
6
LINKAGE II. SPECIAL
EUKARYOTIC CHROMOSOME
MAPPING TECHNIQUES
Accurate Calculation of Large Map
Distances
Analysis of Single Meioses
Mitotic Segregation and
Recombination
Mapping Human Chromosomes
Summary
Euploidy
Aneuploidy
Chromosome Mechanics in Plant
Breeding
Summary
149
150
154
10
162
165
168
GENE M U T A T I O N
178
Somatic Versus Germinal Mutation
Mutant Types
The Occurrence of Mutations
Selective Systems
Mutation and Cancer
Mutagens in Genetic Dissection
Mutation Breeding
Summary
179
181
184
188
195
198
199
200
Concept Map 201 • Chapter Integration
Problem 201 • Solved Problems 201 •
Problems 203
8
CHROMOSOME M U T A T I O N
I: CHANGES IN
CHROMOSOME STRUCTURE
The Topography of Chromosomes
Types of Changes in Chromosome
Structure
205
206
210
241
242
250
257
259
Concept Map 259 • Chapter Integration
Problem 259 • Solved Problems 260 •
Problems 261
RECOMBINATION IN BACTERIA
AND THEIR VIRUSES
Working with Microorganisms
Bacterial Conjugation
Bacterial Recombination and
Mapping the E. coli Chromosome
Bacterial Transformation
Bacteriophage Genetics
Transduction
Mapping of Bacterial Chromosomes
Bacterial Gene Transfer in Review
Summary
Concept Map 169 • Chapter Integration
Problem 169 • Solved Problems 170 •
Problems 172
7
215
229
265
266
267
276
280
282
289
293
294
294
Concept Map 296 • Chapter Integration
Problem 296 • Solved Problems 296 •
Problems 298
11
T H E STRUCTURE OF
DNA
DNA: The Genetic Material
The Structure of DNA
Replication of DNA
Mechanism of DNA Replication
DNA Replication in Eukaryotes
DNA and the Gene
Summary
Concept Map 330 • Chapter Integration
Problem 330 • Solved Problems 330 •
Problems 330
304
305
307
313
320
326
327
329
Contents
IX
THE NATURE OF THE GENE
333
How Genes Work
Gene-Protein Relationships
Genetic Observations Explained by
Enzyme Structure
Genetic Fine Structure
Mutational Sites
Complementation
Summary
334
337
348
350
355
361
365
Concept Map 365 • Chapter Integration
Problem 365 • Solved Problems 366 •
Problems 367
DNA
16
374
FUNCTION
Overview
Transcription
Translation
The Genetic Code
Protein Synthesis
Universality of Genetic «
Information Transfer ^
Eukaryotic RNA
Mechanism of Gene Splicing
Review
Summary
Recombinant DNA Technology in
Eukaryotes: An Overview
Trans genie Yeast
Trans genie Plants
Transgenic Animals
Screening for Genetic Diseases
Identifying Disease Genes
Summary
Concept Map 461 • Chapter Integration
Problem 461 • Solved Problems 464 •
Problems 465
\ 375
375
382
383
391
One DNA Molecule per
Chromosome
The Role of Histone Proteins in
Packaging DNA
Higher Order Coiling
Heterochromatin and Euchromatin
Chromosome Bands
Centromeric DNA
Sequence Organization
Replication and Transcription of
Chromatin
Summary
398
400
402
407
407
Concept
Integration
p
g
p Mapp 410 • Chapter
bl
l d Problems
bl
Problem
410 Solved
410
Problems 411
RECOMBINANT
DNA
Restriction Enzymes
The Formation of Recombinant
DNA
Recombinant DNA Methodology
Recombinant DNA and Social
Responsibility
Summary
419
423
433
434
Concept Map 436 • Chapter Integration
Problem 436 • Solved Problems 436 •
Problems 436
f5
|
APPLICATIONS OF
RECOMBINANT D N A
440
?
i
Applications of Recombinant DNA
Technology Using Prokaryotes
441
450
453
453
459
461
467
468
470
471
474
475
477
478
487
488
Concept Map 488 • Chapter Integration
Problem 488 • Solved Problem 488 •
Problems 488
415
416
THE STRUCTURE AND
FUNCTION OF
EUKARYOTIC CHROMOSOMES
444
445
17
C O N T R O L OF GENE EXPRESSION
491
Basic Control Circuits
Discovery of the lac System:
Negative Control
Catabolite Repression of the lac
Operon: Positive Control
Dual Positive and Negative
Control: The Arabinose Operon
Metabolic Pathways
The Tryptophan Genes: Negative
Control with Superimposed
Attentuation
The I Phage: A Complex of
492
Operons
493
500
503
505
505
509
Contents
Multioperon Repression
Structure of Regulatory Proteins
Transcription: Gene Regulation in
Eukaryotes—An Overview
Cis Control of Transcription
Trans Control of Transcription
5-Methylcytosine Regulation
Post-Transcriptional Control
Control of Ubiquitous Molecules
in Eukaryotic Cells
Summary
511
512
20
512
513
515
521
521
Insertion Sequences
Transposons
Phage mu
Mechanism of Transposition
Rearrangements Mediated by
Transposable Elements
Review of Transposable Elements
in Prokaryotes
Ty Elements in Yeast
Transposable Elements in Drosophila
Retroviruses
Transposition via an RNA
Intermediate
Controlling Elements in Maize
Review of Transposable Elements
in Eukaryotes
Summary
521
524
Concept Map 525 • Chapter Integration
Problem 525 • Solved Problems 525 •
Problems 526
18
MECHANISMS OF GENETIC
CHANGE I: GENE M U T A T I O N
The Molecular Basis of Gene
Mutations
Spontaneous Mutations
Induced Mutations
Reversion Analysis
The Relationship Between
Mutagens and Carcinogens
Biological Repair Mechanisms
Summary
529
531
532
539
547
547
549
558
Concept Map 558 • Chapter Integration
Problem 558 • Solved Problems 558 •
Problems 559
19
MECHANISMS OF GENETIC
CHANGE II: RECOMBINATION
General Homologous
Recombination
The Holliday Model
Enzymatic Mechanism of
Recombination
Site-Specific Recombination
Recombination and Chromosomal
Rearrangements
Duplication and Evolution
Summary
Concept Map 575 • Chapter Integration
Problem 575 • Solved Problems 575 •
Problems 576
561
562
563
571
572
575
575
575
MECHANISMS OF GENETIC
CHANGE III: TRANSPOSABLE
GENETIC ELEMENTS
579
580
583
586
587
592
592
592
593
596
597
598
602
603
Concept Map 603 • Chapter Integration
Problem 603 • Solved Problem 604 •
Problems 604
21
T H E EXTRANUCLEAR GENOME
Variegation in Leaves of Higher
Plants
Cytoplasmic Inheritance in Fungi
Shell Coiling in Snails: A Red
Herring
Extranuclear Genes in
Chlamydomonas
Mitochrondrial Genes in Yeast
An Overview of the
Mitochrondrial Genome
An Overview of the Chloroplast
Genome
Mitochondrial Diseases in Humans
Extragenomic Plasmids in
Eukaryotes
How Many Copies?
Summary
Concept Map 627 • Chapter Integration
Problem 628 • Solved Problems 629 •
Problems 630
605
607
609
611
612
615
620
623
624
625
626
627
Contents
XI
DEVELOPMENTAL GENETICS:,
CELL FATE AND
PATTERN FORMATION
|
Cell Fate: When Do the Cells and
Nuclei of Higher Organisms Lose
Their Totipotency?
Pattern Formation: The Establishment of the Basic Animal Body
Plan
Mutational and Molecular Analyses
of the Basic Body Plan
Communication Between Cells and
the Establishment of Cell Fate
Homeotic Mutations and the
Establishment of Segment Identity^
Applying the Fly and Worm
Lessons to Other Organisms
Summary
24
636
637
640
645
655
Proteins as Determinants of
Cellular Characteristics
Regulating the Synthesis of Proteins
Transcriptional Regulation by
Tissue-Specific Enhancers
Integration of Transcriptional
Control between Different Tissues
Transcript Processing and TissueSpecific Regulation
Applications of Regulatory Mechanisms to Cell Differentiation
Cancer as a Developmental
Genetic Disease
Summary
Concept Map 699 • Chapter Integration
Problem 699 • Solved Problems 700 •
Problems 701
704
713
715
716
718
721
725
727
727
732
737
738
738
747
680
Darwin's Revolution
'
Variation and Its Modulation
The Sources of Variation
The Effect of Sexual Reproduction
on Variation
Selection
Balanced Polymorphism
Multiple Adaptive Peaks
Artificial Selection
Random Events
A Synthesis of Forces
The Origin of Species
Summary
682
Concept Map 770 • Chapter Integration
Problem 770 • Solved Problems 770 •
Problems 772
1)
DEVELOPMENTAL GENETICS:
TOPICS IN GENE REGULATION
AND DIFFERENTIATION
Some Basic Statistical Notions
Genotypes and Phenotypic
Distribution
Norm of Reaction and Phenotypic
Distribution
The Heritability of a Trait
Determining Norms of Reaction
Quantifying Heritability
Counting and Locating the Genes
Gene Action
More on Analyzing Variance
Summary
POPULATION GENETICS
Concept Map 666 • Chapter Integration
Problem 666 • Solved Problems 667 •
Problems 668
»
23
703
Concept Map 733 • Chapter Integration
Problem 733 • Solved Problems 734 •
Problems 734
659
661
665
QUANTITATIVE GENETICS
671
672
672
676
25
750
755
760
762
763
765
766
768
769
682
690
699
Further Reading
Glossary
Answers to Selected Problems
Index
775
783
803
825