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Tables of Contents for Genetic Switch
Chapter/Section Title
Page #
Page Count
Preface to the Third Edition,
xi
 
Preface to the First Edition,
xiii
 
INTRODUCTION
1
10
CHAPTER ONE THE MASTER ELEMENTS OF CONTROL
11
20
Components of the Switch
14
4
DNA
14
1
RNA Polymerase
15
1
The Repressor
16
1
Cro
17
1
The Action of Repressor and Cro
18
4
Negative Control
18
1
Positive Control
18
2
Cooperativity of Repressor Binding
20
2
Induction-Flipping the Switch
22
4
Cooperativity-Switch Stability and Sensitivity
26
2
The Effect of Autoregulation
28
1
Other Cases
28
3
CHAPTER TWO PROTEIN-DNA INTERACTIONS AND GENE CONTROL
31
16
The Operator
31
3
Repressor
34
3
Cro
37
2
Amino Acid-Base Pair Interactions
39
4
The Promoter
43
1
Gene Control
44
3
CHAPTER THREE CONTROL CIRCUITS-SETTING THE SWITCH
47
20
A Brief Overview of λ Growth
48
4
The Genetic Map
48
1
Circularization
49
1
Gene Expression
50
1
Integration
51
1
Control of Transcription
52
4
Very Early
52
1
Early
52
1
Late Lytic
53
2
Late Lysogenic
55
1
The Decision
56
1
Control of Integration and Excision
57
3
Case 1-Establishing Lysogeny
58
1
Case 2-Lytic Growth
58
1
Case 3-Induction
58
2
Other Phages
60
1
The SOS Response
60
2
λ Pathways and Cell Development
62
5
Regulatory Genes
62
1
Switches
63
1
Patterns of Gene Expression
64
3
CHAPTER FOUR HOW DO WE KNOW-THE KEY EXPERIMENTS
67
42
The Repressor Idea
67
4
Clear and Virulent Mutants
67
2
Observations
67
1
Explanation
68
1
Immunity and Heteroimmunity
69
1
Observations
69
1
Explanation
70
1
Asymmetry in Bacterial Mating
70
6
Observations
70
1
Explanation
71
1
The Repressor Problem in the Early 1960's
71
1
Repressor Isolation and DNA Binding
72
2
Making More Repressor
74
2
The Claims of Chapters One and Two
76
27
The repressor is composed of two globular domains held together by a linker of some 40 amino acids
76
1
The repressor dimerizes, largely through interaction between Its carboxyl domains
76
2
A repressor dimer binds, through Its amino domains, to a 17 base pair operator site
78
6
A single operator site binds one dimer of repressor
78
2
Dimers form before DNA binding
80
2
The amino domains contact DNA
82
2
There are three 17 base pair repressor binding sites in the right operator. At each site repressor and Cro bind along the same face of the helix
84
2
Chemical probes
84
1
Operator mutations
85
1
Binding to supercoiled and linear DNA
85
1
Repressor binds to three sites in OR with alternate pairwise cooperativity. The cooperativity is mediated by interactions between carboxyl domains of adjacent dimers
86
1
In a lysogen repressor is typically bound to OR1 and OR2. The bound repressors turn off rightward transcription of cro and stimulate leftward transcription of cl. At higher concentrations, repressor binds to OR3 to turn off transcription of cl
87
5
Cro binds first to OR3, then to OR1 and OR2, thereby first turning off PRS, then PR
92
2
Some background about Cro
92
1
Cro in vivo
93
1
Cro in vitro
94
1
RecA cleaves repressor to trigger induction
94
1
When Cro is bound at 0R3 the switch is thrown
95
1
Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11
95
4
Crystallography
95
1
The "helix swap" experiment
96
2
Specific amino acid-base pair contacts
98
1
The role of the arm of λ repressor
99
1
Repressor activates transcription of cl by binding to OR2 and contacting polymerase with its amino domain
99
10
Positive control mutants
99
3
Positive control in vitro
102
1
Conclusion
103
6
CHAPTER FIVE 2004: NEW DEVELOPMENTS
109
42
1. Long-range Cooperativity and Repression of PRM
109
13
An Octamer of Repressor Binds OR and O,
110
2
Autonegative Regulation of Repressor Synthesis
112
1
How Do We Know
113
9
Long-range Interactions and Repression of PR
113
1
Long-range Interactions and Repression of PRM
114
1
Activation and Repression of PRM
114
1
Repressor Structure
115
7
2. Positive Control (Activation of Transcription)
122
9
Polymerase and Promoter
122
1
The Mechanism of Activation
123
1
How Do We Know
123
8
Activating Region Variants
123
2
A Suppressor of a pc Mutant
125
1
Crystallography
125
1
Activator Bypass
125
2
Changing Activating Regions and Target Context
127
4
3. The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage
131
2
How Do We Know
132
1
4. Evolving the Switch
133
3
Changing the Affinities of Sites in OR for Repressor
133
1
Eliminating Positive Control
134
1
Eliminating Cooperativity between DNA-binding Dimers
134
2
5. CII and the Decision
136
15
Index
151