| Preface to the Third Edition | p. xi |
| Preface to the First Edition | p. xiii |
| Introduction | p. 1 |
| The Master Elements of Control | p. 11 |
| Components of the Switch | p. 14 |
| DNA | p. 14 |
| RNA Polymerase | p. 15 |
| The Repressor | p. 16 |
| Cro | p. 17 |
| The Action of Repressor and Cro | p. 18 |
| Negative Control | p. 18 |
| Positive Control | p. 18 |
| Cooperativity of Repressor Binding | p. 20 |
| Induction--Flipping the Switch | p. 22 |
| Cooperativity--Switch Stability and Sensitivity | p. 26 |
| The Effect of Autoregulation | p. 28 |
| Other Cases | p. 28 |
| Protein-DNA Interactions and Gene Control | p. 31 |
| The Operator | p. 31 |
| Repressor | p. 34 |
| Cro | p. 37 |
| Amino Acid-Base Pair Interactions | p. 39 |
| The Promoter | p. 43 |
| Gene Control | p. 44 |
| Control Circuits--Setting the Switch | p. 47 |
| A Brief Overview of [lambda] Growth | p. 48 |
| The Genetic Map | p. 48 |
| Circularization | p. 49 |
| Gene Expression | p. 50 |
| Integration | p. 51 |
| Control of Transcription | p. 52 |
| Very Early | p. 52 |
| Early | p. 52 |
| Late Lytic | p. 53 |
| Late Lysogenic | p. 55 |
| The Decision | p. 56 |
| Control of Integration and Excision | p. 57 |
| Establishing Lysogeny | p. 58 |
| Lytic Growth | p. 58 |
| Induction | p. 58 |
| Other Phages | p. 60 |
| The SOS Response | p. 60 |
| [lambda] Pathways and Cell Development | p. 62 |
| Regulatory Genes | p. 62 |
| Switches | p. 63 |
| Patterns of Gene Expression | p. 64 |
| How Do We Know--the Key Experiments | p. 67 |
| The Repressor Idea | p. 67 |
| Clear and Virulent Mutants | p. 67 |
| Observations | p. 67 |
| Explanation | p. 68 |
| Immunity and Heteroimmunity | p. 69 |
| Observations | p. 69 |
| Explanation | p. 70 |
| Asymmetry in Bacterial Mating | p. 70 |
| Observations | p. 70 |
| Explanation | p. 71 |
| The Repressor Problem in the Early 1960s | p. 71 |
| Repressor Isolation and DNA Binding | p. 72 |
| Making More Repressor | p. 74 |
| The Claims of Chapters One and Two | p. 76 |
| The repressor is composed of two globular domains held together by a linker of some 40 amino acids | p. 76 |
| The repressor dimerizes, largely through interaction between its carboxyl domains | p. 76 |
| A repressor dimer binds, through its amino domains, to a 17 base pair operator site | p. 78 |
| A single operator site binds one dimer of repressor | p. 78 |
| Dimers form before DNA binding | p. 80 |
| The amino domains contact DNA | p. 82 |
| 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 | p. 84 |
| Chemical probes | p. 84 |
| Operator mutations | p. 85 |
| Binding to supercoiled and linear DNA | p. 85 |
| Repressor binds to three sites in O[subscript R] with alternate pairwise cooperativity. The cooperativity is mediated by interactions between carboxyl domains of adjacent dimers | p. 86 |
| In a lysogen repressor is typically bound to O[subscript R]1 and O[subscript R]2. The bound repressors turn off rightward transcription of cro and stimulate leftward transcription of cl. At higher concentrations, repressor binds to O[subscript R]3 to turn off transcription of cl | p. 87 |
| Cro binds first to O[subscript R]3, then to O[subscript R]1 and O[subscript R]2, thereby first turning off P[subscript RM], then P[subscript R] | p. 92 |
| Some background about Cro | p. 92 |
| Cro in vivo | p. 93 |
| Cro in vitro | p. 94 |
| RecA cleaves repressor to trigger induction | p. 94 |
| When Cro is bound at O[subscript R]3 the switch is thrown | p. 95 |
| Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11 | p. 95 |
| Crystallography | p. 95 |
| The "helix swap" experiment | p. 96 |
| Specific amino acid-base pair contacts | p. 98 |
| The role of the arm of [lambda] repressor | p. 99 |
| Repressor activates transcription of cl by binding to O[subscript R]2 and contacting polymerase with its amino domain | p. 99 |
| Positive control mutants | p. 99 |
| Positive control in vitro | p. 102 |
| Conclusion | p. 103 |
| 2004: New Developments | p. 109 |
| Long-range Cooperativity and Repression of P[subscript RM] | p. 109 |
| An Octamer of Repressor Binds O[subscript R] and O[subscript L] | p. 110 |
| Autonegative Regulation of Repressor Synthesis | p. 112 |
| How Do We Know | p. 113 |
| Long-range Interactions and Repression of P[subscript R] | p. 113 |
| Long-range Interactions and Repression of P[subscript RM] | p. 114 |
| Activation and Repression of P[subscript RM] | p. 114 |
| Repressor Structure | p. 115 |
| Positive Control (Activation of Transcription) | p. 122 |
| Polymerase and Promoter | p. 122 |
| The Mechanism of Activation | p. 123 |
| How Do We Know | p. 123 |
| Activating Region Variants | p. 123 |
| A Suppressor of a pc Mutant | p. 125 |
| Crystallography | p. 125 |
| Activator Bypass | p. 125 |
| Changing Activating Regions and Target Context | p. 127 |
| The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage | p. 131 |
| How Do We Know | p. 132 |
| Evolving the Switch | p. 133 |
| Changing the Affinities of Sites in O[subscript R] for Repressor | p. 133 |
| Eliminating Positive Control | p. 134 |
| Eliminating Cooperativity between DNA-binding Dimers | p. 134 |
| CII and the Decision | p. 136 |
| Index | p. 151 |
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