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| Preface to the Third Edition | |
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| Preface to the First Edition | |
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| Introduction | |
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| The Master Elements of Control | |
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| Components of the Switch | |
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| DNA | |
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| RNA Polymerase | |
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| The Repressor | |
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| Cro | |
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| The Action of Repressor and Cro | |
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| Negative Control | |
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| Positive Control | |
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| Cooperativity of Repressor Binding | |
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| Induction--Flipping the Switch | |
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| Cooperativity--Switch Stability and Sensitivity | |
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| The Effect of Autoregulation | |
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| Other Cases | |
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| Protein-DNA Interactions and Gene Control | |
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| The Operator | |
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| Repressor | |
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| Cro | |
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| Amino Acid-Base Pair Interactions | |
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| The Promoter | |
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| Gene Control | |
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| Control Circuits--Setting the Switch | |
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| A Brief Overview of [lambda] Growth | |
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| The Genetic Map | |
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| Circularization | |
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| Gene Expression | |
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| Integration | |
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| Control of Transcription | |
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| Very Early | |
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| Early | |
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| Late Lytic | |
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| Late Lysogenic | |
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| The Decision | |
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| Control of Integration and Excision | |
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| Establishing Lysogeny | |
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| Lytic Growth | |
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| Induction | |
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| Other Phages | |
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| The SOS Response | |
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| [lambda] Pathways and Cell Development | |
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| Regulatory Genes | |
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| Switches | |
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| Patterns of Gene Expression | |
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| How Do We Know--the Key Experiments | |
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| The Repressor Idea | |
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| Clear and Virulent Mutants | |
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| Observations | |
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| Explanation | |
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| Immunity and Heteroimmunity | |
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| Observations | |
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| Explanation | |
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| Asymmetry in Bacterial Mating | |
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| Observations | |
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| Explanation | |
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| The Repressor Problem in the Early 1960s | |
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| Repressor Isolation and DNA Binding | |
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| Making More Repressor | |
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| The Claims of Chapters One and Two | |
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| The repressor is composed of two globular domains held together by a linker of some 40 amino acids | |
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| The repressor dimerizes, largely through interaction between its carboxyl domains | |
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| A repressor dimer binds, through its amino domains, to a 17 base pair operator site | |
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| A single operator site binds one dimer of repressor | |
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| Dimers form before DNA binding | |
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| The amino domains contact DNA | |
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| 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 | |
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| Chemical probes | |
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| Operator mutations | |
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| Binding to supercoiled and linear DNA | |
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| 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 | |
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| 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 | |
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| 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] | |
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| Some background about Cro | |
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| Cro in vivo | |
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| Cro in vitro | |
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| RecA cleaves repressor to trigger induction | |
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| When Cro is bound at O[subscript R]3 the switch is thrown | |
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| Repressor and Cro bind to the operator as shown in Figures 2.6, 2.8, 2.10, and 2.11 | |
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| Crystallography | |
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| The "helix swap" experiment | |
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| Specific amino acid-base pair contacts | |
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| The role of the arm of [lambda] repressor | |
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| Repressor activates transcription of cl by binding to O[subscript R]2 and contacting polymerase with its amino domain | |
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| Positive control mutants | |
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| Positive control in vitro | |
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| Conclusion | |
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| 2004: New Developments | |
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| Long-range Cooperativity and Repression of P[subscript RM] | |
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| An Octamer of Repressor Binds O[subscript R] and O[subscript L] | |
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| Autonegative Regulation of Repressor Synthesis | |
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| How Do We Know | |
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| Long-range Interactions and Repression of P[subscript R] | |
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| Long-range Interactions and Repression of P[subscript RM] | |
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| Activation and Repression of P[subscript RM] | |
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| Repressor Structure | |
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| Positive Control (Activation of Transcription) | |
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| Polymerase and Promoter | |
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| The Mechanism of Activation | |
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| How Do We Know | |
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| Activating Region Variants | |
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| A Suppressor of a pc Mutant | |
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| Crystallography | |
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| Activator Bypass | |
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| Changing Activating Regions and Target Context | |
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| The Structure of the Repressor Monomer and the Mechanism of Repressor Cleavage | |
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| How Do We Know | |
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| Evolving the Switch | |
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| Changing the Affinities of Sites in O[subscript R] for Repressor | |
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| Eliminating Positive Control | |
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| Eliminating Cooperativity between DNA-binding Dimers | |
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| CII and the Decision | |
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| Index | |