Documente Academic
Documente Profesional
Documente Cultură
Contents
0.1
Preface
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CONTENTS
2.3
2.4
2.5
2.6
2.7
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126
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145
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159
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CONTENTS
II
Life at Rest
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271
274
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285
288
290
CONTENTS
5.6
5.7
5.8
5.9
5.10
6 Entropy Rules!
301
6.1 The Analytical Engine of Statistical Mechanics . . . . . . . . . . 301
6.1.1 A First Look at Ligand-Receptor Binding . . . . . . . . . 307
6.1.2 The Statistical Mechanics of Gene Expression: RNA Polymerase and the Promoter . . . . . . . . . . . . . . . . . . 312
6.1.3 Classic Derivation of the Boltzmann Distribution . . . . . 318
6.1.4 Boltzmann Distribution by Counting . . . . . . . . . . . . 321
6.1.5 Boltzmann Distribution by Guessing . . . . . . . . . . . . 325
6.2 On Being Ideal . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
6.2.1 Average Energy of a Molecule in a Gas . . . . . . . . . . 332
6.2.2 Free Energy of Dilute Solutions . . . . . . . . . . . . . . . 335
6.2.3 Osmotic Pressure as an Entropic Spring . . . . . . . . . . 337
6.3 The Calculus of Equilibrium Applied: Law of Mass Action . . . . 341
6.3.1 Law of Mass Action and Equilibrium Constants . . . . . . 343
6.4 Applications of the Calculus of Equilibrium . . . . . . . . . . . . 345
6.4.1 A Second Look at Ligand-Receptor Binding . . . . . . . . 345
6.4.2 Measuring Ligand-Receptor Binding . . . . . . . . . . . . 347
6.4.3 Beyond Simple Ligand-Receptor Binding: The Hill Function347
6.4.4 ATP Power . . . . . . . . . . . . . . . . . . . . . . . . . . 350
6.5 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . 352
6.6 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
6.7 Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
6.8 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
7 Two-State Systems: From Ion Channels to Cooperative Bind357
ing
7.1 Macromolecules With Multiple States . . . . . . . . . . . . . . . 358
7.1.1 The Internal State Variable Idea . . . . . . . . . . . . . . 358
7.1.2 Ion Channels as an Example of Internal State Variables . 361
7.2 State Variable Description of Binding . . . . . . . . . . . . . . . 366
7.2.1 The Gibbs Distribution: Contact with a Particle Reservoir 367
7.2.2 Simple Ligand-Receptor Binding Revisited . . . . . . . . 369
7.2.3 Phosphorylation as an Example of Two Internal State
Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
7.2.4 Hemoglobin as a Case Study in Cooperativity . . . . . . . 375
7.3 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . 386
7.4 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
7.5 Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . . 388
7.6 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
CONTENTS
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451
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Salty Solutions
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CONTENTS
10.3.1 The Lac Operon and Other Looping Systems . . . . . . .
10.3.2 Energetics of DNA Looping . . . . . . . . . . . . . . . . .
10.3.3 Putting it all together: The J Factor . . . . . . . . . . . .
10.4 DNA Packing: From Viruses to Eukaryotes . . . . . . . . . . . .
10.4.1 The Problem of Viral DNA Packing . . . . . . . . . . . .
10.4.2 Constructing the Nucleosome . . . . . . . . . . . . . . . .
10.4.3 Equilibrium Accessibility of Nucleosomal DNA . . . . . .
10.5 The Cytoskeleton and Beam Theory . . . . . . . . . . . . . . . .
10.5.1 The Cellular Interior: A Structural Perspective . . . . . .
10.5.2 Stiffness of Cytoskeletal Filaments . . . . . . . . . . . . .
10.5.3 Cytoskeletal Buckling . . . . . . . . . . . . . . . . . . . .
10.5.4 Estimate of the Buckling Force . . . . . . . . . . . . . . .
10.6 Beams and Biotechnology . . . . . . . . . . . . . . . . . . . . . .
10.6.1 Biofunctionalized Cantilevers and Molecular Recognition .
10.7 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . .
10.8 Appendix: The Mathematics of the Worm-Like Chain . . . . . .
10.9 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10.10Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . . .
10.11References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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CONTENTS
III
Life in Motion
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CONTENTS
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CONTENTS
16 Dynamics of Molecular Motors
16.1 The Dynamics of Molecular Motors: Life in the Noisy Lane . .
16.1.1 Translational Motors: Beating the Diffusive Speed Limit
16.1.2 Rotary Motors . . . . . . . . . . . . . . . . . . . . . . .
16.1.3 Polymerization Motors: Pushing By Growing . . . . . .
16.1.4 Translocation Motors: Pushing by Pulling . . . . . . . .
16.2 Rectified Brownian Motion and Molecular Motors . . . . . . . .
16.2.1 The Random Walk Yet Again . . . . . . . . . . . . . . .
16.2.2 The One-state Model . . . . . . . . . . . . . . . . . . .
16.2.3 Motor stepping from a free energy perspective . . . . .
16.2.4 The Two-state model . . . . . . . . . . . . . . . . . . .
16.2.5 More General Motor Models . . . . . . . . . . . . . . .
16.2.6 Coordination of Motor Protein Activity . . . . . . . . .
16.2.7 Rotary Motors . . . . . . . . . . . . . . . . . . . . . . .
16.3 Polymerization and Translocation as Motor Action . . . . . . .
16.3.1 The Polymerization Ratchet . . . . . . . . . . . . . . . .
16.3.2 Force Generation by Growth . . . . . . . . . . . . . . .
16.3.3 The Translocation Ratchet . . . . . . . . . . . . . . . .
16.4 Summary and Conclusions . . . . . . . . . . . . . . . . . . . . .
16.5 Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16.6 Further Reading . . . . . . . . . . . . . . . . . . . . . . . . . .
16.7 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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IV
CONTENTS
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1000
1002
CONTENTS
13
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1075
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