The Thermodynamic Machinery of Life (eBook)

Preface 7
Contents 10
1 Biophysics: An Experimental Tool of Biology or the Physics of Animate Matter? 14
2 Statistical Description of Matter 19
2.1 Molecular Structure of Matter 19
2.2 The Principle of Mechanical Determinism 21
2.3 Irreversibility of Macroscopic Processes 24
2.4 Instability of Motion as the Origin of Irreversibility 28
2.5 Statistical Ensembles. 30
2.6 Probability and Entropy. 34
2.7 The Law of Large Numbers. 38
2.8 The Relativity of Thermodynamic Equilibrium 44
3 Thermodynamic State 47
3.1 Global and Structural Thermodynamic Variables 47
3.2 The Clausius Entropy 51
3.3 Temperature and Thermodynamic Forces. 54
3.4 Energy Transformations: Work, Heat and Dissipation 60
3.5 Free Energy and Bound Energy 64
3.6 Open Thermodynamic Systems: Steady State versus Dissipative Structures 69
3.7 Rate of Nonequilibrium Thermodynamic Processes 74
4 Origins and Evolution of Life 77
4.1 History in Physics 77
4.2 Initiation 79
4.3 Origins of the Prokaryotic Cell Machinery 82
4.4 The Photosynthetic Revolution 88
4.5 Origins and Structure of the Eukaryotic Cell. 92
4.6 The Main Metabolic Pathways. Enzymes 97
5 Molecular Biology of the Eukaryotic Cell 102
5.1 The Eukaryotic Cell as a System of Compartments 102
5.2 Membrane Channels and Pumps 105
5.3 Substrate, Oxidative, and Photo Phosphorylation 111
5.4 Cytoskeleton and Cell Motility: Micro.laments 122
5.5 Cytoskeleton and Cell Motility: Microtubules 131
5.6 Regulation of Enzyme Activity 134
5.7 Receptors 138
5.8 The Cell Cycle 148
6 Chemical Reactions 151
6.1 Single Unimolecular Reactions. 151
6.2 Transport Across Membranes 158
6.3 Bimolecular Reactions 162
6.4 Protolysis Reactions 165
6.5 Redox Reactions 168
6.6 Fuel Cells and Photocells. 172
6.7 Two Successive Reactions. 176
6.8 Phenomenological Theory of Reaction Rates 179
7 Enzymatic Catalysis 182
7.1 Chemical Mechanisms of Enzymatic Catalysis 182
7.2 Steady-State Kinetics of Enzymatic Reactions with One Intermediate 186
7.3 Competitive and Noncompetitive Inhibition 192
7.4 Two-Substrate Enzyme 195
7.5 Allosteric Control of Enzymatic Activity 197
7.6 Oscillations in Enzymatic Reactions 201
8 Biological Free Energy Transduction 206
8.1 Isothermal Machines 206
8.2 Chemochemical Machines. 210
8.3 Universality of the Enzymatic Mechanism of Free Energy Transduction 213
8.4 Molecular Pumps and Motors 218
8.5 Flux–Force Dependence 221
8.6 Biological Signal Transduction 228
9 Lack of Partial Thermodynamic Equilibrium 234
9.1 Two Classes of Experiments 234
9.2 Intramolecular Dynamics of Biomolecules 239
9.3 Enzyme in a Multitude of Conformational States 245
9.4 Two Coupled Enzymatic Processes: Case of the Actomyosin Motor 249
9.5 Flux–Force Dependence for the Actomyosin Motor 258
9.6 Biological Molecular Machines as Biased Maxwell Demons 268
A Thermodynamic Supplement 272
A.1 Thermodynamics of Ideal Gases 272
A.2 Legendre Transformations 277
A.3 Capacities and Susceptibilities. 282
A.4 Canonical and Generalized Canonical Probability Distributions 285
A.5 Statistical Interpretation of Thermodynamics 290
B Stochastic Processes 294
B.1 From Liouville’s Equation to the Di.usion Equation 294
B.2 Markov Processes 298
B.3 Stochastic Theory of Reaction Rates 305
B.4 Reaction Rate and the First-Passage Time Problem 311
B.5 One-Dimensional Di.usion in the Presence of a Sink 315
B.6 Diffusion in a Parabolic Potential 319
C Structure of Biomolecules 323
C.1 Elementary Building Blocks 323
C.2 Generalized Ester Bonds 327
C.3 Directionality of Chemical Bonds 331
C.4 Hydrogen Bond. Amphiphilic Molecules in Water Environments 340
C.5 Protein Structures 344
C.6 Nucleic Acid Structures 351
D Dynamics of Biomolecules 357
D.1 Vibrations Versus Conformational Transitions 357
D.2 Conformational Transitions Within the Protein Native State 361
D.3 Protein-Glass Model 367
D.4 Protein-Machine Model 375
D.5 Calculation of Mean First-Passage Time 378
D.6 Nonadiabatic Processes of Charge and Energy Transfer 383
References 397
Index 420