Chemical biophysics quantitative analysis of cellular systems
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| Sprache: | English |
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Cambridge Univ. Press
2008
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| Ausgabe: | 1. publ. |
| Schriftenreihe: | Cambridge texts in biomedical engineering
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| 100 | 1 | |a Beard, Daniel A. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Chemical biophysics |b quantitative analysis of cellular systems |c Daniel A. Beard ; Hong Qian |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Cambridge |b Cambridge Univ. Press |c 2008 | |
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Datensatz im Suchindex
| DE-BY-TUM_call_number | 0202 CHE 802 2009 A 3008 0204 CHE 802 2009 A 3008 |
|---|---|
| DE-BY-TUM_katkey | 1681632 |
| DE-BY-TUM_location | 02 |
| DE-BY-TUM_media_number | 040020760985 040020760974 |
| _version_ | 1820896239190802432 |
| adam_text | Titel: Chemical biophysics
Autor: Beard, Daniel A.
Jahr: 2008
Contents
Preface page xvii
Introduction 1
Computational biology 1
Systems biology 2
Organization of this book 3
Part I Background material 5
1 Concepts from physical chemistry 7
1.1 Macroscopic thermodynamics 7
1.2 Isolated systems and the Boltzmann definition of entropy 9
1.3 Closed isothermal systems 10
1.3.1 Helmholtz free energy 10
1.3.2 Entropy in an NVT system 13
1.3.3 Interpretation of temperature in the NVT system 13
1.4 Isothermal isobaric systems 14
1.4.1 Gibbs free energy 14
1.4.2 Entropy in an NPT system 15
1.5 Thermodynamic driving forces in different systems 15
1.6 Applications and conventions in chemical thermodynamics 16
1.6.1 Systems of non-interacting molecules 16
1.6.2 Gibbs free energy of chemical reactions and
chemical equilibrium 17
1.7 Applications of thermodynamics in biology 19
1.7.1 Enzyme reaction mechanisms 19
1.7.2 Electrostatic potential across a cell membrane 21
2 Conventions and calculations for biochemical systems 24
2.1 Conventional notation in biochemical thermodynamics 24
2.2 Reactants and reactions in biochemistry 26
XI
xii Contents
2.2.1 An example of a biochemical reactant 26
2.2.2 An example of a biochemical reaction 28
2.3 Effects of pH and ion binding on biochemical reaction
thermodynamics 32
2.4 Effects of temperature on biochemical reaction thermodynamics 34
2.5 Effects of ionic strength on biochemical reaction thermodynamics 35
2.6 Treatment of CO2 in biochemical reactions 36
2.7 pH variation in vivo 38
2.7.1 In vivo deviation from the standard state 38
2.7.2 The bicarbonate system in vivo 38
3 Chemical kinetics and transport processes 41
3.1 Well mixed systems 42
3.1.1 Differential equations from mass conservation 42
3.1.2 Reaction thermodynamics revisited 43
3.1.3 Reaction kinetics 45
3.1.4 Using computers to simulate chemical kinetics 53
3.2 Transport processes 58
3.2.1 Advection 59
3.2.2 Diffusion 60
3.2.3 Drift 60
3.2.4 Example: passive permeation across a membrane 61
3.2.5 Example: coupled diffusion and drift in a membrane 62
Part II Analysis and modeling of biochemical systems 67
4 Enzyme-catalyzed reactions: cycles, transients, and
non-equilibrium steady states 69
4.1 Simple Michaelis-Menten reactions revisited 70
4.1.1 Steady state enzyme turnover kinetics 70
4.1.2 Reversible Michaelis-Menten kinetics 73
4.1.3 Non-equilibrium steady states and cycle kinetics 74
4.2 Transient enzyme kinetics 76
4.2.1 Rapid pre-equilibrium 76
4.2.2 A singular perturbation approach to
Michaelis-Menten kinetics 78
4.3 Enzyme with multiple binding sites: cooperativity 81
4.3.1 Sigmoidal equilibrium binding 81
4.3.2 Cooperativity in enzyme kinetics 82
4.3.3 The Hill coefficient 83
4.3.4 Delays and hysteresis in transient kinetics 84
4.4 Enzymatic fluxes with more complex kinetics 86
4.4.1 Reciprocal of flux: the mean time of turnover 87
Contents xiii
4.4.2 The method of King and Altman 89
4.4.3 Enzyme-catalyzed bimolecular reactions 92
4.4.4 Example: enzyme kinetics of citrate synthase 96
5 Biochemical signaling modules 105
5.1 Kinetic theory of the biochemical switch 105
5.1.1 The phosphorylation-dephosphorylation cycle 108
5.1.2 Ultrasensitivity and the zeroth-order
phosphorylation-dephosphorylation cycle 111
5.1.3 Substrate selectivity of the
phosphorylation-dephosphorylation switch 113
5.1.4 The GTPase signaling module 115
5.1.5 Duration of switch activation and a biochemical timer 117
5.1.6 Synergistic action of kinases and phosphatases and
the phosphorylation energy hypothesis 121
5.2 Biochemical regulatory oscillations 122
5.2.1 Gene regulatory networks and the repressilator 122
5.2.2 Biochemical oscillations in cell biology 125
6 Biochemical reaction networks 128
6.1 Formal approach to biochemical reaction kinetics 129
6.1.1 Establishing the components of the biochemical
network model 129
6.1.2 Determining expressions for biochemical fluxes for
the reactions 131
6.1.3 Determining the differential equations 132
6.1.4 Computational implementation and testing 137
6.2 Kinetic model of the TCA cycle 140
6.2.1 Overview 140
6.2.2 Components of the TCA cycle reaction network 140
6.2.3 Flux expressions for TCA cycle reaction network 143
6.2.4 Differential equations for TCA cycle reaction network 152
6.2.5 Simulation of TCA cycle kinetics 153
6.3 Control and stability in biochemical networks 155
6.3.1 Linear analysis near a steady state 156
6.3.2 Metabolic control analysis 157
7 Coupled biochemical systems and membrane transport 162
7.1 Transporters 162
7.1.1 Active versus passive transport 163
7.1.2 Examples: a uniporter and an antiporter 163
7.2 Transport of charged species across membranes 168
7.2.1 Thermodynamics of charged species transport 168
xiv Contents
7.2.2 Electrogenic transporters 170
7.3 Electrophysiology modeling 172
7.3.1 Ion channels 172
7.3.2 Differential equations for membrane potential 173
7.3.3 The Hodgkin-Huxley model 174
7.4 Large-scale example: model of oxidative ATP synthesis 178
7.4.1 Model of oxidative phosphorylation 180
7.4.2 Model behavior 187
7.4.3 Applications to in vivo systems 188
Part III Special topics 193
8 Spatially distributed systems and reaction-diffusion modeling 195
8.1 Diffusion-driven transport of solutes in cells and tissue 195
8.1.1 The diffusion equation: assumptions and applications 196
8.1.2 Oxygen transport to tissue and the Krogh-Erlang
model 197
8.1.3 Facilitated diffusion 203
8.2 Advection-diffusion modeling of solute transport in tissues 209
8.2.1 Axially distributed models of blood-tissue exchange 211
8.2.2 Analysis of solute transport in organs 214
8.2.3 Whole-organ metabolic modeling 216
8.3 Three-dimensional modeling 216
9 Constraint-based analysis of biochemical systems 220
9.1 Motivation for constraint-based modeling and analysis 221
9.2 Mass-balance constraints 221
9.2.1 Mathematical representation for flux balance
analysis 221
9.2.2 Energy metabolism in E. coli 223
9.3 Thermodynamic constraints 227
9.3.1 The basic idea 228
9.3.2 Mathematical details 230
9.3.3 Feasible sign patterns 232
9.4 Further concepts in constraint-based analysis 234
9.4.1 Feasible concentrations from potentials 234
9.4.2 Biochemical conductance and enzyme activity 235
9.4.3 Conserved metabolite pools 235
9.4.4 Biological objective functions and optimization 236
9.4.5 Metabolic engineering 238
9.4.6 Incorporating metabolic control analysis 238
10 Biomacromolecular structure and molecular association 240
10.1 Protein structures and a-helices 241
Contents xv
10.1.1 The theory of helix-coil transition 242
10.2 Protein filaments and actin polymerization 248
10.2.1 Nucleation and critical monomer concentration 249
10.2.2 Theory of nucleation-elongation of actin polymerization 250
10.3 Macromolecular association 252
10.3.1 A combinatorial theory of macromolecular association 252
10.3.2 Statistical thermodynamics of association 256
10.4 A dynamics theory of association 257
10.4.1 Transition-state theory and rate constants 259
11 Stochastic biochemical systems and the chemical master equation 261
11.1 A brief introduction to the chemical master equation 262
11.2 Essential materials from probability theory 265
11.2.1 The law of large numbers 265
11.2.2 Continuous time Markov chain 265
11.3 Single molecules and stochastic models for unimolecular
reaction networks 267
11.3.1 Rate equations for two-state conformational change 267
11.3.2 Michaelis-Menten kinetics of single enzymes 270
11.4 The CME models for non-linear biochemical reactions
with fluctuations 271
11.4.1 Chemical master equation for Michaelis-Menten kinetics 271
11.4.2 A non-linear biochemical reaction system with
concentration fluctuations 273
11.4.3 Bistability and non-equilibrium steady state 276
11.4.4 Stochastic simulation of the CME 276
11.5 The CME model for protein synthesis in a single cell 278
12 Appendix: the statistical basis of thermodynamics 282
12.1 The NVE ensemble 282
12.2 The NVT ensemble 287
12.2.1 Boltzmann statistics and the canonical partition
function: a derivation 287
12.2.2 Another derivation 288
12.2.3 One more derivation 289
12.2.4 Equipartition 291
12.3 The NPT ensemble 293
Bibliography 296
Index 307
|
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| illustrated | Illustrated |
| indexdate | 2024-12-23T21:30:49Z |
| institution | BVB |
| isbn | 9780521870702 0521870704 |
| language | English |
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| spellingShingle | Beard, Daniel A. Chemical biophysics quantitative analysis of cellular systems Mathematik Physical biochemistry Computational biology Biological systems Mathematics Biophysikalische Chemie (DE-588)4291844-3 gnd |
| subject_GND | (DE-588)4291844-3 |
| title | Chemical biophysics quantitative analysis of cellular systems |
| title_auth | Chemical biophysics quantitative analysis of cellular systems |
| title_exact_search | Chemical biophysics quantitative analysis of cellular systems |
| title_full | Chemical biophysics quantitative analysis of cellular systems Daniel A. Beard ; Hong Qian |
| title_fullStr | Chemical biophysics quantitative analysis of cellular systems Daniel A. Beard ; Hong Qian |
| title_full_unstemmed | Chemical biophysics quantitative analysis of cellular systems Daniel A. Beard ; Hong Qian |
| title_short | Chemical biophysics |
| title_sort | chemical biophysics quantitative analysis of cellular systems |
| title_sub | quantitative analysis of cellular systems |
| topic | Mathematik Physical biochemistry Computational biology Biological systems Mathematics Biophysikalische Chemie (DE-588)4291844-3 gnd |
| topic_facet | Mathematik Physical biochemistry Computational biology Biological systems Mathematics Biophysikalische Chemie |
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