Biological Complexity and the Dynamics of Life Processes (eBook)

Front Cover 1
Biological Complexity and the Dynamics of Life Processes 4
Copyright Page 5
Contents 8
Preface 6
Other Volumes in the Series 12
Chapter 1. Complexity and the structure of the living cell 14
1.1. What do we mean by complexity? 14
1.2. The living cell 15
1.3. The living cell is a complex system 24
References 25
Chapter 2. Elementary life processes viewed as dynamic physicochemical events 28
2.1. General phenomenological description of dynamic processes 28
2.2. Enzyme reactions under simple standard conditions 34
2.3. Does the complexity of the living cell affect the dynamics of enzyme-catalysed reactions? 70
Appendix 72
References 73
Chapter 3. Coupling between chemical and (or) vectorial processes as a basis for signal perception and transduction 76
3.1. Coupling between reagent diffusion and bound enzyme reaction rate as an elementary sensing device 76
3.2. Sensitivity amplification for coupled biochemical systems 81
3.3. Bacterial chemotaxis as an example of cell signaling 89
3.4. General features of a signaling process 92
References 93
Chapter 4. Control of metabolic networks under steady state conditions 96
4.1. Metabolic control theory 96
4.2. Biochemical systems theory 110
4.3. An example of the application of Metabolic control theory to a biological problem 113
References 114
Chapter 5. Compartmentalization of the living cell and thermodynamics of energy conversion 116
5.1. Thermodynamic properties of compartmentalized systems 116
5.2. Brief description of molecular events involved in energy coupling 123
5.3. Compartmentalization of the living cell and the kinetics and thermodynamics of coupled scalar and vectorial processes 134
References 147
Chapter 6. Molecular crowding, transfer of information and channelling of molecules within supramolecular edifices 150
6.1. Molecular crowding 151
6.2. Statistical mechanics of ligand binding to supramolecular edifices 152
6.3. Statistical mechanics and catalysis within supramolecular edifices 157
6.4. Statistical mechanics of imprinting effects 164
6.5. Statistical mechanics of instruction transfer within supramolecular edifices 168
6.6. Instruction, chaperones and prion proteins 173
6.7. Multienzyme complexes, instruction and energy transfer 176
6.8. Proteins at the lipid–water interface and instruction transfer to proteins 185
6.9. Information transfer between proteins and enzyme regulation 186
6.10. Channelling of reaction intermediates within multienzyme complexes 187
6.11. The different types of communication within multienzyme complexes 190
References 190
Chapter 7. Cell complexity, electrostatic partitioning of ions and bound enzyme reactions 198
7.1. Enzyme reactions in a homogeneous polyelectrolyte matrix 198
7.2. Enzyme reactions in a complex heterogeneous polyelectrolyte matrix 207
7.3. An example of enzyme behaviour in a complex biological system: the kinetics of an enzyme bound to plant cell walls 217
7.4. Sensing, memorizing and conducting signals by polyelectrolyte-bound enzymes 231
7.5. Complexity of biological polyelectrolytes and the emergence of novel functions 245
References 246
Chapter 8. Dynamics and motility of supramolecular edifices in the living cell 248
8.1. Tubulin. actin and their supramolecular edifices 248
8.2. Dynamics and thermodynamics of tubulin and actin polymerization 253
8.3. Molecular motors and the statistical physics of muscle contraction 266
8.4. Dynamic state of supramolecular edifices in the living cell 275
References 276
Chapter 9. Temporal organization of metabolic cycles and structural complexity: oscillations and chaos 278
9.1. Brief overview of the temporal organization of some metabolic processes 278
9.2. Minimum conditions required for the emergence of oscillations in a model metabolic cycle 280
9.3. Emergence of a temporal organization generated by compartmentalization and electric repulsion effects 286
9.4. Periodic and aperiodic oscillations generated by the complexity of the supramolecular edifices of the cell 304
9.5. ATP synthesis and active transport induced by periodic electric fields 318
9.6. Some functional advantages of complexity 321
References 323
Chapter 10. Spatio-temporal organization during the early stages of development 326
10.1. Turing patterns 326
10.2. Positional information and the existence of gradients of morphogens during early development 327
10.3. The emergence of patterns and forms 332
10.4. Pattern formation and complexity 344
References 344
Chapter 11. Evolution towards complexity 346
11.1. The need for a membrane 346
11.2. How to improve the efficiency of metabolic networks in homogeneous phase 353
11.3. The emergence and functional advantages of compartmentalization 355
11.4. Evolution of molecular crowding and the different types of information transfer 356
11.5. Control of phenotypic expression by a negatively charged cell wall 357
11.6. Evolution of the cell structures associated with motion 358
11.7. The emergence of temporal organization as a consequence of supramolecular complexity 360
11.8. The emergence of multicellular organisms 362
11.9. Is natural selection the only driving force of evolution? 363
References 364
Subject index 366