| Preface |
|
v | |
| Other volumes in the series |
|
xi | |
|
Complexity and the structure of the living cell |
|
|
1 | (14) |
|
What do we mean by complexity? |
|
|
1 | (1) |
|
|
|
2 | (9) |
|
|
|
2 | (4) |
|
|
|
6 | (5) |
|
The living cell is a complex system |
|
|
11 | (4) |
|
|
|
12 | (3) |
|
Elementary life processes viewed as dynamic physicochemical events |
|
|
15 | (48) |
|
General phenomenological description of dynamic processes |
|
|
15 | (6) |
|
Enzyme reactions under simple standard conditions |
|
|
21 | (36) |
|
Simple transition state theory and enzyme reactions |
|
|
21 | (6) |
|
``Complementarity'' between the active site of the enzyme and the transition state |
|
|
27 | (6) |
|
The time-course of an enzyme reaction |
|
|
33 | (4) |
|
Simple enzymes that catalyse simple reactions |
|
|
37 | (5) |
|
Simple enzymes that catalyse complex reactions |
|
|
42 | (15) |
|
Does the complexity of the living cell affect the dynamics of enzyme-catalysed reactions? |
|
|
57 | (6) |
|
|
|
59 | (1) |
|
|
|
60 | (3) |
|
Coupling between chemical and (or) vectorial processes as a basis for signal perception and transduction |
|
|
63 | (20) |
|
Coupling between reagent diffusion and bound enzyme reaction rate as an elementary sensing device |
|
|
63 | (5) |
|
The basic equation of coupling |
|
|
63 | (3) |
|
Hysteresis loops and sensing chemical signals |
|
|
66 | (1) |
|
Control of the substrate gradient |
|
|
67 | (1) |
|
Sensitvity amplification for coupled biochemical systems |
|
|
68 | (8) |
|
Zero-order ultrasensitivity of a monocyclic cascade |
|
|
69 | (1) |
|
Response of the system to changes in effector concentration |
|
|
70 | (2) |
|
Propagation of amplification in multicyclic cascades |
|
|
72 | (2) |
|
Response of a polycyclic cascade to an effector |
|
|
74 | (2) |
|
Bacterial chemotaxis as an example of cell signaling |
|
|
76 | (3) |
|
General features of a signaling process |
|
|
79 | (4) |
|
|
|
80 | (3) |
|
Control of metabolic networks under steady state conditions |
|
|
83 | (20) |
|
|
|
83 | (14) |
|
The parameters of Metabolic control theory |
|
|
83 | (1) |
|
|
|
84 | (3) |
|
Connectivity between flux control coefficients and elasticities |
|
|
87 | (3) |
|
Generalized connectivity relationships and the problem of enzyme interactions and information transfer in Metabolic control theory |
|
|
90 | (5) |
|
Feedback control of a metabolic pathway |
|
|
95 | (1) |
|
Control of branched pathways |
|
|
96 | (1) |
|
Biochemical systems theory |
|
|
97 | (3) |
|
An example of the application of Metabolic control theory to a biological problem |
|
|
100 | (3) |
|
|
|
101 | (2) |
|
Compartmentalization of the living cell and thermodynamics of energy conversion |
|
|
103 | (34) |
|
Thermodynamic properties of compartmentalized systems |
|
|
103 | (7) |
|
Brief description of molecular events involved in energy coupling |
|
|
110 | (11) |
|
|
|
111 | (3) |
|
Energy storage in mitochondria and chloroplasts |
|
|
114 | (7) |
|
Compartmentalization of the living cell and the kinetics and thermodynamics of coupled scalar and vectorial processes |
|
|
121 | (16) |
|
|
|
121 | (4) |
|
The steady state equations of coupled scalar-vectorial processes |
|
|
125 | (3) |
|
Thermodynamics of coupling betwen scalar and vectorial processes |
|
|
128 | (6) |
|
|
|
134 | (3) |
|
Molecular crowding, transfer of information and channelling of molecules within supramolecular edifices |
|
|
137 | (48) |
|
|
|
138 | (1) |
|
Statistical mechanics of ligand binding to supramolecular edifices |
|
|
139 | (5) |
|
Statistical mechanics and catalysis within supramolecular edifices |
|
|
144 | (7) |
|
Statistical mechanics of imprinting effects |
|
|
151 | (4) |
|
Statistical mechanics of instruction transfer within supramolecular edifices |
|
|
155 | (5) |
|
Instruction, chaperones and prion proteins |
|
|
160 | (3) |
|
|
|
160 | (2) |
|
|
|
162 | (1) |
|
Multienzyme complexes, instruction and energy transfer |
|
|
163 | (9) |
|
The plasminogen-streptokinase system |
|
|
163 | (1) |
|
The phosphoribulokinase--glyceraldehyde phosphate dehydrogenase system |
|
|
163 | (8) |
|
|
|
171 | (1) |
|
Proteins at the lipid--water interface and instruction transfer to proteins |
|
|
172 | (1) |
|
|
|
172 | (1) |
|
|
|
173 | (1) |
|
Information transfer between proteins and enzyme regulation |
|
|
173 | (1) |
|
Channelling of reaction intermediates within multienzyme complexes |
|
|
174 | (3) |
|
The different types of communication within multienzyme complexes |
|
|
177 | (8) |
|
|
|
177 | (8) |
|
Cell complexity, electrostatic partitioning of ions and bound enzyme reactions |
|
|
185 | (50) |
|
Enzyme reactions in a homogeneous polyelectrolyte matrix |
|
|
185 | (9) |
|
Electrostatic partitioning of mobile ions by charged matrices |
|
|
185 | (4) |
|
pH effects of polyelectrolyte-bound enzymes |
|
|
189 | (4) |
|
Apparent kinetic co-operativity of a polyelectrolyte-bound enzyme |
|
|
193 | (1) |
|
Enzyme reactions in a complex heterogeneous polyelectrolyte matrix |
|
|
194 | (10) |
|
Can the fuzzy organization of a polyelectrolyte affect a bound enzyme reaction? |
|
|
194 | (2) |
|
Statistical formulation of a fuzzy organization of fixed charges and bound enzyme molecules in a polyanionic matrix |
|
|
196 | (3) |
|
Apparent co-operativity generated by the complexity of the polyelectrolyte matrix |
|
|
199 | (5) |
|
An example of enzyme behaviour in a complex biological system: the kinetics of an enzyme bound to plant cell walls |
|
|
204 | (14) |
|
Brief overview of the structure and dynamics of primary cell wall |
|
|
204 | (2) |
|
Kinetics of a cell wall bound enzyme |
|
|
206 | (2) |
|
The two-state model of the primary cell wall and the process of cell elongation |
|
|
208 | (10) |
|
Sensing, memorizing and conducting signals by polyelectrolyte-bound enzymes |
|
|
218 | (14) |
|
Diffusion of charged substrate and charged product of an enzyme reaction |
|
|
219 | (2) |
|
Electric partition of ions and Donnan potential under gobal nonequilibrium conditions |
|
|
221 | (2) |
|
Coupling between diffusion, reaction and electric partition of the substrate and the product |
|
|
223 | (3) |
|
Conduction of ionic signals by membrane-bound enzymes |
|
|
226 | (6) |
|
Complexity of biological polyelectrolytes and the emergence of novel functions |
|
|
232 | (3) |
|
|
|
233 | (2) |
|
Dynamics and motility of supramolecular edifices in the living cell |
|
|
235 | (30) |
|
Tubulin, actin and their supramolecular edifices |
|
|
235 | (5) |
|
|
|
235 | (2) |
|
Actin, actin filaments and myofibrils |
|
|
237 | (3) |
|
Dynamics and thermodynamics of tubulin and actin polymerization |
|
|
240 | (13) |
|
|
|
241 | (1) |
|
Drug effects on equilibrium polymers |
|
|
242 | (3) |
|
Treadmilling and steady state polymers |
|
|
245 | (5) |
|
Drug action on steady state polymers |
|
|
250 | (3) |
|
Molecular motors and the statistical physics of muscle contraction |
|
|
253 | (9) |
|
Dynamic state of supramolecular edifices in the living cell |
|
|
262 | (3) |
|
|
|
263 | (2) |
|
Temporal organization of metabolic cycles and structural complexity: oscillations and choas |
|
|
265 | (48) |
|
Brief overview of the temporal organization of some metabolic processes |
|
|
265 | (2) |
|
|
|
265 | (1) |
|
|
|
266 | (1) |
|
Minimum conditions required for the emergence of oscillations in a model metabolic cycle |
|
|
267 | (6) |
|
|
|
267 | (1) |
|
Steady states of a model metabolic cycle |
|
|
267 | (4) |
|
Stability analysis of the model metabolic cycle |
|
|
271 | (2) |
|
Emergence of a temporal organization generated by compartmentalization and electric repulsion effects |
|
|
273 | (18) |
|
|
|
273 | (2) |
|
The dynamic equations of the system and the sensitivity coefficients |
|
|
275 | (3) |
|
Local stability of the system |
|
|
278 | (5) |
|
Electrostatic repulsion effects and multiple steady states |
|
|
283 | (2) |
|
pH-effects and the oscillatory dynamics of bound enzyme systems |
|
|
285 | (6) |
|
Periodic and aperiodic oscillations generated by the complexity of the supramolecular edifices of the cell |
|
|
291 | (14) |
|
|
|
291 | (2) |
|
The basic enzyme equations |
|
|
293 | (5) |
|
Homogeneous population of elementary oscillators |
|
|
298 | (3) |
|
Periodic and ``chaotic'' behaviour of the overall growth rate |
|
|
301 | (2) |
|
Periodic and aperiodic oscillations of the elongation rate of plant cells |
|
|
303 | (2) |
|
ATP synthesis and active transport induced by periodic electric fields |
|
|
305 | (3) |
|
Some functional advantages of complexity |
|
|
308 | (5) |
|
|
|
310 | (3) |
|
Spatio-temporal organization during the early stages of development |
|
|
313 | (20) |
|
|
|
313 | (1) |
|
Positional information and the existence of gradients of morphogens during early development |
|
|
314 | (5) |
|
Gradients and the early development of Drosophila egg |
|
|
314 | (4) |
|
Gradients and the development of the chick limb |
|
|
318 | (1) |
|
The emergence of patterns and forms |
|
|
319 | (12) |
|
|
|
319 | (1) |
|
|
|
320 | (1) |
|
Stability analysis of temporal organization |
|
|
321 | (2) |
|
Stability analysis of spatio-temporal organization |
|
|
323 | (6) |
|
Emergence of patterns in finite intervals |
|
|
329 | (2) |
|
Pattern formation and complexity |
|
|
331 | (2) |
|
|
|
331 | (2) |
|
Evolution towards complexity |
|
|
333 | (20) |
|
|
|
333 | (7) |
|
How to improve the efficiency of metabolic networks in homogeneous phase |
|
|
340 | (2) |
|
The possible origin of connected metabolic reactions |
|
|
340 | (1) |
|
The poor efficiency of primitive metabolic networks in homogeneous phase |
|
|
340 | (1) |
|
How to cope with the physical limitations of a homogeneous phase |
|
|
341 | (1) |
|
The emergence and functional advantages of compartmentalization |
|
|
342 | (1) |
|
The symbiotic origin of intracellular membranes |
|
|
342 | (1) |
|
Functional advantages of compartmentalization |
|
|
343 | (1) |
|
Evolution of molecular crowding and the different types of information transfer |
|
|
343 | (1) |
|
Control of phenotypic expression by a negatively charged cell wall |
|
|
344 | (1) |
|
Evolution of the cell structures associated with motion |
|
|
345 | (2) |
|
The emergence of temporal organization as a consequence of supramolecular complexity |
|
|
347 | (2) |
|
The emergence of multicellular organisms |
|
|
349 | (1) |
|
Is natural selection the only driving force of evolution? |
|
|
350 | (3) |
|
|
|
351 | (2) |
| Subject index |
|
353 | |