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Biological Complexity and the Dynamics of Life Processes,9780444500816
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Biological Complexity and the Dynamics of Life Processes


Edition: 1st
Author(s): Ricard
ISBN10:  0444500812
ISBN13:  9780444500816
Format:  Hardcover
Pub. Date:  11/1/1999
Publisher(s): Elsevier Science & Technology

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SummaryTable of Contents
The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry.

The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological problems.

In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo.

The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology.

Univ. of Paris, France. Discusses experimental results, recent and not so recent, in an integrated dynamic physical perspective. Describes how genetic information and biological complexity take part in the emergence of complex functions that stretch beyond the individual properties of biological macromolecules. For researchers.
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)
The living cell
2(9)
The bacterial cell
2(4)
The eukaryotic cell
6(5)
The living cell is a complex system
11(4)
References
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)
Appendix
59(1)
References
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)
References
80(3)
Control of metabolic networks under steady state conditions
83(20)
Metabolic control theory
83(14)
The parameters of Metabolic control theory
83(1)
The summation theorems
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)
References
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)
Carriers and channels
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)
The model
121(4)
The steady state equations of coupled scalar-vectorial processes
125(3)
Thermodynamics of coupling betwen scalar and vectorial processes
128(6)
References
134(3)
Molecular crowding, transfer of information and channelling of molecules within supramolecular edifices
137(48)
Molecular crowding
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)
Chaperones
160(2)
Prions
162(1)
Multienzyme complexes, instruction and energy transfer
163(9)
The plasminogen-streptokinase system
163(1)
The phosphoribulokinase--glyceraldehyde phosphate dehydrogenase system
163(8)
The Ras--Gap complex
171(1)
Proteins at the lipid--water interface and instruction transfer to proteins
172(1)
Protein kinase C
172(1)
Pancreatic lipase
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)
References
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)
References
233(2)
Dynamics and motility of supramolecular edifices in the living cell
235(30)
Tubulin, actin and their supramolecular edifices
235(5)
Tubulin and microtubules
235(2)
Actin, actin filaments and myofibrils
237(3)
Dynamics and thermodynamics of tubulin and actin polymerization
240(13)
Equilibrium polymers
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)
References
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)
Glycolytic oscillations
265(1)
Calcium spiking
266(1)
Minimum conditions required for the emergence of oscillations in a model metabolic cycle
267(6)
The model
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)
The model
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)
The model
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)
References
310(3)
Spatio-temporal organization during the early stages of development
313(20)
Turing patterns
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)
The basic model
319(1)
Dimensionless variables
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)
References
331(2)
Evolution towards complexity
333(20)
The need for a membrane
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)
References
351(2)
Subject index 353

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