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.
Biological Complexity and the Dynamics of Life Processes, 1st Edition
Preface. Chapter 1. Complexity and the structure of the living cell. 1.1. What do we mean by complexity?. 1.2. The living cell. 1.3. The living cell is a complex system. Chapter 2. Elementary life processes viewed as dynamic physicochemical events. 2.1. General phenomenological description of dynamic processes. 2.2. Enzyme reactions under simple standard conditions. 2.3. Does the complexity of the living cell affect the dynamics of enzyme-catalysed reactions? Chapter 3. Coupling between chemical and (or) vectorial processes as a basis for signal perception and transduction. 3.1. Coupling between reagent diffusion and bound enzyme reaction rate as an elementary sensing device. 3.2. Sensitivity amplification for coupled biochemical systems. 3.3. Bacterial chemotaxis as an example of cell signaling. 3.4. General features of a signaling process. Chapter 4. Control of metabolic networks under steady state conditions. 4.1. Metabolic control theory. 4.2. Biochemical systems theory. 4.3. An example of the application of Metabolic control theory to a biological problem. Chapter 5. Compartmentalization of the living cell and thermodynamics of energy conversion. 5.1. Thermodynamic properties of compartmentalized systems. 5.2. Brief description of molecular events involved in energy coupling. 5.3. Compartmentalization of the living cell and the kinetics and thermodynamics of coupled scalar and vectorial processes. Chapter 6. Molecular crowding, transfer of information and channeling of molecules within supramolecular edifices. 6.1. Molecular crowding. 6.2. Statistical mechanics of ligand binding to supramolecular edifices. 6.3. Statistical mechanics and catalysis within supramolecular edificis. 6.4. Statistical mechanics of imprinting effects. 6.5. Statistical mechanics of instruction transfer within supramolecular edifices. 6.6. Instruction, chaperones and prion proteins. 6.7. Multienzyme complexes, instruction and energy transfer. 6.8. Proteins at the lipid-water interface and instruction transfer to proteins. 6.9. Information transfer between proteins and enzyme regulation. 6.10. Channeling of reaction intermediates within multienzyme complexes. 6.11. The different types of communication within multienzyme complexes. Chapter 7. Cell complexity, electrostatic partitioning of ions and bound enzyme reactions. 7.1. Enzyme reactions in a homogeneous polyelectrolyte matrix. 7.2. Enzyme reactions in a complex heterogeneous polyelectrolyte matrix. 7.3. An example of enzyme behaviour in a complex biological system: the kinetics of an enzyme bound to plant cell walls. 7.4. Sensing, memorizing and conducting signals by polyelectrolyte-bound enzymes. 7.5. Complexity of biological polyelectrolytes and the emergence of novel functions. Chapter 8. Dynamics and mobility of supramolecular edifices in the living cell. 8.1. Tubulin, actin and their supramolecular edifices. 8.2. Dynamics and thermodynamics of tubulin and actin polymerization. 8.3. Molecular motors and the statistical physics of muscle contraction. 8.4. Dynamic state of supramolecular edifices in the living cell. Chapter 9. Temporal organization of metabolic cycles and structural complexity: oscillations and chaos. 9.1. Brief overview of the temporal organization of some metabolic processes. 9.2. Minimum conditions required for the emergence of oscillations in a model metabolic cycle. 9.3. Emergence of a temporal organization generated by compartmentalization and electric repulsion effects. 9.4. Periodic and aperiodic oscillations generated by the complexity of the supramolecular edifices of the cell. 9.5. ATP synthesis and active transport induced by periodic electric fields. 9.6. Some functional advantages of complexity. Chapter 10. Spatio-temporal organization during the early stages of development. 10.1. Turing patterns. 10.2. Positional information and the existence of gradients of morphogens during early development. 10.3. The emergence of patterns and forms. 10.4. Pattern formation and complexity. Chapter 11. Evolution towards complexity. 11.1. The need for a membrane. 11.2. How to improve the efficiency of metabolic networks in homogeneous phase. 11.3. The emergence and functional advantages of compartmentalization. 11.4. Evolution of molecular crowding and the different types of information transfer. 11.5. Control of phenotypic expression by a negatively charged cell wall. 11.6. Evolution of the cell structures associated with motion. 11.7. The emergence of temporal organization as a consequence of supramolecular complexity. 11.8. The emergence of multicellular organisms. 11.9. Is natural selection the only driving force of evolution?.