1 Introduction.- 2 Thermodynamics and Chemical Kinetics of Living Systems.- 2.1. How Scientists Learned to Distinguish Energy from Force (Brief Historic Review).- 2.2. Kinetics and Thermodynamics of Chemical Reactions.- 2.3. Applicability of Equilibrium and Nonequilibrium Thermodynamics to Biological Systems and Processes.- 2.4. The Mechanisms of Energy Coupling in Chemical Reactions.- 2.4.1. Indirect Mechanism of Energy Coupling in Equilibrium (Quasi-Equilibrium) Homogeneous Mixtures of Chemical Reagents.- 22.214.171.124. Enthalpic Mechanism of Indirect Coupling.- 126.96.36.199. Entropic Mechanism of Indirect Coupling.- 2.4.2. Entropic Mechanism of Coupling Chemical Reactions in Open Systems.- 3 Molecular Machines: Mechanics and/or Statistics?.- 3.1. The Second Law of Thermodynamics and Its Application to Biochemical Systems.- 3.2. Energy-Transducing Molecular Machines.- 3.2.1. Macroscopic Machines.- 3.2.2. What Are Molecular Machines? Reversibility of Energy-Transducing Devices and the Problem of the Optimal Functioning of Molecular Machines.- 3.2.3. Models for Calculating the Conversion Factor.- 3.3. Statistical Thermodynamics of Small Systems, Fluctuations, and the Violation of the Mass Action Law.- 3.3.1. Structural Peculiarities of Energy-Transducing Organelles of Chloroplasts.- 3.3.2. Chemical Equilibrium Inside Small Vesicles.- 3.3.3. Compartmentalization and the Problem of the Macroscopic Description of "Channeled" Chemical Reactions.- 3.3.4. The Fluctuations, Random Noise, Energy Transduction, and Apparent Violation of the Second Law of Thermodynamics.- 4 Principles of Enzyme Catalysis.- 4.1. Introduction.- 4.2. Earlier Theories of Enzyme Catalysis.- 4.3. The Relaxation Concept of Enzyme Catalysis.- 4.4. Protein Dynamics and Enzyme Functioning.- 4.4.1. Theoretical Aspects of Protein Structural Dynamics.- 4.4.2. Experimental Evidence for Protein Nonequilibrium States and Their Evolution in the Course of Enzyme Turnover.- 5 Energy Transduction in Biological Membranes.- 5.1. Introduction: Two Views on the Problem of Energy Coupling in Biomembranes.- 5.2. Transmembrane Electrochemical Proton Gradients in Chloroplasts.- 5.2.1. Brief Review of the Methods for the ?pH Measurements with pH-Indicating Probes.- 5.2.2. Measurements of ?pH in the Thylakoids with the Kinetic Method.- 5.2.3. Measurements of ?pH in the Thylakoids with a Spin Labeling Technique.- 5.2.4. Lateral Heterogeneity of ?pH in Chloroplasts.- 5.2.5. Membrane-Sequestered Proton Pools and Alternative Pathways of Proton Transport Coupled with ATP Synthesis.- 5.3. Mechanism of ATP Formation Catalyzed by H+ATPsynthases.- 5.3.1. An Elementary Act of ATP Synthesis.- 188.8.131.52. Initial Events of ATP Formation.- 184.108.40.206. Energy-Requiring Step of ATP Formation.- 220.127.116.11. ATP Synthesis from ADP and Pi Catalyzed by Water-Soluble Coupling Factor F1.- 18.104.22.168. ATP Synthesis Induced by the Acid-Base Transitions.- 22.214.171.124. ATP Synthesis from ADP and Pi as Considered from the Viewpoint of the Relaxation Concept of Enzyme Catalysis.- 5.3.2. ATP Synthesis under Steady State Conditions.- 126.96.36.199. The Possible Model for ATPsynthase Cyclic Functioning.- 188.8.131.52. Photophosphorylation in Chloroplasts and Oxidative Phosphorylation in Mitochondria.- Afterword.
This book is aimed at a large audience: from students, who have a high school background in physics, mathematics, chemistry, and biology, to scien tists working in the fields of biophysics and biochemistry. The main aim of this book is to attempt to describe, in terms of physical chemistry and chemi cal physics, the peculiar features of "machines" having molecular dimen sions which play a crucial role in the most important biological processes, viz. , energy transduction and enzyme catalysis. One of the purposes of this book is to analyze the physical background of the high efficiency of molecu lar machines functioning in the living cell. This book begins with a brief review of the subject (Chapter 1). Macro molecular energy-transducing complexes operate with thermal, chemical, and mechanical energy, therefore the appropriate framework to discuss the functioning of biopolymers comes from thermodynamics and chemical kinet ics. That is why we start our analysis with a consideration of the conventional approaches of thermodynamics and classical chemical kinetics, and their application to the description of bioenergetic processes (Chapter 2). Critical analysis of these approaches has led us to the conclusion that the conven tional approaches of physical chemistry to the description of the functioning of individual macromolecular devices, in many cases, appear to be incom plete. This prompted us to consider the general principles ofliving machinery from another point of view.
The main goal of this book is to describe in physical terms the peculiar features of "machines" having molecular dimensions that play the principal role in the most important biological processes. The book is aimed at scientists and graduate students of biochemistry and biophysics as well as biologists and physicians working in this field.