Biophysics | M. V. Volkenshtein

This book is intended for students and post-graduates—biologists mid physicists—who study biophysics. The book has emerged from the lectures given by the author for many years at the Moscow Physico-Technical Institute and from two monographs published earlier. The first of these monographs, Molecular Biophysics, was published in Russian in 1975 and in English by Academic Press in 1977. The second, General Biophysics, was issued in Russian in 1978 and is being prepared for publication by Academic Press. A con­siderable part of the book has been written anew. At the same time the above two monographs are recommended to the reader for a more thorough study of the subject. They are provided with extensive bibliography.

In my opinion, biophysics is not a subsidiary branch of biology -- but a legitimate part of the physical sciences. Biophysics is the physics of living things. Accordingly, an attempt has been made to divorce biophysics from physiology, though these fields overlap to a considerable extent. Though the book is devoted mainly to the theoretical problems of biophysics, it also deals with the most important experimental findings.

 Contents

Preface 5

Chapter 1. Goals and Methods off Biophysics 11 

1.1. The Place of Biophysics in Natural Sciences 11 

1.2. Physics and Biology 13 

1.3. Living and Inanimate Nature 15 

1.4. Biological Individuality 17 

1.5. Finalism and Causality 18 

1.6. The Properties of Open Systems 19 

1.7. Scope and Methods of Biophysics 22

Chapter 2. Chemical Foundations off Biophysics 25 

2.1. Chemistry and Biology 25 

2.2. Amino Acids 27 

2.3. Electrolytes  29 

2.4. The Composition and Primary Structure of Proteins 34 

2.5. Nucleic Acids 36 

2.6. Adenylates 43 

2.7. The Chirality of Biological Molecules 45 

2.8. Carbohydrates and Lipids 49 

2.9. Cofactors, Vitamins, and Hormones 51 

2.10. The Main Biochemical Processes 55 

2.11. Strong and Weak Interactions 58

Chapter 3. Physics off Macromolecules 63 

3.1. Macromolecules and Rubber Elasticity 63 

3.2. Internal Rotation and Rotational Isomerism 66 

3.3. The Rotational-Isomeric Theory of Macromolecules 71 

3.4. The Macromolecule as a Cooperative System 78 

3.5. The Coil and the Globule 82 

3.6. Methods of Investigation of Macromolecules 85 

3.7. Polyelectrolytes 91

Chapter 4. Physics of Proteins 95 

4.1. The Goals of Protein Physics 95 

4.2. Conformations of the Polypeptide C h a in 97 

4.3. The Hydrogen Bond and the Structure of W ater 103 

4.4. Helix-Coil Transitions 108 

4.5. The Protein Globule and Hydrophobic Interactions 114

4.6. Relationship Between the Primary and the Three-Dimensional Structure of Proteins 119 

4.7. The Structure and Stability of theGlobule 125 

4.8. Antibodies and Antigens 132 

4.9. Fibrous Proteins 138

Chapter 5. Methods of Investigation of the Structure of Biopolymers 142 

5.1. X-Ray Diffraction Analysis 142 

5.2. Diffuse Scattering of X-Rays bySolutions of Biopolymers 148 

5.3. Methods of Nuclear Physics 150 5.4. Electronic Absorption Spectra 153 

5.5. Luminescence 157 

5.6. Optical Activity 161 

5.7. Optical Activity of Biopolymers 169 

5.8. Magnetic Optical Activity 174 

5.9. Vibrational Spectra 178

5.10. Nuclear Magnetic Resonance and ElectronParamagnetic Resonance 182

Chapter 6. Physics of Enzymes 188 

6.1. Chemical Kinetics and Catalysis 188 

6.2. Kinetics of Simple EnzymaticReactions 193 

6.3. Chemical Aspects of Enzyme Action 198 

6.4. Conformational Properties of Enzymes 205 

6.5. Physics of Enzyme-Substrate Interactions 209 

6.6. Electronic-Conformational Interactions 212

6.7. Cooperative Properties of Enzymes 217 

6.8. Myoglobin and Hemoglobin 224

Chapter 7. Physics of Nucleic Acids 236 

7.1. Molecular Biology and Physics 236 

7.2. The Structure of Nucleic Acids 239 

7.3. Intramolecular Interactions in the Double Helix 247 

7.4. Thermodynamics of Melting of the Double Helix 250 

7.5. Kinetics of Unwinding of the Double Helix 260 

7.6. Interaction of the Double Helix with SmallMolecules and Ions 265 

7.7. Replication of DNA 268

Chapter 8. Physics of Protein Biosynthesis 275 

8.1. The Problem of the Genetic Code 275 

8.2. Protein Biosynthesis 280 

8.3. Transcription and Reverse Transcription 284

8.4. Transfer RNA  286

8.5. Translation 289

8.6. Deciphering of the Genetic Code and Its Meaning 294 

8.7. Mutations 301 

8.8. Regulation of Genes 306

Chapter 9. Nonequilibrium Thermodynamics in Biology 313 

9.1. Information and Entropy 313 

9.2. Nonequilibrium Processes 319 

9.3. Coupling of Fluxes 322 

9.4. Coupling of Chemical Reactions 325 

9.5. Steady States of Linear Systems 329 

9.6. Coupling of Chemical Reactions to Transport of Matter 335 

9.7. Far-from-Equilibrium Processes 339

Chapter 10. Physics off Membranes 346 

10.1. Cell Membranes 346 

10.2. The Structure of Membranes 348 

10.3. Conformational Properties of Membranes 351 

10.4. Passive Membrane Transport 355 

10.5. Active Membrane Transport 361 

10.6. Transport of Charged Particles Through Membranes 368 

10.7. Molecular Reception 372

Chapter 11. Physics of the Nerve Impulse 377 

11.1. The Axon and the Nerve Impulse 377 

11.2. Propagation of the Nerve Impulse 388 

11.3. Generation of the Nerve Impulse 394

11.4. Ionic Channels 399 

11.5. Synaptic Transmission 402

Chapter 12. Mechanochemical Processes 406

12.1. Thermodynamics of Mechanochemical Processes 406 

12.2. The Structure of the Muscle and Muscle Proteins 411 

12.3. The Chemistry and Physics of the Muscle 417 

12.4. The Theory of Muscular Contraction 423

12.5. The Kinetic Properties of the Muscle 431 

12.6. Mechanochemical Systems 433 

12.7. Biomechanics 437

Chapter 13. Bioenergetics of the Respiratory Chain 440 

13.1. Biological Oxidation 440 

13.2. The Structure and Properties of Mitochondria 446 

13.3. Chemiosmotic Coupling 449 

13.4. Electronic-Conformational Interactions 457 

13.5. Cytochrome c 463

Chapter 14. Photobiological Processes 466 

14.1. Photosynthesis 466 

14.2. Two Photochemical Systems 472 

14.3. Chloroplasts 477 

14.4. The Mechanism of Photosynthesis 481 

14.5. Vision 485 

14.6. The Molecular Mechanism of Photoreception 489 

14.7. Bacteriorhodopsin 497

Chapter 15. Modelling of Dynamic BiologicalProcesses 501

15.1. Dynamic Order 501

15.2. Physico-Mathematical Foundations of the Dynamics of Nonlinear Processes 504

15.3. Lotka-Volterra Models 515

15.4. Autocatalytic Systems 521 

15.5. Phase Transitions 527 

15.6. Stochastic Processes 532 

15.7. Dynamics and Regulation 535

Chapter 16. Periodic Chemical and BiologicalProcesses .538 

16.1. Introduction 538 

16.2. Belousov-Zhabotinsky Reactions 539 

16.3. Auto-oscillations in Glycolysis 547 

16.4. Auto-oscillations in Photosynthesis 551 

16.5. Nonlinear Dynamics of Membranes 554 

16.6. Autowave Processes in the Cardiac Muscle 559

Chapter 17. Problems of Biological Evolution and Development 564 

17.1 The Origin of Life 564 

17.2. Modelling of Prebiotic Evolution 568 

17.3. Game Models and Informational Aspects of Self-Organization 572 

17.4. Hypercycles 575 

17.5. Other Models of Prebiological Evolution 579 

17.6. Biological Evolution 585 

17.7. Ontogenesis 589 

17.8. Immunity 596 

17.9. Biological Evolution and Information Theory 602

17.10. Complexity and Evolution 611 

Recommended Literature 619 

Name Index  624 

Subject Index  627