《Molecular Biophysics》

CHAPTER 1．PHYSICS AND BIOLOGY1

1-1Introduction1

1-2 History of biophysics3

1-3 Life － order or chaos?6

1-4 Summary7

CHAPTER 2．THE BIOPHYSICIST＇S VIEW OF THE LIVING CELL10

2-1The broad characteristics of a typical cell10

2-2 Cell organelles13

2-3 The molecular composition of a cell16

2-4 Biological molecules and their general character17

2-5 Cell behavior26

2-6 Viruses31

2-7 Genetics and biophysics36

2-8 Molecular biophysics38

CHAPTER 3．ENERGETIC AND STATISTICAL RELATIONS IN THE LIVING CELL42

3-1Introduction42

3-2 The conservation of energy in biological processes43

3-3 Metabolism，or chemical and energy turnover45

3-4 Statistical thermodynamics and biology49

3-5 The theory of absolute reaction rates57

3-6 Thermal inactivation62

3-7 The entropy transfer of living organisms63

3-8 Information theory．Relation between information and entropy66

3-9 Information content of some biological systems68

3-10 Information content of a bacterial cell71

CHAPTER 4．PHYSICAL METHODS OF DETERMINING THE SIZES AND SHAPES OF MOLECULES77

4-1Introduction77

4-2 Random motion79

4-3 Diffusion82

4-4 Measurement of diffusion constants87

4-5 Sedimentation91

4-6 Sedimentation-equilibrium method93

4-7 Sedimentation-velocity method95

4-8 Analytical centrifuges and optical detection methods98

4-9 Rotational diffusion and birefringence105

4-10 Conclusion109

CHAPTER 5．X-RAY ANALYSIS AND MOLECULAR STRUCTURES113

5-1Introduction113

5-2 Production of x-rays115

5-3 Diffraction of x-rays118

5-4 Crystal structure and the unit cell121

5-5 Layer lines and crystal arrays124

5-6 Vector representation of amplitudes and the width of diffraction maxima126

5-7 Density distribution within a unit cell128

5-8 The diffraction patterns of some protein fibers132

5-9 The structure of globular proteins135

5-10 The structure of polypeptide chains139

5-11 The pleated sheets and β-keratin141

5-12 The α-helix and α-keratin143

5-13 The structure of nucleic acid polymers145

5-14 The structure of nucleoproteins150

5-15 The analysis of virus structures151

5-16 Conclusion153

CHAPTER 6．INTRAMOLECULAR AND INTERMOLECULAR FORCES156

6-1Strong and weak forces156

6-2 The uncertainty principle and the Pauli principle157

Ⅰ．Strong Interactions161

6-3The covalent bond161

6-4 The ionic bond163

6-5 Resonance164

Ⅱ．Weak Interactions165

6-6Dipole-dipole interaction165

6-7 Permanent-dipole，induced-dipole interaction169

6-8 Transient-dipole，induced-dipole interaction170

6-9 Dispersion forces between large molecules172

6-10 The hydrogen-bond interaction174

6-11 Charge-fluctuation interaction175

Ⅲ．molecules in Solution176

6-12Debye-Hückel theory176

6-13 Antigens and antibodies as examples of short-range forces in solution181

CHAPTER 7．ABSORPTION SPECTROSCOPY AND MOLECULAR STRUCTURE189

7-1Introduction189

7-2 Atomic energy levels190

7-3 Molecular energy levels193

7-4 Vibrational energy levels195

7-5 Vibrations of polyatomic molecules199

7-6 Characteristic bond frequencies201

7-7 Raman spectra and the dipolar nature of amino acids203

7-8 The vibrational spectra of proteins205

7-9 The energy levels of hydrogen-bonded structures206

7-10 Absorption coefficient and cross section208

7-11 Experimental techniques for absorption measurements212

7-12 Absorption by oriented dipoles214

7-13 Dichroic ratios of proteins and nucleic acids217

7-14 Electronic energy levels220

7-15 Electronic spectra of polyatomic molecules223

7-16 Ultraviolet absorption by proteins and nucleic acids225

7-17 The fine structure in spectra228

7-18 Polarized ultraviolet light229

7-19 Electron spin resonance230

7-20 Nuclear magnetic resonance234

CHAPTER 8．ENZYMES239

8-1Introduction239

8-2 The temperature dependence of enzyme kinetics239

8-3 The enzyme-substrate complex242

8-4 Observation of the enzyme-substrate complex245

8-5 Heat inactivation and the structure of enzymes251

8-6 The relation between enzyme structure and function253

8-7 Enzyme specificity257

8-8 Speculations about the mechanism of enzyme action262

8-9 Speculations about the minimum size of an enzyme264

CHAPTER 9．ACTION SPECTRA AND QUANTUM YIELDS267

9-1Introduction267

9-2 Light sources and materials269

9-3 Monochromators271

9-4 Intensity measurements274

9-5 Definition of action spectra277

9-6 Action spectra theory278

9-7 Inactivation of proteins and nucleic acids281

9-8 Light action on respiratory pigments288

9-9 Photosynthesis291

9-10 Sensitized fluorescence294

9-11 Viruses and microorganisms295

9-12 Cooperative events in light action;the Poisson distribution296

9-13 Photoreversal303

CHAPTER 10．THE ACTION OF IONIZING RADIATION ON CELLULAR CONSTITUENTS306

10-1Introduction306

10-2 The nature of ionizing radiation307

10-3 The measure of radiation:the roentgen315

10-4 Ionization by x-rays，gamma rays，or neutrons315

10-5 Dosimetry318

10-6 Action of ionizing radiation on molecular systems321

10-7 Experimental results of bombarding large biological molecules323

10-8 Target theory326

10-9 Variable linear energy transfer328

10-10 Effect of secondary electrons，or delta rays331

10-11 Features of the radiation sensitivity of large molecules333

10-12 Molecular effects by agents that diffuse334

10-13 Protective action against diffusing agents336

10-14 The oxygen effect338

10-15 A theoretical analysis of radiation effects on a cell339

10-16 The action of ionizing radiation on chromosomes343

10-17 The effects of ionizing radiation on human beings347

CHAPTER 11．THE USE OF IONIZING RADIATION TO STUDY CELL STRUCTURE352

11-1Introduction352

11-2 The principle of the method352

11-3 Early radiation studies of structure356

11-4 Radiation studies of the structure of viruses358

11-5 Differential radiation studies on bacteria366

11-6 Bombardment of bacteria by particles limited in penetration374

11-7 Orientation studies377

11-8 Conclusion378

CHAPTER 12．MICROSCOPES380

12-1Introduction380

12-2 Magnification380

12-3 Resolution384

12-4 Contrast391

12-5 Staining393

12-6 Fluorescence393

12-7 Polarization393

12-8 Ultraviolet microscopes396

12-9 Interference microscopes399

12-10 Phase microscopes403

12-11 Electron microscopy410

CHAPTER 13．ISOTOPIC TRACERS IN MOLECULAR BIOPHYSICS417

13-1Introduction417

13-2 Detection and measurement of isotopes420

13-3 Experimental use of isotopic tracers424

13-4 The permeability of the bacterial cell to small molecules424

13-5 Amino acid incorporation;isotopic competition426

13-6 The induction of adaptive enzymes432

13-7 Effect of incorporated phosphorus-32 on the viability of a bacterial virus434

13-8 Radioautographic studies of biological duplication436

13-9 Remarks about commonly used isotopes443

13-10 Summary and conclusion446

CHAPTER 14．MOLECULAR BIOPHYSICS AND MUSCLE，NERVE，AND EYE STUDIES448

14-1Introduction448

Ⅰ．Muscle Studies449

14-2Muscle fiber as a model449

14-3 Biochemical character of muscle451

14-4 The molecular architecture of the muscle fiber454

14-5 Muscle behavior456

14-6 Molecular biophysics and muscle action458

Ⅱ．Nerve Studies467

14-7Cell membranes467

14-8 Electrical effects associated with membranes469

14-9 Nature of a nerve and a nerve cell474

Ⅲ．Studies of the Eye479

14-10The eye as a model479

14-11 The retina480

14-12 Quantum nature of vision483

14-13 The biochemistry of retinal detection485

Ⅳ．Conclusion487

CHAPTER 15．THE PHYSICS OF CELLULAR PROCESSES489

15-1Introduction489

15-2 Growth489

15-3 Protein synthesis494

15-4 Random collison and specific selection495

15-5 Content of the volume around a ribosome496

15-6 Random collisions and the rates of each step in synthesis497

15-7 Temporary complex formation501

15-8 The speed of diffusion in the cell502

15-9 Electrical effects in diffusion504

15-10 Specificity of transport509

15-11 Fluctuations in the cell511

15-12 The duplication of DNA512

15-13 Random diffusion and specific selection in DNA synthesis513

15-14 The formation of ribosomes518

15-15 ＂Long-range＂forces519

15-16 The process of cell division520

15-17 Conclusion522

ANSWERS TO SELECTED PROBLEMS525

CONVERSION TABLE527

INDEXES531