The field of biophysics employs the principles of physics to study biological systems, and introduces the concept of the living state. It is a multidisciplinary approach to the study of the living state combining physics, biochemistry, molecular and cell biology, medicine and engineering. The physics of macromolecules and macromolecular assemblies is a particularly important aspect of this broader field.
Biophysics: Physical Processes Underlying the living state offers an introduction to the general principles of the living state and their biological applications. Beginning with an historical overview of fundamental scientific theories and fields, the book then provides a brief introduction to cell biology and biochemistry, and then an overview of basic thermodynamics, kinetics, information theory, electrostatics in solution, fluid mechanics and macromolecular physics, and their relationship to the living state. After a presentation of physical methods, with an emphasis on light scattering, different biological macromolecules, selected aspects of their functions, and their physical properties and interactions are surveyed. A brief introduction to vision, biomotion, and theoretical biology is also provided. Exploration of some frontier issues in prebiotic origins of life, consciousness, and astrobiology round out the book. The result is a multifaceted window into the broad and evolving field of biophysics.
Biophysics readers will also find: - Problems at the conclusion of each chapter to reinforce and focus student knowledge- A gathering of topics in basic physics and physical chemistry which are seldom found in a single source
This textbook is suitable for physics and engineering students studying biophysics, macromolecular science, and biophysical chemistry, as well as for polymer scientists, chemists, biochemists, cell and molecular biologists, bioengineers, and others.
Table of Contents
Preface xvi
Acknowledgments xx
About the Companion Website xxi
Part I Scientific Overview, Biological and Biochemical Surveys 1
1 Background Notions, Histories, and Fundamental Issues in Physics and Biophysics 3
1.1 The Evolution of Scientific Thought 3
1.2 Historical Sketch of Atomic Theory and Evolutionary and Genetic Thought 7
1.3 Historical Developments in Biophysics 15
1.4 Subfields in Biophysics 19
1.5 Interdisciplinarity 20
1.6 Disciplinary Physics 23
1.7 Are Currently Known Physical Laws Adequate for Understanding Living State Phenomena? 28
1.8 Unifying Characteristics of the Living State 29
1.9 Summary 30
2 Overview of Biological Cell Structure 34
2.1 The Prokaryotic Cell 34
2.2 The Eukaryotic Cell 36
2.3 Plant Cell 37
2.4 Where Do Viruses Fit in? 37
2.5 Overview of Cell Functions 39
2.6 Specialized Cell Types and Structures 44
2.7 Molecular Biology Methods 50
2.8 Summary 52
3 Biochemistry Survey 53
3.1 Amino Acids and Proteins 53
3.2 Nucleic Acids 58
3.3 Carbohydrates 62
3.4 Lipids 64
3.5 Metabolism 67
3.6 Summary 73
Part II Physical Processes Underlying the Living State 75
4 Thermodynamics, Reaction Kinetics, and Information Theory 77
4.1 Thermodynamically Based Forces 77
4.2 Thermodynamic Laws 78
4.3 Thermodynamic Processes Involving Ideal Gases 82
4.4 Connection Between Ideal Gas Law and Molecular Kinetic Energy 84
4.5 The Boltzmann Distribution 86
4.6 The Partition Function 91
4.7 Statistical Interpretation of Entropy 93
4.8 Ideal Osmotic Solutions 94
4.9 Working Substances and Bioenergetics Cycles 99
4.10 The Hydrophobic Effect 99
4.11 Surface Tension 99
4.12 Thermodynamics of Multicomponent Solutions 102
4.13 Chemical Potential for Nonideal Solutions 107
4.14 Excluded Volume Approach to Nonideal Solutions 112
4.15 Chemical Equilibrium 117
4.16 Reaction Kinetics 122
4.17 Phase Transitions 125
4.18 Nonequilibrium Thermodynamics 126
4.19 Information Theory 126
4.20 Summary 132
5 Electrostatics in Solution 137
5.1 Review of Electrostatics (in MKSA Units) 137
5.2 Covalent Bonds in the Living State are Stable Against Thermal Energy 144
5.3 “Weak Electrostatic Forces” Allow for Self-organization and Rapid Dynamic Processes 144
5.4 Hydrogen Bonds 147
5.5 Electrically Charged Macromolecules and Colloids in Solution 148
5.6 Poisson-Boltzmann Equation 148
5.7 Osmotic Pressure of an Ideal Polyelectrolyte Solution with a Semi-Permeable Membrane: Donnan Equilibrium 158
5.8 Self-energy of a Hydrated Ion 161
5.9 Force on an Ion near an Interface of Two Media with Different Dielectric Constants 162
5.10 Bjerrum Length and Counterion Condensation 163
5.11 Summary 163
6 Fluid Mechanics and Transport Processes 167
6.1 Conceptual Approach to Viscosity 168
6.2 The Stress Tensor 170
6.3 Navier-Stokes Equation of Motion for Incompressible, Viscous Fluids 170
6.4 Applications of Navier-Stokes for Steady Flow 173
6.5 Hemodynamics 177
6.6 The Intrinsic Viscosity [η] of Particles in a Fluid 177
6.7 Force-Flux Relations 180
6.8 Diffusion 184
6.9 The Nernst-Planck Equation 189
6.10 Fluctuation-Dissipation and a Qualitative Overview of Its Consequences 191
6.11 Coupled Forces and Flows: Onsager’s Reciprocal Relationships 195
6.12 Fluid Transport in Plants 196
6.13 Diffusional Versus Directed Motion 197
6.14 Time Reversal Symmetry and Its Breaking 198
6.15 Techniques for Determining Transport Properties 198
6.16 Summary 199
Part III Polymer Science 205
7 Overview of Polymer Science 207
7.1 Biological and Synthetic Polymers 207
7.2 Brief Overview of Classes of Organic Molecules 208
7.3 Synthetic Polymers 215
7.4 Polymerization Reactions 221
7.5 Free Radicals and Chain Reactions 224
7.6 Free Radical Polymerization Kinetics 225
7.7 Ideal Living Polymerization 232
7.8 Chain Growth Copolymerization Kinetics 234
7.9 Cumulative and Instantaneous Polymer Characteristics During Free Radical Reactions 238
7.10 Fully Automatic Feedback Control of Molar Mass and Conversion During Chain Growth Polymerization 239
7.11 Linear Step Growth Reactions 243
7.12 Molar Mass Distributions (MMD) and Averages 244
7.13 Experimental Methods for Determining Molar Mass Distributions 251
7.14 Summary 256
8 Polymer Physics 260
8.1 Polymer Conformations and Dimensions 260
8.2 Polymer Excluded Volume (EV) 276
8.3 Hydrodynamic Characteristics of Polymers in Solution 278
8.4 Electrically Charged Polymers: Polyelectrolytes 281
8.5 Case Study of Polystyrene Characteristics in Tetrahydrofuran 285
8.6 Thermodynamics of Polymer Solutions 285
8.7 Rheology 288
8.8 Solid-state Properties 290
8.9 Summary 290
9 Light Scattering and Cognate Methods 295
9.1 Overview of Light Scattering 295
9.2 The Maxwell Electromagnetic Equations and the Prediction of Electromagnetic Waves and Their Properties, in Gaussian (CGS) Units 297
9.3 Radiation Emitted by an Accelerated Charge 304
9.4 Basic Scattering Theory: Light Emitted from an Oscillating Electric Dipole 305
9.5 Relation of Light Scattering by Pure Liquids to Thermodynamic Fluctuations 311
9.6 The Angular Dependence of Scattered Light: Intramolecular Interference Effects on Scattering 315
9.7 The Angular Dependence of Scattered Light: Intermolecular Interference Effects on Scattering: The structure factor S(q,c) 326
9.8 Mie Scattering 328
9.9 Scattering Model for Index of Refraction 330
9.10 Scattering at Interfaces 331
9.11 Single Photon Scattering 337
9.12 Dynamic Light Scattering 338
9.13 X-ray Diffraction and Crystallography 342
9.14 Raman Scattering 342
9.15 Optical Activity 343
9.16 Superconducting Quantum Interference Devices (SQUIDs) 344
9.17 Antimatter and PET Imaging 345
9.18 Electron Microscopy 346
9.19 Summary 347
Part IV Examples of Specific Living State Phenomena 353
10 Proteins: Structure, Folding, Enzyme Kinetics, and Cooperativity 355
10.1 The Protein Folding Problem 355
10.2 Protein Aggregation 360
10.3 Enzyme Kinetics 370
10.4 Cooperative Binding in Proteins 377
10.5 Cooperativity in the Helix-Coil Transition 381
10.6 Histones and Other Chromosomal Proteins 383
10.7 The Action of Proteins Often Depends on Correlated Internal Motions 383
10.8 Directed Protein Motion and Protein Motors 384
10.9 Allostery and Feedback Regulation 385
10.10 Energetics of Iscosahedral Viral Self-assembly 385
10.11 Summary 387
11 DNA and RNA Properties and Structures: The Genetic Code 391
11.1 Structure and Macromolecular Properties of RNA and DNA 391
11.2 The Genetic Code 393
11.3 Brief Description of Gene Expression with a Focus on Protein Synthesis 395
11.4 Chromatin and DNA Mechanics 397
11.5 Summary 399
12 Some Polysaccharide Phenomena 403
12.1 Polymer and Polyelectrolyte Properties of Polysaccharides 403
12.2 Proteoglycans and Extracellular Matrix Functions 404
12.3 Proteoglycan Degradation Mechanisms Found by Light Scattering 408
12.4 Summary 411
13 Phospholipids Membranes: Channels and Nerve Impulses 413
13.1 General Properties of Membranes 413
13.2 Membrane Potentials 413
13.3 The Voltage Clamp and Patch Clamp 418
13.4 Membrane Current-Voltage Curves 419
13.5 Membrane Channel Proteins 420
13.6 Passive Propagation of Potentials Along an Axon 421
13.7 Action Potentials and Nerve Impulse Propagation 423
13.8 Summary 428
14 Integrated Biological Systems 430
14.1 Light and Life 430
14.2 Vision 432
14.3 Cilial and Flagellar Biomotion 439
14.4 Theoretical Biology: Cycles, Instabilities, and Attractors 439
14.5 Dissipative, Far from Equilibrium Spatially Self-organizing Systems 444
14.6 Summary 448
15 On the Frontier 450
15.1 Prebiotic Origins of Life 450
15.2 Quantum Biology 454
15.3 Neuroscience and the Question of Consciousness 456
15.4 Artificial Intelligence 460
15.5 Astrobiology and Exoplanets 463
15.6 Summary 467
Afterword 472
Appendix I: Probability Distributions and Their Averages 473
Appendix II: Review of Vector Calculus and Notation Used 479
Index 483
