Preface to First Edition xv
Preface to Second Edition xvii
THERMODYNAMICS 1
1. Heat, Work, and Energy 3
1.1 Introduction 3
1.2 Temperature 4
1.3 Heat 5
1.4 Work 6
1.5 Definition of Energy 9
1.6 Enthalpy 11
1.7 Standard States 12
1.8 Calorimetry 13
1.9 Reaction Enthalpies 16
1.10 Temperature Dependence of the Reaction Enthalpy 18
References 19
Problems 20
2. Entropy and Gibbs Energy 23
2.1 Introduction 23
2.2 Statement of the Second Law 24
2.3 Calculation of the Entropy 26
2.4 Third Law of Thermodynamics 28
2.5 Molecular Interpretation of Entropy 29
2.6 Gibbs Energy 30
2.7 Chemical Equilibria 32
2.8 Pressure and Temperature Dependence of the Gibbs Energy 35
2.9 Phase Changes 36
2.10 Additions to the Gibbs Energy 39
Problems 40
3. Applications of Thermodynamics to Biological Systems 43
3.1 Biochemical Reactions 43
3.2 Metabolic Cycles 45
3.3 Direct Synthesis of ATP 49
3.4 Establishment of Membrane Ion Gradients by Chemical Reactions 51
3.5 Protein Structure 52
3.6 Protein Folding 60
3.7 Nucleic Acid Structures 63
3.8 DNA Melting 67
3.9 RNA 71
References 72
Problems 73
4. Thermodynamics Revisited 77
4.1 Introduction 77
4.2 Mathematical Tools 77
4.3 Maxwell Relations 78
4.4 Chemical Potential 80
4.5 Partial Molar Quantities 83
4.6 Osmotic Pressure 85
4.7 Chemical Equilibria 87
4.8 Ionic Solutions 89
References 93
Problems 93
CHEMICAL KINETICS 95
5. Principles of Chemical Kinetics 97
5.1 Introduction 97
5.2 Reaction Rates 99
5.3 Determination of Rate Laws 101
5.4 Radioactive Decay 104
5.5 Reaction Mechanisms 105
5.6 Temperature Dependence of Rate Constants 108
5.7 Relationship Between Thermodynamics and Kinetics 112
5.8 Reaction Rates Near Equilibrium 114
5.9 Single Molecule Kinetics 116
References 118
Problems 118
6. Applications of Kinetics to Biological Systems 121
6.1 Introduction 121
6.2 Enzyme Catalysis: The Michaelis-Menten Mechanism 121
6.3 alpha-Chymotrypsin 126
6.4 Protein Tyrosine Phosphatase 133
6.5 Ribozymes 137
6.6 DNA Melting and Renaturation 142
References 148
Problems 149
QUANTUM MECHANICS 153
7. Fundamentals of Quantum Mechanics 155
7.1 Introduction 155
7.2 Schrödinger Equation 158
7.3 Particle in a Box 159
7.4 Vibrational Motions 162
7.5 Tunneling 165
7.6 Rotational Motions 167
7.7 Basics of Spectroscopy 169
References 173
Problems 174
8. Electronic Structure of Atoms and Molecules 177
8.1 Introduction 177
8.2 Hydrogenic Atoms 177
8.3 Many-Electron Atoms 181
8.4 Born-Oppenheimer Approximation 184
8.5 Molecular Orbital Theory 186
8.6 Hartree-Fock Theory and Beyond 190
8.7 Density Functional Theory 193
8.8 Quantum Chemistry of Biological Systems 194
References 200
Problems 201
SPECTROSCOPY 203
9. X-ray Crystallography 205
9.1 Introduction 205
9.2 Scattering of X-Rays by a Crystal 206
9.3 Structure Determination 208
9.4 Neutron Diffraction 212
9.5 Nucleic Acid Structure 213
9.6 Protein Structure 216
9.7 Enzyme Catalysis 219
References 222
Problems 223
10. Electronic Spectra 225
10.1 Introduction 225
10.2 Absorption Spectra 226
10.3 Ultraviolet Spectra of Proteins 228
10.4 Nucleic Acid Spectra 230
10.5 Prosthetic Groups 231
10.6 Difference Spectroscopy 233
10.7 X-Ray Absorption Spectroscopy 236
10.8 Fluorescence and Phosphorescence 236
10.9 RecBCD: Helicase Activity Monitored by Fluorescence 240
10.10 Fluorescence Energy Transfer: A Molecular Ruler 241
10.11 Application of Energy Transfer to Biological Systems 243
10.12 Dihydrofolate Reductase 245
References 247
Problems 248
11. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization 253
11.1 Introduction 253
11.2 Optical Rotary Dispersion 254
11.3 Circular Dichroism 256
11.4 Optical Rotary Dispersion and Circular Dichroism of Proteins 257
11.5 Optical Rotation and Circular Dichroism of Nucleic Acids 259
11.6 Small Molecule Binding to DNA 260
11.7 Protein Folding 263
11.8 Interaction of DNA with Zinc Finger Proteins 266
11.9 Fluorescence Polarization 267
11.10 Integration of HIV Genome Into Host Genome 269
11.11 alpha-Ketoglutarate Dehydrogenase 270
References 272
Problems 273
12. Vibrations in Macromolecules 277
12.1 Introduction 277
12.2 Infrared Spectroscopy 278
12.3 Raman Spectroscopy 279
12.4 Structure Determination with Vibrational Spectroscopy 281
12.5 Resonance Raman Spectroscopy 283
12.6 Structure of Enzyme-Substrate Complexes 286
12.7 Conclusion 287
References 287
Problems 288
13. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance 289
13.1 Introduction 289
13.2 NMR Spectrometers 292
13.3 Chemical Shifts 293
13.4 Spin-Spin Splitting 296
13.5 Relaxation Times 298
13.6 Multidimensional NMR 300
13.7 Magnetic Resonance Imaging 306
13.8 Electron Spin Resonance 306
References 310
Problems 310
14. Applications of Magnetic Resonance to Biology 315
14.1 Introduction 315
14.2 Regulation of DNA Transcription 315
14.3 Protein-DNA Interactions 318
14.4 Dynamics of Protein Folding 320
14.5 RNA Folding 322
14.6 Lactose Permease 325
14.7 Proteasome Structure and Function 328
14.8 Conclusion 329
References 329
STATISTICAL MECHANICS 331
15. Fundamentals of Statistical Mechanics 333
15.1 Introduction 333
15.2 Kinetic Model of Gases 333
15.3 Boltzmann Distribution 338
15.4 Molecular Partition Function 343
15.5 Ensembles 346
15.6 Statistical Entropy 349
15.7 Helix-Coil Transition 350
References 353
Problems 354
16. Molecular Simulations 357
16.1 Introduction 357
16.2 Potential Energy Surfaces 358
16.3 Molecular Mechanics and Docking 364
16.4 Large-Scale Simulations 365
16.5 Molecular Dynamics 367
16.6 Monte Carlo 373
16.7 Hybrid Quantum/Classical Methods 373
16.8 Helmholtz and Gibbs Energy Calculations 375
16.9 Simulations of Enzyme Reactions 376
References 379
Problems 379
SPECIAL TOPICS 383
17. Ligand Binding to Macromolecules 385
17.1 Introduction 385
17.2 Binding of Small Molecules to Multiple Identical Binding Sites 385
17.3 Macroscopic and Microscopic Equilibrium Constants 387
17.4 Statistical Effects in Ligand Binding to Macromolecules 389
17.5 Experimental Determination of Ligand Binding Isotherms 392
17.6 Binding of Cro Repressor Protein to DNA 395
17.7 Cooperativity in Ligand Binding 397
17.8 Models for Cooperativity 402
17.9 Kinetic Studies of Cooperative Binding 406
17.10 Allosterism 408
References 412
Problems 412
18. Hydrodynamics of Macromolecules 415
18.1 Introduction 415
18.2 Frictional Coefficient 415
18.3 Diffusion 418
18.4 Centrifugation 421
18.5 Velocity Sedimentation 422
18.6 Equilibrium Centrifugation 424
18.7 Preparative Centrifugation 425
18.8 Density Centrifugation 427
18.9 Viscosity 428
18.10 Electrophoresis 429
18.11 Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein 432
18.12 Ultracentrifuge Analysis of Protein-DNA Interactions 434
References 435
Problems 435
19. Mass Spectrometry 441
19.1 Introduction 441
19.2 Mass Analysis 441
19.3 Tandem Mass Spectrometry (MS/MS) 445
19.4 Ion Detectors 445
19.5 Ionization of the Sample 446
19.6 Sample Preparation/Analysis 449
19.7 Proteins and Peptides 450
19.8 Protein Folding 452
19.9 Other Biomolecules 455
References 455
Problems 456
APPENDICES 457
Appendix 1. Useful Constants and Conversion Factors 459
Appendix 2. Structures of the Common Amino Acids at Neutral pH 461
Appendix 3. Common Nucleic Acid Components 463
Appendix 4. Standard Gibbs Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength 465
Appendix 5. Standard Gibbs Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25M Ionic Strength 467
Appendix 6. Introduction to Electrochemistry 469
A6-1 Introduction 469
A6-2 Galvanic Cells 469
A6-3 Standard Electrochmical Potentials 471
A6-4 Concentration Dependence of the Electrochemical Potential 472
A6-5 Biochemical Redox Reactions 473
References 473
Index 475
