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Physical Chemistry for the Biological Sciences

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ÁöÀºÀÌ :  Hammes
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ISBN :  9781118859001
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Synthesis, Properties and Mineralogy of Important Inorganic Materials
Physics and Chemistry of Interfaces 4/e

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This book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.
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  • 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 -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 -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