Physical Chemistry for the Biological Sciences

Responsibility
Gordon Hammes, Sharon Hammes-Schiffer.
Edition
Second edition / Gordon G. Hammes, Sharon Hammes-Schiffer.
Publication
Hoboken, NJ : Wiley, [2015]
Physical description
1 online resource.
Series
Methods of biochemical analysis volume 55.

Online

Available online

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Description

Creators/Contributors

Author/Creator
Hammes, Gordon G., 1934- author.
Contributor
Hammes-Schiffer, Sharon, author.

Contents/Summary

Bibliography
Includes bibliographical references at the end of each chapters and index.
Contents
  • 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 Schroedinger 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.
  • (source: Nielsen Book Data)
Publisher's summary
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.
(source: Nielsen Book Data)

Bibliographic information

Publication date
2015
Series
Wiley series in methods of biochemical analysis ; volume 55
Note
Includes index.
ISBN
9781118858912 electronic bk.
1118858913 electronic bk.
9781118859001 (cloth)
9781118859148
1118859146
1118859006
9781118859001
9781118858837
1118858832

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