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Physical Chemistry for the Biological Sciences, Second Edition
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Table of 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 Schrodinger 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

About the Author

Gordon G. Hammes, PhD, is the Distinguished Service Professor of Biochemistry Emeritus at Duke University. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences, and has received several national awards, including the American Chemical Society Award in Biological Chemistry and the American Society for Biochemistry and Molecular Biology William C. Rose Award. Dr. Hammes was Editor of the journal Biochemistry from 1992-2003. Sharon Hammes-Schiffer, PhD, is the Swanlund Professor of Chemistry at the University of Illinois at Urbana-Champaign. She is a fellow of the American Physical Society, the American Chemical Society, the Biophysical Society, and the American Association for the Advancement of Science. She is a member of the American Academy of Arts and Sciences, the National Academy of Sciences, and the International Academy of Quantum Molecular Science. Dr. Hammes-Schiffer has served as the Deputy Editor of The Journal of Physical Chemistry B and is currently the Editor-in-Chief of Chemical Reviews.

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