Cover -- Title Page -- Copyright -- Contents -- Preface to First Edition -- Preface to Second Edition -- THERMODYNAMICS -- Chapter 1 Heat, Work, and Energy -- 1.1 Introduction -- 1.2 Temperature -- 1.3 Heat -- 1.4 Work -- 1.5 Definition of Energy -- 1.6 Enthalpy -- 1.7 Standard States -- 1.8 Calorimetry -- 1.9 Reaction Enthalpies -- 1.10 Temperature Dependence of the Reaction Enthalpy -- References -- Problems -- Chapter 2 Entropy and Gibbs Energy -- 2.1 Introduction -- 2.2 Statement of the Second Law -- 2.3 Calculation of the Entropy -- 2.4 Third Law of Thermodynamics -- 2.5 Molecular Interpretation of Entropy -- 2.6 Gibbs Energy -- 2.7 Chemical Equilibria -- 2.8 Pressure and Temperature Dependence of the Gibbs Energy -- 2.9 Phase Changes -- 2.10 Additions to the Gibbs Energy -- Problems -- Chapter 3 Applications of Thermodynamics to Biological Systems -- 3.1 Biochemical Reactions -- 3.2 Metabolic Cycles -- 3.3 Direct Synthesis of ATP -- 3.4 Establishment of Membrane Ion Gradients by Chemical Reactions -- 3.5 Protein Structure -- 3.6 Protein Folding -- 3.7 Nucleic Acid Structures -- 3.8 DNA Melting -- 3.9 RNA -- References -- Problems -- Chapter 4 Thermodynamics Revisited -- 4.1 Introduction -- 4.2 Mathematical Tools -- 4.3 Maxwell Relations -- 4.4 Chemical Potential -- 4.5 Partial Molar Quantities -- 4.6 Osmotic Pressure -- 4.7 Chemical Equilibria -- 4.8 Ionic Solutions -- References -- Problems -- CHEMICAL KINETICS -- Chapter 5 Principles of Chemical Kinetics -- 5.1 Introduction -- 5.2 Reaction Rates -- 5.3 Determination of Rate Laws -- 5.4 Radioactive Decay -- 5.5 Reaction Mechanisms -- 5.6 Temperature Dependence of Rate Constants -- 5.7 Relationship Between Thermodynamics and Kinetics -- 5.8 Reaction Rates Near Equilibrium -- 5.9 Single Molecule Kinetics -- References -- Problems.

Chapter 6 Applications of Kinetics to Biological Systems -- 6.1 Introduction -- 6.2 Enzyme Catalysis: The Michaelis-Menten Mechanism -- 6.3 α-Chymotrypsin -- 6.4 Protein Tyrosine Phosphatase -- 6.5 Ribozymes -- 6.6 DNA Melting and Renaturation -- References -- Problems -- QUANTUM MECHANICS -- Chapter 7 Fundamentals of Quantum Mechanics -- 7.1 Introduction -- 7.2 Schrödinger Equation -- 7.3 Particle in a Box -- 7.4 Vibrational Motions -- 7.5 Tunneling -- 7.6 Rotational Motions -- 7.7 Basics of Spectroscopy -- References -- Problems -- Chapter 8 Electronic Structure of Atoms and Molecules -- 8.1 Introduction -- 8.2 Hydrogenic Atoms -- 8.3 Many-Electron Atoms -- 8.4 Born-Oppenheimer Approximation -- 8.5 Molecular Orbital Theory -- 8.6 Hartree-Fock Theory and Beyond -- 8.7 Density Functional Theory -- 8.8 Quantum Chemistry of Biological Systems -- References -- Problems -- SPECTROSCOPY -- Chapter 9 X-ray Crystallography -- 9.1 Introduction -- 9.2 Scattering of X-Rays by a Crystal -- 9.3 Structure Determination -- 9.4 Neutron Diffraction -- 9.5 Nucleic Acid Structure -- 9.6 Protein Structure -- 9.7 Enzyme Catalysis -- References -- Problems -- Chapter 10 Electronic Spectra -- 10.1 Introduction -- 10.2 Absorption Spectra -- 10.3 Ultraviolet Spectra of Proteins -- 10.4 Nucleic Acid Spectra -- 10.5 Prosthetic Groups -- 10.6 Difference Spectroscopy -- 10.7 X-Ray Absorption Spectroscopy -- 10.8 Fluorescence and Phosphorescence -- 10.9 RecBCD: Helicase Activity Monitored by Fluorescence -- 10.10 Fluorescence Energy Transfer: A Molecular Ruler -- 10.11 Application of Energy Transfer to Biological Systems -- 10.12 Dihydrofolate Reductase -- References -- Problems -- Chapter 11 Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization -- 11.1 Introduction -- 11.2 Optical Rotary Dispersion -- 11.3 Circular Dichroism.

11.4 Optical Rotary Dispersion and Circular Dichroism of Proteins -- 11.5 Optical Rotation and Circular Dichroism of Nucleic Acids -- 11.6 Small Molecule Binding to DNA -- 11.7 Protein Folding -- 11.8 Interaction of DNA with Zinc Finger Proteins -- 11.9 Fluorescence Polarization -- 11.10 Integration of HIV Genome Into Host Genome -- 11.11 α-Ketoglutarate Dehydrogenase -- References -- Problems -- Chapter 12 Vibrations in Macromolecules -- 12.1 Introduction -- 12.2 Infrared Spectroscopy -- 12.3 Raman Spectroscopy -- 12.4 Structure Determination with Vibrational Spectroscopy -- 12.5 Resonance Raman Spectroscopy -- 12.6 Structure of Enzyme-Substrate Complexes -- 12.7 Conclusion -- References -- Problems -- Chapter 13 Principles of Nuclear Magnetic Resonance and Electron Spin Resonance -- 13.1 Introduction -- 13.2 NMR Spectrometers -- 13.3 Chemical Shifts -- 13.4 Spin-Spin Splitting -- 13.5 Relaxation Times -- 13.6 Multidimensional NMR -- 13.7 Magnetic Resonance Imaging -- 13.8 Electron Spin Resonance -- References -- Problems -- Chapter 14 Applications of Magnetic Resonance to Biology -- 14.1 Introduction -- 14.2 Regulation of DNA Transcription -- 14.3 Protein-DNA Interactions -- 14.4 Dynamics of Protein Folding -- 14.5 RNA Folding -- 14.6 Lactose Permease -- 14.7 Proteasome Structure and Function -- 14.8 Conclusion -- References -- STATISTICAL MECHANICS -- Chapter 15 Fundamentals of Statistical Mechanics -- 15.1 Introduction -- 15.2 Kinetic Model of Gases -- 15.3 Boltzmann Distribution -- 15.4 Molecular Partition Function -- 15.5 Ensembles -- 15.6 Statistical Entropy -- 15.7 Helix-Coil Transition -- References -- Problems -- Chapter 16 Molecular Simulations -- 16.1 Introduction -- 16.2 Potential Energy Surfaces -- 16.3 Molecular Mechanics and Docking -- 16.4 Large-Scale Simulations -- 16.5 Molecular Dynamics -- 16.6 Monte Carlo.

16.7 Hybrid Quantum/Classical Methods -- 16.8 Helmholtz and Gibbs Energy Calculations -- 16.9 Simulations of Enzyme Reactions -- References -- Problems -- SPECIAL TOPICS -- Chapter 17 Ligand Binding to Macromolecules -- 17.1 Introduction -- 17.2 Binding of Small Molecules to Multiple Identical Binding Sites -- 17.3 Macroscopic and Microscopic Equilibrium Constants -- 17.4 Statistical Effects in Ligand Binding to Macromolecules -- 17.5 Experimental Determination of Ligand Binding Isotherms -- 17.6 Binding of Cro Repressor Protein to DNA -- 17.7 Cooperativity in Ligand Binding -- 17.8 Models for Cooperativity -- 17.9 Kinetic Studies of Cooperative Binding -- 17.10 Allosterism -- References -- Problems -- Chapter 18 Hydrodynamics of Macromolecules -- 18.1 Introduction -- 18.2 Frictional Coefficient -- 18.3 Diffusion -- 18.4 Centrifugation -- 18.5 Velocity Sedimentation -- 18.6 Equilibrium Centrifugation -- 18.7 Preparative Centrifugation -- 18.8 Density Centrifugation -- 18.9 Viscosity -- 18.10 Electrophoresis -- 18.11 Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein -- 18.12 Ultracentrifuge Analysis of Protein-DNA Interactions -- References -- Problems -- Chapter 19 Mass Spectrometry -- 19.1 Introduction -- 19.2 Mass Analysis -- 19.3 Tandem Mass Spectrometry (MS/MS) -- 19.4 Ion Detectors -- 19.5 Ionization of the Sample -- 19.6 Sample Preparation/Analysis -- 19.7 Proteins and Peptides -- 19.8 Protein Folding -- 19.9 Other Biomolecules -- References -- Problems -- APPENDICES -- Appendix 1 Useful Constants and Conversion Factors -- Appendix 2 Structures of the Common Amino Acids at Neutral pH 481 -- Appendix 3 Common Nucleic Acid Components.

Appendix 4 Standard Gibbs Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength -- Appendix 5 Standard Gibbs Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25 M Ionic Strength -- Appendix 6 Introduction to Electrochemistry -- A6-1 Introduction -- A6-2 Galvanic Cells -- A6-3 Standard Electrochmical Potentials -- A6-4 Concentration Dependence of the Electrochemical Potential -- A6-5 Biochemical Redox Reactions -- References -- Index -- Methods of Biochemical Analysis -- EULA.