Biophysical Chemistry

1 Molecules, Membranes, and Modeling.- I Review of Thermodynamics.- 2 Thermodynamics: An Introductory Glance.- 2.1. Overview.- 2.1.1. The First Law: "The Energy of the Universe Is Conserved".- 2.1.2. The Second Law: "The Entropy of the Universe Increases".- 2.2. Defining Thermodynamic Terms.- 2.2.1. Systems, Surroundings, and Boundaries.- 2.2.2. Properties of a System.- 2.2.3. State Functions and the State of a System.- 2.2.4. Changes in State.- 2.3. Work.- 2.3.1. Electrical Work.- 2.3.2. Pressure-Volume Work.- 2.3.3. Mechanical Work.- 2.3.4. A Return to the Laws.- 3 The First Law.- 3.1. Understanding the First Law.- 3.1.1. Specialized Boundaries as Tools.- 3.1.2. Evaluating the Energy of a System.- 3.2. Derivation of the Heat Capacity.- 3.3. A System Constrained by Pressure: Defining Enthalpy.- 4 The Second Law.- 4.1. Understanding the Second Law of Thermodynamics.- 4.2. A Thought Problem: Designing a Perfect Heat Engine.- 4.2.1. Reversible Versus Irreversible Path.- 4.2.2. A Carnot Cycle.- 4.3. Statistical Derivation of Entropy.- 4.3.1. Limits of the Second Law.- 4.3.2. Statistical Distributions.- 4.3.3. The Boltzmann Distribution.- 4.3.4. A Statistical Mechanical Problem in Entropy.- 4.4. The Third Law and Entropy.- 5 Free Energy.- 5.1. The Gibbs Free Energy.- 5.2. A Moment of Retrospection Before Pushing On.- 5.3. The Properties of the Gibbs Free Energy.- 5.4. Introduction of , the Free Energy per Mole.- 5.5. Transforming the General Ideal Equation to a General Real Equation.- Appendix 5.1. Derivation of the Statement, qrev > qirrev.- 6 Multiple-Component Systems.- 6.1. New Systems, More Components.- 6.2. Chemical Potential and Chemical Systems.- 6.2.1. Characteristics of ?.- 6.2.2. An Immediate Biological Relevance of the Chemical Potential.- 6.3. The Entropy and Enthalpy and Free Energy of Mixing.- 6.4. Free Energy When Components Change Concentration.- 6.4.1. A Side Trip: Derivation of a General Term, the Activity.- 6.4.2. Activity of the Standard State.- 6.4.3. Returning to the Problem at Hand.- 6.5. The Thermodynamics of Galvanic Cells.- 7 Phase Equilibria.- 7.1. Principles of Phase Equilibria.- 7.1.1. Thermodynamics of Transfer Between Phases.- 7.1.2. The Phase Rule.- 7.2. Pure Substances and Colligative Properties.- 7.2.1. Colligative Properties and the Ideal Solution.- 7.2.2. Measurements of the Activity Coefficient Using Colligative Properties.- 7.3. Surface Phenomena.- Appendix 7.1. Equilibrium Dialysis and Scatchard Plots.- Appendix 7.2. Derivation of the Clausius-Clapeyron Equation.- Appendix 7.3. Derivation of the van't Hoff Equation for Osmotic Pressure.- 8 Engineering the Cell: A Modeling Approach to Biological Problem Solving.- II The Nature of Aqueous Solutions.- 9 Water: A Unique Structure, A Unique Solvent.- 9.1. Introduction.- 9.2. Hydrogen Bonds in Water.- 9.3. The Structure of Crystalline Water.- 9.4. Theories of the Structure of Liquid Water.- 10 Introduction to Electrolytic Solutions.- 10.1. Introduction to Ions and Solutions.- 10.1.1. The Nature of Electricity.- 10.2. Intermolecular Forces and the Energies of Interaction.- 10.3. The Nature of Ionic Species.- Appendix 10.1. Derivation of the Energy of Interaction Between Two Ions.- 11 Ion-Solvent Interactions.- 11.1. Understanding the Nature of Ion-Solvent Interactions Through Modeling.- 11.1.1. Overview.- 11.1.2. The Born Model.- 11.2. Adding Water Structure to the Continuum.- 11.3. The Energy of Ion-Dipole Interactions.- 11.4. Dipoles in an Electric Field: A Molecular Picture of Dielectric Constants.- 11.5. What Happens When the Dielectric Is Liquid Water?.- 11.6. Extending the Ion-Solvent Model Beyond Born.- 11.7. Recalculating the Born Model.- 11.7.1. Ion-Solvent Interactions in Biological Systems.- Appendix 11.1. Derivation of the Work to Charge and Discharge a Rigid Sphere.- Appendix 11.2. Derivation of Xext = 4? (q - qdipole) by Gauss's Law.- 12 Ion-Ion Interactions.- 12.1. Ion-Ion Interactions.- 12.2. Testing the Debye-Huckel Model.- 12.3. A More Rigorous Treatment of the Debye-Hu qirrev.- 6 Multiple-Component Systems.- 6.1. New Systems, More Components.- 6.2. Chemical Potential and Chemical Systems.- 6.2.1. Characteristics of ?.- 6.2.2. An Immediate Biological Relevance of the Chemical Potential.- 6.3. The Entropy and Enthalpy and Free Energy of Mixing.- 6.4. Free Energy When Components Change Concentration.- 6.4.1. A Side Trip: Derivation of a General Term, the Activity.- 6.4.2. Activity of the Standard State.- 6.4.3. Returning to the Problem at Hand.- 6.5. The Thermodynamics of Galvanic Cells.- 7 Phase Equilibria.- 7.1. Principles of Phase Equilibria.- 7.1.1. Thermodynamics of Transfer Between Phases.- 7.1.2. The Phase Rule.- 7.2. Pure Substances and Colligative Properties.- 7.2.1. Colligative Properties and the Ideal Solution.- 7.2.2. Measurements of the Activity Coefficient Using Colligative Properties.- 7.3. Surface Phenomena.- Appendix 7.1. Equilibrium Dialysis and Scatchard Plots.- Appendix 7.2. Derivation of the Clausius-Clapeyron Equation.- Appendix 7.3. Derivation of the van't Hoff Equation for Osmotic Pressure.- 8 Engineering the Cell: A Modeling Approach to Biological Problem Solving.- II The Nature of Aqueous Solutions.- 9 Water: A Unique Structure, A Unique Solvent.- 9.1. Introduction.- 9.2. Hydrogen Bonds in Water.- 9.3. The Structure of Crystalline Water.- 9.4. Theories of the Structure of Liquid Water.- 10 Introduction to Electrolytic Solutions.- 10.1. Introduction to Ions and Solutions.- 10.1.1. The Nature of Electricity.- 10.2. Intermolecular Forces and the Energies of Interaction.- 10.3. The Nature of Ionic Species.- Appendix 10.1. Derivation of the Energy of Interaction Between Two Ions.- 11 Ion-Solvent Interactions.- 11.1. Understanding the Nature of Ion-Solvent Interactions Through Modeling.- 11.1.1. Overview.- 11.1.2. The Born Model.- 11.2. Adding Water Structure to the Continuum.- 11.3. The Energy of Ion-Dipole Interactions.- 11.4. Dipoles in an Electric Field: A Molecular Picture of Dielectric Constants.- 11.5. What Happens When the Dielectric Is Liquid Water?.- 11.6. Extending the Ion-Solvent Model Beyond Born.- 11.7. Recalculating the Born Model.- 11.7.1. Ion-Solvent Interactions in Biological Systems.- Appendix 11.1. Derivation of the Work to Charge and Discharge a Rigid Sphere.- Appendix 11.2. Derivation of Xext = 4? (q - qdipole) by Gauss's Law.- 12 Ion-Ion Interactions.- 12.1. Ion-Ion Interactions.- 12.2. Testing the Debye-Huckel Model.- 12.3. A More Rigorous Treatment of the Debye-Huckel Model.- 12.4. Consideration of Other Interactions.- 12.4.1. Bjerrum and Ion Pairs.- 12.5. Perspective.- 13 Molecules in Solution.- 13.1. Solutions of Inorganic Ions.- 13.2. Solutions of Small Nonpolar Molecules.- 13.3. Solutions of Organic Ions.- 13.3.1. Solutions of Small Organic Ions.- 13.3.2. Solutions of Large Organic Ions.- 14 Macromolecules in Solution.- 14.1. Solutions of Macromolecules.- 14.1.1. Nonpolar Polypeptides in Solution.- 14.1.2. Polar Polypeptides in Solution.- 14.2. Transitions of State.- III Membranes and Surfaces in Biological Systems.- 15 Lipids in Aqueous Solution: The Formation of the Cell Membrane.- 15.1 The Form and Function of Biological Membranes.- 15.2. Lipid Structure: Components of the Cell Membrane.- 15.3. Aqueous and Lipid Phases in Contact.- 15.4. The Physical Properties of Lipid Membranes.- 15.4.1. Phase Transitions in Lipid Membranes.- 15.4.2. Motion and Mobility in Membranes.- 15.5. Biological Membranes: The Complete Picture.- 16 Irreversible Thermodynamics.- 16.1. Transport: An Irreversible Process.- 16.2. Principles of Nonequilibrium Thermodynamics.- 17 Flow in a Chemical Potential Field: Diffusion.- 17.1. Transport Down a Chemical Potential Gradient.- 17.2. The Random Walk: A Molecular Picture of Movement.- 18 Flow in an Electric Field: Conduction.- 18.1. Transport in an Electric Field.- 18.2. A Picture of Ionic Conduction.- 18.3. The Empirical Observations Concerning Conduction.- 18.4. A Second Look at Ionic Conduction.- 18.5. How Do Interionic Forces Affect Conductivity?.- 18.6. The Special Case of Proton Conduction.- 19 The Electrified Interface.- 19.1. When Phases Meet: The Interphase.- 19.2. A More Detailed Examination of the Interphase Region.- 19.3. The Simplest Picture: The Helmholtz-Perrin Model.- 19.4. A Diffuse Layer Versus a Double Layer.- 19.5. Combining the Capacitor and the Diffuse Layers: The Stern Model.- 19.6. The Complete Picture of the Double Layer.- 20 Electrokinetic Phenomena.- 20.1. The Cell and Interphase Phenomena.- 20.2. Electrokinetic Phenomena.- 21 Colloidal Properties.- 21.1. Colloidal Systems and the Electrified Interface.- 21.2. Salting Out Revisited.- 22 Forces Across Membranes.- 22.1. Energetics, Kinetics, and Force Equations in Membranes.- 22.1.1. The Donnan Equilibrium.- 22.1.2. Electric Fields Across Membranes.- 22.1.3. Diffusion Potentials and the Transmembrane Potential.- 22.1.4. Goldman Constant Field Equation.- 22.1.5. Electrostatic Profiles of the Membrane.- 22.1.6. The Electrochemical Potential.- 22.2. Molecules Through Membranes: Permeation of the Lipid Bilayer.- 22.2.1. The Next Step: The Need for Some New Tools.- Appendices.- Appendix I Further Reading List.- Appendix II Study Questions.- Appendix III Symbols Used.- Appendix IV Glossary.