Biophysical Chemistry

Biophysical Chemistry: Molecules to Membranes is a one-semester textbook for graduate and senior undergraduate students. Developed over several years of teaching, the approach differs from that of other texts by emphasizing thermodynamics of aqueous solutions, by rigorously treating electrostatics and irreversible phenomena, and by applying these principles to topics of biochemistry and biophysics. The main sections are: (1) Basic principles of equilibrium thermodynamics. (2) Structure and behavior of solutions of ions and molecules. The discussions range from properties of bulk water to the solvent structure of solutions of small molecules and macromolecules. (3) Physical principles are extended for the non-homogenous and non-equilibrium nature of biological processes. Areas included are lipid/water systems, transport phenomena, membranes, and bio-electrochemistry. This new textbook will provide an essential foundation for research in cellular physiology, biochemistry, membranebiology, as well as the derived areas bioengineering, pharmacology, nephrology, and many others.

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 µ, 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—Hückel Model.- 12.3. A More Rigorous Treatment of the Debye—Hückel 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.