Biophysical Chemistry

PrefaceSymbols1. Biochemistry and Geochemistry Distribution of the Chemical Elements in Living Organisms The Relative Abundance of the Chemical Elements in the Universe The Structure of the Earth and Its Crust Early History of the Earth The Ocean The Central Role of Carbon in Biology References2. Water and Its Biological Significance Heat Capacity of Water and Other Substances Heat of Vaporization Latent Heat of Fusion The Expansion of Water in Freezing Surface Tension Dielectric Constant of Water Solubility References3. Problems of Protein Structure Proteins; Some General Considerations Amino Acids and Peptides as Dipolar Ions Characteristics of the Amino Acids Derived from Proteins Amino Acid Analysis of Proteins Polypeptide Chains and Their Presence in Proteins Determination of Arrangement of Peptide Chains and Their Linkage within Protein Molecules The Number of Peptide Chains in the Molecule, and the Nature of the Terminal Groups Cross-Linkages Between Peptide Chains: Disulfide and Phosphate Cross-Linkages Phosphate Cross-Linkages Other Cross-Linkages Sequence of Amino Acid Residues in Peptide Chains Disulfide Linkages in Insulin and Ribonuclease Spatial Configurations of Polypeptide Chains Silk Fibroin β-Keratin α-Keratin and Synthetic Polypeptides: the α-Helix and Other Possible Helical Structures Collagen Amino Acid Composition Heat Shrinkage The Structural Pattern—Evidence from X-Ray and Electron Microscope Studies Collagen Structure The Stability of Helical Structures The Significance of Disulfide Bonds; Cross-Linkages and Loops in Peptide Chains Possible Stereochemistry of Insulin Stereochemistry and Enzyme Activity of Ribonuclease Helical and Nonhelical Regions in Globular Proteins References4. Thermodynamics Introduction Systems and Phases Temperature Dimensions of Temperature First Law Second Law Irreversible Processes Maximum Work, Equilibrium, and Free Energy Heat Content, or Enthalpy Expressions for the Change of the Fundamental Thermodynamic Functions Partial Molal Quantities Chemical Potentials Phase Rule Activities Ideal or Perfect Solutions and Raoult's Law Activity Coefficients and the Choice of Standard States Activity and Chemical Potential of a Nonvolatile Solute from the Vapor Pressure of the Solvent Equilibrium Between Phases; Activities in Relation to Distribution Coefficients and Solubilities Activity of Strong Electrolytes Mass Law The Malate-Fumarate Equilibrium Peptide Bond Synthesis in the Reaction Between Benzoyl-L-Tyrosine and Glycinamide The Standard Free Energy of Hydrolysis of Adenosine Triphosphate Systems Involving Other Variables Elastic Bodies Systems in Gravitational or Centrifugal Fields Statistical Interpretation of Entropy Entropy of a Perfect Crystal at 0°K Entropy Change on Mixing of Components in an Ideal Solution The Residual Entropy of Ice Standard Free Energies of Formation and Their Use in Determining Thermodynamic Equilibria The Fumarate-Malate Equilibrium The First Ionization of Carbonic Acid Standard Free Energy of Peptide Bond Synthesis References5. Electrostatics: Its Application to Polar Molecules and Ionic Solutions Definition of the Potential Gauss's Law Poisson's Equation for Regions Containing a Space Charge Free Energy of a Charged Sphere The Potential and Energy of a Dipole Image Charges The Salting-Out Effect Salting Out of Proteins Effects of Dipolar Ions Debye's Theory of Salting Out by Redistribution of Solvent Molecules Around the Ions Ionic Interactions and the Debye-Hückel Theory Ion-Dipole Interactions Experimental Studies on the Solubility of Dipolar Ions, and Their Interaction with Ions Solubilities and Activity Coefficients in Water and Other Media Solubilities in the Presence of Salt References6. Dielectric Constants and Their Significance Introduction to Dielectric Constants and Dipole Moments Dielectric Polarization in Relation t o Molecular Properties The Debye Theory of the Dielectric Constant Application of the Debye Theory The Breakdown of the Debye Theory in Polar Liquids Modifications of the Debye Theory The Onsager Theory Kirkwood's Theory Polar Liquids and Dipolar Ions Dielectric Constants and Dipole Moments of Dipolar Ions in Solution Methods of Measuring Dielectric Constant References7. Conductivity of Electrolytes Conductance and Resistance Electrolytes as Conductors Faraday's Law Equivalent Conductivity Ion Mobilities Ion Conductances Transference Numbers Hittorf Method of Determining Transference Numbers The Moving Boundary Method of Determining Transference Numbers Theoretical Considerations Regarding Equivalent Conductance; Effects of Interionic Forces Measurement of Conductivity References8. Acid-Base Equilibria The Nature of Acids and Bases The Concept of pH; a Preliminary Statement Calculations of pH in Systems of Acids of Known Acid Strengths The Titration of a Weak Acid with a Strong Base; Buffer Action The Experimental Determination of Acidity Constants (KA Values) The Conductivity Method The Indicator Method for Determining Relative Strengths of Acids Electromotive Force Measurements and pH Determination Standard Potentials of Half-Cells, Choice of Conventions Evaluation of pKA from Cells without Liquid Junction Cells Containing Liquid Junctions The Liquid Junction Potential Variation of pH with Ionic Strength for Acid-Base Pairs of Different Charge Types Choice of a Standard for Calibrating pH Measurements The Glass Electrode Determination of pKA Values and Related Thermodynamic Functions in Relation to Structure Effect of Neighboring Charged Groups and Dipoles on pKA Values Other Acidic Groups of Biochemical Interest Phenolic Hydroxyl Groups Imidazole Groups Sulfhydryl Groups The Guanidinium Group The Peptide Linkage Purines, Pyrimidines, Nucleosides, and Nucleotides Effects of Variation in Dielectric Constant of Solvent on Relative Strength of Acids of Different Charge Types Problems References9. Polybasic Acids, Bases, and Ampholytes, Including Proteins Dibasic Acids Polyvalent Acids: General Relations A Specific Case: Glutamic Acid Spectroscopic Determination of Microscopic Constants: The Ionization of Cysteine Isoelectric Points of Amphoteric Substances Isoelectric Points of Polyvalent Ampholytes Equilibrium Between Different Ionic Forms in Polyvalent Acids and Ampholytes: The Equation of Linderstrøm-Lang Electrostatic Effects on Ionization in Polybasic Acids. The Charged Sphere Model Formulation in Terms of Association Constants Acid-Base Equilibria in β-Lactoglobulin Solutions Ovalbumin Serum Albumins Ribonuclease Hemoglobin Other Proteins Synthetic Polyelectrolytes, Including Polypeptides Effects of Internal Hydrogen Bonding on Titration Curves Calculations with a Dielectric Sphere Model Containing Fixed Charges References10. Carbon Dioxide and Carbonic Acid Carbon Dioxide in Nature Structural Considerations The Fundamental Equilibria in Systems Containing Carbon Dioxide and Carbonic Acid Absorption Coefficients of Carbon Dioxide in Water The Reversible Hydration of Carbon Dioxide and the Ionization of Carbonic Acid Carbon Dioxide Dissociation Curves The Formation of Carbamates Rates of the Reactions CO2 + H2O → H2CO3 The Velocity of the Dehydration Reaction: H2CO3 → H2O + CO2 The Hydration Reaction: CO2 + H2O → H2CO3 Carbonic Anhydrase References11. Some General Aspects of Molecular Interactions Some Methods of Measuring Binding Equilibrium Dialysis Ultrafiltration Spectroscopic Measurements Electromotive Force Measurements Ultracentrifuge Measurements Electrophoresis Effects of pH Changes When Salts Are Added: Isoionic Points Isoelectric and Isoionic Solutions Some Fundamental Considerations Regarding Certain Types of Binding Interactions of Bound Groups Competition Effects Interactions Between Different Kinds of Bound Groups Formation of Chelate Complexes Binding by a Set of Equivalent and Independent Groups The Logarithmic Plot: Bjerrum's "Formation Function" The Reciprocal Plot The Scatchard Plot of v/(A) against v Relation of Equations for Binding to Those of Enzyme Kinetics General Equation for Binding by a Molecule or Ion with n Sites Available for Combination Binding by an Equivalent Set of Groups with Interactions Between Them Complexes of Biochemical Substances with Metallic Ions: Some General Considerations Electrostatic Effects on Binding of Ions Effects of Competition Between Different Ligands for the Same Binding Site Linked Functions References