Thermodynamic Data for Biochemistry and Biotechnology

Section I Introduction.- 1 Present and Future Uses and a Bit of History.- 1 Some Early History.- 2 Acids, Bases, and Oxidation-Reduction Equilibria.- 3 Thermodynamics of Major Metabolic Processes.- 4 Thermodynamics of Amino Acids and Proteins: Electrostatic and Hydrophobic Interactions.- 5 Thermodynamics of Ligand Binding to Macromolecules.- 6 The Contributions of this Book.- References.- Appendix: Physical Quantities, Units, and Conversion Factors.- Section II Nonreacting Systems.- 2 Partial Molar Volumes of Biochemical Model Compounds in Aqueous Solution.- 1 Introduction.- 2 Definitions.- 3 Extrapolation to Infinite Dilution.- 4 Tabulation of the Experimental Data.- 5 Alcohols, Polyols, and Phenols.- 6 Ethers, Ketones, and Aldehydes.- 7 Carboxylic Acids, Sodium Carboxylates, and Esters.- 8 Amines, Amides, and Ureas.- 9 Carbohydrates.- 10 Amino Acids and Low Molar Mass Proteins.- 11 Group Additivity of Partial Molar Volumes.- 12 Models Based on van der Waals Volumes.- 13 Conclusions.- 14 Addendum.- References.- 3 Specific Volumes of Biological Macromolecules and Some Other Molecules of Biological Interest.- 1 Introduction.- 2 Definitions.- 2.1 Volume and Density.- 2.2 Specific Volumes.- 3 Determination of Specific Volumes.- 3.1 Calculation.- 3.1.1 Traube’s Additivity Principle.- 3.1.2 Native Nonconjugated Proteins.- 3.1.3 Native Conjugated Proteins.- 3.1.4 Protein Complexes.- 3.1.5 Denatured Proteins.- 3.2 Experimental Determination.- 3.2.1 Methods.- 3.2.2 Digital Densimetry.- 4 Tabulation and Interpretation of Data.- 4.1 Specific Volumes.- 4.1.1 Small Molecules.- 4.1.2 Polyamino Acids and Peptides.- 4.1.3 Native Nonconjugated Proteins.- 4.1.4 Native Conjugated Proteins.- 4.1.5 Denatured Proteins.- 4.1.6 Polysaccharides.- 4.1.7 Lipids, Membranes, and Micelles.- 4.1.8 Polynucleotides and Nucleic Acids.- 4.2 Specific Volume Changes.- 4.2.1 Proteins.- 4.2.1.1 Protein Concentration.- 4.2.1.2 Temperature.- 4.2.1.3 Aging, Thermal Denaturation.- 4.2.1.4 Acid and Alkaline Denaturation.- 4.2.1.5 Different Buffers.- 4.2.1.6 Addition of Salts.- 4.2.1.7 Addition of Sugars of Polyols.- 4.2.1.8 Addition of Denaturants.- 4.2.1.9 Binding of Specific Ligands.- 4.2.2 Other Substances.- 5 Conclusions.- 6 Tables.- References.- 4 Partial Molar Compressibilities of Organic Solutes in Water.- 1 Introduction.- 2 Definitions.- 3 Tabulation of Experimental Results.- 4 Alcohols, Diols, and Ethers.- 5 Carboxylic Acids and Sodium Carboxylates.- 6 Amines, Amides, and Ureas.- 7 Carbohydrates.- 8 Amino Acids and Dipeptides.- 9 Proteins.- 10 Nucleobases and Nucleosides.- 11 Summary.- References.- 5 Heat Capacities of Biological Macromolecules.- 1 Introduction.- 2 Calorimetric Measurements.- 3 Experimental Results.- 3.1 Heat Capacity and Thermodynamic Properties of Amino Acid Residues over the Temperature Range 1.5–350 K.- 3.2 Heat Capacity and Thermodynamic Properties of Polypeptides over the Temperature Range 1.5–300 K.- 3.3 Heat Capacity and Thermodynamic Properties of Globular Proteins over the Temperature Range 10–350 K.- 3.4 Thermodynamic Properties of Fibrous Collagen in the Helical and Coil States at Temperatures 4–400 K.- 3.5 Heat Capacity of DNA.- 4 Concluding Remarks.- References.- 6 Thermodynamics of Carbohydrate Monomers and Polymers in Aqueous Solution.- 1 Introduction.- 2 Rationale for Concentration Dependence.- 3 Experimental Data for Simple Carbohydrates in Solution.- 4 Molecular Calculations of Thermodynamic Properties.- 4.1 Conformational Properties.- 4.2 Comparison of Experimental Data with Those from Energy Calculations.- 5 Inclusion Complexes.- 5.1 Cyclodextrin Complexes.- 5.2 Energetics of the Amylose-Iodine Complex.- 6 Ionic Polysaccharides.- 6.1 Premise.- 6.2 The Polyelectrolytic Contrast Effect.- 6.3 Enthalpies of Dilution in Water.- 6.4 Enthalpies of Protonation of Carboxylated Polysaccharides.- 6.5 Enthalpy of Mixing with Ions.- 7 Conclusions.- References.- Section III Interactions in Solution.- 7 Thermodynamic Data for Protein-Ligand Interaction.- 1 Introduction.- 2 Thermodynamic Quantities and Their Measurements.- 2.1 Gibbs Energy Changes.- 2.2 Enthalpy Changes.- 2.3 Changes in Entropy.- 2.4 Changes in Heat Capacity.- 2.5 Potential Errors in Microcalorimetric Measurements of Protein-Ligand Interactions.- 2.6 Sensitivity of Microcalorimeters and Calibration Procedures.- 2.7 Criteria of Selection and Arrangement of Tables .215 References.- 8 Thermodynamics of Protein-Protein Association.- 1 Introduction.- 2 Explanation of Table 1.- 3 Commentary on Methods of Gibbs Energy Determination.- 4 Commentary on Experimental Methodology.- 5 Commentary on Specific Systems.- 6 Conclusion.- References.- 9 Hemoglobin.- 1 Introduction.- 2 Molecular Parameters of Human Hemoglobin.- 3 Nonideality and Gelation of Concentrated Hb Solutions.- 4 Methemoglobin and the Redox Behavior of Hemoglobin.- 5 The Bohr Effect.- 6 Equilibrium Binding of O2 to Hemoglobin — Classical Models.- 7 Linked Subunit Assembly and Ligand Binding in Hemoglobin.- 8 Oxygen-Linked Binding of Anions to Hemoglobin.- 9 Miscellaneous Data.- 10 Conclusion.- References.- Section IV Solution Processes.- 10 Gas-Liquid and Solid-Liquid Phase Equilibria in Binary Aqueous Systems of Nonelectrolytes.- 1 Introduction.- 2 Solubility of Gases in Pure Water.- 3 Solubility of Gases in Aqueous Solutions of Electrolytes.- 4 Partition Coefficients of Vapors Between Water and the Gas Phase.- 5 Solubility of Solid Substances.- 6 Previsions of the Solubility in Water of Nonelectrolytes.- References.- Notes Added in Proof.- 11 Thermodynamic Parameters of Biopolymer-Water Systems.- 1 Introduction.- 2 Experimental Methods, Their Sources of Error, and Criteria for Selection of “Best Values”.- 2.1 Vapor Pressure Measurements.- 2.1.1 Sources of Error.- 2.1.2 Criteria for Selection of Best Values.- 2.2 Calorimetry.- 2.2.1 Heat Capacity Calorimeters.- 2.2.2 Differential Scanning Calorimetry (DSC).- 2.3 Densitometry.- 3 Tables of Selected Values.- 3.1 Thermodynamic Data Obtained from Vapor Pressure Studies.- 3.2 Thermodynamic Data Obtained by Calorimetry.- 3.3 Thermodynamic Parameters Obtained by Densitometry.- 4 Discussion and Correlation of the Thermodynamic Parameters of Biopolymer Hydration.- References.- Section V Phase Changes.- 12 The Formation of Micelles.- 1 Behavior of Detergents in Water.- 2 Aggregation Behavior of Surfactants.- 2.1 Determination of the Critical Micelle Concentration cmc.- 2.2 Influence of the Nature of Surfactants and External Parameters on the cmc.- 3 Thermodynamic Parameters of Micelle Formation.- 3.1 General Considerations of the Thermodynamics of Micelle Formation.- 3.2 Experimental Techniques for the Determination of the Thermodynamic Parameters of Micelle Formation.- 3.3 Partial Molal Quantities of Surfactants in Aqueous Solutions.- 3.4 Thermodynamic Functions of Micelle Formation.- 3.5 Molecular Interpretation of Thermodynamic Parameters.- 4 Models for the Micellar Aggregation Process.- 4.1 Theoretical Considerations on Micellar Aggregation.- 4.1.1 Size and Shape of Micellar Aggregates.- 4.1.2 Determination of Higher cmc’s and Their Dependence on the Structure of the Detergent and External Parameters.- 4.1.3 Methods for the Determination of Size and Shape of Micelles.- 4.3 Configuration of the Monomers Inside Micelles.- 4.4 Interaction Between Micellar Aggregates.- 5 The Behavior of Surfactants in Nonpolar Solvents; Formation of Reversed Micelles.- 6 Dynamics of Micelle Formation.- References.- 13 Unfolding of Proteins.- 1 Introduction.- 2 The Approaches in Determining ?Gunf.- References.- 14 The Thermodynamics of Conformation Transitions in Polynucleotides.- 1 Introduction.- 2 The Thermodynamics of Conformational Transitions in Single-Stranded Polynucleotides.- 3 Thermodynamic Parameters of the Polynucleotide Complexes.- 3.1 Complexes of Polyribonucleotides.- 3.2 Complexes of Polydesoxyribonucleotides.- 4 Thermodynamics of RNA Unfolding.- 5 Concluding Remarks.- References.- 15 Methods for Obtaining Thermodynamic Data on Oligonucleotide Transitions.- 1 Introduction.- 2 Why Are We Interested in Thermodynamic Data?.- 3 Why Study Oligonucleotides?.- 4 Methods for Obtaining Thermodynamic Data.- 4.1 Optical Techniques for Determining Transition Enthalpies.- 4.1.1 Shape Analysis of Absorbance Versus Temperature Profiles.- 4.1.2 Analysis of the Shape of a Differentiated Absorbance versus Temperature Melting Curve.- 4.1.3 Temperature Dependence of the Equilibrium Constant.- 4.1.4 Concentration Dependence of the Melting Temperature.- 4.1.5 Calculating Complete Thermodynamic Transition Profiles from the Enthalpy Data.- 5 Concluding Remarks.- References.- Section VI Enzyme Catalyzed Processes.- 16 Thermodynamic of Enzymatic Reactions.- 1 Introduction.- 2 Principle for the Systematization of Thermodynamic Data for Enzymatic Reactions.- 2.1 Thermodynamics of Enzymatic Reactions Catalyzed by Oxidoreductases.- 2.2 Thermodynamics of Enzymatic Reactions Catalyzed by Transferases.- 2.3 Thermodynamics of Enzymatic Reactions Catalyzed by Hydrolases.- 2.4 Thermodynamics of Enzymatic Reactions Catalyzed by Lyases.- 2.5 Thermodynamics of Enzymatic Reactions Catalyzed by Isomerases.- 2.6 Thermodynamics of Enzymatic Reactions Catalyzed by Ligases.- 3 Conclusion.- References.