Biophysical Chemistry (eBook)

Front Cover 1
Thermodynamics, Electrostatics, and the Biological Significance of the Properties of Matter 4
Copyright Page 5
Table of Contents 10
Preface 6
Symbols 15
Chapter 1. Biochemistry and Geochemistry 18
Distribution of the Chemical Elements in Living Organisms 20
The Relative Abundance of the Chemical Elements in the Universe 24
The Structure of the Earth and Its Crust 25
Early History of the Earth 28
The Ocean 34
The Central Role of Carbon in Biology 40
References 42
Chapter 2. Water and Its Biological Significance 44
Heat Capacity of Water and Other Substances 54
Heat of Vaporization 55
Latent Heat of Fusion 56
The Expansion of Water in Freezing 57
Surface Tension 59
Dielectric Constant of Water 60
Solubility 62
References 62
Chapter 3. Problems of Protein Structure 64
Proteins Some General Considerations
Amino Acids and Peptides as Dipolar Ions 71
Characteristics of the Amino Acids Derived from Proteins 73
Amino Acid Analysis of Proteins 82
Polypeptide Chains and Their Presence in Proteins 91
Determination of Arrangement of Peptide Chains and Their Linkage within Protein Molecules 97
The Number of Peptide Chains in the Molecule, and the Nature of the Terminal Groups 99
Cross-Linkages between Peptide Chains: Disulfide and Phosphate Cross-Linkages 102
Other Cross-Linkages 105
Sequence of Amino Acid Residues in Peptide Chains 106
Disulfide Linkages in Insulin and Ribonuclease 113
Spatial Configurations of Polypeptide Chains 116
Silk Fibroin 121
ß-Keratin 123
a-Keratin and Synthetic Polypeptides: the a-Helix and Other Possible Helical Structures 127
Collagen 132
The Stability of Helical Structures 140
The Significance of Disulfide Bonds Cross-Linkages and Loops in Peptide Chains
Possible Stereochemistry of Insulin 143
Stereochemistry and Enzyme Activity of Ribonuclease 145
Helical and Nonhelical Regions in Globular Proteins 146
References 149
Chapter 4. Thermodynamics 153
Introduction 153
Systems and Phases 153
Temperature 155
Dimensions of Temperature 157
First Law 159
Second Law 163
Irreversible Processes 174
Maximum Work, Equilibrium, and Free Energy 176
Heat Content, or Enthalpy 179
Expressions for the Change of the Fundamental Thermodynamic Functions 179
Partial Molal Quantities 187
Chemical Potentials 191
Phase Rule 193
Activities 198
Ideal (or Perfect) Solutions and Raoult's Law 201
Activity Coefficients and the Choice of Standard States 206
Activity and Chemical Potential of a Nonvolatile Solute from the Vapor Pressure of the Solvent 212
Equilibrium between Phases Activities in Relation to Distribution Coefficients and Solubilities
Activity of Strong Electrolytes 217
Mass Law 218
Systems Involving Other Variables 234
Statistical Interpretation of Entropy 241
Standard Free Energies of Formation and Their Use in Determining Thermodynamic Equilibria 249
References 255
Chapter 5. Electrostatics: Its Application to Polar Molecules and Ionic Solutions 258
Definition of the Potential 260
Gauss's Law 263
Poisson's Equation for Regions Containing a Space Charge 266
Free Energy of a Charged Sphere 269
The Potential and Energy of a Dipole 271
Image Charges 275
The Salting-Out Effect 280
Ionic Interactions and the Debye-Hückel Theory 299
Ion-Dipole Interactions 313
Experimental Studies on the Solubility of Dipolar Ions, and Their Interaction with Ions 323
References 337
Chapter 6. Dielectric Constants and Their Significance 340
Introduction to Dielectric Constants and Dipole Moments 340
Dielectric Polarization in Relation to Molecular Properties 345
Application of the Debye Theory 352
The Breakdown of the Debye Theory in Polar Liquids 358
Modifications of the Debye Theory 359
The Onsager Theory 364
Kirkwood's Theory 373
Polar Liquids and Dipolar Ions 381
Methods of Measuring Dielectric Constant 395
References 402
Chapter 7. Conductivity of Electrolytes 403
Conductance and Resistance 403
Electrolytes as Conductors 404
Faraday's Law 405
Equivalent Conductivity 406
Ion Mobilities 407
Ion Conductances 410
Transference Numbers 410
Hittorf Method of Determining Transference Numbers 411
The Moving Boundary Method of Determining Transference Numbers 412
Theoretical Considerations Regarding Equivalent Conductance Effects of Interionic Forces
Measurement of Conductivity 421
References 421
Chapter 8. Acid-Base Equilibria 423
The Nature of Acids and Bases 423
The Concept of pH a Preliminary Statement
Calculations of pH in Systems of Acids of Known Acid Strengths 431
The Titration of a Weak Acid with a Strong Base Buffer Action
The Experimental Determination of Acidity Constants ( K A Values) 437
Standard Potentials of Half-Cells, Choice of Conventions 451
Cells Containing Liquid Junctions 454
The Glass Electrode 466
Determination of pKA Values and Related Thermodynamic Functions in Relation to Structure 467
Effect of Neighboring Charged Groups and Dipoles on pKA Values 474
Other Acidic Groups of Biochemical Interest 480
Effects of Variation in Dielectric Constant of Solvent on Relative Strength of Acids of Different Charge Types 488
Problems 490
References 492
Chapter 9. Polybasic Acids, Bases, and Ampholytes, Including Proteins 494
Dibasic Acids 494
Polyvalent Acids: General Relations 504
A Specific Case: Glutamic Acid 511
Spectroscopic Determination of Microscopic Constants: The Ionization of 
513 
Isoelectric Points of Amphoteric Substances 521
Isoelectric Points of Polyvalent Ampholytes 524
Equilibrium between Different Ionic Forms in Polyvalent Acids and Ampholytes: The Equation of Linderstr.m-Lang 527
Electrostatic Effects on Ionization in Polybasic Acids. The Charged Sphere Model 529
Formulation in Terms of Association Constants 535
Acid-Base Equilibria in ß-Lactoglobulin Solutions 539
Ovalbumin 547
Serum Albumins 549
Ribonuclease 553
Hemoglobin 554
Other Proteins 557
Synthetic Polyelectrolytes, Including Polypeptides 557
Effects of Internal Hydrogen Bonding on Titration Curves 562
Calculations with a Dielectric Sphere Model Containing Fixed Charges 563
References 564
Chapter 10. Carbon Dioxide and Carbonic Acid 567
Carbon Dioxide in Nature 567
Structural Considerations 570
The Fundamental Equilibria in Systems Containing Carbon Dioxide and Carbonic Acid 572
Carbon Dioxide Dissociation Curves 578
The Formation of Carbamates 588
Rates of the Reactions CO2 + H2O . H2CO2 595
Carbonic Anhydrase 604
References 606
Chapter 11. Some General Aspects of Molecular Interactions 608
Some Methods of Measuring Binding 611
Some Fundamental Considerations Regarding Certain Types of Binding 622
Interactions of Bound Groups 623
Competition Effects 624
Interactions between Different Kinds of Bound Groups 624
Formation of Chelate Complexes 625
Binding by a Set of Equivalent and Independent Groups 627
Relation of Equations for Binding to Those of Enzyme Kinetics 637
General Equation for Binding by a Molecule or Ion with n Sites Available for Combination 640
Binding by an Equivalent Set of Groups with Interactions between Them 643
Complexes of Biochemical Substances with Metallic Ions: Some General Considerations 655
Electrostatic Effects on Binding of Ions 662
Effects of Competition between Different Ligands for the Same Binding Site 668
Linked Functions 670
References 677
Author Index 680
Subject Index 686