THERMODYNAMICS ANDKINETICS FOR TH EBIOLOGICAL SCIENCES

Gordon G . Hammes

Preface

ix

1. Heat, Work, and Energy

1

1 .1 Introduction

11 .2 Temperature

21 .3 Heat

31 .4 Work

41 .5 Definition of Energy

71 .6 Enthalpy

91 .7 Standard States

10

1 .8 Calorimetry

1 1

1 .9 Reaction Enthalpies

151 .10 Temperature Dependence of the Reaction Enthalpy

17

References

1 8Problems

1 8

2. Entropy and Free Energy

21

2.1 Introduction

2 12.2 Statement of the Second Law

22

2.3 Calculation of the Entropy

24

2.4 Third Law of Thermodynamics

262.5 Molecular Interpretation of Entropy

27

2.6 Free Energy

282.7 Chemical Equilibria

302 .8 Pressure and Temperature Dependence of the Free Energy

332.9 Phase Changes

35

2.10 Additions to the Free Energy

37Problems

37

3. Applications of Thermodynamics to Biological Systems

41

3 .1 Biochemical Reactions

413 .2 Metabolic Cycles

423 .3 Direct Synthesis of ATP

47

3 .4 Establishment of Membrane Ion Gradients by Chemical Reactions

48

3 .5 Protein Structure

503 .6 Protein Folding

5 63 .7 Nucleic Acid Structures

593.8 DNA Melting

623.9 RNA

66References

6 8

Problems

6 8

4. Chemical Kinetics

71

4.1 Introduction

7 14 .2 Reaction Rates

73

4.3 Determination of Rate Laws

7 54 .4 Radioactive Decay

784.5 Reaction Mechanisms

794.6 Temperature Dependence of Rate Constants

8 34.7 Relationship Between Thermodynamics and Kinetics

8 64.8 Reaction Rates Near Equilibrium

8 8References

9 1Problems

9 1

5. Applications of Kinetics to Biological Systems

9 4

5 .1 Introduction

945 .2 Enzyme Catalysis : The Michaelis-Menten Mechanism

9 4

5 .3 a-Chymotrypsin

995.4 Protein Tyrosine Phosphatase

1065 .5 Ribozymes

1095 .6 DNA Melting and Renaturation

11 3References

119Problems

120

6. Ligand Binding to Macromolecules

124

6.1 Introduction

1246.2 Binding of Small Molecules to Multiple Identical Binding Sites

1246.3 Macroscopic and Microscopic Equilibrium Constants

1276 .4 Statistical Effects in Ligand Binding to Macromolecules

1286 .5 Experimental Determination of Ligand Binding Isotherms

1326 .6 Binding of Cro Repressor Protein to DNA

1356.7 Cooperativity in Ligand Binding

13 86.8 Models for Cooperativity

1436 .9 Kinetic Studies of Cooperative Binding

1476 .10 Allosterism

14 8References

15 1Problems

152

Appendixes

1. Standard Free Energies and Enthalpies of Formation at 298 K ,1 Atmosphere, pH 7, and 0 .25 M Ionic Strength

154

2. Standard Free Energy and Enthalpy Changes for BiochemicalReactions at 298 K, 1 Atmosphere, pH 7 .0, pMg 3 .0, and 0 .25 MIonic Strength

156

3. Structures of the Common Amino Acids at Neutral pH

157

4. Useful Constants and Conversion Factors

159

Index

161