Preface |
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xvii | |
Acknowledgments |
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xix | |
Authors |
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xxi | |
Part I Thermodynamics |
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Chapter 1 Systems and their Surroundings |
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3 | (2) |
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4 | (1) |
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Chapter 2 State Functions and the Laws of Thermodynamics |
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5 | (62) |
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2.1 General Considerations: State Variables and State Functions |
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5 | (2) |
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2.2 The Internal Energy U and the First Law of Thermodynamics |
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7 | (19) |
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2.2.1 Internal Energy, Heat, and Work |
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7 | (1) |
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2.2.2 The First Law of Thermodynamics |
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8 | (1) |
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2.2.3 The Ideal Gas: A Convenient System to Understand Thermodynamic Principles |
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9 | (3) |
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2.2.4 Changes in the State of an Ideal Gas |
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12 | (8) |
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2.2.4.1 Irreversible Isothermal Expansion and Compression |
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12 | (1) |
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2.2.4.2 Reversible Isothermal Expansion and Compression |
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13 | (1) |
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2.2.4.3 Comparison of Reversible and Irreversible Changes of State |
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14 | (2) |
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2.2.4.4 Adiabatic Expansion and Compression |
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16 | (4) |
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2.2.5 Thermodynamic Cycles: Back and Forth or Round and Round |
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20 | (5) |
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2.2.5.1 The Carnot Process |
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21 | (4) |
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2.2.6 The Temperature Dependence of the Internal Energy U |
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25 | (1) |
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26 | (3) |
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2.4 The Entropy S and the Second Law of Thermodynamics |
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29 | (8) |
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2.4.1 Predicting Spontaneity of Processes: Dissipation of Heat and Matter |
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29 | (1) |
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30 | (2) |
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2.4.3 Temperature Dependence of the Entropy |
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32 | (1) |
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2.4.4 The Third Law of Thermodynamics and Absolute Entropy |
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33 | (1) |
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2.4.5 Entropy and Order: The Statistic Interpretation |
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34 | (3) |
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2.5 The Free Energy G: Combining System and Surroundings |
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37 | (9) |
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2.5.1 Entropy- and Enthalpy-Driven Reactions |
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39 | (2) |
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2.5.2 Pressure and Temperature Dependence of the Free Energy |
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41 | (2) |
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43 | (1) |
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2.5.4 Relation of Free Energy, Enthalpy, and Entropy to Molecular Properties |
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44 | (2) |
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2.6 The Chemical Potential p |
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46 | (18) |
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2.6.1 The Chemical Potential as a Driving Force for Chemical Reactions |
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46 | (2) |
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2.6.2 The Chemical Potential and Stable States: Phase Diagrams |
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48 | (3) |
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2.6.3 Pressure and Temperature Dependence of the Chemical Potential |
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51 | (1) |
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2.6.4 The Chemical Potential as a Partial Molar Property |
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51 | (1) |
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2.6.5 The Chemical Potential of Compounds in Mixtures |
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52 | (3) |
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2.6.6 The Chemical Potential of Solutions |
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55 | (2) |
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2.6.7 Colligative Properties |
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57 | (7) |
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64 | (1) |
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65 | (2) |
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Chapter 3 Energetics and Chemical Equilibria |
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67 | (18) |
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3.1 The Free Energy Change and the Equilibrium Constant |
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67 | (4) |
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3.1.1 Temperature Dependence of the Equilibrium Constant |
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69 | (1) |
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3.1.2 The Principle of Le Chatelier |
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70 | (1) |
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3.2 Binding and Dissociation Equilibria and Affinity |
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71 | (3) |
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3.3 Protolysis Equilibria: The Dissociation of Acids and Bases in Water |
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74 | (1) |
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3.4 Thermodynamic Cycles, Linked Functions and Apparent Equilibrium Constants |
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75 | (7) |
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82 | (1) |
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83 | (2) |
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Chapter 4 Thermodynamics of Transport Processes |
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85 | (16) |
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85 | (5) |
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4.2 The Chemiosmotic Hypothesis |
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90 | (2) |
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4.3 Active and Passive Transport |
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92 | (2) |
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4.4 Directed Movement by the Brownian Ratchet |
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94 | (4) |
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98 | (1) |
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98 | (3) |
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Chapter 5 Electrochemistry |
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101 | (18) |
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5.1 Redox Reactions and Electrochemical Cells |
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101 | (3) |
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104 | (1) |
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5.3 Standard Electrode Potentials |
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105 | (1) |
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106 | (2) |
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108 | (1) |
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5.6 Redox Reactions in Biology |
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109 | (2) |
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5.6.1 The Respiratory Chain |
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109 | (1) |
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5.6.2 The Light Reaction in Photosynthesis |
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110 | (1) |
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5.7 The Electrochemical Potential and Membrane Potentials |
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111 | (3) |
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5.8 Electrophysiology: Patch-Clamp Methods to Measure Ion Flux through Ion Channels |
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114 | (1) |
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115 | (1) |
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116 | (3) |
Part II Kinetics |
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Chapter 6 Reaction Velocities and Rate Laws |
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119 | (6) |
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123 | (2) |
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Chapter 7 Integrated Rate Laws for Uni- and Bimolecular Reactions |
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125 | (12) |
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135 | (2) |
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137 | (10) |
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137 | (3) |
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140 | (2) |
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8.3 Consecutive Reactions |
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142 | (4) |
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146 | (1) |
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146 | (1) |
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Chapter 9 Rate-Limiting Steps |
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147 | (6) |
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151 | (1) |
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151 | (2) |
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Chapter 10 Binding Reactions: One-Step and Two-Step Binding |
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153 | (8) |
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159 | (1) |
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159 | (2) |
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Chapter 11 Steady-State (Enzyme) Kinetics |
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161 | (30) |
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11.1 Rapid Equilibrium (Michaelis-Menten Formalism) |
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162 | (2) |
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11.2 Steady-State Approximation (Briggs-Haldane Formalism) |
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164 | (3) |
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167 | (5) |
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11.4 Two or More Non-Interacting Active Sites |
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172 | (3) |
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11.5 Two or More Interacting Active Sites: Cooperativity and the Hill Equation |
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175 | (4) |
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11.6 Inhibition of Enzyme Activity |
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179 | (8) |
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11.6.1 Product Inhibition in Reversible Reactions |
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179 | (3) |
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11.6.2 Competitive Inhibition |
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182 | (1) |
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11.6.3 Non-Competitive Inhibition |
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183 | (2) |
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185 | (2) |
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187 | (2) |
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189 | (2) |
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Chapter 12 Complex Reaction Schemes and their Analysis |
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191 | (12) |
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12.1 Binding of Two Substrates |
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191 | (5) |
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191 | (2) |
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193 | (3) |
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196 | (1) |
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12.3 Net Rate Constants and Transit Times |
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197 | (3) |
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200 | (1) |
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200 | (3) |
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Chapter 13 Temperature Dependence of Rate Constants |
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203 | (6) |
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13.1 The Arrhenius Equation |
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203 | (1) |
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13.2 Transition State Theory |
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203 | (3) |
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206 | (1) |
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13.4 Kinetic and Thermodynamic Control of Reactions |
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207 | (1) |
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208 | (1) |
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Chapter 14 Principles of Catalysis |
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209 | (12) |
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209 | (2) |
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211 | (4) |
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14.3 Electrostatic and Covalent Catalysis |
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215 | (1) |
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14.4 Intramolecular Catalysis and Effective Concentrations |
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216 | (1) |
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216 | (1) |
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217 | (4) |
Part III Molecular Structure and Stability |
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Chapter 15 Molecular Structure and Interactions |
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221 | (18) |
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15.1 Configuration and Conformation |
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221 | (3) |
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15.2 Covalent Interactions |
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224 | (3) |
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225 | (1) |
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15.2.2 Bond Angles and Torsion Angles |
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225 | (2) |
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15.3 Non-Covalent Interactions |
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227 | (10) |
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15.3.1 Ionic Interactions |
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229 | (1) |
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15.3.2 Interactions between Ions and Dipoles |
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229 | (3) |
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232 | (2) |
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15.3.4 Interactions between Induced Dipoles: van der Waals Interactions |
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234 | (3) |
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237 | (1) |
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237 | (2) |
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239 | (64) |
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16.1 Amino Acids and the Peptide Bond |
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239 | (12) |
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16.1.1 Properties of the Twenty Canonical Amino Acids |
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239 | (2) |
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241 | (2) |
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16.1.3 Side-Chain Rotamers |
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243 | (1) |
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16.1.4 Post-Translational Modifications |
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244 | (7) |
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245 | (1) |
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245 | (1) |
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246 | (1) |
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247 | (1) |
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248 | (1) |
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248 | (3) |
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251 | (28) |
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16.2.1 Helical Secondary Structure Elements |
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253 | (4) |
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253 | (2) |
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16.2.1.2 310-, poly-Pro, and Collagen Helices |
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255 | (2) |
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16.2.2 p-Strands and their Super-Secondary Structures (p-Sheets) |
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257 | (3) |
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260 | (2) |
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16.2.4 Protein Domains & Tertiary Structure |
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262 | (3) |
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16.2.5 Quaternary Structure & Protein-Protein Interactions |
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265 | (3) |
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265 | (2) |
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16.2.5.2 Hetero-Oligomers |
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267 | (1) |
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16.2.6 Protein-Protein Interactions |
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268 | (3) |
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16.2.6.1 Surface Complementarity and Buried Surface Area |
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268 | (1) |
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16.2.6.2 Energetics of Macromolecular Interactions |
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269 | (1) |
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16.2.6.3 Role of Water - The Hydrophobic Effect |
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269 | (2) |
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16.2.7 Protein-Ligand Interactions |
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271 | (2) |
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16.2.8 Membrane Proteins and their Lipid Environment |
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273 | (6) |
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16.2.8.1 Biological Roles of Lipids and Membranes |
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273 | (2) |
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275 | (1) |
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16.2.8.3 Super-Structures Formed by Lipids and Detergents |
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275 | (2) |
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16.2.8.4 Properties and Structure of Membrane Proteins |
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277 | (2) |
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16.3 Folding and Stability |
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279 | (20) |
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16.3.1 Driving Forces for Protein Folding |
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280 | (2) |
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16.3.2 First Folding Experiments and the Levinthal Paradox |
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282 | (1) |
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16.3.3 Energy Landscapes for Protein Folding |
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283 | (2) |
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16.3.4 Mathematical Description of the Two-State Model |
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285 | (5) |
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16.3.5 Folding Pathways and Mechanisms of Protein Folding |
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290 | (7) |
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16.3.5.1 Fast Steps in Protein Folding: Secondary Structure Formation |
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292 | (1) |
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16.3.5.2 Rate-Limiting Steps and Protein Folding In Vivo |
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293 | (2) |
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16.3.5.3 Kinetics of Protein Folding |
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295 | (1) |
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16.3.5.4 Folding Intermediates in Monomers and Oligomers |
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296 | (1) |
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16.3.6 Protein Folding Diseases |
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297 | (2) |
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299 | (1) |
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300 | (2) |
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302 | (1) |
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303 | (38) |
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17.1 Nucleobases, Nucleosides and Nucleotides |
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304 | (3) |
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17.1.1 Non-Standard Nucleobases in DNA |
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305 | (1) |
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17.1.2 Non-Standard Nucleobases in RNA |
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306 | (1) |
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17.2 Ribose and Nucleobase Conformations |
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307 | (2) |
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307 | (1) |
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17.2.2 Syn- and Anti-Conformations |
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308 | (1) |
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17.3 Primary Structure of Nucleic Acids |
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309 | (2) |
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17.4 Base Pairing and Stacking |
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311 | (4) |
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17.4.1 H-bonds between Nucleobases |
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311 | (2) |
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17.4.2 Importance of Base Pair Stacking for Double Helix Formation |
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313 | (1) |
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17.4.3 Base Pair Geometries |
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314 | (1) |
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17.5 DNA Structures and Conformations |
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315 | (19) |
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17.5.1 DNA Double Helical Structures |
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315 | (3) |
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17.5.2 Triple and Quadruple DNA Helices |
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318 | (2) |
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318 | (1) |
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17.5.2.2 Quadruplexes and Telomeres |
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319 | (1) |
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17.5.3 Higher Order DNA Structures |
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320 | (9) |
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320 | (2) |
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17.5.3.2 DNA Supercoiling |
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322 | (6) |
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17.5.3.3 DNA Bending and Kinking |
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328 | (1) |
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17.5.4 DNA Interactions with Proteins and Ligands |
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329 | (5) |
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17.5.4.1 DNA Recognition by Proteins |
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329 | (4) |
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17.5.4.2 Small Molecule Binding to DNA |
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333 | (1) |
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334 | (4) |
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17.6.1 RNA Secondary Structure |
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335 | (1) |
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17.6.2 RNA Tertiary Structure |
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336 | (2) |
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338 | (1) |
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338 | (1) |
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339 | (1) |
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340 | (1) |
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Chapter 18 Computational Biology |
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341 | (24) |
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341 | (7) |
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18.1.1 Sequence Composition, Global Properties, and Motifs |
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341 | (4) |
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342 | (1) |
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18.1.1.2 RNA Secondary Structure Prediction |
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342 | (1) |
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18.1.1.3 Protein Sequence Composition and Properties |
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343 | (2) |
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18.1.2 Sequence Alignment |
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345 | (3) |
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18.1.3 Secondary Structure Prediction |
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348 | (1) |
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348 | (11) |
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349 | (1) |
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18.2.2 Energy Minimization |
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350 | (2) |
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18.2.3 Molecular Mechanics and Dynamics |
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352 | (4) |
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18.2.3.1 Boundary Conditions and Solvation |
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353 | (1) |
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18.2.3.2 Integration of the Newtonian Equations |
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354 | (1) |
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18.2.3.3 Trajectory Analysis |
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355 | (1) |
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18.2.4 Applications of Molecular Modeling to Macromolecules |
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356 | (9) |
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18.2.4.1 Fold Recognition |
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357 | (1) |
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18.2.4.2 Homology Modeling |
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358 | (1) |
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18.2.4.3 Simulated Annealing |
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358 | (1) |
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18.2.4.4 Coarse-Grained Modeling |
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359 | (1) |
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359 | (1) |
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360 | (1) |
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360 | (5) |
Part IV Methods |
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Chapter 19 Optical Spectroscopy |
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365 | (96) |
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19.1 Interaction of Light and Matter |
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365 | (4) |
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19.1.1 Light as an Electromagnetic Wave |
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365 | (2) |
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19.1.2 Principles of Spectroscopy: Transitions in Two-State Systems |
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367 | (2) |
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369 | (18) |
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19.2.1 Electronic, Vibronic, and Rotational Energy Levels |
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369 | (1) |
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19.2.2 Transitions and Transition Dipoles |
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370 | (2) |
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19.2.3 The Lambert-Beer Law |
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372 | (2) |
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19.2.4 Solvent Effects and Influence of the Local Environment |
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374 | (1) |
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375 | (1) |
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19.2.6 Biological Chromophores |
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375 | (5) |
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380 | (6) |
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19.2.7.1 Concentration Determination |
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380 | (1) |
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19.2.7.2 Spectroscopic Assays for Enzymatic Activity |
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381 | (2) |
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19.2.7.3 Spectroscopic Tests for Functional Groups |
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383 | (1) |
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19.2.7.4 Absorption as a Probe for Structural Changes |
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384 | (2) |
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19.2.8 Potential Pitfalls |
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386 | (1) |
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19.3 Linear and Circular Dichroism |
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387 | (11) |
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19.3.1 Linearly Polarized Light and Linear Dichroism |
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387 | (3) |
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19.3.2 Circularly Polarized Light and Circular Dichroism |
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390 | (5) |
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395 | (1) |
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19.3.4 Biological Chromophores that Show Circular Dichroism |
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395 | (1) |
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396 | (2) |
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19.3.6 Potential Pitfalls |
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398 | (1) |
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19.4 Infrared Spectroscopy |
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398 | (6) |
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19.4.1 Bond Vibrations: The Harmonic Oscillator |
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398 | (2) |
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19.4.2 Molecule Geometry, Degrees of Freedom, and Vibrational Modes |
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400 | (2) |
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402 | (1) |
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403 | (1) |
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404 | (49) |
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19.5.1 General Considerations |
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404 | (2) |
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406 | (1) |
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19.5.3 Quantum Yield and Lifetime |
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407 | (1) |
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19.5.4 Fluorophores and Fluorescent Labeling |
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408 | (10) |
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19.5.4.1 Biological Fluorophores |
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408 | (1) |
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19.5.4.2 Extrinsic Fluorophores and their Introduction into Proteins, Nucleic Acids, and Lipids |
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409 | (9) |
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418 | (6) |
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19.5.5.1 Fluorescence as a Probe for Binding: Equilibrium Titrations |
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418 | (4) |
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19.5.5.2 Fluorescence as a Probe for the Chemical Micro- and Macro-Environment |
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422 | (1) |
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19.5.5.3 Fluorescence and Imaging: Fluorescence Recovery after Photobleaching |
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423 | (1) |
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19.5.6 Potential Pitfalls |
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424 | (2) |
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19.5.7 Fluorescence Quenching |
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426 | (3) |
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19.5.8 Fluorescence Anisotropy |
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429 | (4) |
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19.5.8.1 Principle of Fluorescence Anisotropy |
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429 | (2) |
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431 | (1) |
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19.5.8.3 Potential Pitfalls of Polarization/Anisotropy Measurements |
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432 | (1) |
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19.5.9 Time-Resolved Fluorescence |
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433 | (8) |
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19.5.9.1 Measurement of Fluorescence Lifetimes |
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435 | (3) |
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19.5.9.2 Fluorescence Anisotropy Decays and Rotational Correlation Times |
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438 | (1) |
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19.5.9.3 Rotational Correlation Time and Molecular Size |
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439 | (1) |
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440 | (1) |
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19.5.10 Forster Resonance Energy Transfer |
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441 | (20) |
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19.5.10.1 Principle of FRET |
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441 | (2) |
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19.5.10.2 Experimental Determination of FRET Efficiencies |
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443 | (3) |
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446 | (3) |
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19.5.10.4 Potential Pitfalls |
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449 | (1) |
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19.5.10.5 FRET Efficiencies from Lifetimes |
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449 | (3) |
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19.5.10.6 FRET Efficiencies from Single Molecules |
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452 | (1) |
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453 | (2) |
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455 | (6) |
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Chapter 20 Magnetic Resonance |
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461 | (46) |
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20.1 Nuclear Magnetic Resonance |
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461 | (29) |
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20.1.1 Nuclear Spins and the Zeeman Effect |
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461 | (2) |
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20.1.2 A One-Dimensional NMR Spectrum: Larmor Frequency, Chemical Shift, J-Coupling, and Multiplicity |
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463 | (5) |
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20.1.2.1 The Larmor Frequency |
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463 | (1) |
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20.1.2.2 The Local Magnetic Field and the Chemical Shift |
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463 | (3) |
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20.1.2.3 Scalar Coupling and Multiplets |
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466 | (1) |
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20.1.2.4 Shape of NMR Lines |
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467 | (1) |
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468 | (1) |
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20.1.3 The Nuclear Overhauser Effect: Distance Information |
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468 | (4) |
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20.1.4 Magnetization and Its Relaxation to Equilibrium: Fourier Transform-NMR and the Free Induction Decay |
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472 | (4) |
|
20.1.5 Two-Dimensional FT-NMR: COSY and NOESY |
|
|
476 | (8) |
|
20.1.5.1 Principle of a 2D-FT-NMR Experiment |
|
|
477 | (1) |
|
20.1.5.2 Correlated Spectroscopy |
|
|
478 | (1) |
|
20.1.5.3 Nuclear Overhauser Enhancement Spectroscopy |
|
|
479 | (1) |
|
20.1.5.4 Spin Systems and Sequential Assignment of Protein NMR Spectra |
|
|
479 | (4) |
|
20.1.5.5 Structure Calculation |
|
|
483 | (1) |
|
20.1.6 Extending NMR to Structure Determination of Large Molecules |
|
|
484 | (2) |
|
|
486 | (2) |
|
20.1.8 Solid State NMR and Biology |
|
|
488 | (1) |
|
|
489 | (1) |
|
20.2 Electron Paramagnetic Resonance |
|
|
490 | (10) |
|
20.2.1 Principle of Electron Paramagnetic Resonance |
|
|
490 | (1) |
|
20.2.2 Spin-Spin Interactions: Hyperfine Coupling of Unpaired Electrons with Nuclei |
|
|
491 | (1) |
|
20.2.3 EPR Probes and Spin Labeling |
|
|
492 | (2) |
|
20.2.4 EPR as a Probe for Mobility and Dynamics |
|
|
494 | (1) |
|
20.2.5 EPR as a Probe for Accessibility |
|
|
495 | (1) |
|
20.2.6 Measuring Spin-Spin Distances |
|
|
496 | (1) |
|
20.2.7 Distance Determination by Pulsed EPR: PELDOR/DEER |
|
|
497 | (3) |
|
|
500 | (1) |
|
|
501 | (6) |
|
Chapter 21 Solution Scattering |
|
|
507 | (24) |
|
|
507 | (8) |
|
21.1.1 Static Light Scattering |
|
|
507 | (4) |
|
21.1.2 Dynamic Light Scattering |
|
|
511 | (2) |
|
|
513 | (2) |
|
21.2 Small Angle Scattering |
|
|
515 | (13) |
|
21.2.1 Scattering of X-rays and Neutrons |
|
|
515 | (3) |
|
21.2.2 SAS Intensity Distribution |
|
|
518 | (4) |
|
21.2.3 Distance Distribution Function |
|
|
522 | (1) |
|
21.2.4 Small Angle X-ray Scattering |
|
|
523 | (3) |
|
|
523 | (1) |
|
21.2.4.2 Excluded Volume and Molecular Mass |
|
|
524 | (1) |
|
|
524 | (1) |
|
21.2.4.4 Modeling of Scattering Curves |
|
|
525 | (1) |
|
21.2.5 Small Angle Neutron Scattering |
|
|
526 | (28) |
|
21.2.5.1 Generation of Neutrons |
|
|
526 | (1) |
|
21.2.5.2 Contrast Variation |
|
|
527 | (1) |
|
|
528 | (1) |
|
|
529 | (2) |
|
Chapter 22 X-ray Crystallography |
|
|
531 | (40) |
|
22.1 Generation of X-rays |
|
|
532 | (4) |
|
22.2 Phase Problem and Requirement for Crystals |
|
|
536 | (1) |
|
22.3 Crystallization of Macromolecules |
|
|
536 | (6) |
|
22.4 Symmetry and Space Groups |
|
|
542 | (5) |
|
22.5 X-ray Diffraction from Crystals |
|
|
547 | (4) |
|
22.6 Diffraction Data Collection and Analysis |
|
|
551 | (3) |
|
|
554 | (8) |
|
22.7.1 Isomorphous Replacement |
|
|
554 | (2) |
|
22.7.2 Anomalous Diffraction |
|
|
556 | (4) |
|
22.7.3 Molecular Replacement |
|
|
560 | (2) |
|
22.8 Electron Density and Model Building |
|
|
562 | (3) |
|
22.9 Model Refinement and Validation |
|
|
565 | (3) |
|
|
568 | (1) |
|
|
569 | (1) |
|
|
570 | (1) |
|
Chapter 23 Imaging and Microscopy |
|
|
571 | (52) |
|
23.1 Fluorescence Microscopy |
|
|
571 | (37) |
|
23.1.1 Optical Principles of Microscopy |
|
|
572 | (6) |
|
23.1.1.1 Focusing and Collecting Light by Optical Lenses |
|
|
572 | (2) |
|
23.1.1.2 Microscopes: How to Achieve Magnification with Optical Lenses |
|
|
574 | (2) |
|
23.1.1.3 The Diffraction Limit of Optical Resolution |
|
|
576 | (2) |
|
23.1.2 Wide-Field Fluorescence Microscopy |
|
|
578 | (1) |
|
23.1.3 Confocal Scanning Microscopy |
|
|
579 | (2) |
|
23.1.4 Total Internal Reflection Microscopy |
|
|
581 | (2) |
|
23.1.5 Fluorescence Lifetime Imaging Microscopy |
|
|
583 | (1) |
|
23.1.6 Fluorescence (Cross-)Correlation Spectroscopy |
|
|
584 | (8) |
|
23.1.6.1 Fluorescence Correlation Spectroscopy |
|
|
585 | (2) |
|
23.1.6.2 FCS to Monitor Binding Events |
|
|
587 | (3) |
|
23.1.6.3 Fluorescence Cross-Correlation Spectroscopy |
|
|
590 | (2) |
|
23.1.7 Single-Molecule Fluorescence Microscopy |
|
|
592 | (13) |
|
23.1.7.1 Principles of Single-Molecule Microscopy |
|
|
592 | (3) |
|
23.1.7.2 Why Single Molecules? |
|
|
595 | (1) |
|
23.1.7.3 Localization and Tracking of Single Molecules |
|
|
596 | (1) |
|
23.1.7.4 Kinetic Information from Single-Molecule Microscopy |
|
|
597 | (1) |
|
23.1.7.5 Colocalization of Molecules |
|
|
598 | (2) |
|
23.1.7.6 Single-Molecule FRET |
|
|
600 | (5) |
|
23.1.8 Super-Resolution Microscopy |
|
|
605 | (3) |
|
|
608 | (10) |
|
23.2.1 Principle of Electron Microscopy |
|
|
608 | (1) |
|
23.2.2 Sample Preparation |
|
|
609 | (1) |
|
23.2.3 Image Generation and Analysis |
|
|
610 | (1) |
|
23.2.4 Three-Dimensional Electron Microscopy: Cryo-Electron Tomography and Single Particle Cryo-EM |
|
|
611 | (6) |
|
23.2.5 Scanning Probe Microscopy: Scanning Tunneling, Scanning Force, and Atomic Force Microscopy |
|
|
617 | (1) |
|
|
618 | (1) |
|
|
619 | (4) |
|
Chapter 24 Force Measurements |
|
|
623 | (24) |
|
24.1 Force Spectroscopy by AFM |
|
|
625 | (6) |
|
|
631 | (7) |
|
|
638 | (4) |
|
|
642 | (1) |
|
|
642 | (5) |
|
Chapter 25 Transient Kinetic Methods |
|
|
647 | (10) |
|
|
647 | (3) |
|
|
650 | (1) |
|
25.3 Laser Flash Photolysis |
|
|
651 | (2) |
|
25.4 Relaxation Kinetics: Pressure- and Temperature-Jump |
|
|
653 | (1) |
|
|
654 | (1) |
|
|
655 | (2) |
|
Chapter 26 Molecular Mass, Size, and Shape |
|
|
657 | (52) |
|
|
657 | (19) |
|
|
658 | (2) |
|
26.1.1.1 Matrix-Assisted Laser Desorption Ionization |
|
|
658 | (1) |
|
26.1.1.2 Electrospray Ionization |
|
|
659 | (1) |
|
26.1.2 Ion Storage and Manipulation |
|
|
660 | (7) |
|
26.1.2.1 Time of Flight Analysis |
|
|
660 | (1) |
|
26.1.2.2 Quadrupoles and Ion Traps |
|
|
661 | (3) |
|
|
664 | (1) |
|
26.1.2.4 Ion Fragmentation and Sequencing |
|
|
665 | (2) |
|
|
667 | (2) |
|
|
669 | (1) |
|
|
669 | (7) |
|
26.1.5.1 Mass Analysis for the Identification of Molecules |
|
|
669 | (1) |
|
26.1.5.2 Isotope Distribution and Isotope Exchange |
|
|
670 | (1) |
|
26.1.5.3 Protein Identification from One- and Two-Dimensional Gels |
|
|
671 | (1) |
|
26.1.5.4 Native Mass Spectrometry |
|
|
671 | (1) |
|
26.1.5.5 Ion Mobility and Molecular Shape |
|
|
672 | (1) |
|
26.1.5.6 Identifying Protein-RNA Interaction Sites after Photo-Crosslinking |
|
|
673 | (1) |
|
26.1.5.7 Secondary Ion Mass Spectrometry |
|
|
673 | (1) |
|
26.1.5.8 Quantitative Mass Spectrometry |
|
|
674 | (2) |
|
26.2 Analytical Ultracentrifugation |
|
|
676 | (17) |
|
26.2.1 Instrumentation and Detection Systems |
|
|
676 | (2) |
|
26.2.2 Behavior of a Molecule in a Gravitational Field |
|
|
678 | (4) |
|
26.2.3 Sedimentation Velocity |
|
|
682 | (5) |
|
26.2.3.1 Determination of Sedimentation Coefficients |
|
|
683 | (1) |
|
26.2.3.2 Solvent and Concentration Dependence of the Sedimentation Coefficient |
|
|
684 | (1) |
|
26.2.3.3 Measuring Polydispersity and Association |
|
|
685 | (2) |
|
26.2.4 Sedimentation Equilibrium |
|
|
687 | (3) |
|
26.2.4.1 Determination of Molecular Mass Using Sedimentation Equilibrium |
|
|
687 | (2) |
|
26.2.4.2 Association in Sedimentation Equilibrium |
|
|
689 | (1) |
|
26.2.5 Zonal, Band, or Isopycnic Centrifugation |
|
|
690 | (3) |
|
26.3 Surface Plasmon Resonance |
|
|
693 | (9) |
|
26.3.1 Physical Background of SPR |
|
|
693 | (2) |
|
26.3.2 Principle and Information Content of an SPR Experiment |
|
|
695 | (2) |
|
26.3.3 Mass Transport Limitation |
|
|
697 | (1) |
|
26.3.4 Receptor Immobilization on the Sensor Surface |
|
|
697 | (4) |
|
26.3.4.1 Covalent Receptor Immobilization |
|
|
698 | (2) |
|
26.3.4.2 Non-Covalent Receptor Immobilization |
|
|
700 | (1) |
|
26.3.5 Stoichiometry of Binding in an SPR Experiment |
|
|
701 | (1) |
|
26.3.6 Specificity of Binding in an SPR Experiment |
|
|
702 | (1) |
|
|
702 | (4) |
|
|
706 | (1) |
|
|
707 | (2) |
|
|
709 | (22) |
|
27.1 Isothermal Titration Calorimetry |
|
|
709 | (11) |
|
|
709 | (2) |
|
|
711 | (2) |
|
27.1.3 Origin of Enthalpic Changes |
|
|
713 | (2) |
|
27.1.4 Practical Considerations |
|
|
715 | (2) |
|
27.1.5 Measuring High Affinities with ITC by Competition |
|
|
717 | (1) |
|
27.1.6 Measuring Michaelis-Menten Enzyme Kinetics with ITC |
|
|
717 | (3) |
|
27.2 Differential Scanning Calorimetry |
|
|
720 | (6) |
|
|
720 | (3) |
|
27.2.2 Two-State Unfolding of Macromolecules |
|
|
723 | (2) |
|
27.2.3 Two-State Unfolding with Subunit Dissociation |
|
|
725 | (1) |
|
|
726 | (1) |
|
|
726 | (5) |
Appendix |
|
|
Chapter 28 Prefixes, Units, Constants |
|
|
731 | (4) |
|
|
731 | (1) |
|
28.2 SI (Systeme International) or Base Units |
|
|
732 | (1) |
|
28.3 Derived Units Used in this Book |
|
|
732 | (1) |
|
28.4 Natural Constants Used in This Book |
|
|
733 | (2) |
|
Chapter 29 Mathematical Concepts Used in This Book |
|
|
735 | (20) |
|
|
735 | (1) |
|
|
736 | (1) |
|
29.3 Binomial Coefficients |
|
|
736 | (1) |
|
|
737 | (1) |
|
29.5 Logarithms and Exponentials |
|
|
737 | (2) |
|
29.6 Differentiation and Integration |
|
|
739 | (3) |
|
|
742 | (1) |
|
|
743 | (1) |
|
|
743 | (2) |
|
|
744 | (1) |
|
|
744 | (1) |
|
|
745 | (2) |
|
29.11 Basic Elements of Statistics |
|
|
747 | (1) |
|
|
748 | (1) |
|
|
749 | (2) |
|
|
749 | (1) |
|
|
749 | (2) |
|
29.14 Fourier Transformation |
|
|
751 | (2) |
|
|
753 | (2) |
Index |
|
755 | |