153. Enzyme Kinetics

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153. Enzyme Kinetics

 

 

CATEGORY: Diet Nutrition Supplementation – 500 Courses

COURSE NUMBER: 153

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Syllabus

PREFACE xiii
1 TOOLS AND TECHNIQUES OF KINETIC ANALYSIS 1
1.1 Generalities / 1
1.2 Elementary Rate Laws / 2
1.2.1 Rate Equation / 2
1.2.2 Order of a Reaction / 3
1.2.3 Rate Constant / 4
1.2.4 Integrated Rate Equations / 4
1.2.4.1 Zero-Order Integrated Rate
Equation / 4
1.2.4.2 First-Order Integrated Rate
Equation / 5
1.2.4.3 Second-Order Integrated Rate
Equation / 7
1.2.4.4 Third-Order Integrated Rate
Equation / 8
1.2.4.5 Higher-Order Reactions / 9
1.2.4.6 Opposing Reactions / 9
1.2.4.7 Reaction Half-Life / 11

1.2.5 Experimental Determination of Reaction
Order and Rate Constants / 12
1.2.5.1 Differential Method (Initial Rate
Method) / 12
1.2.5.2 Integral Method / 13
1.3 Dependence of Reaction Rates on
Temperature / 14
1.3.1 Theoretical Considerations / 14
1.3.2 Energy of Activation / 18
1.4 Acid–Base Chemical Catalysis / 20
1.5 Theory of Reaction Rates / 23
1.6 Complex Reaction Pathways / 26
1.6.1 Numerical Integration and Regression / 28
1.6.1.1 Numerical Integration / 28
1.6.1.2 Least-Squares Minimization
(Regression Analysis) / 29
1.6.2 Exact Analytical Solution
(Non-Steady-State Approximation) / 39
1.6.3 Exact Analytical Solution (Steady-State
Approximation) / 40

2 HOW DO ENZYMES WORK? 41
3 CHARACTERIZATION OF ENZYME ACTIVITY 44
3.1 Progress Curve and Determination of Reaction
Velocity / 44
3.2 Catalysis Models: Equilibrium and Steady
State / 48
3.2.1 Equilibrium Model / 48
3.2.2 Steady-State Model / 49
3.2.3 Plot of v versus [S] / 50
3.3 General Strategy for Determination of the
Catalytic Constants Km and Vmax / 52
3.4 Practical Example / 53
3.5 Determination of Enzyme Catalytic Parameters
from the Progress Curve / 58

CONTENTS ix
4 REVERSIBLE ENZYME INHIBITION 61
4.1 Competitive Inhibition / 61
4.2 Uncompetitive Inhibition / 62
4.3 Linear Mixed Inhibition / 63
4.4 Noncompetitive Inhibition / 64
4.5 Applications / 65
4.5.1 Inhibition of Fumarase by Succinate / 65
4.5.2 Inhibition of Pancreatic Carboxypeptidase
A by β-Phenylpropionate / 67
4.5.3 Alternative Strategies / 69

5 IRREVERSIBLE ENZYME INHIBITION 70
5.1 Simple Irreversible Inhibition / 72
5.2 Simple Irreversible Inhibition in the Presence of
Substrate / 73
5.3 Time-Dependent Simple Irreversible
Inhibition / 75
5.4 Time-Dependent Simple Irreversible Inhibition in
the Presence of Substrate / 76
5.5 Differentiation Between Time-Dependent and
Time-Independent Inhibition / 78
6 pH DEPENDENCE OF ENZYME-CATALYZED
REACTIONS 79
6.1 The Model / 79
6.2 pH Dependence of the Catalytic Parameters / 82
6.3 New Method of Determining pK Values of
Catalytically Relevant Functional Groups / 84
7 TWO-SUBSTRATE REACTIONS 90
7.1 Random-Sequential Bi Bi Mechanism / 91
7.1.1 Constant [A] / 93
7.1.2 Constant [B] / 93
7.2 Ordered-Sequential Bi Bi Mechanism / 95
7.2.1 Constant [B] / 95

7.2.2 Constant [A] / 96
7.2.3 Order of Substrate Binding / 97
7.3 Ping-Pong Bi Bi Mechanism / 98
7.3.1 Constant [B] / 99
7.3.2 Constant [A] / 99
7.4 Differentiation Between Mechanisms / 100
8 MULTISITE AND COOPERATIVE ENZYMES 102
8.1 Sequential Interaction Model / 103
8.1.1 Basic Postulates / 103
8.1.2 Interaction Factors / 105
8.1.3 Microscopic versus Macroscopic
Dissociation Constants / 106
8.1.4 Generalization of the Model / 107
8.2 Concerted Transition or Symmetry Model / 109
8.3 Application / 114
8.4 Reality Check / 115
9 IMMOBILIZED ENZYMES 116
9.1 Batch Reactors / 116
9.2 Plug-Flow Reactors / 118
9.3 Continuous-Stirred Reactors / 119
10 INTERFACIAL ENZYMES 121
10.1 The Model / 122
10.1.1 Interfacial Binding / 122
10.1.2 Interfacial Catalysis / 123
10.2 Determination of Interfacial Area per Unit
Volume / 125
10.3 Determination of Saturation Interfacial Enzyme
Coverage / 127

11 TRANSIENT PHASES OF ENZYMATIC REACTIONS 129
11.1 Rapid Reaction Techniques / 130
11.2 Reaction Mechanisms / 132

11.2.1 Early Stages of the Reaction / 134
11.2.2 Late Stages of the Reaction / 135
11.3 Relaxation Techniques / 135
12 CHARACTERIZATION OF ENZYME STABILITY 140
12.1 Kinetic Treatment / 140
12.1.1 The Model / 140
12.1.2 Half-Life / 142
12.1.3 Decimal Reduction Time / 143
12.1.4 Energy of Activation / 144
12.1.5 Z Value / 145
12.2 Thermodynamic Treatment / 146
12.3 Example / 150
12.3.1 Thermodynamic Characterization of
Stability / 151
12.3.2 Kinetic Characterization of Stability / 156

13 MECHANISM-BASED INHIBITION 158
Leslie J. Copp
13.1 Alternate Substrate Inhibition / 159
13.2 Suicide Inhibition / 163
13.3 Examples / 169
13.3.1 Alternative Substrate Inhibition / 169
13.3.2 Suicide Inhibition / 170

14 PUTTING KINETIC PRINCIPLES INTO PRACTICE 174
Kirk L. Parkin
14.1 Were Initial Velocities Measured? / 175
14.2 Does the Michaelis–Menten Model Fit? / 177
14.3 What Does the Original [S] versus Velocity Plot
Look Like? / 179
14.4 Was the Appropriate [S] Range Used? / 181
14.5 Is There Consistency Working Within the Context
of a Kinetic Model? / 184
14.6 Conclusions / 191

15 USE OF ENZYME KINETIC DATA IN THE STUDY
OF STRUCTURE–FUNCTION RELATIONSHIPS OF
PROTEINS 193
Takuji Tanaka and Rickey Y. Yada
15.1 Are Proteins Expressed Using Various Microbial
Systems Similar to the Native Proteins? / 193
15.2 What Is the Mechanism of Conversion of a
Zymogen to an Active Enzyme? / 195
15.3 What Role Does the Prosegment Play in the
Activation and Structure–Function of the Active
Enzyme? / 198
15.4 What Role Do Specific Structures and/or Residues
Play in the Structure–Function of Enzymes? / 202
15.5 Can Mutations be Made to Stabilize the Structure
of an Enzyme to Environmental Conditions? / 205
15.5.1 Charge Distribution / 205
15.5.2 N-Frag Mutant / 208
15.5.3 Disulfide Linkages / 210
15.6 Conclusions / 212
15.7 Abbreviations Used for the Mutation
Research / 213

BIBLIOGRAPHY 217
Books / 217
Selection of Classic Papers / 218
INDEX 221

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