How Enzymes Work From Structure to Function 2nd Edition by Haruo Suzuki ISBN 042934144X 9780429341441

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ISBN 10: 042934144X 
ISBN 13: 9780429341441
Author: Haruo Suzuki

How Enzymes Work From Structure to Function 2nd Table of contents:

1. Introduction

1.1 General Properties of Enzyme
1.1.1 Enzyme Specificity
1.1.2 Rate Enhancement
1.2 Examples of Enzyme
1.2.1 Neurotransmission and Muscular Action
1.2.2 Gastric Juice and Proton Pump
1.2.3 Genetic Test of Alcohol Sensitivity and DNA Polymerase
1.2.4 Enzyme Sensor Determination of Glucose

2. Overall Reaction Kinetics

2.1 Road to the Steady State Kinetics
2.1.1 Sucrose Hydrolysis
2.1.2 Henri’s Treatment of the Enzymatic Reaction
2.1.3 Michaelis–Menten Equation
2.1.4 Briggs and Haldane’s Steady State Method
2.2 Demonstration of the Enzyme–Substrate Complex
2.2.1 Peroxidase Reaction
2.2.2 Crystallization of the ES Complex
2.3 Meaning of Steady State
2.3.1 Steady State Model: Tab Model
2.3.2 Application of the Tab Model to the Enzymatic Reaction
2.4 Kinetic Parameters
2.4.1 kcat
2.4.2 kcat/Km

3. Factors That Affect Enzyme Activity

3.1 Enzyme Concentration
3.2 Substrate Concentration
3.2.1 One-Substrate Reaction
3.2.2 Two-Substrate Reaction
3.2.2.1 Ordered bi-bi mechanism
3.2.2.2 Random bi-bi mechanism
3.2.2.3 Ping-Pong bi-bi mechanism
3.3 Inhibitor
3.3.1 Reversibility
3.3.2 Derivation of Rate Equations
3.3.2.1 Competitive inhibition
3.3.2.2 Non-competitive inhibition
3.3.2.3 Uncompetitive inhibition
3.3.2.4 Mixed-type inhibition
3.3.3 Graphical Method for the Determination of the Type of Inhibition and Dissociation Constants

4. Effect of pH, Temperature, and High Pressure on Enzymatic Activity

4.1 Effect of pH
4.1.1 A Basic Model
4.1.2 Graphical Methods to Determine pK Value
4.1.3 Meaning of pK Values
4.2 Thermodynamics in the Enzymatic Reaction
4.2.1 Basics of Thermodynamics
4.2.2 Transition State Theory
4.2.3 Determination of Thermodynamic Parameters of the Enzymatic Reaction
4.3 Temperature Dependence of the Enzymatic Reaction
4.4 Effect of Pressure
4.4.1 Effect of Pressure on the Rate of Reaction
4.4.2 Meaning of the Activation Volume
4.5 The Effect of Temperature and Pressure on α-Chymotrypsin-Catalyzed Reaction
4.5.1 Effect of Temperature
4.5.2 Effect of Pressure

5. Measurement of Individual Rate Constants

5.1 Rapid-Mixing Techniques
5.2 Analysis of the First-Order Reaction
5.2.1 Order of Reaction
5.2.2 Practical Methods to Determine the First-Order Rate Constant

6. Structure of Protein

6.1 Amino Acids
6.2 Polypeptide and Protein
6.3 Analysis of Primary Structure
6.3.1 Protein Chemical Methods
6.3.2 cDNA Sequencing: Dideoxy Method
6.4 Three-Dimensional Structure
6.4.1 Weak Interactions
6.4.1.1 Electrostatic interaction
6.4.1.2 Hydrogen bond
6.4.1.3 Hydrophobic interaction
6.4.1.4 van der Waals force
6.4.2 Secondary Structures and Their Determination
6.4.2.1 α helix
6.4.2.2 β sheet and β turn
6.4.2.3 Determination of secondary structures
6.5 Tertiary and Quaternary Structures
6.6 Structural Motif and Loop
6.6.1 Supersecondary Structures: Motifs

7. Cofactors

7.1 Active Site and Active Center
7.2 Cofactor, Coenzyme, Prosthetic Group
7.2.1 Nicotinamide Adenine Dinucleotide and Nicotinamide Adenine Dinucleotide Phosphate
7.2.2 Coenzyme A
7.2.3 Flavin Mononucleotide, Flavin Adenine Dinucleotide
7.2.4 Heme
7.2.5 Pyridoxal Phosphate
7.2.6 Folate
7.2.7 Thiamine Pyrophosphate
7.2.8 Biotin
7.2.9 Lipoamide
7.3 Protein-Derived Cofactors
7.3.1 Pyrroloquinoline Quinone
7.3.2 Topaquinone
7.3.3 Lysine Tyrosylquinone
7.3.4 Tryptophan Tryptophylquinone
7.3.5 Cysteine Tryptophylquinone
7.3.6 Pyruvoyl (Pyruvate)
7.3.7 4-Methylidene-5-Imidazole-5-One
7.3.8 Formyl Glycine
7.3.9 Cysteine Sulfinic Acid, Cysteine-Sulfenic Acid

8. Search of Active Site

8.1 Chemical Modification
8.1.1 Amino Group
8.1.2 Carbonyl Group
8.1.3 Carboxyl Group
8.1.4 Sulfhydryl Group
8.1.5 Hydroxyl Group
8.1.6 Guanidino Group
8.1.7 Imidazole Group
8.1.8 Indole Group
8.2 Site-Directed Mutagenesis
8.3 Examples of Active Site Studies
8.3.1 Chemical Modification of L-Phe Oxidase
8.3.2 Chemical Modification of Aspergillus niger Amine Oxidase
8.3.2.1 Stoichiometry of the reaction catalyzed by the enzyme
8.3.2.2 Chemical modification of SH groups
8.3.2.3 Site-directed mutagenesis of thermostable L-lactate dehydrogenase

9. Control of Enzyme Activity

9.1 Regulation by Non-Covalent Interaction
9.2 Regulation by Covalent Modification
9.2.1 Activation of Enzymes by Cleavage of Polypeptide Chain
9.2.2 Regulation by the Side Chain Phosphorylation
9.2.2.1 cAMP-dependent protein kinase, protein kinaseA (PKA) and glycogen metabolism
9.2.2.2 Regulatory subunit of PKA
9.2.2.3 Catalytic subunit and overall reaction mechanism of catalysis
9.2.2.4 Phosphoryl transfer reactions at the active site of the C subunit

10. Channeling of Substrates and Products

10.1 Tryptophan Synthase
10.1.1 Introduction
10.1.2 Structure of TRPS
10.1.3 Allosteric Regulation of TRPS Reactions
10.2 Heterotetrameric Sarcosine Oxidase
10.2.1 Introduction
10.2.2 X-ray Structure of HTSO
10.2.3 Channeling of Substrates and Products in HTSO
10.2.3.1 Tunnel analyses
10.2.3.2 Selective migration of substrates and products

11. Preparation of Enzyme

11.1 Extraction of Enzyme
11.2 Purification of Enzyme
11.2.1 Method to Use the Solubility of Proteins
11.2.1.1 Salting-out
11.2.1.2 Precipitation with organic solvents
11.2.2 Column Chrom

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Tags: Haruo Suzuki, Enzymes, Function