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E-raamat: How Enzymes Work: From Structure to Function 2nd edition [Taylor & Francis e-raamat]

(Kitasato University, Kanagawa-ken, Japan)
  • Formaat: 284 pages, 15 Tables, black and white; 19 Illustrations, color; 137 Illustrations, black and white
  • Ilmumisaeg: 10-Sep-2019
  • Kirjastus: Pan Stanford Publishing Pte Ltd
  • ISBN-13: 9780429341441
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  • Taylor & Francis e-raamat
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How Enzymes Work: From Structure to Function 2nd editionSuurem pilt
  • Formaat: 284 pages, 15 Tables, black and white; 19 Illustrations, color; 137 Illustrations, black and white
  • Ilmumisaeg: 10-Sep-2019
  • Kirjastus: Pan Stanford Publishing Pte Ltd
  • ISBN-13: 9780429341441
Teised raamatud teemal:
Taylor & Francis e-raamatudRohkem infot Taylor & Francis e-raamatute kohta
Raamatu kodulehekülg: https://www.taylorfrancis.com/books/9780429341441

The first edition of this book covered the basic treatment of the enzyme reaction using the overall reaction kinetics and stopped-flow method, the general properties of protein and cofactors, the control of enzyme reaction, and the preparation of enzyme protein. These topics are the basis of the enzyme research and thus suitable for the beginner in the field. The second edition presents the cofactors produced via post-translational modification of the enzyme’s active site. These cofactors expand the function of enzymes and open a new research field. The carbonyl reagent phenylhydrazine and related compounds have been useful in finding some of the newly discovered cofactors and thus have been discussed in this edition. The topic of the control of enzyme activity through the channel of substrates and products in polyfunctional enzymes has also been expanded in this book.

Preface
xiii
1 Introduction 1(16)
1.1 General Properties of Enzyme
1(4)
1.1.1 Enzyme Specificity
2(1)
1.1.2 Rate Enhancement
2(3)
1.2 Examples of Enzyme
5(12)
1.2.1 Neurotransmission and Muscular Action
5(1)
1.2.2 Gastric Juice and Proton Pump
6(3)
1.2.3 Genetic Test of Alcohol Sensitivity and DNA Polymerase
9(3)
1.2.4 Enzyme Sensor Determination of Glucose
12(5)
2 Overall Reaction Kinetics 17(18)
2.1 Road to the Steady State Kinetics
17(7)
2.1.1 Sucrose Hydrolysis
17(2)
2.1.2 Henri's Treatment of the Enzymatic Reaction
19(1)
2.1.3 Michaelis-Menten Equation
20(4)
2.1.4 Briggs and Haldane's Steady State Method
24(1)
2.2 Demonstration of the Enzyme-Substrate Complex
24(3)
2.2.1 Peroxidase Reaction
25(1)
2.2.2 Crystallization of the ES Complex
26(1)
2.3 Meaning of Steady State
27(3)
2.3.1 Steady State Model: Tab Model
27(2)
2.3.2 Application of the Tab Model to the Enzymatic Reaction
29(1)
2.4 Kinetic Parameters
30(5)
2.4.1 kcat
30(1)
2.4.2 kcat/Km
31(4)
3 Factors That Affect Enzyme Activity 35(18)
3.1 Enzyme Concentration
35(2)
3.2 Substrate Concentration
37(6)
3.2.1 One-Substrate Reaction
37(3)
3.2.2 Two-Substrate Reaction
40(3)
3.2.2.1 Ordered bi-bi mechanism
41(1)
3.2.2.2 Random bi-bi mechanism
41(1)
3.2.2.3 Ping-Pong bi-bi mechanism
42(1)
3.3 Inhibitor
43(10)
3.3.1 Reversibility
43(1)
3.3.2 Derivation of Rate Equations
44(2)
3.3.2.1 Competitive inhibition
44(1)
3.3.2.2 Non-competitive inhibition
45(1)
3.3.2.3 Uncompetitive inhibition
46(1)
3.3.2.4 Mixed-type inhibition
46(1)
3.3.3 Graphical Method for the Determination of the Type of Inhibition and Dissociation Constants
46(7)
4 Effect of pH, Temperature, and High Pressure on Enzymatic Activity 53(22)
4.1 Effect of pH
53(6)
4.1.1 A Basic Model
53(2)
4.1.2 Graphical Methods to Determine pK Value
55(3)
4.1.3 Meaning of pK Values
58(1)
4.2 Thermodynamics in the Enzymatic Reaction
59(6)
4.2.1 Basics of Thermodynamics
60(1)
4.2.2 Transition State Theory
61(3)
4.2.3 Determination of Thermodynamic Parameters of the Enzymatic Reaction
64(1)
4.3 Temperature Dependence of the Enzymatic Reaction
65(1)
4.4 Effect of Pressure
66(2)
4.4.1 Effect of Pressure on the Rate of Reaction
67(1)
4.4.2 Meaning of the Activation Volume
67(1)
4.5 The Effect of Temperature and Pressure on a-Chymotrypsin-Catalyzed Reaction
68(7)
4.5.1 Effect of Temperature
69(2)
4.5.2 Effect of Pressure
71(4)
5 Measurement of Individual Rate Constants 75(12)
5.1 Rapid-Mixing Techniques
75(4)
5.2 Analysis of the First-Order Reaction
79(8)
5.2.1 Order of Reaction
79(4)
5.2.2 Practical Methods to Determine the First-Order Rate Constant
83(4)
6 Structure of Protein 87(30)
6.1 Amino Acids
87(5)
6.2 Polypeptide and Protein
92(1)
6.3 Analysis of Primary Structure
92(7)
6.3.1 Protein Chemical Methods
93(3)
6.3.2 cDNA Sequencing: Dideoxy Method
96(3)
6.4 Three-Dimensional Structure
99(7)
6.4.1 Weak Interactions
99(3)
6.4.1.1 Electrostatic interaction
99(1)
6.4.1.2 Hydrogen bond
100(1)
6.4.1.3 Hydrophobic interaction
100(1)
6.4.1.4 van der Waals force
101(1)
6.4.2 Secondary Structures and Their Determination
102(6)
6.4.2.1 α helix
103(1)
6.4.2.2 β sheet and β turn
104(1)
6.4.2.3 Determination of secondary structures
104(2)
6.5 Tertiary and Quaternary Structures
106(2)
6.6 Structural Motif and Loop
108(9)
6.6.1 Supersecondary Structures: Motifs
108(9)
7 Cofactors 117(28)
7.1 Active Site and Active Center
117(1)
7.2 Cofactor, Coenzyme, Prosthetic Group
118(9)
7.2.1 Nicotinamide Adenine Dinucleotide and Nicotinamide Adenine Dinucleotide Phosphate
119(1)
7.2.2 Coenzyme A
119(1)
7.2.3 Flavin Mononucleotide, Flavin Adenine Dinucleotide
120(1)
7.2.4 Heme
121(1)
7.2.5 Pyridoxal Phosphate
122(1)
7.2.6 Folate
122(2)
7.2.7 Thiamine Pyrophosphate
124(1)
7.2.8 Biotin
125(1)
7.2.9 Lipoamide
126(1)
7.3 Protein-Derived Cofactors
127(18)
7.3.1 Pyrroloquinoline Quinone
129(1)
7.3.2 Topaquinone
130(2)
7.3.3 Lysine Tyrosylquinone
132(1)
7.3.4 Tryptophan Tryptophylquinone
133(1)
7.3.5 Cysteine Tryptophylquinone
134(1)
7.3.6 Pyruvoyl (Pyruvate)
135(1)
7.3.7 4-Methylidene-5-Imidazole-5-One
136(1)
7.3.8 Formyl Glycine
137(1)
7.3.9 Cysteine Sulfinic Acid, Cysteine-Sulfenic Acid
138(7)
8 Search of Active Site 145(20)
8.1 Chemical Modification
145(6)
8.1.1 Amino Group
146(1)
8.1.2 Carbonyl Group
146(1)
8.1.3 Carboxyl Group
147(1)
8.1.4 Sulfhydryl Group
147(2)
8.1.5 Hydroxyl Group
149(1)
8.1.6 Guanidino Group
150(1)
8.1.7 Imidazole Group
150(1)
8.1.8 Indole Group
151(1)
8.2 Site-Directed Mutagenesis
151(1)
8.3 Examples of Active Site Studies
152(13)
8.3.1 Chemical Modification of L-Phe Oxidase
152(4)
8.3.2 Chemical Modification of Aspergillus niger Amine Oxidase
156(17)
8.3.2.1 Stoichiometry of the reaction catalyzed by the enzyme
156(4)
8.3.2.2 Chemical modification of SH groups
160(1)
8.3.2.3 Site-directed mutagenesis of thermostable L-lactate dehydrogenase
161(4)
9 Control of Enzyme Activity 165(30)
9.1 Regulation by Non-Covalent Interaction
165(8)
9.2 Regulation by Covalent Modification
173(22)
9.2.1 Activation of Enzymes by Cleavage of Polypeptide Chain
173(5)
9.2.2 Regulation by the Side Chain Phosphorylation
178(17)
9.2.2.1 cAMP-dependent protein kinase, protein kinaseA (PKA) and glycogen metabolism
179(2)
9.2.2.2 Regulatory subunit of PKA
181(3)
9.2.2.3 Catalytic subunit and overall reaction mechanism of catalysis
184(4)
9.2.2.4 Phosphoryl transfer reactions at the active site of the C subunit
188(7)
10 Channeling of Substrates and Products 195(20)
10.1 Tryptophan Synthase
195(6)
10.1.1 Introduction
195(3)
10.1.2 Structure of TRPS
198(1)
10.1.3 Allosteric Regulation of TRPS Reactions
199(2)
10.2 Heterotetrameric Sarcosine Oxidase
201(14)
10.2.1 Introduction
201(1)
10.2.2 X-ray Structure of HTSO
201(1)
10.2.3 Channeling of Substrates and Products in HTSO
202(14)
10.2.3.1 Tunnel analyses
202(3)
10.2.3.2 Selective migration of substrates and products
205(10)
11 Preparation of Enzyme 215(14)
11.1 Extraction of Enzyme
215(1)
11.2 Purification of Enzyme
216(7)
11.2.1 Method to Use the Solubility of Proteins
216(2)
11.2.1.1 Salting-out
216(2)
11.2.1.2 Precipitation with organic solvents
218(1)
11.2.2 Column Chromatography
218(5)
11.2.2.1 Ion exchangers
219(1)
11.2.2.2 Gel filtration
220(1)
11.2.2.3 Affinity chromatography
221(2)
11.3 Purity Analysis of Enzyme
223(6)
11.3.1 Electrophoresis
223(1)
11.3.2 Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis
223(2)
11.3.3 Isoelectric Focusing
225(4)
12 A Case Study: L-Phenylalanine Oxidase (Deaminating and Decarboxylating) 229(24)
12.1 Introduction
229(1)
12.2 Preparation of PAO
230(2)
12.2.1 Preparation of the Cell Extracts
230(1)
12.2.2 Purification of PAO by Column Chromatographies
230(2)
12.3 Catalytic Properties of PAO
232(8)
12.3.1 Stoichiometry of the Reaction Catalyzed by PAO
232(1)
12.3.2 Overall Reaction Kinetics
232(2)
12.3.3 Determination of Kinetic Constants
234(2)
12.3.4 Hydrogen Quantum Tunneling in the PAO-Catalyzed Reaction
236(4)
12.3.4.1 Hydrogen quantum tunneling (hydrogen tunneling)
236(3)
12.3.4.2 Hydrogen tunneling in the PAO-catalyzed reaction
239(1)
12.4 Structural Properties of PAO
240(4)
12.4.1 Nucleotide and Its Deduced Amino Sequences of PAO Gene and Its Expression
240(2)
12.4.2 3D Structures of proPAO and PAOpt
242(2)
12.5 Substrate Specificity and Reaction Specificity of PAO
244(9)
Appendix 253(4)
Solutions 257(8)
Index 265
Haruo Suzuki is professor emeritus at Kitasato University, Tokyo, Japan. He graduated from Tokyo Metropolitan University in 1966. He then majored in biochemistry from the Graduate School of the University of Tokyo in 1971 and received a DSci degree in the same year. After postdoc in the United States, Dr. Suzuki worked at Aichi Prefectural Colony, Japan, and then at Kitasato University. His research was on the structurefunction relationship of enzymes and on the control of hemoglobin biosynthesis.
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