Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis

579 Pages·2023·20.129 MB·English

by  Robert A. Copeland

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ENZYMES
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ENZYMES
A Practical Introduction
to Structure, Mechanism,
and Data Analysis
THIRD EDITION
(cid:2) Robert A. Copeland (cid:2)
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Thisthirdeditionfirstpublished2023
©2023JohnWiley&Sons,Inc.
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LibraryofCongressCataloging-in-PublicationData
Names:Copeland,RobertAllen,author.
Title:Enzymes:apracticalintroductiontostructure,mechanism,anddata
analysis/RobertA.Copeland.
Description:Thirdedition.|Hoboken,NJ:Wiley,2023.|Revisededition
of:Enzymes/RobertA.Copeland.2nded.c2000.|Includes
bibliographicalreferencesandindex.
Identifiers:LCCN2022048916(print)|LCCN2022048917(ebook)|ISBN
9781119793250(cloth)|ISBN9781119793281(adobepdf)|ISBN
9781119793298(epub)
Subjects:LCSH:Enzymes.|Enzymology.
Classification:LCCQP601.C7532023(print)|LCCQP601(ebook)|DDC
572/.7–dc23/eng/20221128
LCrecordavailableathttps://lccn.loc.gov/2022048916
LCebookrecordavailableathttps://lccn.loc.gov/2022048917
CoverDesign:Wiley
CoverImage:CourtesyofRobertA.Copeland
Setin11/13ptTimesLTStdbyStraive,Chennai,India
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To Clyde Worthen for teaching me all the important
lessons: arigato sensei.
And to Theodore (Doc) Janner for stoking the fire.
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CONTENTS
Preface to the Third Edition xvii
Preface to the Second Edition xix
Preface to the First Edition xxi
Acknowledgments xxiii
1 A Brief History of Enzymology 1
KeyLearningPoints / 1
1.1 EnzymesinAntiquity / 2
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1.2 EarlyEnzymology / 3
1.3 TheDevelopmentofMechanisticEnzymology / 4
1.4 StudiesofEnzymeStructure / 5
1.5 EnzymologyToday / 7
1.6 Summary / 9
ReferencesandFurtherReading / 9
2 Chemical Bonds and Reactions in Biochemistry 11
KeyLearningPoints / 11
2.1 AtomicandMolecularOrbitals / 12
2.1.1 AtomicOrbitals / 12
2.1.2 MolecularOrbitals / 15
2.1.3 HybridOrbitals / 16
2.1.4 ResonanceandAromaticity / 18
2.1.5 DifferentElectronicConfigurationsHaveDifferentPotential
Energies / 20
2.2 ThermodynamicsofChemicalReactions / 22
2.2.1 TheTransitionStateofChemicalReactions / 24
2.3 Acid–baseChemistry / 27
vii
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viii CONTENTS
2.4 NoncovalentInteractionsinReversibleBinding / 29
2.4.1 ElectrostaticInteractions / 30
2.4.2 HydrogenBonding / 30
2.4.3 HydrophobicInteractions / 31
2.4.4 VanderWaalsForces / 31
2.5 RatesofChemicalReactions / 33
2.5.1 ReactionOrder / 35
2.5.2 ReversibleChemicalReactions / 36
2.5.3 MeasurementofInitialVelocity / 37
2.6 Summary / 38
ReferencesandFurtherReading / 38
3 Structural Components of Enzymes 39
KeyLearningPoints / 39
3.1 TheAminoAcids / 40
3.1.1 PropertiesofAmino-AcidSideChains / 42
3.1.1.1 Hydrophobicity / 42
3.1.1.2 HydrogenBonding / 42
3.1.1.3 Salt-BridgeFormation / 43
(cid:2) 3.1.2 AminoAcidsasAcidsandBases / 44 (cid:2)
3.1.3 CationandMetalBinding / 45
3.1.4 AnionandPolyanionBinding / 46
3.1.5 CovalentBondFormation / 46
3.1.5.1 DisulfideBonds / 46
3.1.5.2 Phosphorylation / 46
3.1.5.3 Glycosylation / 47
3.1.6 StericBulk / 47
3.2 ThePeptideBond / 48
3.3 AminoAcidSequenceorPrimaryStructure / 51
3.4 SecondaryStructure / 54
3.4.1 TheRight-Handed𝛼 Helix / 55
3.4.2 The𝛽-PleatedSheet / 56
3.4.3 𝛽 Turns / 58
3.4.4 OtherSecondaryStructures / 58
3.4.5 SupersecondaryStructures / 59
3.5 TertiaryStructure / 60
3.5.1 Domains / 62
3.6 SubunitsandQuaternaryStructure / 64
3.7 CofactorsinEnzymes / 67
3.8 ConformationalDynamicsandEnzymeFunction / 70
3.9 MethodsofProteinStructureDetermination / 75
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