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

579 Pages·2023·20.129 MB·English
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(cid:2) ENZYMES (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) ENZYMES A Practical Introduction to Structure, Mechanism, and Data Analysis THIRD EDITION (cid:2) Robert A. Copeland (cid:2) (cid:2) (cid:2) Thisthirdeditionfirstpublished2023 ©2023JohnWiley&Sons,Inc. EditionHistory JohnWiley&Sons,Inc.(1e,1996);JohnWiley&Sons,Inc.(2e,2000) Allrightsreserved.Nopartofthispublicationmaybereproduced,storedinaretrievalsystem,ortransmitted,inanyformorby anymeans,electronic,mechanical,photocopying,recordingorotherwise,exceptaspermittedbylaw.Adviceonhowtoobtain permissiontoreusematerialfromthistitleisavailableathttp://www.wiley.com/go/permissions. TherightofauthorRobertA.Copelandtobeidentifiedastheauthorofthisworkhasbeenassertedinaccordancewithlaw. RegisteredOffice JohnWiley&Sons,Inc.,111RiverStreet,Hoboken,NJ07030,USA Fordetailsofourglobaleditorialoffices,customerservices,andmoreinformationaboutWileyproductsvisitusat www.wiley.com. Wileyalsopublishesitsbooksinavarietyofelectronicformatsandbyprint-on-demand.Somecontentthatappearsinstandard printversionsofthisbookmaynotbeavailableinotherformats. Trademarks:WileyandtheWileylogoaretrademarksorregisteredtrademarksofJohnWiley&Sons,Inc.and/oritsaffiliatesin theUnitedStatesandothercountriesandmaynotbeusedwithoutwrittenpermission.Allothertrademarksarethepropertyof theirrespectiveowners.JohnWiley&Sons,Inc.isnotassociatedwithanyproductorvendormentionedinthisbook. LimitofLiability/DisclaimerofWarranty Inviewofongoingresearch,equipmentmodifications,changesingovernmentalregulations,andtheconstantflowofinformation relatingtotheuseofexperimentalreagents,equipment,anddevices,thereaderisurgedtoreviewandevaluatetheinformation providedinthepackageinsertorinstructionsforeachchemical,pieceofequipment,reagent,ordevicefor,amongotherthings, anychangesintheinstructionsorindicationofusageandforaddedwarningsandprecautions.Whilethepublisherandauthors (cid:2) (cid:2) haveusedtheirbesteffortsinpreparingthiswork,theymakenorepresentationsorwarrantieswithrespecttotheaccuracyor completenessofthecontentsofthisworkandspecificallydisclaimallwarranties,includingwithoutlimitationanyimplied warrantiesofmerchantabilityorfitnessforaparticularpurpose.Nowarrantymaybecreatedorextendedbysalesrepresentatives, writtensalesmaterialsorpromotionalstatementsforthiswork.Thefactthatanorganization,website,orproductisreferredtoin thisworkasacitationand/orpotentialsourceoffurtherinformationdoesnotmeanthatthepublisherandauthorsendorsethe informationorservicestheorganization,website,orproductmayprovideorrecommendationsitmaymake.Thisworkissold withtheunderstandingthatthepublisherisnotengagedinrenderingprofessionalservices.Theadviceandstrategiescontained hereinmaynotbesuitableforyoursituation.Youshouldconsultwithaspecialistwhereappropriate.Further,readersshouldbe awarethatwebsiteslistedinthisworkmayhavechangedordisappearedbetweenwhenthisworkwaswrittenandwhenitisread. Neitherthepublishernorauthorsshallbeliableforanylossofprofitoranyothercommercialdamages,includingbutnotlimited tospecial,incidental,consequential,orotherdamages. 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 (cid:2) (cid:2) To Clyde Worthen for teaching me all the important lessons: arigato sensei. And to Theodore (Doc) Janner for stoking the fire. (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) (cid:2) 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 (cid:2) (cid:2) 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 (cid:2) (cid:2) 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 (cid:2)

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