Microbial Biochemistry: Second Edition PDF
Preview Microbial Biochemistry: Second Edition
Microbial Biochemistry . G.N. Cohen Microbial Biochemistry Second Edition Prof.G.N.Cohen InstitutPasteur rueduDocteurRoux28 75724Paris France [email protected] ISBN978-90-481-9436-0 e-ISBN978-90-481-9437-7 DOI10.1007/978-90-481-9437-7 SpringerDordrechtHeidelbergLondonNewYork LibraryofCongressControlNumber:2010938472 #SpringerScience+BusinessMediaB.V.2011 Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmittedinanyformorbyany means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permissionfromthePublisher,withtheexceptionofanymaterialsuppliedspecificallyforthepurpose ofbeingenteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Foreword This book originates from almost 60 years of living in the company of micro- organisms,mainlywithEscherichiacoli.Myscientificlifehastakenplacealmost exclusively at the Institut Pasteur in Paris, where many concepts of modern molecularbiologywerebornordeveloped. Thepresentworkemphasizestheinterestofmicrobialphysiology,biochemistry andgenetics.Ittakesintoaccounttheconsiderableadvanceswhichhavebeenmade inthefieldinthelast30yearsbytheintroductionofgenecloningandsequencing andbytheexponentialdevelopmentofphysicalmethodssuchasX-raycrystallog- raphyofproteins. Theyoungergenerationofbiochemistsislegitimatelyinterestedintheproblems raisedbydifferentiationanddevelopmentinhigherorganisms,andalsoinneuros- ciences.Itishowevermyfeelingthatthestudyofprokaryoteswillremainforalong timethebestintroductiontogeneralbiology. A particular emphasis has been given to particular systems which have been extensively studied from historical, physiological, enzymological, structural, genetic and evolutionary points of view: I present my apologies to those who mayfindthatthischoiceistoopersonalandreflectstoomuchmypersonalinterest insubjectsinwhichIhaveeitherapersonalcontributionorwhereimportantresults havebeenobtainedbysomeofmybestfriends. I am grateful to the Philippe Foundation for the help it has given to me and to manyofmystudentsformanyyears. My thanks are due to my wife, Louisette Cohen for her patience and help, not onlywhilethisbookwaswritten,butalsoduringournear70yearscommonlife. This work is a tribute to the memory of my beloved colleagues, my mentor Jacques Monod, and the late Harold Amos, Dean B. Cowie, Michael Doudoroff, BenNisman,EarlR.Stadtman,RogerY.Stanier,GermaineStanier,Huguetteand KisselSzulmajster. Paris,France G.N.Cohen v . Contents 1 BacterialGrowth ..............................................................1 TheLagPhase ..................................................................1 TheExponentialPhase..........................................................1 LinearGrowth...................................................................2 TheYieldofGrowth............................................................3 VariationoftheGrowthRateatLimitingCarbonSource Concentrations ..................................................................4 ContinuousGrowth:TheChemostat ...........................................5 AdvantagesoftheContinuousExponentialCulture ...........................7 DiauxicGrowth.................................................................7 SelectedReferences........................................................... 10 2 TheOuterMembraneofGram-negativeBacteria andtheCytoplasmicMembrane ........................................... 11 TheOuterMembraneofGram-NegativeBacteria........................... 11 TheCytoplasmicMembrane.................................................. 12 EnergyGeneration............................................................ 13 ATPSynthase .............................................................. 13 SubunitCompositionoftheATPSynthase .................................. 14 ATPSynthesisinArchaea.................................................... 16 SelectedReferences........................................................... 16 3 PeptidoglycanSynthesisandCellDivision ................................ 17 GeneralStructure ............................................................. 17 AssemblyofthePeptidoglycanUnit ......................................... 18 TheMembraneSteps ......................................................... 19 AssemblyoftheMureinSacculus............................................ 20 PenicillinSensitivity.......................................................... 20 CellDivision.................................................................. 21 SelectedReferences........................................................... 22 vii viii Contents 4 CellularPermeability ....................................................... 23 Accumulation,Crypticity,andSelectivePermeability....................... 24 b-GalactosidePermease....................................................... 25 AccumulationinInducedCells:KineticsandSpecificity................. 26 TheInducedSynthesisofGalactosidePermease.......................... 29 FunctionalSignificanceofGalactosidePermease:SpecificCrypticity ... 30 FunctionalRelationshipsofPermease:Induction ......................... 32 GeneticRelationshipsofGalactosidaseandGalactoside Permease.................................................................... 32 GalactosidePermeaseasProtein........................................... 33 PeriplasmicBindingProteinsandATPBindingCassettes................... 36 Phosphotransferases:ThePTSSystem....................................... 39 TRAPTransporters ........................................................... 41 AFewWell-identifiedCasesofSpecificCellularPermeability............. 42 AminoAcidPermeases .................................................... 42 PeptidePermeases.......................................................... 43 Porins.......................................................................... 45 IronUptake.................................................................... 47 Conclusion .................................................................... 48 SelectedReferences........................................................... 48 5 AllostericEnzymes .......................................................... 51 AllostericInhibitionandActivation.......................................... 54 AnAlternativeModel......................................................... 61 Conclusion .................................................................... 62 SelectedReferences........................................................... 62 6 Glycolysis,GluconeogenesisandGlycogenSynthesis .................... 63 GlycogenDegradation........................................................ 63 Glycolysis..................................................................... 63 Hexokinase................................................................. 65 Glucose6-PhosphateIsomerase............................................ 65 Phosphofructokinase ....................................................... 66 Fructose1,6-BisphosphateAldolase....................................... 68 TriosePhosphateIsomerase................................................ 68 Glyceraldehyde-3-PhosphateDehydrogenase(GAPDH).................. 68 PhosphoglycerateKinase................................................... 69 Phosphoglyceromutase..................................................... 69 Enolase ..................................................................... 69 PyruvateKinase............................................................ 70 Gluconeogenesis.............................................................. 70 FructoseBisphosphataseinMicroorganisms................................. 70 GlycogenSynthesis........................................................... 71 GlycogenSynthase......................................................... 71 Contents ix ControlofGlycogenBiosynthesis............................................ 72 BranchingEnzyme............................................................ 72 7 ThePentosePhosphateandEntner–DoudoroffPathways ............... 73 ThePentosePhosphatePathway.............................................. 73 TheEnzymesoftheOxidativePhase......................................... 73 Glucose6-PhosphateDehydrogenase...................................... 73 6-Phosphogluconolactonase................................................ 74 6-PhosphogluconateDehydrogenase(Decarboxylating) .................. 74 RibosePhosphateIsomerase............................................... 74 TheEnzymesoftheNon-oxidativePhase.................................... 74 Transketolase............................................................... 75 Transaldolase............................................................... 76 Ribulose-5-Phosphate-3-Epimerase........................................ 76 RegulationofthePentosePhosphatePathway............................... 77 TheEntner–DoudoroffPathway........................................... 77 8 TheTricarboxylicAcidCycleandtheGlyoxylateBypass ............. 79 TheoriginofacetylCoA:ThePyruvateDehydrogenaseComplex ........ 79 OverviewoftheTricarboxylicAcid(TCA)Cycle.......................... 81 OriginoftheOxaloacetate................................................ 81 OrganizationoftheEnzymesoftheTricarboxylicAcidCycle............. 96 TheTricarboxylicAcidCycleIsaSourceofBiosynthetic Precursors.................................................................... 97 TheAnapleroticGlyoxylicPathwayBypass................................ 97 9 ATP-GeneratingProcesses:RespirationandFermentation .......... 101 Respiration..................................................................101 Fermentation................................................................104 Acetone-ButanolFermentation.............................................104 TheSticklandReaction.....................................................105 OrnithineFermentation.....................................................105 GlycineandProlineDegradation...........................................106 ThreonineDegradation......................................................106 GlutamateDegradation .....................................................107 LysineDegradation.........................................................108 ArginineFermentation......................................................109 MethionineDegradation....................................................110 D-SelenocystineandD-CysteineDegradation .............................110 SelectedReferences.........................................................111 10 BiosynthesisofLipids .................................................... 115 BiosynthesisofShortChainFattyAcids...................................115 BiosynthesisofLong-ChainFattyAcids...................................116 SynthesisofAcetylCoA.................................................116
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