Alberts. .molecular.biology.of.the.cell.5th.ed

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Transcript of Alberts. .molecular.biology.of.the.cell.5th.ed

  1. 1. MolecularBiologyof FifthEdition
  2. 2. FifthEdition MolecularBiologyof BruceAlberts AlexanderJohnson JulianLewis MartinRaff KeithRoberts PeterWalter Withproblemsby JohnWilson TimHunt GarlandScience Taylor& FrancisGroup
  3. 3. Garland Science Vice President:Denise Schanck AssistantEditor: Sigrid Masson Production Editor and Layout: Emma leffcock Senior Publisher: JackieHarbor Illustrator: Nigel Orme Designer:Matthew McClements,Blink Studio,Ltc. Editors:Marjorie Anderson and SherryGranum Copy Editor: Bruce Goatly Indexer: Merrall-RossInternational, Ltd. PermissionsCoordinator: Marv Disoenza Cell Biology Interactiue Artistic and Scientific Direction: PeterWalter Narrated by: Julie Theriot Production Design and Development: Michael Morales @2008, 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Rafi Keith Roberts,and PeterWalter. @ f 983, f 989, 1994by Bruce Alberts, Dennis Bray,Iulian Lewis, Martin Raff, Keith Roberts,and lames D.Watson. Bruce Alberts received his Ph.D. from Harvard university and is professor of Biochemistry and Biophysicsat the university of california, san Francisco.For 12years,he servedas Presidentofthe u.s. NationalAcademy ofSciences (1993-2005). Alexander Johnson received his Ph.D. from Harvard University and is professor of Microbiology and Immunology and Director of the Biochemistry cell Biology,Genetics, and Developmental Biology Graduate Program at the University of california, San Francisco. Iulian Lewis received his D.Phil. from the University of Oxford and is a Principal Scientistat the London ResearchInstitute of CancerResearchUK. Martin Raffreceived his M.D. from McGill University and is at the Medical Research Council Laboratory for Molecular Cell Biology and the Biology Department at University College London. Keith Roberts received his Ph.D. from the University of Cambridge and is Emeritus Fellow at the John Innes Centre, Norwich. peterWalter received his ph.D. from The Rockefeller University in Newyork and is professor and chairman of the Department of Biochemistry and Biophysics at the University of california, san Francisco, and an Investigator of the Howard Hughes Medical Institute. All rights reserved. No part of this book covered by the copyright heron may be reproduced or used in any format in any form or by any means-graphic, electronic, or mechanical, including photocopying, recording, taping, or information storage and retrieval systems-without permission of the publisher. Library of CongressCataloging-in-Publication Data Molecularbiologyof the cell / BruceAlberts... [etal.].--5th ed. p.cm ISBN978-0-8153-4r05-5(hardcover)---ISBN978-0-8f5g-4t06_Z(paperback) L Cytology.2. Molecular biology.I. Alberts, Bruce. QHsB1.2.M642008 571.6--dc22 2007005475CIP Published by Garland science, Taylor & Francis Group, LLC, an informa business, 270 Madison Avenue,NewYork NY f 0016,USA,and 2 park Square,Milton park, Abingdon,OXl4 4RN,UK. Printed in the United Statesof America 15 14 13 12 lt 1 0 I B 7 6 5 4 3 2 |
  4. 4. Preface In many respects,we understandthe structureof the universebetter than the workingsof living cells.Scientistscan calculatethe ageof the Sunand predict when it will ceaseto shine,but we cannotexplainhow it is that a human being may live for eighty yearsbut a mouse for only two. We know the complete genomesequencesof theseandmany other species,but we still cannotpredict how a cell will behaveif we mutate a previouslyunstudiedgene.Starsmay be l0a3times bigger,but cellsaremore complex,more intricately structured,and moreastonishingproductsof thelawsofphysicsandchemistry.Throughhered- ity and natural selection,operatingfrom the beginningsof life on Earthto the presentday-that is,for about20Voof theageof the universe-living cellshave been progressivelyrefining and extending their molecular machinery and recordingthe resultsof their experimentsin the geneticinstructionsthey pass on to their progeny. With eachedition of this book,we marvelat the new information that cell biologistshavegatheredin just a fewyears.But we areevenmore amazedand dauntedatthe sophisticationofthe mechanismsthat weencounter.Thedeeper weprobeinto the cell,themorewe reafizehowmuch remainsto beunderstood. In the daysof our innocence,working on the first edition,we hailedthe identi- fication of asingleprotein-a signalreceptol say-as agreatstepforward'Now we appreciatethat eachprotein isgenerallypart of acomplexwith manyothers, working togetherasa system,regulatingone another'sactivitiesin subtleways, andheldin specificpositionsbybinding to scaffoldproteinsthat givethechem- ical factorya definite spatialstructure.Genomesequencinghasgivenusvirtu- ally completemolecularparts-listsfor many different organisms;geneticsand biochemistryhavetold us a greatdeal about what thoseparts are capableof individually and which onesinteract with which others;but we haveonly the most primitive graspof the dynamicsof thesebiochemicalsystems,with all their interlocking control loops.Therefore,although there are great achieve- mentsto report,cellbiologistsfaceevengreaterchallengesfor the future. In this edition,wehaveincludednewmaterialon manytopics,rangingfrom epigenetics,histonemodifications,smallRNAs,and comparativegenomics,to geneticnoise,cytoskeletaldlmamics,cell-cyclecontrol,apoptosis,stemcells, and novelcancertherapies.As in previouseditions,we havetried aboveall to givereadersa conceptualframeworkfor the massof information that we now haveabout cells.This meansgoingbeyondthe recitationof facts.Thegoalis to learn how to put the facts to use-to reason,to predict, and to control the behaviorof living systems. Tohelp readerson the wayto an activeunderstanding,we havefor the first time incorporatedend-of-chapterproblems,written by Iohn Wilsonand Tim Hunt. Theseemphasizea quantitativeapproachand the art of reasoningfrom experiments.A companionvolume,MolecularBiologyof theCelI,Fifth Edition: TheProblemsBook0SBN978-0-8153-4110-9),by the sameauthors,givescom- pleteanswersto theseproblemsand alsocontainsmorethan 1700additional problemsandsolutions. A further major adjunctto the main book is the attachedMediaDVD-ROM disc.Thisprovideshundredsofmoviesandanimations,includingmanythat are new in this edition, showingcellsand cellularprocessesin action and bringing thetextto life;thediscalsonowincludesall thefiguresandtablesfrom themain
  5. 5. book,pre-loadedintoPowerPoint@presentations.Otherancillariesavailablefor thebookincludeabankof testquestionsandlectureoutlines,availableto qual- ifiedinstructors,anda setof 200full-coloroverheadtransparencies. Perhapsthe biggestchangeis in the physicalstructureof the book. In an effort to make the standardStudentEdition somewhatmore portable,we are providing chapters 2r-25, coveringmulticellular systems,in electronic (pDF) form on the accompanyingdisc,while retainingin theprinted volumechapters l-20, coveringthe core of the usual cell biology curriculum. But we should emphasizethat the final chaptershavebeenrevisedand updatedasthoroughly asthe restof the book andwe sincerelyhopethat theywill beread!A Reference Edition(ISBN97s-0-8153-4r11-6),containingthefull setof chaptersasprinred pages,is alsoavailablefor thosewho preferit. Full detailsof the conventionsadoptedin the book aregivenin the Noteto the Readerthat followsthis Preface.Asexplainedthere,we havetakena drastic approachin confrontingthe differentrulesfor thewriting of genenamesin dif- ferent species:throughout this book, we use the same style, regardlessof species,andoftenin defianceofthe usualspecies-specificconventions. As always,we areindebtedto many people.Full acknowledgmentsfor sci- entifichelparegivenseparately,but wemustheresingleout someexceptionally important contributions:Iulie Theriot is almost entirely responsiblefor chap- ters 16(cytoskeleton)and 24 (Pathogens,Infection,and InnateImmunity), and David Morganlikewisefor chapter 17(cell cycle).wallaceMarshalland Laura Attardi provided substantialhelp with chapters 8 and 20,respectively,as did Maynardolsonfor thegenomicssectionofchapter4,Xiaodongwangfor chap- ter 18,andNicholasHarberdfor theplantsectionof Chapter15. we also owe a huge debt to the staff of Garlandscienceand otherswho helped convert writers' efforts into a polished final product. Deniseschanck directedthe whole enterpriseand shepherdedthe waywardauthorsalongthe roadwith wisdom,skill,and kindness.Nigelorme put the artworkinto its final form andsupervisedthevisualaspectsof thebook,includingthebackcover,with his usual flair. Matthew Mcclements designedthe book and its front cover. EmmaJeffcocklaid out its pageswith extraordinaryspeedand unflappableeffi- ciency,dealingimpeccablywithinnumerablecorrections.MichaelMoralesman- agedthe transformationof a massof animations,video clips,and othermateri- als into a user-friendly DVD-ROM. Eleanor Lawrence and sherry Granum updatedandenlargedtheglossary.JackieHarborandSigridMassonkeptusorga- nized.AdamSendroffkeptusawareofour readersandtheir needsandreactions. MarjorieAnderson,BruceGoatly,andsherryGranumcombedthetextfor obscu- rities,infelicities,and errors.we thank them all, not only for their professional skill and dedicationand for efficiencyfar surpassingour own,but alsofor their unfailinghelpftrlnessandfriendship:theyhavemadeit apleasureto work on the book. Lastly,and with no lessgratitude,we thank our spouses,families,friends andcolleagues.without theirpatient,enduringsupport,wecouldnot havepro- ducedanyof the editionsof thisbook.
  6. 6. Contents Speci.alFeatures DetailedContents Acknowledgments A Noteto theReader PARTI I. 2. 3. PARTII 4. 5. 6. 7. PARTIII B. 9. PARTIV 10. 11. 12. 13. 14. 15. 16. t7. tB. PARTV 19. 20. 2I, 22. 23, 24. 25. Glossary Index TabIes uiii ix xxui xxxi INTRODUCTIONTOTHECELL CellsandGenomes CellChemistryandBiosynthesis Proteins BASICGENETICMECHANISMS DNA,Chromosomes,andGenomes DNA Replication,Repair,and Recombination HowCellsReadthe Genome:FromDNAto Protein Controlof GeneExpression METHODS Manipulating Proteins,DNA,and RNA VisualizingCells INTERNALORGANIZATIONOFTHECELL MembraneStructure MembraneTransportof SmallMoleculesandthe Electrical Propertiesof Membranes IntracellularCompartmentsand ProteinSorting IntracellularVesicularTraffic EnergyConversion:MitochondriaandChloroplasts Mechanismsof CellCommunication TheCytoskeleton The CellCycle Apoptosis CELLSINTHEIRSOCIALCONTEXT Celllunctions, CellAdhesion,and the ExtracellularMatrix Cancer Chapters2I-25 availableon MediaDVD-ROM SexualReproduction:Meiosis,GermCells,andFertilization Developmentof MulticellularOrganisms SpecializedTissues,StemCells,andTissueRenewal Pathogens,Infection, and InnateImmunity TheAdaptiveImmune System The Genetic Code,Amino Acids 195 263 329 41I I 45 t25 50r 579 6t7 651 695 749 Br3 879 965 1053 1115 1131 I205 1269 r305 L4l7 1485 1539 G-1 L1 T-1
  7. 7. SpecialFeatures Table l-l Table l-2 Table2-1 Table2-2 Table 2-3 Table2-4 Panel2-l Panel2-2 Panel 2-3 Panel2-4 Panel 2-5 Panel 2-6 Panel2-7 Panel 2-B Panel2-9 Panel3-l Panel 3-2 Table3-1 Panel 3-3 Table4-l Table 5-3 Table6-l PanelB-l Table 10-l Thble11-l Panel1l-2 Panelll-3 Table l2-l Table l2-2 Table l4-l Panel l4-l Thble r5-5 Panel 16-2 Panel 16-3 Table I7-2 Panel l7-l SomeGenomesThatHaveBeenCompletelySequenced TheNumbersof GeneFamilies,classifiedby Function,ThatArecommon to All ThreeDomainsof the LivingWorld CovalentandNoncovalentChemicalBonds TheTypesof MoleculesThatForma BacterialCell ApproximateChemicalCompositionsof aTypicalBacteriumandaTypical MammalianCell RelationshipBetweenthe StandardFree-EnergyChange,AG, andthe EquilibriumConstant ChemicalBondsandGroupsCommonlyEncounteredin BiologicalMolecules WaterandItsInfluenceon theBehaviorof BiologicalMolecules ThePrincipalTypesofweakNoncovalentBondsthat HoldMacromolecules Together An Outlineof Someof theTypesof SugarsCommonlyFoundin Cells FattyAcidsandOtherLipids A Surveyof the Nucleotides FreeEnergyandBiologicalReactions Detailsof the t0 Stepsof Glycolysis TheCompleteCitricAcidCycle The20AminoAcidsFoundin Proteins FourDifferentWaysof Depictinga SmallProtein,the SH2Domain SomeCommonTypesof Enzymes Someof the MethodsUsedto StudyEnzymes SomeVitalStatisticsfor theHumanGenome ThreeMajorClassesofTransposableElements PrincipalTlpesof RNAsProducedin Cells Reviewof ClassicalGenetics pp. ApproximateLipid Compositionsof DifferentCellMembranes A Comparisonof Ion ConcentrationsInsideandOutsideaTypicalMammalianCell TheDerivationof the NernstEquation SomeClassicalExperimentson the SquidGiantAxon RelativeVolumesOccupiedby theMajorIntracellularCompartmentsin a Liver Cell(Hepatocyre) RelativeAmounts of MembraneTypesin TwoKindsof Eucaryoticcells ProductYieldsfrom the Oxidationof SugarsandFats RedoxPotentials TheRasSuperfamilyof MonomericGTpases The Polymerizationof Actin andTubulin pp. 978-979 AccessoryProteinsthat ControltheAssemblyandpositionof Cvtoskeletal Filaments pp.994-995 Summaryof theMajorCell-CycleRegulatoryproteins p. 1066 The Princinle Stases of M Phasp (Mitnsis nnrl Crrfnlrinpcic in qn Animal /-oll nn rATo rA?a p. 18 p.24 p.53 p.55 p.63 p.77 pp. 106-107 pp. 108-109 pp. pp. pp. pp. pp. pp. pp. pp. pp. r10-111 112-113 I l4-1I5 I 16-1r7 I IB-t 19 r20-I2l I22-t23 tzg-729 132-133 p.159 162-163 p.206 p.318 p.336 554-555 p.624 p.652 p.670 p.679 p.697 p.697 p.824 p.830 p.926 pp.
  8. 8. DetailedContents Chapter 1 Cells and Genomes THEUNIVERSALFEATURESOFCELLSON EARTH AllCellsStoreTheirHereditaryInformationintheSameLinear ChemicalCode(DNA) AllCellsReplicateTheirHereditaryInformationbyTemplated Polymerization AllCellsTranscribePortionsofTheirHereditaryInformationinto theSameIntermediaryForm(RNA) AllCellsUseProteinsasCatalysts AllCellsTranslateRNAintoProteinin theSameWay TheFragmentof GeneticInformationCorrespondingto One ProteinlsOneGene LifeRequiresFreeEnergy AllCellsFunctionasBiochemicalFactoriesDealingwiththe SameBasicMolecularBuildingBlocks AllCellsAreEnclosedina PlasmaMembraneAcrossWhich NutrientsandWasteMaterialsMustPass A LivingCellCanExistwith FewerThan500Genes Summary THEDIVERSITYOFGENOMESANDTHETREEOFLIFE CellsCanBePoweredbyaVarietyof FreeEnergySources SomeCellsFixNitrogenandCarbonDioxideforOthers TheGreatestBiochemicalDiversityExistsAmongProcaryoticCells TheTreeof LifeHasThreePrimaryBranches:Bacteria,Archaea, andEucaryotes SomeGenesEvolveRapidly;OthersAreHighlyConserved MostBacteriaandArchaeaHave1000-6000Genes NewGenesAreGeneratedfromPreexistingGenes GeneDuplicationsGiveRiseto Familiesof RelatedGenesWithin a SingleCell GenesCanBeTransferredBetweenOrganisms,Bothinthe Laboratoryandin Nature SexResultsin HorizontalExchangesof GeneticInformation Withina Species TheFunctionof aGeneCanOftenBeDeducedfromltsSequence MoreThan200GeneFamiliesAreCommonto AllThreePrimary Branchesof theTreeof Life MutationsRevealtheFunctionsof Genes MolecularBiologistsHaveFocuseda SpotlightonE coli Summary GENETICINFORMATIONIN EUCARYOTES EucaryoticCellsMayHaveOriginatedasPredators ModernEucaryoticCellsEvolvedfroma Symbiosis EucaryotesHaveHybridGenomes EucaryoticGenomesAreBig EucaryoticGenomesAreRichin RegulatoryDNA TheGenomeDefinestheProgramof MulticellularDevelopment ManyEucaryotesLiveasSolitaryCells:theProtists AYeastServesasa MinimalModelEucaryote TheExpressionLevelsof AllTheGenesof AnOrganismCanBe MonitoredSimultaneously ToMakeSenseof Cells,WeNeedMathematics,Computers,and QuantitativeInformation ArabidopsisHasBeenChosenOutof 300,000SpeciesAsa Model Plant 1 1 TheWorldof AnimalCellslsRepresentedByaWorm,a Fly, a Mouse,anda Human 36 Studiesin DrosophilaProvidea Keyto VertebrateDevelopment 37 TheVertebrateGenomelsa Productof RepeatedDuplication 38 GeneticRedundancylsa ProblemforGeneticists,Butlt Creates Opportunitiesfor EvolvingOrganisms TheMouseServesasa ModelforMammals HumansReportonTheirOwnPeculiarities WeAreAllDifferentin Detail Summory Problems References Chapter2 CellChemistryand Biosynthesis THECHEMICALCOMPONENTSOFACELL CellsAreMadeFroma FewTypesof Atoms TheOutermostElectronsDetermineHowAtomslnteract CovalentBondsFormbytheSharingof Electrons ThereAreDifferentTypesof CovalentBonds AnAtomOftenBehavesasif lt Hasa FixedRadius WaterlstheMostAbundantSubstanceinCells SomePolarMoleculesAreAcidsandBases FourTypesof NoncovalentAttractionsHelpBringMolecules 5 4 5 o 8 9 1 0 1 1 1 1 1 2 1 3 1 4 t 5 t o 1 7 1 8 1 9 2 1 39 5> 40 41 42 42 44 45 45 45 46 48 50 51 51 52 7 8 58 59 61 oz 63 65 65 66 22 2 2 23 z ) 24 26 Togetherin Cells 53 A CelllsFormedfromCarbonCompounds 54 CellsContainFourMajorFamiliesof SmallOrganicMolecules 55 SugarsProvideanEnergySourceforCellsandAretheSubunits of Polysaccharides 55 FattyAcidsAreComponentsof CellMembranes,asWellasa Sourceof EnergY AminoAcidsAretheSubunitsof Proteins NucleotidesAretheSubunitsof DNAandRNA TheChemistryof CellslsDominatedbyMacromoleculeswith RemarkableProperties NoncovalentBondsSpecifyBoththePreciseShapeof a MacromoleculeanditsBindingto OtherMolecules Summary CATALYSISANDTHEUSEOFENERGYBYCELLS CellMetabolismlsOrganizedbyEnzymes BiologicalOrderlsMadePossiblebytheReleaseof HeatEnergy fromCells PhotosyntheticOrganismsUseSunlightto SynthesizeOrganic Molecules CellsObtainEnergybytheOxidationof OrganicMolecules OxidationandReductionInvolveElectronTransfers EnzymesLowertheBarriersThatBlockChemicalReactions HowEnzymesFindTheirSubstrates:TheEnormousRapidityof MolecularMotions TheFree-EnergyChangefora ReactionDeterminesWhetherlt CanOccur TheConcentrationof ReactantsInfluencestheFree-Energy Changeanda Reaction'sDirection ForSequentialReactions,AG"ValuesAreAdditive ActivatedCarrierMoleculesAreEssentialfor Biosynthesis TheFormationof anActivatedCarrierlsCoupledto an EneroeticallvFavorableReaction 26 26 30 30 3 1 3 1 5Z 33 34 35 JO 66 68 70 71 72 74 75 76 77 78
  9. 9. ATPlstheMostWidelyUsedActivatedCarrierMolecule EnergyStoredin ATPlsOftenHarnessedto JoinTwoMolecules Together NADHandNADPHArelmportantElectronCarriers ThereAreManyOtherActivatedCarrierMoleculesinCells TheSynthesisof BiologicalPolymerslsDrivenbyATpHydrolysis Summary HOWCELLSOBTAINENERGYFROMFOOD Glycolysislsa CentralATP-producingpathway FermentationsProduceATPintheAbsenceof Oxygen GlycolysislllustratesHowEnzymesCoupleOxidationto Energy Storage OrganismsStoreFoodMoleculesin SpecialReservoirs MostAnimalCellsDeriveTheirEnergyfromFattyAcidsBetween Meals SugarsandFatsAreBothDegradedto AcetylCoAin Mitochondria TheCitricAcidCycleGeneratesNADHbyOxidizingAcetylGroups to CO2 ElectronTransportDrivestheSynthesisof theMajorityof theATp inMostCells AminoAcidsandNucleotidesArepartof theNitrogenCycle MetabolismlsOrganizedandRegulated Summary Problems References Chapter3 Proteins THESHAPEANDSTRUCTUREOFPROTEINS TheShapeof a ProteinlsSpecifiedbyltsAminoAcidSequence ProteinsFoldintoaConformationof LowestEnergy ThecrHelixandtheBSheetAreCommonFoldingpatterns ProteinDomainsAreModularUnitsfromwhichLargerproteins AreBuilt Fewof theManyPossiblePolypeptideChainsWillBeUsefur to Cells ProteinsCanBeClassifiedintoManyFamilies SequenceSearchesCanldentifyCloseRelatives SomeProteinDomainsFormpartsof ManyDifferentproteins CertainPairsof DomainsAreFoundTogetherin Manyproteins TheHumanGenomeEncodesaComplexSetof proteins, RevealingMuchThatRemainsUnknown LargerProteinMoleculesOftenContainMoreThanOne PolypeptideChain SomeProteinsFormLongHelicalFilaments ManyProteinMoleculesHaveElongated,FibrousShapes ManyProteinsContaina SurprisinglyLargeAmountof UnstructuredPolypeptideChain CovalentCross-LinkagesOftenStabilizeExtracellularproteins ProteinMoleculesOftenServeasSubunitsfortheAssembry of LargeStructures ManyStructuresinCellsAreCapableof Self-Assembly AssemblyFactorsOftenAidthe Formationof Comolex BiologicalStructures Summary PROTEINFUNCTION AllProteinsBindto OtherMolecules TheSurfaceConformationof a ProteinDeterminesltsChemistrv SequenceComparisonsBetweenproteinFamilyMembers HighlightCrucialLigand-BindingSites ProteinsBindto OtherProteinsThroughSeveralTypesof Interfaces AntibodyBindingSitesAreEspeciallyVersatile TheEquilibriumConstantMeasuresBindingStrength EnzymesArePowerfulandHighlySpecificCatalysts SubstrateBindinglstheFirstStepin EnzymeCatalysis EnzymesSpeedReactionsbySelectivelyStabilizingTransitron States EnzymesCanUseSimultaneousAcidandBaseCatalysis LysozymelllustratesHowanEnzymeWorks TightlyBoundSmallMoleculesAddExtraFunctionsto prorerns MolecularTunnelsChannelSubstratesin Enzymeswith MultipleCatalyticSites MultienzymeComplexesHelpto IncreasetheRateof Cell Metabolism TheCellRegulatestheCatalyticActivitiesof itsEnzymes AllostericEnzymesHaveTwoor MoreBindingSitesThatInteract TwoLigandsWhoseBindingSitesAreCoupledMust ReciprocallyAffectEachOther'sBinding SymmetricProteinAssembliesProduceCooperativeAllosteflc Transitions TheAllostericTransitionin AspartateTranscarbamoylasels Understoodin AtomicDetail 173 ManyChangesin ProteinsAreDrivenbyProtein Phosphorylation A EucaryoticCellContainsa LargeCollectionof ProteinKinases andProteinPhosphatases TheRegulationof CdkandSrcProteinKinasesShowsHowa ProteinCanFunctionasa Microchip ProteinsThatBindandHydrolyzeGTPAreUbiquitousCellular Regulators RegulatoryProteinsControltheActivityof GTP-Bindingproteins byDeterminingWhetherGTPor GDPlsBound LargeProteinMovementsCanBeGeneratedFromSmallOnes MotorProteinsProduceLargeMovementsin Cells Membrane-BoundTransportersHarnessEnergyto Pump MoleculesThroughMembranes ProteinsOftenFormLargeComplexesThatFunctionasProtein Machines ProteinMachineswithInterchangeablePartsMakeEfficientUse of Geneticlnformation TheActivationof ProteinMachinesOftenInvolvesPositioning Themat SpecificSites ManyProteinsAreControlledbyMultisiteCovalentModification A ComplexNetworkof ProteinInteractionsUnderliesCellFunction Summary Problems References Chapter4 DNA,Chromosomes,and Genomes THESTRUCTUREANDFUNCTIONOFDNA A DNAMoleculeConsistsofTwoComplementaryChains of Nucleotides TheStructureof DNAProvidesa Mechanismfor Heredity InEucaryotes,DNAlsEnclosedina CellNucleus Summory CHROMOSOMALDNA AND ITSPACKAGINGINTHE CHROMATINFIBER EucaryoticDNAlsPackagedintoa Setof Chromosomes ChromosomesContainLongStringsof Genes TheNucleotideSequenceoftheHumanGenomeShowsHow OurGenesAreArranged GenomeComparisonsRevealEvolutionarilyConservedDNA )equences 207 ChromosomesExistin DifferentStatesThroughouttheLife ofa Cell 2OB EachDNAMoleculeThatFormsa LinearChromosomeMust Containa Centromere,TwoTelomeres,andReplicationOrigins 2Og DNAMoleculesAreHighlyCondensedin Chromosomes 210 NucleosomesArea BasicUnitof EucaryoticChromosome Structure 211 TheStructureofthe NucleosomeCoreParticleRevealsHow DNAlsPackaged Z'tZ NucleosomesHavea DynamicStructure,andAreFrequentry Subjectedto ChangesCatalyzedbyATp-DependentChromatin- RemodelingComplexes 215 NucleosomesAreUsuallyPackedTogetherintoaCompact 80 8 1 82 83 84 87 88 88 Rq '167 168 169 171 171 172 175 176 177 178 179 179 1 8 1 182 184 184 185 t 6 0 187 190 1 9 1 193 9 1 9 1 95 vo o7 100 1 0 0 1 0 1 103 103 124 125 125 t z J 1 3 0 1 3 1 t J ) I Jt) 137 1 3 9 140 141 142 "t42 143 t 4 ) "146 147 148 149 1 5 1 't52 152 1 5 3 154 1 5 5 tf,o 1 5 6 157 1 5 8 i5 9 195 197 197 199 200 201 202 202 204 205 ChromatinFiber Summary l t o 218 THEREGULATIONOFCHROMATINSTRUCTURE 219 SomeEarlyMysteriesConcerningChromatinStructure 220 160 160 16"1 166
  10. 10. HeterochromatinlsHighlyOrganizedandUnusuallyResistant to GeneExoression TheCoreHistonesAreCovalentlyModifiedat ManyDifferentSites ChromatinAcquiresAdditionalVarietythroughtheSite-Specific lnsertionof a SmallSetof HistoneVariants TheCovalentModificationsandtheHistoneVariantsActin Concertto Producea"HistoneCode"ThatHelpsto DetermineBiologicalFunction AComolexof Code-ReaderandCode-WriterProteinsCanSpread SpecificChromatinModificationsfor LongDistancesAlonga Chromosome BarrierDNASequencesBlocktheSpreadof Reader-WriterComplexes andTherebySeparateNeighboringChromatinDomains TheChromatinin CentromeresRevealsHowHistoneVariants CanCreateSpecialStructures ChromatinStructuresCanBeDirectlyInherited ChromatinStructuresAddUniqueFeaturesto Eucaryotic ChromosomeFunction Summary THEGLOBALSTRUCTUREOFCHROMOSOMES ChromosomesAreFoldedintoLargeLoopsof Chromatin PolyteneChromosomesAreUniquelyUsefulforVisualizing ChromatinStructures ThereAreMultipleFormsof Heterochromatin ChromatinLoopsDecondenseWhentheGenesWithinThemAre Exoressed ChromatinCanMoveto SpecificSitesWithintheNucleusto AlterTheirGeneExoression Networksof MacromoleculesForma Setof DistinctBiochemical EnvironmentsinsidetheNucleus MitoticChromosomesAreFormedfromChromatinin ltsMost CondensedState Summary HOWGENOMESEVOLVE GenomeAlterationsAreCausedbyFailuresof theNorma MechanismsforCopyingandMaintainingDNA TheGenomeSequencesofTwoSpeciesDifferin Proportionto theLengthofTimeThatTheyHaveSeparatelyEvolved PhylogeneticTreesConstructedfroma Comparisonof DNA SequencesTracethe Relationshipsof AllOrganisms A Comoarisonof HumanandMouseChromosomesShows HowtheStructuresof GenomesDiverge TheSizeof aVertebrateGenomeReflectsthe RelativeRatesof DNAAdditionandDNALossina Lineage WeCanReconstructtheSequenceof SomeAncientGenomes MultispeciesSequenceComparisonsldentifylmportantDNA Sequencesof UnknownFunction AcceleratedChangesin PreviouslyConservedSequencesCan HelpDecipherCriticalStepsin HumanEvolution GeneDuplicationProvidesanlmportantSourceof Genetic NoveltyDuringEvolution DuplicatedGenesDiverge TheEvolutionof theGlobinGeneFamilyShowsHowDNA DuplicationsContributeto theEvolutionof Organisms GenesEncodingNewProteinsCanBeCreatedbythe Recombinationof Exons NeutralMutationsOftenSpreadto BecomeFixedin a Population, witha ProbabilitythatDependson PopulationSize A GreatDealCanBeLearnedfromAnalysesoftheVariation AmongHumans Summary Problems References Chapter5 DNAReplication,Repair,and Recombination THEMAINTENANCEOFDNASEQUENCES MutationRatesAreExtremelyLow LowMutationRatesAreNecessaryfor LifeasWeKnowlt Summory DNAREPLICATIONMECHANISMS Base-PairingUnderliesDNAReplicationandDNARepair TheDNAReplicationForklsAsymmetrical TheHighFidelityof DNAReplicationRequiresSeveralProofreading Mechanisms OnlyDNAReplicationin the5'-to-3'DirectionAllowsEfficientError Correction A 5pecialNucleotide-PolymerizingEnzymeSynthesizesShortRNA PrimerMoleculesontheLaggingStrand SpecialProteinsHelpto OpenUptheDNADoubleHelixin Front oftheReplicationFork A SlidingRingHoldsa MovingDNAPolymeraseontotheDNA TheProteinsata ReplicationForkCooperateto Forma Replication Machine A Strand-DirectedMismatchRepairSystemRemovesReplication ErrorsThatEscapefromtheReplicationMachine DNATopoisomerasesPreventDNATanglingDuringReplication DNAReplicationlsFundamentallySimilarin Eucaryotesand Bacteria Summary THEINITIATIONANDCOMPLETIONOFDNAREPLICATION INCHROMOSOMES DNASynthesisBeginsat ReplicationOrigins BacterialChromosomesTypicallyHavea SingleOriginof DNA Reolication EucaryoticChromosomesContainMultipleOriginsof Replication InEucaryotesDNAReplicationTakesPlaceDuringOnlyOnePart of thecellcycle DifferentRegionsontheSameChromosomeReplicateat Distinct Timesin SPhase HighlyCondensedChromatinReplicatesLate,WhileGenesin LessCondensedChromatinTendto ReplicateEarly Well-DefinedDNASequencesServeasReplicationOriginsin a SimpleEucaryote,theBuddingYeast A LargeMultisubunitComplexBindsto EucaryoticOriginsof Reolication TheMammalianDNASequencesThatSpecifythe Initiationof ReplicationHaveBeenDifficultto ldentify NewNucleosomesAreAssembledBehindtheReplicationFork TheMechanismsof EucaryoticChromosomeDuplicationEnsure ThatPatternsof HistoneModificationCanBeInheriteo TelomeraseReplicatesthe Endsof Chromosomes TelomereLengthlsRegulatedbyCellsandOrganisms Summary DNAREPAIR WithoutDNARepair,SpontaneousDNADamageWouldRapidly ChangeDNASequences TheDNADoubleHelixlsReadilyRepaired DNADamageCanBeRemovedbyMoreThanOnePathway CouplingDNARepairto TranscriptionEnsuresThattheCell'sMost lmportantDNAlsEfficientlyRepaired TheChemistryof theDNABasesFacilitatesDamageDetection SpecialDNAPolymerasesAreUsedin Emergenciesto RepairDNA Double-StrandBreaksAreEfficientlyRepaired DNADamageDelaysProgressionof theCellCycle Summary HOMOLOGOUSRECOMBINATION HomologousRecombinationHasManyUsesintheCell HomologousRecombinationHasCommonFeaturesin AllCells DNABase-PairingGuidesHomologousRecombination TheRecAProteinanditsHomologsEnablea DNA5ingleStrand to Pairwitha HomologousRegionof DNADoubleHelix BranchMigrationCanEitherEnlargeHetroduplexRegionsor ReleaseNewlySynthesizedDNAasa SingleStrand HomologousRecombinationCanFlawlesslyRepairDouble- StrandedBreaksin DNA CellsCarefullyRegulatethe Useof HomologousRecombination in DNARepair HollidayJunctionsAreOftenFormedDuringHomologous RecombinationEvents 220 266 too 266 27"1 272 273 273 275 276 z I d 280 281 281 281 26l 282 zt6 230 231 233 233 234 236 256 239 239 241 243 245 245 246 247 248 249 251 251 2s2 284 285 285 260 287 288 289 290 292 zY5 294 253 z > 5 254 295 296 296 297 299 300 302 302 303 304 304 257 304 305 305 307 308 308 3 1 0 3 1 1 257 258 260 lou 262 263 263 205 265 265
  11. 11. MeioticRecombinationBeginswitha programmedDouble- StrandBreak HomologousRecombinationOftenResultsin GeneConversron MismatchProofreadingPreventspromiscuousRecombinatron BetweenTwoPoorlyMatchedDNASequences Summary TRANSPOSITIONAND CONSERVATIVESITE-SPECIFIC RECOMBINATION FROMRNATOPROTEIN 366 An mRNASequencelsDecodedin SetsofThreeNucleotide 367 IRNAMoleculesMatchAminoAcidsto Codonsin mRNA 368 tRNAsAreCovalentlyModifiedBeforeTheyExitfromthe Nucleus 369 SpecificEnzymesCoupleEachAminoAcidto ltsAppropriateIRNA Molecule EditingbyRNASynthetasesEnsuresAccuracy AminoAcidsAreAddedto theC-terminalEndof a Growing PolypeptideChain TheRNAMessagelsDecodedin Ribosomes ElongationFactorsDriveTranslationForwardandlmprovelts Accuracy 377 TheRibosomelsa Ribozyme 379 NucleotideSequencesin mRNASignalWhereto StartProtein Synthesis 379 StopCodonsMarktheEndofTranslation 381 ProteinsAreMadeon Polyribosomes 391 ThereAreMinorVariationsin theStandardGeneticCode 392 Inhibitorsof ProcaryoticProteinSynthesisAreUsefulas Antibiotics AccuracyinTranslationRequiresthe Expenditureof FreeEnergy QualityControlMechanismsActto PreventTranslationof Damaqed mRNAs SomeProteinsBeginto FoldWhileStillBeingSynthesized MolecularChaperonesHelpGuidethe Foldingof Mostproteins ExposedHydrophobicRegionsProvideCritical5ignalsfor protein QualityControl TheProteasomelsa CompartmentalizedProteasewith SequesteredActiveSites An ElaborateUbiquitin-ConjugatingSystemMarksProteinsfor Destruction ManyProteinsAreControlledbyRegulatedDestruction AbnormallyFoldedProteinsCanAggregateto CauseDestructive HumanDiseases 396 ThereAreManyStepsFromDNAto Protein 3gg Summory 3gg THERNAWORLDANDTHEORIGINSOFLIFE 4OO LifeRequiresStoredInformation 401 PolynucleotidesCanBothStoreInformationandCatalyze 312 314 3 1 5 5 t o 3 1 6 329 331 345 346 347 349 349 351 352 370 371 5 t 5 373 ThroughTransposition,MobileGeneticElementsCanInsertlnto AnyDNASequence y7 DNA-OnlyTransposonsMovebyBothCut-and-pasteandReplicative Mechanisms 317 SomeVirusesUseaTranspositionMechanismto MoveThemselves intoHostCellChromosomes 319 Retroviral-likeRetrotransposonsResembleRetroviruses,but Lacka ProteinCoat 320 A LargeFractionof the HumanGenomelsComoosedof NonretroviralRetrotransposons 32,l DifferentTransposableElementspredominatein Different Organisms 322 GenomeSequencesRevealtheApproximateTimesthat TransposableElementsHaveMoved 323 ConservativeSite-SpecificRecombinationCanReversibly RearrangeDNA 323 ConservativeSite-SpecificRecombinationWasDiscoveredin Bacteriophage), n+ ConservativeSite-SpecificRecombinationCanBeUsedto Turn GenesOnorOff Summary Problems References Chapter6 HowCellsReadthe Genome:From DNAto Protein FROMDNATORNA Portionsof DNASequenceAreTranscribedintoRNA TranscriptionProducesRNAComplementaryto OneStrandof DNA CellsProduceSeveralTypesof RNA SignalsEncodedin DNATellRNApolymeraseWhereto Startand Stop TranscriptionStartandStopSignalsAreHeterogeneousin NucleotideSequence TranscriptionInitiationin EucaryotesRequiresManyproteins RNAPolymerasell RequiresGeneralTranscriptionFactors Polymerasell AlsoRequiresActivator,Mediator,andChromatin- ModifyingProteins TranscriptionElongationProducesSuperhelicalTensionin DNA TranscriptionElongationin EucaryoteslsTightlyCoupledto RNA Processing RNACappinglstheFirstModificationof Eucaryoticpre-mRNAs RNASplicingRemovesIntronSequencesfromNewlyTranscribed Pre-mRNAs NucleotideSequencesSignalWhereSplicingOccurs RNASplicinglsPerformedbytheSpliceosome TheSpliceosomeUsesATPHydrolysisto producea ComplexSeries of RNA-RNARearrangements OtherPropertiesof Pre-mRNAandltsSynthesisHelpto Explain theChoiceof ProperSpliceSites A Second5etof snRNPsSplicea SmallFractionof IntronSequences inAnimalsandPlants RNASplicingShowsRemarkableplasticity Spliceosome-CatalyzedRNASplicingprobablyEvolvedfrom Self-SplicingMechanisms RNA-ProcessingEnzymesGeneratethe3,Endof EucaryoticmRNAs MatureEucaryoticmRNAsAreSelectivelyExportedfromtne Nucleus ManyNoncodingRNAsAreAlsoSynthesizedandprocessedinthe Nucleus TheNucleoluslsa Ribosome-producingFactory TheNucleusContainsaVarietyof SubnuclearStructures Summarv ChemicalReactions A Pre-RNAWorldMayPredatetheRNAWorld Single-StrandedRNAMoleculesCanFoldintoHighlyElaborate Structures Self-ReplicatingMoleculesUndergoNaturalSelection HowDidProteinSynthesisEvolve? AllPresent-DayCellsUseDNAasTheirHereditaryMaterial Summary Problems References Chapter7 Controlof GeneExpression PathwayfromDNAto RNAto Protein Summary AN OVERVIEWOFGENECONTROL 4'11 TheDifferentCellTypesof a MulticellularOrganismContainthe SameDNA 411 DifferentCellTypesSynthesizeDifferentSetsof proteins 412 ExternalSignalsCanCausea Cellto ChangetheExpressionof ItsGenes 413 GeneExpressionCanBeRegulatedat Manyofthe Stepsinthe 324 326 327 328 383 385 385 387 388 390 391 393 39s 552 5 5 5 335 336 338 339 340 342 343 401 402 403 404 407 408 408 409 410 411 353 J 5 5 355 5 t / 358 360 502 50J 366 415 415 DNA-BINDINGMOTIFSINGENEREGULATORYPROTEINS 416 GeneRegulatoryProteinsWereDiscoveredUsingBacterial Genetics TheOutsideof the DNAHelixCanBeReadbyproteins ShortDNASequencesAreFundamentalComponentsof Genetic Switches GeneRegulatoryProteinsContainStructuralMotifsThatCan ReadDNASeouences TheHelix-Turn-HelixMotiflsOneof theSimplestandMost CommonDNA-B|ndingMotifs 416 416 418 418 419
  12. 12. HomeodomainProteinsConstitutea SpecialClassof Helix-Turn- HelixProteins ThereAreSeveralTypesof DNA-B|ndingZincFingerMotifs p sheetsCanAlsoRecognizeDNA SomeProteinsUseLoopsThatEntertheMajorandMinorGroove to RecognizeDNA TheLeucineZipperMotifMediatesBothDNABindingandProtein Dimerization HeterodimerizationExpandstheRepertoireof DNASequencesThat GeneRegulatoryProteinsCanRecognize TheHelix-Looo-HelixMotifAlsoMediatesDimerizationandDNA Binding It lsNotYetPossibleto PredicttheDNASequencesRecognized byAllGeneRegulatoryProteins A Gel-MobilityShiftAssayReadilyDetectsSequence-Specific DNA-BindingProteins DNAAffinityChromatographyFacilitatesthePurificationof Sequence-SpecificDNA-BindingProteins TheDNASequenceRecognizedbya GeneRegulatoryProtein CanBeDeterminedExperimentally PhylogeneticFootprintingldentifiesDNARegulatorySequences ThroughComparativeGenomics ChromatinlmmunoprecipitationldentifiesManyof theSites ThatGeneRegulatoryProteinsOccupyin LivingCells Summary HOWGENETICSWITCHESWORK TheTryptophanRepressorlsa SimpleSwitchThatTurnsGenes OnandOffin Bacteria TranscriptionalActivatorsTurnGenesOn ATranscriptionalActivatorandaTranscriptionalRepressor ControltheLocOperon DNALoopingOccursDuringBacterialGeneRegulation BacteriaUseInterchangeableRNAPolymeraseSubunitsto Help RegulateGeneTranscription ComplexSwitchesHaveEvolvedto ControlGeneTranscription in Eucaryotes A EucaryoticGeneControlRegionConsistsof a PromoterPlus RegulatoryDNASequences EucaryoticGeneActivatorProteinsPromotetheAssemblyof RNA PolymeraseandtheGeneralTranscriptionFactorsatthe StartpointofTranscription EucaryoticGeneActivatorProteinsAlsoModifyLocalChromatin Structure GeneActivatorProteinsWorkSynergistically EucaryoticGeneRepressorProteinsCanInhibitTranscription inVariousWays EucaryoticGeneRegulatoryProteinsOftenBindDNA Cooperatively ComplexGeneticSwitchesThatRegulateDrosophilaDevelopment AreBuiltUpfromSmallerModules fhe DrosophilaEveGenelsRegulatedbyCombinatorialControls ComplexMammalianGeneControlRegionsAreAlsoConstructed fromSimpleRegulatoryModules InsulatorsAreDNASequencesThatPreventEucaryoticGene RegulatoryProteinsfromInfluencingDistantGenes GeneSwitchesRapidlyEvolve Summary THEMOLECULARGENETICMECHANISMSTHATCREATE SPECIALIZEDCELLTYPES DNARearrangementsMediatePhaseVariationin Bacteria A Setof GeneRegulatoryProteinsDeterminesCellTypein a BuddingYeast TwoProteinsThatRepressEachOther! SynthesisDeterminethe HeritableStateof BacteriophageLambda SimpleGeneRegulatoryCircuitsCanBeUsedto MakeMemory Devices TranscriptionalCircuitsAllowtheCellto CanyOutLogicOperations SyntheticBiologyCreatesNewDevicesfromExistingBiologicalParts CircadianClocksAreBasedon FeedbackLoopsin GeneRegulation A SingleGeneRegulatoryProteinCanCoordinatethe Expression of a Setof Genes Expressionof a CriticalGeneRegulatoryProteinCanTrigger the Expressionof aWholeBatteryof DownstreamGenes CombinatorialGeneControlCreatesManyDifferentCellTypes in Eucaryotes A SingleGeneRegulatoryProteinCanTriggerthe Formation of anEntireOrgan ThePatternof DNAMethylationCanBeInheritedWhen VertebrateCellsDivide GenomiclmprintinglsBasedon DNAMethylation CG-RichlslandsAreAssociatedwith ManyGenesin Mammals EpigeneticMechanismsEnsureThatStablePatternsof GeneExpressionCanBeTransmittedto DaughterCells Chromosome-WideAlterationsin ChromatinStructure CanBeInherited TheControlof GeneExpressionisIntrinsicallyNoisy Summary POST-TRANSCRIPTIONALCONTROLS TranscriptionAttenuationCausesthe PrematureTermination of SomeRNAMolecules RiboswitchesMightRepresentAncientFormsof GeneControl AlternativeRNASplicingCanProduceDifferentFormsof a ProteinfromtheSameGene TheDefinitionof a GeneHasHadto BeModifiedSincethe Discoveryof AlternativeRNASplicing SexDeterminationinDrosophiloDependsona Regulated Seriesof RNASplicingEvents A ChangeintheSiteof RNATranscriptCleavageandPoly-A AdditionCanChangetheC-terminusof a Protein RNAEditingCanChangetheMeaningoftheRNAMessage RNATransportfromthe NucleusCanBeRegulated SomemRNAsAreLocalizedto SpecificRegionsof theCytoplasm The5'and3'UntranslatedRegionsof mRNAsControl TheirTranslation ThePhosphorylationof anlnitiationFactorRegulatesProtein SynthesisGlobally lnitiationatAUGCodonsUpstreamof theTranslationStart CanRegulateEucaryoticTranslationInitiation InternalRibosomeEntrySitesProvideOpportunitiesfor TranslationControl Changesin mRNAStabilityCanRegulateGeneExpression CytoplasmicPoly-AAdditionCanRegulateTranslation SmallNoncodingRNATranscriptsRegulateManyAnimaland PlantGenes RNAInterferencelsa CellDefenseMechanism RNAInterferenceCanDirectHeterochromatinFormation RNAlnterferenceHasBecomea PowerfulExperimentalTool Summory Problems References Chapter8 ManipulatingProteins,DNA,and RNA ISOLATINGCELLSANDGROWINGTHEMINCULTURE CellsCanBelsolatedfromIntactTissues CellsCanBeGrownin Culture EucaryoticCellLinesAreaWidelyUsedSourceof HomogeneousCells EmbryonicStemCellsCouldRevolutionizeMedicine SomaticCellNuclearTransplantationMayProvideaWayto GeneratePersonalizedStemCells HybridomaCellLinesAreFactoriesThatProduceMonoclonal Antibodies Summary PURIFYINGPROTEINS CellsCanBeSeparatedintoTheirComponentFractions 510 CellExtractsProvideAccessibleSystemsto StudyCellFunctions 511 ProteinsCanBeSeparatedbyChromatography 512 AffinityChromatographyExploitsSpecificBindingSiteson Proteins 513 Genetically-EngineeredTagsProvideanEasyWayto Purify Proteins 514 420 421 422 423 423 424 425 426 427 428 429 431 464 465 467 468 470 471 473 476 477 477 431 432 432 433 435 435 437 438 439 440 477 478 479 480 481 482 483 485 486 488 488 489 491 492 493 493 495 496 497 497 497 499 50r 501 502 s02 50s 505 s07 508 s 1 0 5 1 0 441 442 444 445 450 +)z 453 453 454 454 455 458 459 460 460 445 447 448
  13. 13. PurifiedCell-FreeSystemsAreRequiredforthepreciseDissectionof MolecularFunctions Summory ANALYZINGPROTEINS ProteinsCanBeSeparatedbySDSpolyacrylamide-Gel Electrophoresis SpecificProteinsCanBeDetectedbyBlottingwithAntibodies MassSpectrometryProvidesa HighlySensitiveMethod for ldentifyingUnknownproteins Two-DimensionalSeparationMethodsareEspeciallypowerful HydrodynamicMeasurementsRevealtheSizeandShapeof a Proteincomolex Setsof InteractingProteinsCanBeldentifiedbyBiochemical Methods Protein-ProteinInteractionsCanAlsoBeldentifiedbya Two-HybridTechniqueinyeast CombiningDataDerivedfromDifferentTechniquesproduces ReliableProtein-lnteractionMaDs OpticalMethodsCanMonitorProteinInteractionsin RealTime SomeTechniquesCanMonitorSingleMolecules ProteinFunctionCanBeSelectivelyDisruptedwithSmall Molecules ProteinStructureCanBeDeterminedUsingX-RayDiffraction NMRCanBeUsedto DetermineproteinStructurein Solutron ProteinSequenceandStructureprovideCluesAboutprotein Function Summory ANALYZINGAND MANIPULATINGDNA RestrictionNucleasesCutLargeDNAMoleculesintoFragments GelElectrophoresisSeparatesDNAMoleculesof DifferentSizes PurifiedDNAMoleculesCanBeSpecificallyLabeledwith RadioisotopesorChemicalMarkersin yitro NucleicAcidHybridizationReactionsprovidea SensitiveWayof DetectingSpecificNucleotideSequences NorthernandSouthernBlottingFacilitateHybridizationwith ElectrophoreticallySeparatedNucleicAcidMolecules GenesCanBeClonedUsingDNALibraries TwoTypesof DNALibrariesServeDifferentpurooses cDNAClonesContainUninterruptedCodingSequences GenesCanBeSelectivelyAmplifiedbypCR CellsCanBeUsedAsFactoriesto produceSoecificproteins ProteinsandNucleicAcidsCanBeSynthesizedDirectlyby ChemicalReactions DNACanBeRapidlySequenced NucleotideSequencesAreUsedto predicttheAminoAcio Sequencesof Proteins TheGenomesof ManyOrganismsHaveBeenFullySequenceo Summary STUDYINGGENEEXPRESSIONAND FUNCTION ClassicalGeneticsBeginsbyDisruptingaCellprocessbyRanoom Mutagenesis GeneticScreensldentifyMutantswith SpecificAbnormalirres MutationsCanCauseLossor Gainof proteinFunction ComplementationTestsRevealWhetherTwoMutationsAre intheSameGeneor DifferentGenes GenesCanBeOrderedin Pathwaysby EpistasisAnalysis GenesldentifiedbyMutationsCanBeCloned HumanGeneticsPresents5pecialproblemsandSpecial Opportunities HumanGenesAreInheritedin HaplotypeBlocks,WhichCan Aidin theSearchforMutationsThatCauseDisease ComplexTraitsAreInfluencedbyMultipleGenes ReverseGeneticsBeginswitha KnownGeneandDetermines WhichCellProcessesRequireltsFunction GenesCanBeRe-Engineeredin SeveralWays EngineeredGenesCanBeInsertedintotheGermLineof ManyOrganisms AnimalsCanBeGeneticallyAltered TransgenicPlantsArelmportantfor BothCellBiologyand Agriculture LargeCollectionsofTaggedKnockoutsProvideaToolfor ExaminingtheFunctionof EveryGeneinanOrganism RNAInterferencelsa SimpleandRapidWayto TestGeneFunction ReporterGenesand/nSituHybridizationRevealWhenano WhereaGenelsExpressed Expressionof IndividualGenesCanBeMeasuredUsino QuantitativeRT-PCR Lipidsin CellMembranes PhospholioidsSoontaneouslvFormBilavers MicroarraysMonitorthe ExpressionofThousandsof Genesat Once 574 5ingle-CellGeneExpressionAnalysisRevealsBiological"Noise" 575 Summary 576 Problems 576 References 579 Chapter 9 Visualizing Cells LOOKINGATCELLSINTHELIGHTMICROSCOPE TheLightMicroscopeCanResolveDetails0.2pm Apart LivingCellsAreSeenClearlyin a Phase-Contrastora Differential- Interference-ContrastMicroscooe lmagesCanBeEnhancedandAnalyzedbyDigitalTechniques IntactTissuesAreUsuallyFixedandSectionedbeforeMicroscopy SpecificMoleculesCanBeLocatedinCellsbyFluorescence Microscopy AntibodiesCanBeUsedto DetectSpecificMolecules lmagingof ComplexThree-DimensionalObjectslsPossible withtheOpticalMicroscope TheConfocalMicroscopeProducesOpticalSectionsbyExcluding 579 579 s80 583 583 585 586 588 589 Out-of-FocusLight 590 FluorescentProteinsCanBeUsedtoTagIndividualproteinsin LivingCellsandOrganisms 592 ProteinDynamicsCanBeFollowedin LivingCells 593 Light-EmittingIndicatorsCanMeasureRapidlyChanging IntracellularlonConcentrations 596 SeveralStrategiesAreAvailablebyWhichMembrane-lmpermeant SubstancesCanBeIntroducedintoCells 597 LightCanBeUsedto ManipulateMicroscopicObjectsAsWell Asto lmageThem 598 SingleMoleculesCanBeVisualizedbyUsingTotalInternal ReflectionFluorescenceMicroscopy 5gg IndividualMoleculesCanBeTouchedandMovedUsingAtomic ForceMicroscopy 600 MoleculesCanBeLabeledwithRadioisotopes 600 RadioisotopesAreUsedtoTraceMoleculesinCellsandOrganisms602 Summary 603 LOOKINGATCELLSANDMOLECULESINTHEELECTRON MtcRoScoPE 604 TheElectronMicroscopeResolvesthe FineStructureofthe Cell 604 BiologicalSpecimensRequireSpecialPreparationfortheElectron Microscope 605 SpecificMacromoleculesCanBeLocalizedbylmmunogoldElectron Microscopy 606 lmagesof SurfacesCanBeObtainedbyScanningElectron Microscopy 607 MetalShadowingAllowsSurfaceFeaturesto BeExaminedat HighResolutionbyTransmissionElectronMicroscopy 60g NegativeStainingandCryoelectronMicroscopyBothAllow Macromoleculesto BeViewedat HighResolution 6l O MultiplelmagesCanBeCombinedto IncreaseResolution 610 DifferentViewsof a SingleObjectCanBeCombinedto Givea Three-DimensionalReconstruction Summary Problems References Chapter10MembraneStructure 612 o t 2 614 o t ) 6",7 THELIPIDBILAYER 617 Phosphoglycerides,Sphingolipids,andSterolsAretheMajor ) t o ) t o 517 517 5 1 8 5 1 9 5 2 1 522 523 523 524 524 526 J 2 / i l l 529 530 ) J l 532 s32 534 s35 ) J ) s38 540 541 544 544 546 569 571 572 573 548 548 550 5 5 1 ))z 553 553 556 558 558 s59 s63 564 s60 561 s63 565 foo )oaJ 6 1 8 A)6
  14. 14. TheLipidBilayerlsaTwo-DimensionalFluid TheFluidityof a LipidBilayerDependson ltsComposition DespiteTheirFluidity,LipidBilayersCanFormDomainsof DifferentCompositions LipidDropletsAreSurroundedbya PhospholipidMonolayer TheAsymmetryof theLipidBilayerlsFunctionallylmportant GlycolipidsAreFoundontheSurfaceof AllPlasmaMembranes Summary MEMBRANEPROTEINS MembraneProteinsCanBeAssociatedwiththe LipidBilayerin VariousWays LipidAnchorsControltheMembraneLocalizationof Some SignalingProteins InMostTransmembraneProteinsthePolypeptideChainCrosses theLipidBilayerin ano-HelicalConformation TransmembranecrHelicesOftenlnteractwithOneAnother Somep BarrelsFormLargeTransmembraneChannels ManyMembraneProteinsAreGlycosylated MembraneProteinsCanBeSolubilizedandPurifiedin Detergents Bacteriorhodopsinlsa Light-DrivenProtonPumpThatTraverses the LipidBilayerasSevens Helices MembraneProteinsOftenFunctionasLargeComplexes ManyMembraneProteinsDiffuseinthePlaneof theMembrane CellsCanConfineProteinsandLipidsto SpecificDomainsWithin a Membrane TheCorticalCytoskeletonGivesMembranesMechanicalStrength andRestrictMembraneProteinDiffusion Summary Problems References Patch-ClampRecordingIndicatesThatIndividualGatedChannels Openin anAll-or-NothingFashion 680 Voltage-GatedCationChannelsAreEvolutionarilyandStructurally Related 682 TransmittercatedlonChannelsConvertChemicalSignalsinto ElectricalOnesatChemicalSynapses 682 ChemicalSynapsesCanBeExcitatoryor Inhibitory 684 TheAcetylcholineReceptorsatthe NeuromuscularJunctionAre Transmitter-GatedCationChannels 684 TransmitterGatedlonChannelsAreMajorTargetsfor Psychoactive Drugs 686 NeuromuscularTransmissionInvolvestheSequentialActivation of FiveDifferentSetsof lonChannels SingleNeuronsAreComplexComputationDevices NeuronalComputationRequiresa Combinationof at Least ThreeKindsof K+Channels Long-TermPotentiation(LTP)intheMammalianHippocampus DependsonCa2+EntryThroughNMDA-ReceptorChannels Summary Problems References Chapter12IntracellularCompartmentsand ProteinSorting 695 THECOMPARTMENTALIZATIONOFCELLS 695 AllEucaryoticCellsHavetheSameBasicSetofMembrane- EnclosedOrganelles 695 EvolutionaryOriginsExplaintheTopologicalRelationshipsof Organelles ProteinsCanMoveBetweenCompartmentsin DifferentWays SignalSequencesDirectProteinsto theCorrectCellAddress MostOrganellesCannotBeConstructedDeNovo:TheyRequire Informationin theOrganelleltself Summary THETRANSPORTOF MOLECULESBETWEENTHENUCLEUS ANDTHECYTOSOL NuclearPoreComplexesPerforatethe NuclearEnvelope NuclearLocalizationSignalsDirectNuclearProteinsto theNucleus NuclearlmportReceptorsBindto BothNuclearLocalization SignalsandNPCProteins NuclearExportWorksLikeNuclearlmport,Butin Reverse TheRanGTPaselmposesDirectionalityonTransportThrough NPCs TransportThroughNPCsCanBeRegulatedbyControlling Accessto theTransPortMachinerY DuringMitosisthe NuclearEnvelopeDisassembles Summary THETRANsPORTOF PROTEINSINTOMITOCHONDRIA AND CHLOROPLASTS 713 TranslocationintoMitochondriaDependson SignalSequences andProteinTranslocators 7'13 MitochondrialPrecursorProteinsArelmportedasUnfolded PolypeptideChains 715 ATPHydrolysisanda MembranePotentialDriveProteinlmport IntotheMatrixSpace 716 BacteriaandMitochondriaUseSimilarMechanismsto lnsert PorinsintotheirOuterMembran2 717 TransDortIntothe InnerMitochondrialMembraneand IntermembraneSpaceOccursViaSeveralRoutes 717 TwoSignalSequencesDirectProteinsto theThylakoid o l l 622 624 ot> 626 628 629 629 629 630 631 632 634 o5f 636 640 642 642 645 646 648 648 650 6s3 654 654 656 o)t 658 oou 661 663 667 687 688 689 691 692 693 694 697 699 701 702 704 Chapter11MembraneTransportof SmallMolecules and the ElectricalPropertiesof Membranes 651 PRINCIPLESOFMEMBRANETRANSPORT 651 Protein-FreeLipidBilayersAreHighlylmpermeableto lons 652 ThereAreTwoMainClassesof MembraneTransportProteins: TransportersandChannels 652 ActiveTransportlsMediatedbyTransportersCoupledto an EnergySource Summary TRANSPORTERSAND ACTIVEMEMBRANETRANSPORT ActiveTransportCanBeDrivenbylonGradients Transportersin thePlasmaMembraneRegulateCytosolicpH AnAsymmetricDistributionofTransportersin EpithelialCells UnderliestheTranscellularTransportof Solutes ThereAreThreeClassesof ATP-DrivenPumps TheCa2+PumplstheBest-UnderstoodP-typeATPase ThePlasmaMembraneP-typeNa+-K+PumpEstablishesthe Na+GradientAcrossthePlasmaMembrane ABCTransportersConstitutetheLargestFamilyof Membrane TransoortProteins Summary IONCHANNELSANDTHEELECTRICALPROPERTIESOF MEMBRANES 667 lonChannelsArelon-SelectiveandFluctuateBetweenOpenand closedStates 667 TheMembranePotentialin AnimalCellsDependsMainlyon K+Leak ChannelsandtheK+GradientAcrossthePlasmaMembrane 669 TheRestingPotentialDecaysOnlySlowlyWhenthe Na+-K+Pump lsStopped 669 TheThree-DimensionalStructureof a BacterialK+ChannelShows HowanlonChannelCanWork AquaporinsArePermeableto WaterButlmpermeableto lons TheFunctionofa NeuronDependson ltsElongatedStructure Voltage-GatedCationChannelsGenerateActionPotentialsin ElectricallyExcitableCells MyelinationIncreasestheSpeedandEfficiencyof ActionPotential Propagationin NerveCells MembraneinChloroplasts Summary PEROXISOMES PeroxisomesUseMolecularOxygenandHydrogenPeroxideto PerformOxidativeReactions A ShortSignalSequenceDirectsthe lmportof Proteinsinto Peroxisomes Summary 704 705 705 671 673 675 676 o / 6 707 708 708 709 7't0 712 719 720 721 721 722 t 2 5
  15. 15. THEENDOPLASMICRETICULUM 723 TheERlsStructurallyandFunctionallyDiverse 724 SignalSequencesWereFirstDiscoveredin proteinslmoorteo intotheRoughER 726 A Signal-RecognitionParticle(SRp)DirectsERSignalSequences to a SpecificReceptorintheRoughERMembrane 727 ThePolypeptideChainPassesThroughanAqueousporeinthe Translocator 730 TranslocationAcrossthe ERMembraneDoesNotAlwaysRequire OngoingPolypeptideChainElongation 731 InSingle-PassTransmembraneProteins,a SingleInternalERSignal SequenceRemainsintheLipidBilayerasa Membrane-spanning o Helix 732 Combinationsof Start-TransferandStop-TransferSignalsDetermine theTopologyof MultipassTransmembraneproteins 734 TranslocatedPolypeptideChainsFoldandAssemblein theLumen oftheRoughER n6 MostProteinsSynthesizedin theRoughERAreGlycosylatedby theAdditionofa CommonN-LinkedOligosaccharide 736 OligosaccharidesAreUsedasTagsto MarktheStateof protein Folding 738 lmproperlyFoldedProteinsAreExportedfromthe ERand Degradedin theCytosol 739 MisfoldedProteinsintheERActivateanUnfoldedprotein TRANSPORTFROMTHEIRANSGOLGINETWORK TO LYSOSOMES 779 LysosomesArethe PrincipalSitesof IntracellularDigestion 779 LysosomesAreHeterogeneous 780 PlantandFungalVacuolesAreRemarkablyVersatileLysosomes 781 MultiplePathwaysDeliverMaterialsto Lysosomes 792 A Mannose6-PhosphateReceptorRecognizesLysosomalProteins in thelronsGolgiNetwork TheM6PReceptorShuttlesBetweenSpecificMembranes A SignalPatchinthe HydrolasePolypeptideChainProvides theCuefor M6PAddition Defectsin theGlcNAcPhosphotransferaseCausea Lysosomal StorageDiseasein Humans SomeLysosomesUndergoExocytosis Summary TRANSPORTINTOTHECELLFROMTHEPLASMA MEMBRANE:ENDOCYTOSIS SpecializedPhagocyticCellsCanIngestLargeParticles PinocyticVesiclesFormfromCoatedPitsinthePlasmaMemorane NotAllPinocyticVesiclesAreClathrin-Coated CellsUseReceptor-MediatedEndocytosisto lmportSelected ExtracellularMacromolecules EndocytosedMaterialsThatAreNotRetrievedfromEndosomes EndUpin Lysosomes SpecificProteinsAreRetrievedfromEarlyEndosomesand Returnedto thePlasmaMembrane MultivesicularBodiesFormonthe Pathwayto LateEndosomes TranscytosisTransfersMacromoleculesAcrossEpithelial CellSheets EpithelialCellsHaveTwoDistinctEarlyEndosomalCompartments buta CommonLateEndosomalComoartment Summory TRANSPORTFROMTHEIRANSGOLGINETWORK TOTHECELLEXTERIOR:EXOCYTOSIS ManyProteinsandLipidsSeemto BeCarriedAutomaticallv fromtheGolgiApparatusto theCellSurface SecretoryVesiclesBudfromthefuonsGolgiNetwork ProteinsAreOftenProteolyticallyProcessedDuringthe Formationof SecretoryVesicles SecretoryVesiclesWaitNearthePlasmaMembraneUntil Signaledto ReleaseTheirContents RegulatedExocytosisCanBea LocalizedResponseofthe PlasmaMembraneandltsUnderlyingCytoplasm SecretoryVesicleMembraneComponentsAreeuicklyRemoved fromthePlasmaMembrane SomeRegulatedExocytosisEventsServeto Enlargetheplasma Membrane PolarizedCellsDirectProteinsfromthelransGolgiNetworkto theAppropriateDomainofthePlasmaMembrane DifferentStrategiesGuideMembraneProteinsandLipidsSelectively to theCorrectPlasmaMembraneDomains SynapticVesiclesCanFormDirectlyfromEndocyticVesicles >ummary Problems References Chapter14EnergyConversion:Mitochondria and Chloroplasts 813 THEMITOCHONDRION 815 TheMitochondrionContainsanOuterMembrane,anInner Membrane,andTwoInternalCompartments 916 TheCitricAcidCycleGeneratesHigh-EnergyElectrons 817 AChemiosmoticProcessConvertsOxidationEnergyintoATp 917 NADHTransfersitsElectronsto OxygenThroughThreeLarge RespiratoryEnzymeComplexes gl9 AsElectronsMoveAlongthe RespiratoryChain,EnergylsStored asanElectrochemicalProtonGradientAcrossthe lnner 783 784 785 785 786 786 Resoonse SomeMembraneProteinsAcquireaCovalentlyAttached Glycosylphosphatidylinositol(Gpl)Anchor TheERAssemblesMostLipidBilayers Summory Problems References Chapter 13 IntracellularVesicularTraffic THEMOLECULARMECHANISMSOFMEMBRANE TRANSPORTANDTHEMAINTENANCEOF COMPARTMENTALDIVERSITY ThereAreVariousTypesofCoatedVesicles TheAssemblyofaClathrinCoatDrivesVesicleFormation NotAllCoatsFormBasket-likeStructures PhosphoinositidesMarkOrganellesandMembraneDomarns CytoplasmicProteinsRegulatethepinching-OffandUncoarrng of CoatedVesicles MonomericGTPasesControlCoatAssembly NotAllTransportVesiclesAreSpherical RabProteinsGuideVesicleTargeting SNAREsMediateMembraneFusion InteractingSNAREsNeedto BepriedApartBeforeTheyCan FunctionAgain ViralFusionProteinsandSNAREsMayUseSimilarFusion 740 742 743 745 746 748 749 750 751 754 757 t ) I 758 760 760 toz 764 787 787 789 790 791 792 793 795 797 798 799 800 801 803 803 804 799 805 806 807 809 8 1 0 812 820 a2'l 805 80s Mechanisms 764 Summary 766 TRANSPORTFROMTHEERTHROUGHTHEGOLGI APPARATUS 766 ProteinsLeavetheERin COPII-CoatedTransportVesicles 767 OnlyProteinsThatAreproperlyFoldedandAssembledCanLeave theER 767 VesicularTubularClustersMediateTransportfromtheERto the GolgiApparatus 768 TheRetrievalPathwayto theERUsesSortingSignals 769 ManyProteinsAreSelectivelyRetainedintheCompartmentsin WhichTheyFunction 771 TheGolgiApparatusConsistsof anOrderedSeriesof Compartments 771 OligosaccharideChainsAreProcessedintheGolgiApparatus 773 ProteoglycansAreAssembledin theGolgiApparatus 775 WhatlsthePurposeof Glycosyfationt 776 TransportThroughtheGolgiApparatusMayOccurbyVesicular TransportorCisternalMaturation 777 GolgiMatrixProteinsHelpOrganizetheStack 77g Summory 77g Membrane TheProtonGradientDrivesATPSynthesis
  16. 16. TheProtonGradientDrivesCoupledTransportAcrosstheInner Membrane 822 ProtonGradientsProduceMostof theCell'sATP 822 MitochondriaMaintaina HighATP:ADPRatioinCells 823 A LargeNegativeValueof AGforATPHydrolysisMakesATP Usefulto theCell 824 ATPSynthaseCanFunctionin Reverseto HydrolyzeATPand PumoHr 826 Summary 827 ELECTRON-TRANSPORTCHAINSANDTHEIRPROTOI' PUMPS 827 ProtonsAreUnusuallyEasyto Move 827 TheRedoxPotentiallsa Measureof ElectronAffinities 828 EfectronTransfersReleaseLargeAmountsofEnergy 829 SpectroscopicMethodsldentifiedManyElectronCarriersinthe RespiratoryChain 829 TheRespiratoryChainIncludesThreeLargeEnzymeComplexes EmbeddedintheInnerMembrane 831 Anlron-CopperCenterin CytochromeOxidaseCatalyzesEfficient 02 Reduction 832 ElectronTransfersinthe InnerMitochondrialMembraneAreMediated byElectronTunnelingduringRandomCollisions 834 A LargeDropin RedoxPotentialAcrossEachoftheThreeRespiratory EnzymeComplexesProvidesthe Energyfor H+Pumping 835 TheH+PumpingOccursbyDistinctMechanismsintheThreeMajor EnzymeComplexes 835 H+lonophoresUncoupleElectronTransportfromATPSynthesis 836 RespiratoryControlNormallyRestrainsElectronFlowThrough theChain 837 NaturalUncouolersConverttheMitochondriain BrownFatinto Heat-GeneratingMachines 838 TheMitochondrionPlaysManyCriticalRolesin CellMetabolism 838 BacteriaAlsoExploitChemiosmoticMechanismsto Harness Energy 839 Summary 840 CHLOROPLASTSAND PHOTOSYNTHESIS 840 TheChloroplastlsOneMemberof the PlastidFamilyof Organelles 841 ChloroplastsResembleMitochondriaButHaveanExtra Compartment 842 ChloroplastsCaptureEnergyfromSunlightandUselt to Fix Carbon 843 CarbonFixationlsCatalyzedbyRibuloseBisphosphate Carboxylase 844 EachCO2MoleculeThatlsFixedConsumesThreeMolecules ofATPandTwoMoleculesofNADPH 845 CarbonFixationin SomePlantslsCompartmentalizedto Facilitate Growthat LowCO2Concentrations 846 PhotosynthesisDependsonthe Photochemistryof Chlorophyll Molecules 847 A PhotochemicalReactionCenterPlusanAntennaComplex Forma Photosystem 848 Ina ReactionCenter,LightEnergyCapturedbyChlorophyll Createsa StrongElectronDonorfromaWeakOne 849 NoncyclicPhotophosphorylationProducesBothNADPHandATP 850 ChloroplastsCanMakeATPbyCyclicPhotophosphorylation WithoutMakingNADPH 853 PhotosystemsI andll HaveRelatedStructures,andAlsoResemble BacterialPhotosystems TheProton-MotiveForcelstheSamein Mitochondriaand Chloroplasts CarrierProteinsintheChloroplastInnerMembraneControl MetaboliteExchangewiththeCytosol ChloroplastsAlsoPerformOtherCrucialBiosyntheses Summary THEGENETICSYSTEMSOFMITOCHONDRIAAND PLASTIDS MitochondriaandChloroplastsContainCompleteGeneticSystems OrganelleGrowthandDivisionDeterminetheNumberof MitochondriaandPlastidsina Cell 8s3 6 f J 854 855 855 MitochondriaandChloroplastsHaveDiverseGenomes 859 MitochondriaandChloroplastsProbablyBothEvolvedfrom EndosymbioticBacteria 859 MitochondriaHavea RelaxedCodonUsageandCanHavea VariantGeneticCode AnimalMitochondriaContaintheSimplestGeneticSystemsKnown SomeOrganelleGenesContainIntrons TheChloroplastGenomeof HigherPlantsContainsAbout 120Genes MitochondrialGenesAreInheritedbya Non-Mendelian Mechanism OrganelleGenesAreMaternallyInheritedin ManyOrganisms PetiteMutantsinYeastsDemonstratetheOverwhelming lmportanceoftheCellNucleusforMitochondrialBiogenesis MitochondriaandPlastidsContainTissue-SpecificProteinsthat AreEncodedintheCellNucleus MitochondrialmportMostofTheirLipids;ChloroplastsMake MostofTheirs MitochondriaMayContributeto theAgingof CellsandOrganisms WhyDoMitochondriaandChloroplastsHaveTheirOwnGenetic Systems? Summary THEEVOLUTIONOFELECTRON-TRANSPORTCHAINS TheEarliestCellsProbablyUsedFermentationto ProduceATP Electron-TransoortChainsEnabledAnaerobicBacteriato Use NonfermentableMoleculesasTheirMajorSourceof Energy ByProvidinganInexhaustibleSourceof ReducingPower, PhotosyntheticBacteriaOvercamea MajorEvolutionary Obstacle ThePhotosyntheticElectron-TransportChainsof Cyanobacteria ProducedAtmosphericOxygenandPermittedNewLife-Forms Summary Problems References Chapter 15 Mechanisms of Cell Communication 879 GENERALPRINCIPLESOFCELLCOMMUNICATION 879 ExtracellularSignalMoleculesBindto SpecificReceptors 880 ExtracellularSignalMoleculesCanActOverEitherShortor Long Distances 881 GapJunctionsAllowNeighboringCellsto ShareSignaling lnformation 884 EachCelllsProgrammedto Respondto SpecificCombinationsof ExtracellularSignalMolecule5 884 DifferentTypesof CellsUsuallyRespondDifferentlyto theSame ExtracellularSignalMolecule 885 TheFateof SomeDevelopingCellsDependsonTheirPositionin MorphogenGradients 886 A CellCanAltertheConcentrationof anlntracellularMolecule QuicklyOnlylf theLifetimeof the MoleculelsShort 886 NitricOxideGasSignalsbyDirectlyRegulatingtheActivityof SpecificProteinsInsidetheTargetCell 887 NuclearReceptorsAreLigand-ModulatedGeneRegulatory Proteins 889 TheThreeLargestClassesof Cell-SurfaceReceptorProteinsArelon- Channel-Coupled,G-Protein-Coupled,andEnzyme-Coupled Receptors 891 MostActivatedCell-SurfaceReceptorsRelaySignalsViaSmall Moleculesanda Networkof IntracellularSignalingProteins 893 ManyIntracellularSignalingProteinsFunctionasMolecularSwitches ThatAreActivatedbyPhosphorylationorGTPBinding 895 IntracellularSignalingComplexesEnhancetheSpeed,Efficiency, andSpecificityofthe Response 897 ModularInteractionDomainsMediatelnteractionsBetween IntracellularSignalingProteins 897 CellsCanUseMultipleMechanismsto RespondAbruptlyto a GraduallyIncreasingConcentrationofan ExtracellularSignal 899 IntracellularSignalingNetworksUsuallyMakeUseof 861 862 863 863 864 866 866 867 867 606 868 870 870 870 871 872 873 875 877 878 85s 856 857 FeedbackLoops CellsCanAdjustTheirSensitivityto a Signal Summary 901 902 903
  17. 17. SIGNALINGTHROUGHG-PROTEIN-COUPLEDCELL- sURFACERECEPTORS(GPCRs)ANDSMALL INTRACELLULARMEDIATORS TrimericGProteinsRelaySignalsfromGpCRs SomeGProteinsRegulatetheProductionof CyclicAMp Cyclic-AMP-DependentProteinKinase(pKA)MediatesMosr of theEffectsof CyclicAMP SomeG ProteinsActivateAnInositolPhospholipidSignaling PathwaybyActivatingPhospholipaseC-p Ca2+Functionsasa UbiquitousIntracellularMediator TheFrequencyof Ca2+OscillationslnfluencesaCell!Response Ca2+/Calmodulin-DependentproteinKinases(CaM-Kinases) MediateManyoftheResponsesto Ca2+SignalsinAnimalCells SomeGProteinsDirectlyRegulatelonChannels SmellandVisionDependonGPCRsThatRegulateCyclic- Nucleotide-GatedlonChannels IntracellularMediatorsandEnzymaticCascadesAmplify ExtracellularSignals GPCRDesensitizationDependson Receptorphosphorylation Summory SIGNALINGTHROUGHENZYME-COUPLEDCELL-SURFACE RECEPTORS ActivatedReceptorTyrosineKinases(RTKs)phosphorylate Themselves PhosphorylatedTyrosineson RTKsServeasDockingSitesfor IntracellularSignalingProteins ProteinswithSH2DomainsBindto phosphorylatedTyrosines RasBelongsto a LargeSuperfamilyof MonomericGTpases RTKsActivateRasViaAdaptorsandGEFs:Evidencefromthe DevelopingDrosophilaEye RasActivatesa MAPKinaseSignalingModule ScaffoldProteinsHelpPreventCross-TalkBetweenparallelMAp KinaseModules RhoFamilyGTPasesFunctionallyCoupleCell-SurfaceReceptors to theCytoskeleton Pl3-KinaseProducesLipidDockingSitesintheplasmaMemorane ThePl-3-Kinase-AktSignalingPathwayStimulatesAnimalCellsto SurviveandGrow TheDownstreamSignalingPathwaysActivatedByRTKsandGpCRs Overlao Tyrosine-Kinase-AssociatedReceptorsDependonCytoplasmic TyrosineKinases CytokineReceptorsActivatetheJAK-STATSignalingpathway, Providinga FastTrackto theNucleus ProteinTyrosinePhosphatasesReverseTyrosinephosphorylations SignalProteinsof theTGFBSuperfamilyActThroughReceptor Serine/ThreonineKinasesandSmads Serine/ThreonineandTyrosineproteinKinasesAreStructurally Related BacterialChemotaxisDependson aTwo-ComponentSignaling PathwayActivatedbyHistidine-Kinase-AssociatedReceptors ReceptorMethylationlsResponsibleforAdaptationin Bacterial Chemotaxis Summory SIGNALINGPATHWAYSDEPENDENTON REGULATED PROTEOLYSISOF LATENTGENEREGULATORYPROTEINS TheReceptorProteinNotchlsa LatentGeneRegulatoryprotein WntProteinsBindto FrizzledReceptorsandInhibitthe Degradationof p-Catenin HedgehogProteinsBindto patchedRelievingltsInhibition of Smoothened ManyStressfulandInflammatoryStimuliActThroughan NFrB-DependentSignalingPathway Summory SIGNALINGIN PLANTS MulticellularityandCellCommunicationEvolvedIndependently in PlantsandAnimals ReceptorSerine/ThreonineKinasesArethe LargestClassof Cell-SurfaceReceptorsin Plants EthyleneBlockstheDegradationof SpecificGeneRegulatory Proteinsin theNucleus 957 RegulatedPositioningof AuxinTransportersPatternsPlantGrowth 959 PhytochromesDetectRedLight,andCryptochromesDetectBlue Light Summory Problems References Chapter16 TheCytoskeleton 960 961 964 965 THESELF-AssEMBLYAND DYNAMICSTRUCTUREOF CYTOSKELETALFILAMENTS 965 CytoskeletalFilamentsAreDynamicandAdaptable 966 TheCytoskeletonCanAlsoFormStableStructures 969 EachTypeof CytoskeletalFilamentlsConstructedfromSmaller ProteinSubunits 970 FilamentsFormedfromMultipleProtofilamentsHave AdvantageousProperties 971 NucleationlstheRate-LimitingStepintheFormationof aCytoskeletalPolymer 973 TheTubulinandActinSubunitsAssembleHead-to-Tailto CreatePolarFilaments 973 MicrotubulesandActinFilamentsHaveTwoDistinctEnds ThatGrowat DifferentRates 975 FilamentTreadmillingandDynamicInstabilityAreConsequences of NucleotideHydrolysisbyTubulinandActin 976 TreadmillingandDynamicInstabilityAidRapidCytoskeletal Rearrangement 980 TubulinandActinHaveBeenHighlyConservedDuring EucaryoticEvolution 982 IntermediateFilamentStructureDependsonTheLateral BundlingandTwistingof CoiledCoils 983 IntermediateFilamentslmpartMechanicalStabilityto AnimalCells 985 DrugsCanAlterFilamentPolymerization 987 BacterialCellOrganizationandCellDivisionDependon Homologsofthe EucaryoticCytoskeleton 999 Summary 991 HOWCELLSREGULATETHEIRCYTOSKELETALFILAMENTS 992 A ProteinComplexContainingyTubulinNucleatesMicrotubules 992 MicrotubulesEmanatefromtheCentrosomeinAnimalCells 992 ActinFilamentsAreOftenNucleatedatthe PlasmaMembrane 996 TheMechanismof NucleationInfluencesLarge-ScaleFilament Organization 999 ProteinsThatBindto theFreeSubunitsModifyFilamentElongation999 SeveringProteinsRegulatetheLengthandKineticBehaviorof ActinFilamentsandMicrotubules 1000 ProteinsThatBindAlongtheSidesof FilamentsCanEitherStabilize or DestabilizeThem 1OO1 ProteinsThatInteractwithFilamentEndsCanDramaticallyChange FilamentDynamics 1OO2 DifferentKindsof ProteinsAlterthe Propertiesof RapidlyGrowing MicrotubuleEnds FilamentsAreOrganizedintoHigher-OrderStructuresin Cells IntermediateFilamentsAreCross-LinkedandBundledlnto StrongArrays Cross-LinkingProteinswith DistinctPropertiesOrganizeDifferent 1003 1005 1005 AssembliesofActinFilaments 1006 FilaminandSpectrinFormActinFilamentWebs l OOg CytoskeletalElementsMakeManyAttachmentsto Membrane 1009 Summary l0l0 MOLECULARMOTORS Actin-BasedMotorProteinsAreMembersof theMvosin Superfamily ThereAreTwoTypesof MicrotubuleMotorProteins:Kinesinsand Dyneins rc14 TheStructuralSimilarityof MyosinandKinesinIndicatesa CommonEvolutionaryOrigin 1015 MotorProteinsGenerateForcebyCouplingATPHydrolysisto ConformationalChanqes 1016 904 90s 90s 908 909 912 912 914 916 917 919 920 921 921 922 923 924 926 927 928 930 931 932 934 v5) 935 937 938 939 941 941 943 944 946 946 948 950 952 954 955 1 0 1 0 1 0 11 955 vf,o
  18. 18. MotorProteinKineticsAreAdaptedto CellFunctions 1020 MotorProteinsMediatethe IntracellularTransportof Membrane- Microtubule-DependentMotorProteinsGovernSpindle AssemblyandFunction 1077 TwoMechanismsCollaborateintheAssemblyof a BipolarMitoticEnclosedOrganelles TheCytoskeletonLocalizesSpecificRNAMolecules CellsRegulateMotorProteinFunction Summary THECYTOSKELETONAND CELLBEHAVIOR Slidingof Myosinll andActinFilamentsCausesMusclesto Contract A SuddenRisein CytosolicCa2+ConcentrationInitiatesMuscle Contraction HeartMusclelsa PreciselyEngineeredMachine of theActinCytoskeleton ExtracellularSignalsCanActivatetheThreeRhoProtein FamilyMembers ExternalSignalsCanDictatetheDirectionof CellMigration CiliaandFlagellaAreMotileStructuresBuiltfromMicrotubules andDyneins 1031 Constructionof theMitoticSpindleRequiresMicrotubule DynamicsandtheInteractionsof ManyMotorProteins ManyCellsCanCrawlAcrossA SolidSubstratum ActinPolymerizationDrivesPlasmaMembraneProtrusion CellAdhesionandTractionAllowCellsto PullThemselves Forward 1040 Membersof the RhoProteinFamilyCauseMajorRearrangements Soindle CentrosomeDuplicationOccursEarlyin theCellCycle M-CdkInitiatesSpindleAssemblyin Prophase TheCompletionof SpindleAssemblyin AnimalCellsRequires NuclearEnvelopeBreakdown MicrotubuleInstabilityIncreasesGreatlyin Mitosis MitoticChromosomesPromoteBipolarSpindleAssembly KinetochoresAttachSisterChromatidsto theSpindle Bi-OrientationlsAchievedbyTrialandError MultipleForcesMoveChromosomesontheSpindle TheAPC/CTriggersSister-ChromatidSeparationandthe Completionof Mitosis UnattachedChromosomesBlockSister-ChromatidSeparation: TheSpindleAssemblYCheckPoint ChromosomesSegregatein AnaphaseA andB Reproduction Summory CYTOKINESIS ActinandMyosinll intheContractileRingGeneratethe Forcefor Cytokinesis SegregatedChromosomesArePackagedin DaughterNucleiat Teloohase 1o9o Meiosislsa SoecialFormof NuclearDivisionInvolvedin Sexual 1021 1022 1023 1025 1025 1026 1028 1031 1077 l 078 1078 1079 1080 1081 1082 1083 1085 1087 1088 1089 1034 1036 1037 1041 1043 1045 1090 1092 1092 1093CommunicationBetweentheMicrotubuleandActinCytoskeletons CoordinatesWhole-CellPolarizationandLocomotion 1046 TheComplexMorphologicalSpecializationof NeuronsDepends ontheCytoskeleton Summary Problems References Chapter17TheCellCycle OVERVIEWOFTHECELLCYCLE TheEucaryoticCellCyclelsDividedintoFourPhases Cell-CycleControllsSimilarinAllEucaryotes Cell-CycleControlCanBeDissectedGeneticallybyAnalysisof YeastMutants Cell-CycleControlCanBeAnalyzedBiochemicallyin Animal Embryos Cell-CycleControlCanBeStudiedin CulturedMammalianCells Cell-CycleProgressionCanBeStudiedinVariousWays Summary THECELL-CYCLECONTROLSYSTEM TheCell-CycleControlSystemTriggerstheMajorEventsofthe CellCycle 1060 TheCell-CycleControlSystemDependsonCyclicallyActivated Cyclin-DependentProteinKinases(Cdks) 1062 InhibitoryPhosphorylationandCdkInhibitoryProteins(CKls) CanSuppressCdkActivity TheCell-CycleControlSystemDependsonCyclicalProteolysis Cell-CycleControlAlsoDependsonTranscriptionalRegulation TheCell-CycleControlSystemFunctionsasa Networkof BiochemicalSwitches Summaty 5 PHASE S-CdkInitiatesDNAReplicationOncePerCycle ChromosomeDuplicationRequiresDuplicationof Chromatin Structure CohesinsHelpHoldSisterChromatidsTogether Summory MITOSIS M-CdkDrivesEntryIntoMitosis DephosphorylationActivatesM-CdkattheOnsetof Mitosis CondensinHelpsConfigureDuplicatedChromosomesfor Separation TheMitoticSpindlelsa Microtubule-BasedMachine LocalActivationof RhoATriggersAssemblyandContractionof the ContractileRing 1094 TheMicrotubulesof theMitoticSpindleDeterminethe Planeof1047 1050 1050 1052 1053 1054 1054 1056 1056 1057 1059 1059 1060 1060 AnimalCellDivision ThePhragmoplastGuidesCytokinesisin HigherPlants Membrane-EnclosedOrganellesMustBeDistributedto Daughter CellsDuringCytokinesis SomeCellsRepositionTheirSpindleto DivideAsymmetrically MitosisCanOccurWithoutCytokinesis TheG1Phaselsa StableStateof Cdklnactivity Summary CONTROLOFCELLDIVISIONAND CELLGROWTH MitogensStimulateCellDivision CellsCanDelayDivisionbyEnteringa SpecializedNondividing AbnormalProliferationSignalsCauseCell-CycleArrestor Apoptosis,Exceptin CancerCells OrganismandOrganGrowthDependon CellGrowth ProliferatingCellsUsuallyCoordinateTheirGrowthandDivision NeighboringCellsCompetefor ExtracellularSignalProteins AnimalsControlTotalCellMassbyUnknownMechanisms Summary Problems References Chapter18APoPtosis State 1103 MitogensStimulateGr-CdkandGrlS-CdkActivities 1103 DNADamageBlocksCellDivision:TheDNADamageResponse 1105 ManyHumanCellsHavea Built-lnLimitationontheNumber ofTimesTheyCanDivide 1oo7 1095 1097 1098 1099 1099 1100 1101 11 0 1 1102 1107 r 108 1108 1 1 1 0 1 1 1 1 1112 1112 1 1 1 3 1115 1 1 1 8 1063 1064 I uof, 1065 't067 't067 1067 1069 1070 1071 1071 1071 1074 1075 1075 ProgrammedCellDeathEliminatesUnwantedCells 1115 ApoptoticCellsAreBiochemicallyRecognizable 1117 ApoptosisDependsonanIntracellularProteolyticCascade ThatlsMediatedbYCasPases Cell-SurfaceDeathReceptorsActivatethe ExtrinsicPathway ofApoptosis 1120 TheIntrinsicPathwayof ApoptosisDependsonMitochondria 1121 Bcf2ProteinsRegulatetheIntrinsicPathwayof Apoptosis 1121 lAPsInhibitCaspases 1124 ExtracellularSurvivalFactorsInhibitApoptosisinVariousWays '1126 EitherExcessiveor InsufficientApoptosisCanContributeto Disease1127 Summary 1128 problems 1128 References 1129
  19. 19. Chapter19CellJunctions,CellAdhesion,and the ExtracellularMatrix CADHERINSANDCELL-CELLADHESION CadherinsMediateCa2+-DependentCell-CellAdhesionin AllAnimals TheCadherinSuperfamilyinVertebratesIncludesHundredsof DifferentProteins,IncludingManywithSignaling Functions CadherinsMediateHomophilicAdhesion 5electiveCell-CellAdhesionEnablesDissociatedVertebrare Cellsto ReassembleintoOrganizedTissues CadherinsControltheSelectiveAssortmentof Cells TwistRegulatesEpithelial-MesenchymaITransitions CateninsLinkClassicalCadherinsto theActinCytoskeleton AdherensJunctionsCoordinatetheActin-BasedMotilityof AdjacentCells DesmosomeJunctionsGiveEpitheliaMechanicalStrenqth Cell-CellJunctionsSendSignalsintotheCellInterior SelectinsMediateTransientCell-CellAdhesionsinthe Bloodstream Membersofthelmmunoglobulin5uperfamilyof proteins MediateCa2+-lndependentCell-CellAdhesion ManyTypesof CellAdhesionMoleculesActin parallelto Create a Synapse ScaffoldProteinsOrganizeJunctionalComplexes Summary TIGHTJUNCTIONSANDTHEORGANIZATIONOF EPITHELIA TightJunctionsForma SealBetweenCellsanda FenceBetween MembraneDomains ScaffoldProteinsinJunctionalComplexesplaya KeypartIn theControlof CellProliferation Cell-CellJunctionsandtheBasalLaminaGovernAoico-Basal Polarityin Epithelia A SeparateSignalingSystemControlsplanarCellpolarity Summary PASSAGEWAYSFROMCELLTOCELL:GApJUNCT|ONS AND PLASMODESMATA GapJunctionsCoupleCellsBothElectricallyandMetabolically A Gap-JunctionConnexonlsMadeUpof SixTransmembrane ConnexinSubunits GapJunctionsHaveDiverseFunctions CellsCanRegulatethePermeabilityofTheirGapJunctions In Plants,PlasmodesmataperformManyof theSameFunctions asGapJunctions Summary THEBASALLAMINA BasalLaminaeUnderlieAllEpitheliaandSurroundSome NonepithelialCellTypes Lamininlsa PrimaryComponentoftheBasalLamina TypelVCollagenGivestheBasalLaminaTensileStrenoth BasalLaminaeHaveDiverseFunctions Summary INTEGRINSANDCELL-MATRIXADHESION IntegrinsAreTransmembraneHeterodimersThatLinkto tne Cytoskeleton IntegrinsCanSwitchBetweenanActiveandanInactive Conformation IntegrinDefectsAreResponsiblefor ManyDifferentGenetic Diseases IntegrinsClusterto FormStrongAdhesions ExtracellularMatrixAttachmentsActThroughIntegrinsto ControlCellProliferationandSurvival IntegrinsRecruitIntracellularSignalingproteinsatSitesofCell- SubstratumAdhesion IntegrinsCanProduceLocalizedIntracellularEffects Summory THEEXTRACELLULARMATRIXOFANIMALCONNECTIVE TlsSuES 1178 TheExtracellularMatrixlsMadeandOrientedbytheCells Withinlt j179 Glycosaminoglycan(GAG)ChainsOccupyLargeAmountsof SpaceandFormHydratedGels 1179 HyaluronanActsasa SpaceFilleranda FacilitatorofCellMigration DuringTissueMorphogenesisandRepair 1180 ProteoglycansAreComposedof GAGChainsCovalentlyLinked to a CoreProtein ProteoglycansCanRegulatetheActivitiesof SecretedProterns Cell-SurfaceProteoglycansActasCo-Receptors CollagensAretheMajorProteinsof theExtracellularMatrix CollagenChainsUndergoa Seriesof Post-Translational Modifications PropeptidesAreClippedOffProcollagenAfterltsSecretion to AllowAssemblyof Fibrils SecretedFibril-AssociatedCollagensHelpOrganizetheFibrils CellsHelpOrganizetheCollagenFibrilsTheySecreteby ExertingTensiononthe Matrix ElastinGivesTissuesTheirElasticitv FibronectinlsanExtracellularProteinThatHelpsCellsAttach to theMatrix 1191 TensionExertedbyCellsRegulatesAssemblyof Fibronectin Fibrils FibronectinBindsto IntegrinsThroughanRGDMotif CellsHaveto BeAbleto DegradeMatrix,asWellasMakeit MatrixDegradationlsLocalizedto theVicinityof Cells Summary THEPLANTCELLWALL TheCompositionof theCellWallDependsontheCellType TheTensileStrengthof theCellWallAllowsPlantCellsto DevelopTurgorPressure ThePrimaryCellWalllsBuiltfromCelluloseMicrofibrils Interwovenwitha Networkof PecticPolysaccharides OrientedCell-WallDepositionControlsplantCellGrowth MicrotubulesOrientCell-WallDeposition Summary Problems References Chapter20 Cancer CANCERA5AMICROEVOLUTIONARYPROCESS CancerCellsReproduceWithoutRestraintandColonize OtherTissues MostCancersDerivefroma SingleAbnormalCell CancerCellsContainSomaticMutations A SingleMutationlsNotEnoughto CauseCancer CancersDevelopGraduallyfromIncreasinglyAberrantCells CervicalCancersArePreventedbyEarlyDetection TumorProgressionInvolvesSuccessiveRoundsof Random InheritedChangeFollowedbyNaturalSelection TheEpigeneticChangesThatAccumulatein CancerCellsInvolve InheritedChromatinStructuresandDNAMethylation HumanCancerCellsAreGeneticallyUnstable CancerousGrowthOftenDependson DefectiveControlof CellDeath,CellDifferentiation,or Both CancerCellsAreUsuallyAlteredinTheirResponsesto DNA DamageandOtherFormsof Stress HumanCancerCellsEscapea Built-lnLimitto Cellproliferation A SmallPopulationof CancerStemCellsMaintainsMany Tumors HowDoCancerStemCellsArise? ToMetastasize,MalignantCancerCellsMustSurviveand Proliferateina ForeignEnvlronment TumorsInduceAngiogenesis TheTumorMicroenvironmentInfluencesCancer Development ManyPropertiesTypicallyContributeto CancerousGrowth Summary I 131 1133 11 3 5 t t 5 0 1137 1 3 9 140 141 142 1142 1143 1"t45 1145 1146 1147 1148 1149 11 5 0 11 5 0 11 5 3 11 5 5 1157 11 5 8 11 5 8 11 5 8 11 5 9 11 6 1 11 6 1 1162 11 6 3 ^t't64 1164 11 6 5 't166 1167 1169 1169 1170 1"170 "1172 1174 1175 1176 11 7 7 1178 11 8 1 1182 1183 1184 1186 1187 't187 1189 1189 't't91 1193 1193 1194 1195 11 9 5 1195 't't97 1197 1199 1200 1202 1202 1204 1205 1205 1206 1207 I208 1209 1210 1211 1212 1213 1214 1215 1216 12'.t7 1217 1218 1220 1220 1222 1223 1223
  20. 20. THEPREVENTABLECAU5E5OFCANCER Many,ButNotAll,Cancer-CausingAgentsDamageDNA TumorInitiatorsDamageDNA;TumorPromotersDoNot VirusesandOtherInfectionsContributeto a Significant Proportionof HumanCancers ldentificationof CarcinogensRevealsWaysto Avoid Cancer Summary FINDINGTHECANCER-CRITICALGENES Theldentificationof Gain-of-FunctionandLoss-of-Function MutationsRequiresDifferentMethods RetrovirusesCanActasVectorsforOncogenesThatAlter CellBehavior DifferentSearchesforOncogenesHaveConvergedonthe SameGene-Ras Studiesof RareHereditaryCancerSyndromesFirstldentified TumorSuppressorGenes TumorSuopressorGenesCanAlsoBeldentifiedfromStudies ofTumors BothGeneticandEpigeneticMechanismsCanInactivateTumor SuppressorGenes GenesMutatedinCancerCanBeMadeOveractivein Many Ways TheHuntforCancerCriticalGenesContinues Summary THEMOLECULARBASISOFCANCER-CELLBEHAVIOR Studiesof BothDevelopingEmbryosandGenetically EngineeredMiceHaveHelpedto UncovertheFunctionof Cancer-CriticalGenes ManyCancer-CriticalGenesRegulateCellProliferation DistinctPathwaysMayMediatetheDisregulationof Cell-Cycle ProgressionandtheDisregulationof CellGrowthin CancerCells MutationsinGenesThatRegulateApoptosisAllowCancerCells to SurviveWhenTheyShouldNot Mutationsinthep53GeneAllowManyCancerCellsto Survive andProliferateDespiteDNADamage DNATumorVirusesBlocktheActionof KeyTumorSuppressor Proteins TheChangesinTumorCellsThatLeadto MetastasisAreStill Largelya Mystery ColorectalCancersEvolveSlowlyViaa SuccessionofVisible Changes A FewKeyGeneticLesionsAreCommonto a LargeFractionof ColorectalCancers SomeColorectalCancersHaveDefectsin DNAMismatchRepair TheStepsofTumorProgressionCanOftenBeCorrelatedwith SDecificMutations EachCaseof CancerlsCharacterizedbyltsOwnArrayof Genetic Lesions Summary CANCERTREATMENT:PRESENTANDFUTURE TheSearchforCancerCureslsDifficultbutNotHopeless TraditionalTherapiesExploittheGeneticInstabilityandLossof Cell-CycleCheckpointResponsesinCancerCells NewDrugsCanExploittheSpecificCauseof aTumor'sGenetic Instability GeneticInstabilityHelpsCancersBecomeProgressivelyMore ResistanttoTherapies NewTherapiesAreEmergingfromOurKnowledgeof Cancer Biology SmallMoleculesCanBeDesignedto InhibitSpecificOncogenic Proteins TumorBloodVesselsAreLogicalTargetsforCancerTherapy ManyCancersMayBeTreatablebyEnhancingthelmmune ResponseAgainsta SpecificTumor TreatingPatientswithSeveralDrugsSimultaneouslyHas PotentialAdvantagesforCancerTherapy GeneExpressionProfilingCanHelpClassifyCancersinto ClinicallyMeaningfulSubgroups TherelsStillMuchMoreto Do 1264 Summory 1265 problems 1265 References 1267 Chapters21-25availableon MediaDVD-ROM Chapter2t SexualReproduction:Meiosis, GermCells,andFertilization OVERVIEWOFSEXUALREPRODUCTIOII 1269 TheHaploidPhasein HigherEucaryoteslsBrief 1269 MeiosisCreatesGeneticDiversity 1271 SexualReproductionGivesOrganismsa CompetitiveAdvantage 1271 Summary 1272 ME|OS|S 1272 GametesAreProducedbyTwoMeioticCellDivisions 1272 DuplicatedHomologs(andSexChromosomes)PairDuringEarly proohase1 1274 1224 1225 1226 1 2 2 7 1229 1230 1230 1231 1232 1233 1234 I l 5 > 1235 1237 1239 1240 1240 1241 1242 1244 1245 1246 1247 1249 1250 1251 1254 1254 I z)o Iz>o 1256 1257 1257 1257 1259 1260 1260 I loz | 202 | 205 1264 1269 HomologPairingCulminatesintheFormationof a Synaptonemal Complex HomologSegregationDependson Meiosis-Specific,Kinetochore- AssociatedProteins MeiosisFrequentlyGoesWrong Crossing-OverEnhancesGeneticReassortment Crossing-OverlsHighlyRegulated MeiosislsRegulatedDifferentlyin MaleandFemaleMammals Summary PRIMORDIALGERMCELLSAND sEXDETERMINATIONIN MAMMALS 1275 1276 1278 1279 1280 1280 1281 1282 SignalsfromNeighborsSpecifyPGCsin MammalianEmbryos 1282 PGCSMigrateintotheDevelopingGonads 1283 TheSryGeneDirectstheDevelopingMammalianGonadto BecomeaTestis 1283 ManyAspectsof SexualReproductionVaryGreatlybetween AnimalsPecies 1285 Summary 1286 EGGS 1287 AnEgglsHighlySpecializedfor IndependentDevelopment 1287 EggsDevelopinStages 1288 OocytesUseSpecialMechanismsto Growto TheirLargeSize 1290 MostHumanOocytesDieWithoutMaturing 1291 Summary 1292 SPERM 't292 SpermAreHighlyAdaptedfor DeliveringTheirDNAto anEgg 1292 SpermAreProducedContinuouslyin theMammalianTestis 1293 SpermDevelopasa SYncYtium 1294 Summary 1296 FERTILIZATION 1297 EjaculatedSpermBecomeCapacitatedinthe FemaleGenitalTract 1297 CapacitatedSpermBindto theZonaPellucidaandUndergoan AcrosomeReaction 1298 TheMechanismof Sperm-EggFusionlsStillUnknown 1298 SpermFusionActivatestheEggbyIncreasingCa2+intheCytosol 1299 Ti'reCorticalReactionHelpsEnsureThatOnlyOneSpermFertilizes theEgg 1300 TheSoermProvidesCentriolesasWellasltsGenometo theZygote1301 IVFandlCSlHaveRevolutionizedtheTreatmentof Human Infertility Summary References Chapter22Developmentof Multicellular Organisms UNIVERSALMECHANISMSOFANIMALDEVELOPMENT 1305 AnimalsShareSomeBasicAnatomicalFeatures 1307 1301 1303 1304 1305
  21. 21. MulticellularAnimalsAreEnrichedin proteinsMediatinoCell InteractionsandGeneRegulation RegulatoryDNADefinestheprogramof Development Manipulationof theEmbryoRevealstheInteractionsBetween ItsCells Studiesof MutantAnimalsldentifytheGenesThatControl DevelopmentalProcesses A CellMakesDevelopmentalDecisionsLongBeforelt Shows aVisibleChange CellsHaveRememberedPositionalValuesThatReflectTheir Locationin theBody InductiveSignalsCanCreateOrderlyDifferencesBetween InitiallyldenticalCells SisterCellsCanBeBornDifferentbyanAsymmetricCell Division PositiveFeedbackCanCreateAsymmetryWhereThereWas NoneBefore PositiveFeedbackGeneratespatterns,CreatesAll-or-None Outcomes,andProvidesMemory A SmallSetof SignalingPathways,UsedRepeatedly,Controls DevelopmentalPatterning MorphogensAreLong-RangeInducersThatExertGradedEffects ExtracellularInhibitorsof SignalMoleculesShapetheResponse to theInducer DevelopmentalSignalsCanSpreadThroughTissuein Severar DifferentWays ProgramsThatAreIntrinsicto a CellOftenDefinetheTime-Course of itsDevelooment InitialPatternsAreEstablishedinSmallFieldsof Cellsano RefinedbySequentialInductionastheEmbrvoGrows Summory CAENORHABDITISELEGANS:DEVELOPMENTFRoMTHE PERSPECTIVEOFTHEINDIVIDUALCELL CaenorhabditiseleganslsAnatomicallySimple CellFatesinthe DevelopingNematodeAreAlmostperfectly Predictable Productsof Maternal-EffectGenesOrganizetheAsymmetric DivisionoftheEgg ProgressivelyMoreComplexpatternsAreCreatedbyCell-Cell Interactions MicrosurgeryandGeneticsRevealtheLogicof Developmental Control;GeneCloningandSequencingRevealltsMolecular Mechanisms CellsChangeOverTimeinTheirResponsivenessto DevelopmentalSignals HeterochronicGenesControltheTimingof Development CellsDoNotCountCellDivisionsinTimingTheirInternal Programs SelectedCellsDiebyApoptosisaspartof theproqramof Development Summary DROSOPHILAANDTHEMOLECULARGENETICSOF PATTERNFORMATION:GENESISOFTHEBODYPLAN TheInsectBodylsConstructedasa Seriesof SegmentalUnits DrosophiloBeginsltsDevelopmentasa Syncytium GeneticScreensDefineGroupsofGenesRequiredforSpecific Aspectsof EarlyPatterning Interactionsof theOocyteWithltsSurroundingsDefinethe Axesof theEmbryo:theRoleof theEgg-polarityGenes TheDorsoventralSignalingGenesCreatea Gradientof a NuclearGeneRegulatoryprotern DppandSogSetUpa SecondaryMorphogenGradientto RefinethePatternof theDorsalpartof the Embrvo TheInsectDorsoventralAxisCorrespondsto theVeriebrate VentrodorsalAxis ThreeClassesof SegmentationGenesRefinetheAnterior_posterior MaternalPatternandSubdividethe Embrvo TheLocalizedExpressionof SegmentationGeneslsRegulated bya Hierarchyof PositionalSignals TheModularNatureof RegulatoryDNAAllowsGenesto Have MultipleIndependentlyControlledFunctions HomeoticSelectorGenesCodeforDNA-BindingproteinsThat lnteractwithOtherGeneRegulatoryProteins 1342 TheHomeoticSelectorGenesAreExpressedSequentially Accordingto TheirOrderin theHoxComplex TheHoxComplexCarriesa PermanentRecordof Positional Information TheAnteroposteriorAxislsControlledbyHoxSelectorGenesIn vertebratesAlso Summary ORGANOGENESISANDTHEPATTERNINGOF APPENDAGES ConditionalandInducedSomaticMutationsMakeit possibleto AnalyzeGeneFunctionsLatein Development BodyPartsof theAdultFlyDevelopFromlmaginalDiscs HomeoticSelectorGenesAreEssentialfortheMemoryof PositionalInformationin lmaginalDiscCells SpecificRegulatoryGenesDefinetheCellsThatWillForman Appendage TheInsectWingDisclsDividedintoCompartments FourFamiliarSignalingPathwaysCombineto Patternthe WingDisc:Wingless,Hedgehog,Dpp,andNotch TheSizeof EachCompartmentlsRegulatedbyInteractions AmongltsCells SimilarMechanismsPatterntheLimbsofVertebrates LocalizedExpressionof SpecificClassesof GeneRegulatory ProteinsForeshadowsCellDifferentiation LateralInhibitionSinglesOutSensoryMotherCellsWithin ProneuralClusters LateralInhibitionDrivestheProgenyoftheSensoryMotherCell TowardDifferentFinalFates 857 PlanarPolarityofAsymmetricDivisionsisControlledbySignaling viathe ReceptorFrizzled 1359 AsymmetricStem-CellDivisionsGenerateAdditionalNeurons intheCentralNervousSystem 1359 AsymmetricNeuroblastDivisionsSegregateanInhibitorof Cell Egg-Polarity,Gap,andPair-RuleGenesCreateaTransient PatternThatlsRememberedbvOtherGenes Summary HOMEOTICSELECTORGENESANDTHEPATTERNINGOF THEANTEROPOSTERIORAXIS The Hox Code SpecifiesAnterior-PosteriorDifferences DivisionintoJustOneoftheDaughterCells NotchSignalingRegulatestheFine-Grainedpatternof DifferentiatedCellTypesin ManyDifferentTissues SomeKeyRegulatoryGenesDefinea CellType;OthersCan ActivatetheProgramforCreationof anEntireOrgan Summary CELLMOVEMENTSANDTHESHAPINGOFTHE VERTEBRATEBODY ThePolarityoftheAmphibianEmbryoDependsonthepolarity of theEgg CleavageProducesManyCellsfromOne GastrulationTransformsa HollowBallof CellsintoaThree-Lavered Structurewitha PrimitiveGut TheMovementsof GastrulationArePreciselypredictable ChemicalSignalsTriggertheMechanicalProcesses ActiveChangesof CellPackingProvidea DrivingForcefor Gastrulation ChangingPatternsof CellAdhesionMoleculesForceCells IntoNewArrangements TheNotochordElongates,WhiletheNeuralplateRollsUpro Formthe NeuralTube A Gene-ExpressionOscillatorControlsSegmentationof the MesodermlntoSomites DelayedNegativeFeedbackMayGeneratetheOscillations oftheSegmentationClock 1308 1309 13 1 0 1 3 11 1 3 11 1312 13 1 3 1 3 1 3 1314 t 5 t ) 13 1 6 13 1 6 1317 13 1 8 1 3 1 9 13 1 9 1320 13 2 1 't321 1322 1323 1324 | 5l) 1325 1326 1327 1327 1328 1328 1329 1330 1332 1333 1334 1336 1336 1336 1337 I 339 1340 1341 1341 1342 1343 1344 1344 1347 1347 1348 1349 t S f l 1351 1352 I 353 13s3 1355 1356 1357 1361 1362 1362 1363 1363 1364 l 365 I J O ) | 500 1367 1368 1369 1370 't371 1373 EmbryonicTissuesAreInvadedina StrictlyControlledFashion byMigratoryCells 1373 TheDistributionof MigrantCellsDependsonSurvivalFactors asWellasGuidanceCues 1375
  22. 22. Left-RightAsymmetryof theVertebrateBodyDerivesFrom MolecularAsymmetryintheEarlyEmbryo Summary THEMOUSE MammalianDevelopmentBeginsWitha SpecializedPreamble TheEarlyMammalianEmbryolsHighlyRegulative TotipotentEmbryonicStemCellsCanBeObtainedFroma MammalianEmbryo InteractionsBetweenEpitheliumandMesenchymeGenerate BranchingTubularStructures Summary NEURALDEVELOPMENT NeuronsAreAssignedDifferentCharactersAccordingto the TimeandPlaceWhereTheyAreBorn TheCharacterAssignedto a Neuronat ltsBirthGovernsthe Connectionslt WillForm EachAxonor DendriteExtendsbyMeansof aGrowthConeat ItsTip TheGrowthConePilotstheDevelopingNeuriteAlonga Precisely DefinedPath/nVlvo GrowthConesCanChangeTheirSensibilitiesasTheyTravel TargetTissuesReleaseNeurotrophicFactorsThatControlNerve CellGrowthandSurvival NeuronalSpecificityGuidestheFormationof OrderlyNeural Maps AxonsFromDifferentRegionsofthe RetinaRespondDifferently to aGradientof ReoulsiveMoleculesintheTectum DiffusePatternsof SynapticConnectionsAreSharpenedby Activity-DependentRemodeling ExperienceMoldsthePatternof SynapticConnectionsinthe Brain AdultMemoryandDevelopmentalSynapseRemodelingMay DependonSimilarMechanisms Summary PLANTDEVELOPMENT ArabidopsisServesasa ModelOrganismforPlantMolecular Genetics fhe ArabidopsisGenomelsRichin DevelopmentalContro Genes EmbryonicDevelopmentStartsbyEstablishinga Root-Shoot AxisandThenHaltsInsidetheSeed ThePartsof a PlantAreGeneratedSequentiallybyMeristems De