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Libro: Molecular Biology of THE CELL (Alberts)

Contenido:
INTRODUCTIOTNO T HEC ELL
Cells and Genomes
Cell Chemistry and Biosynthesis
Proteins
BASICG ENETIMC ECHANISMS
DNA, Chromosomesa, nd Genomes
DNA Replication, Repair, and Recombination
How Cells Read the Genome: From DNA to Protein
Control of Gene Expression
METHODS
Manipulating Proteins, DNA, and RNA
Visualizing Cells
INTERNAOLR GANIZATIOONF T HEC ELL
Membrane Structure
Membrane Transport of Small Molecules and the Electrical
Propertieso f Membranes
Intracellular Compartments and Protein Sorting
Intracellular Vesicular Traffi c
EnergyC onversionM: itochondriaa nd Chloroplasts
Mechanismso f CellC ommunication
The Cytoskeleton
The Cell Cycle
Apoptosis
CELLSIN T HEIRS OCIALC ONTEXT
Cell lunctions, Cell Adhesion, and the Extracellular Matrix
Cancer
Chapters2 I-25 availableo n Media DVD-ROM
SexuaRl eproductionM: eiosis,G erm Cells,a nd Fertilization
Development of Multicellular Organisms
SpecializedT issuesS, temC ells,a nd TissueR enewal
PathogensI,n fection, and Innate Immunity
The Adaptive Immune System

Chapter 1 Cells and Genomes
THEU NIVERSAFLE ATUREOSF CELLSO N EARTH
AllC ellsS toreT heirH ereditarIyn formatioinn theS ameL inear
ChemicaCl ode( DNA)
AllC ellsR eplicateTheHier reditarIyn formatiobny Templated
Polymerization
All CellsTranscribPeo rtionso f TheirH ereditarIyn formationin to
the SameI ntermediarFyo rm( RNA)
All CellsU seP roteinsa sC atalysts
AllC ellsT ranslatRe NAi nto Proteinin the SameW ay
TheF ragmenot f GeneticIn formationC orrespondintgo One
Proteinls O neG ene
LifeR equireFs reeE nergy
AllC ellsF unctioans B iochemicFaal ctorieDse alingw itht he
SameB asicM oleculaBru ildingB locks
AllC ellsA reE ncloseidn a PlasmMa embranAec rosWs hich
Nutrientsa ndW asteM aterialMs ustP ass
A LivingC ellC anE xiswt ith FeweTr han5 00G enes
Summary
THED IVERSITOYF G ENOMESA NDT HET REEO F LIFE
CellsC anB eP oweredb y a Varietyo f FreeE nergyS ources
SomeC ellsF ixN itrogena ndC arbonD ioxidefo r Others
TheG reatesBt iochemicaDl iversityE xistsA mongP rocaryotiCce lls
TheT reeo f LifeH asT hreeP rimaryB ranchesB:a cteriaA,r chaea,
and Eucaryotes
SomeG enesE volveR apidlyO; thersA reH ighlyC onserved
MostB acteria ndA rchaeaH ave1 000-6000G enes
NewG enesA reG eneratefdr om PreexistinGg enes
GeneD uplicationGs iveR iseto Familieosf RelatedG enesW ithin
a SingleC ell
GenesC anB eT ransferreBde tweenO rganismsB,o thi n the
Laboratorayn d in Nature
SexR esultisn HorizontaEl xchangeosf GeneticIn formation
Within a Species
TheF unctiono f a GeneC anO ftenB eD educedfr om lts Sequence
MoreT han2 00G eneF amilieAs reC ommont o AllT hreeP rimary
Brancheosf theT reeo f Life
MutationsR eveatlh e Functionos f Genes
MoleculaBr iologistHs aveF ocusead Spotlighot n E coli
Summary
GENETICIN FORMATIONIN EUCARYOTES
EucaryotiCc ellsM ayH aveO riginateda sP redators
ModernE ucaryotiCc ellsE volvedfr oma Symbiosis
EucaryoteHsa veH ybridG enomes
EucaryotiGc enomesA reB ig
EucaryotiGc enomesA reR ichi n RegulatorDy NA
TheG enomeD efinesth e Programo f MulticellulaDr evelopment
ManyE ucaryoteLsi vea sS olitaryC ellst:h e Protists
A YeasSt ervesa sa MinimalM odelE ucaryote
TheE xpressioLne velso f AllT heG eneso f An OrganismC anB e
MonitoredS imultaneously
ToM akeS enseo f CellsW, eN eedM athematicCs,o mputersa,n d
QuantitativIen formation
ArabidopsHisa sB eenC hosenO ut of 300,000S pecieAs sa Model
Plant
TheW orldo f AnimalC ellsls R epresenteBdy a Worm,a Fly,
a Mousea, nda Human 36
Studiesin DrosophilPar ovidea Keyt o VertebrateD evelopment 37
TheVertebratGe enomels a Producot f RepeatedD uplication 38
GeneticR edundanclys a Problemfo r GeneticistBs,u tl t Creates
Opportunitiefso r EvolvingO rganisms
TheM ouseS erveas sa Modelf or Mammals
HumanRs eporot nT heirO wnP eculiarities
WeA reA ll Differenitn Detail
Summory
Problems
References
Chapter 2 Cell Chemistry and Biosynthesis
THEC HEMICCAOL MPONEONTFAS C ELL
CellsA reM adeF roma FewTypeosf Atoms
TheO utermosEt lectronDs etermineH owA tomsl nteract
CovalenBt ondsF ormb y the Sharingo f Electrons
ThereA reD ifferenTt ypeso f CovalenBt onds
An AtomO ftenB ehaveass i f lt Hasa FixedR adius
Waterls t heM ostA bundanSt ubstancine C ells
SomeP olarM oleculeAs reA cidsa nd Bases
FourTypeosf NoncovalenAt ttractionsH elpB ringM olecules
Togetheirn Cells
A Celll s Formedfr om CarbonC ompounds 54
CellsC ontainF ourM ajorF amilieosf SmalOl rganiMc olecules 55
SugarsP rovidea n EnergyS ourcefo r Cellsa ndA ret he Subunits
of Polysaccharides 55
FattyA cidsA reC omponentosf CellM embranesa,s W ella sa
Sourceo f EnergY
AminoA cidsA ret he Subunitso f Proteins
NucleotideAsr et heS ubunitosf DNAa ndR NA
TheC hemistroy f Cellsls Dominatedb y Macromoleculewsit h
RemarkablPer operties
NoncovalenBt ondsS pecifyB otht he PrecisSe hapeo f a
Macromolecualned i tsB indingto OtherM olecules
Summary
CATALYSIASN D THEU SEO F ENERGYB YC ELLS
CellM etabolismls O rganizedb y Enzymes
BiologicaOl rderl s MadeP ossiblbey the Releasoef HeatE nergy
from Cells
PhotosynthetOicr ganismUs seS unlightto SynthesizOer ganic
Molecules
CellsO btainE nergyb y the Oxidationo f OrganicM olecules
Oxidationa ndR eductionIn volveE lectronT ransfers
EnzymeLs owert he BarrierTsh atB lockC hemicaRl eactions
HowE nzymeFs indT heirS ubstrateTs:h eE normouRs apidityo f
MoleculaMr otions
TheF ree-EnergCyh angefo r a ReactionD etermineWs hetherlt
Can Occur
TheC oncentratioonf ReactantIsn fluencetsh e Free-Energy
Changea nda ReactionD'si rection
ForS equentiaRl eactionAs,G "V aluesA reA dditive
ActivatedC arrieMr oleculeAs reE ssentiafol r Biosynthesis
TheF ormationo f an ActivatedC arrielrs C oupledto an
EneroeticalFlva vorablRe eaction

ATPls t he MostW idelyU sedA ctivatedC arrieMr olecule
EnergyS toredin ATPls O ftenH arnessetdo JoinT woM olecules
Together
NADHa nd NADPHA rel mportantE lectronC arriers
ThereA reM anyO therA ctivatedC arrieMr oleculeisn Cells
TheS ynthesiosf BiologicaPl olymerlss Drivenb y ATpH ydrolysis
Summary
HOW CELLSO BTAINE NERGYF ROMF OOD
Glycolysils a CentraAl TP-producinpga thway
FermentationPsr oduceA TPin the Absenceo f Oxygen
Glycolysilsll ustrateHs owE nzymeCs oupleO xidationto Energy
Storage
OrganismSs toreF oodM oleculeisn SpeciaRl eservoirs
MostA nimalC ellsD eriveT heirE nergyfr om FattyA cidsB etween
Meals
Sugarsa nd FatsA reB othD egradedto AcetyCl oAi n Mitochondria
TheC itricA cidC ycleG enerateNs ADHb y OxidizingA cetyGl roups
to CO2
ElectronT ransporDt rivesth e Synthesiosf the Majorityo f the ATp
in Most Cells
AminoA cidsa nd NucleotideAsr ep arto f the NitrogenC ycle
Metabolismls O rganizeadn d Regulated
Summary
Problems
References
Chapter 3 Proteins
THES HAPAEN DS TRUCTUORFPE R OTEINS
TheS hapeo f a Proteinls Specifiedb y ltsA minoA cidS equence
ProteinsF oldi nto a Conformatioonf LowesEt nergy
Thec rH elixa ndt he B SheetA reC ommonF oldingp atterns
ProteinD omainsA reM odularU nitsf romw hichL argerp roteins
Are Built
Fewo f the ManyP ossiblPe olypeptidCe hainsW illB eU sefur
to Cells
ProteinCs anB eC lassifieindt oM anyF amilies
SequencSe earcheCsa nl dentifyC loseR elatives
SomeP roteinD omainsF ormp artso f ManyD ifferenpt roteins
CertainP airso f DomainsA reF oundT ogetheirn Manyp roteins
TheH umanG enomeE ncodeas ComplexS eto f proteins,
RevealinMgu chT hatR emainUs nknown
LargerP roteinM oleculeOs ftenC ontainM oreThanO ne
PolypeptidCe hain
SomeP roteinsF ormL ongH elicaFl ilaments
ManyP roteinM oleculeHs aveE longatedF,i brousS hapes
ManyP roteinCs ontaina SurprisinglLya rgeA mounto f
UnstructurePd olypeptidCe hain
CovalenCt ross-LinkagOesft enS tabilizeE xtracellulaprr oteins
ProteinM oleculeOs ftenS ervea sS ubunitsfo r the Assembry
of Large Structures
ManyS tructureisn CellsA reC apableo f Self-Assembly
AssemblyF actorOs ftenA idt he Formationo f Comolex
BiologicaSl tructures
Summary
PROTEINF UNCTION
AllP roteinBsi ndt o OtherM olecules
TheS urfaceC onformatioonf a ProteinD eterminelsts C hemistrv
SequencCe omparisonBse tweenp roteinF amilyM embers
HighlighCt ruciaLl igand-BindiSngit es
ProteinsB indt o OtherP roteinTs hroughS everaTl ypeso f
Interfaces
AntibodyB indingS itesA reE specialVlye rsatile
TheE quilibriuCmo nstanMt easureBsi ndingS trength
EnzymeAs reP owerfual ndH ighlyS pecifiCc atalysts
SubstratBe indingls t he FirstS tepi n EnzymeC atalysis
EnzymeSs peedR eactionbsy SelectivelSyt abilizinTgr ansitron
States
EnzymeCsa nU seS imultaneouAsc ida ndB aseC atalysis
Lysozymlell ustrateHs owa n EnzymeW orks
TightlyB oundS malMl oleculeAs dd ExtraF unctiontso prorerns
MolecularTunnCelhsa nneSl ubstrateins E nzymewsi th
MultipleC atalytiSc ites
MultienzymeC omplexeHs elpt o Increasteh e Rateo f Cell
Metabolism
TheC ellR egulatetsh e CatalytiAc ctivitieso f its Enzymes
AllostericE nzymeHs aveT woo r MoreB indingS itesT hatI nteract
TwoL igandsW hoseB indingS itesA reC oupledM ust
ReciprocalAlyf fectE achO ther'sB inding
SymmetricP roteinA ssembliePsr oduceC ooperativAel losteflc
Transitions
TheA llosteriTc ransitionin AspartatTe ranscarbamoylalsse
Understoodin AtomicD etail 173
ManyC hangesin ProteinAs reD rivenb y Protein
Phosphorylation
A EucaryotiCc ellC ontainsa LargeC ollectiono f ProteinK inases
and ProteinP hosphatases
TheR egulatioonf Cdka ndS rcP roteinK inaseSs howsH owa
ProteinC anF unctiona sa Microchip
ProteinTs hatB inda nd HydrolyzGe TPA reU biquitousC ellular
Regulators
RegulatorPy roteinCs ontrotl he Activityo f GTP-Bindinpgr oteins
by DetermininWg hetherG TPo r GDPl s Bound
LargeP roteinM ovementCs anB eG eneratedF romS malOl nes
MotorP roteinsP roduceL argeM ovementsin Cells
Membrane-BounTdra nsporterHsa rnesEs nergyto Pump
MoleculeTsh roughM embranes
ProteinsO ftenF ormL argeC omplexeTsh atF unctiona sP rotein
Machines
ProteinM achinews ith InterchangeabPlea rtsM akeE fficienUt se
of Geneticln formation
TheA ctivationo f ProteinM achineOs ftenI nvolvesP ositioning
Thema t SpecificS ites
ManyP roteinsA reC ontrolledb y MultisiteC ovalenMt odification
A ComplexN etworko f ProteinIn teractionUs nderlieCs ellF unction
Summary
Problems
References
Chapter4 DNA,C hromosomesa,n d Genomes
THES TRUCTUARNEDF UNCTIONFD NA
A DNAM oleculeC onsistosf TwoC omplementarCyh ains
of Nucleotides
TheS tructureo f DNAP rovideas Mechanismfo r Heredity
In EucaryoteDs,N Al s Encloseidn a CellN ucleus
Summory
CHROMOSOMALD NA AND ITSP ACKAGINGIN THE
CHROMATINFI BER
EucaryotiDc NAl s Packageidn toa Seto f Chromosomes
ChromosomeCso ntainL ongS tringso f Genes
TheN ucleotidSee quencoef the HumanG enomeS howsH ow
OurG enesA reA rranged
GenomeC omparisonRse veaEl volutionariClyo nserveDd NA
)equences 207
ChromosomeEsx istin DifferenSt tatesThroughotuhte Life
ofa Cell 2OB
EachD NAM oleculeT hatF ormsa LinearC hromosomMe ust
Containa CentromereT,w oT elomereas,n d ReplicatioOn rigins 2Og
DNAM oleculeAs reH ighlyC ondenseidn Chromosomes 210
NucleosomeAsr ea BasicU nito f EucaryotiCc hromosome
Structure 211
TheS tructureo fthe NucleosomCe oreP articleR evealHs ow
DNA ls Packaged Z'tZ
NucleosomeHsa vea DynamicS tructurea,n dA reF requentry
Subjectedto ChangesC atalyzebdy ATp-DependeCnth romatin-
RemodelinCg omplexes 215
NucleosomeAsr eU suallyP ackedT ogetheirn to a Compac
HeterochromaltsinH ighlyO rganizeadn dU nusuallRye sistant
to Gene Exoression
TheC oreH istonesA reC ovalentlMy odifieda t ManyD ifferenSt ites
ChromatinA cquiresA dditionaVl arietyth rought he Site-Specific
lnsertioonf a SmalSl eto f HistonVe ariants
TheC ovalenMt odificationasn dt he HistoneV ariantsA cti n
Concertto Producea "HistoneC ode"ThaHt elpst o
DeterminBei ologicaFlu nction
A Comolexo f Code-Readearn dC ode-WritePrr oteinCs anS pread
SpecifiCc hromatinM odificationfso r LongD istanceAsl onga
Chromosome
BarrieDr NAS equenceBsl ockth e Spreado f Reader-WriteCro mplexes
andT herebSy eparatNee ighborinCgh romatiDn omains
TheC hromatinin CentromereRse vealHs owH istoneV ariants
CanC reateS peciaSl tructures
ChromatinS tructureCs anB eD irectlyIn herited
ChromatinS tructureAs dd UniqueF eaturetso Eucaryotic
ChromosomFeu nction
Summary
THEG LOBALS TRUCTUROEF CHROMOSOMES
ChromosomeAsr eF oldedin to LargeL oopso f Chromatin
PolyteneC hromosomeAsr eU niquelyU sefuflo r Visualizing
ChromatinS tructures
ThereA reM ultipleF ormso f Heterochromatin
ChromatinL oopsD econdensWe hent he GenesW ithinT hemA re
Exoressed
ChromatinC anM ovet o SpecificS itesW ithint he Nucleusto
Alter Their Gene Exoression
Networkso f MacromoleculeFso rma Seto f DistinctB iochemical
Environmenitnss ideth e Nucleus
MitoticC hromosomeAsr eF ormedfr omC hromatinin lts Most
CondenseSd tate
Summary
HOWG ENOMESE VOLVE
GenomeA lterationAs reC ausedb y Failureosf the Norma
Mechanismfosr C opyinga ndM aintaininDgN A
TheG enomeS equenceosf TwoS pecieDs ifferi n Proportionto
the Lengtho fTimeThatTheyH aveS eparatelEyv olved
PhylogenetTicr eesC onstructefdro m a Comparisoonf DNA
SequenceTsr aceth e Relationshiposf All Organisms
A Comoarisoonf Humana ndM ouseC hromosomeSsh ows
Howt he Structureosf GenomesD iverge
TheS izeo f a VertebratGe enomeR eflecttsh e RelativeR ateso f
DNAA dditiona ndD NAL ossin a Lineage
WeC anR econstructht e Sequencoef SomeA ncientG enomes
MultispecieSse quencCeo mparisonldse ntifylm portanDt NA
Sequenceosf UnknownF unction
AccelerateCdh angesin PreviouslCy onserveSd equenceCsa n
HelpD ecipheCr riticaSl tepsin HumanE volution
GeneD uplicationP rovideasn lmportantS ourceo f Genetic
NoveltyD uringE volution
DuplicatedG enesD iverge
TheE volutiono f the GlobinG eneF amilyS howsH owD NA
DuplicationCso ntributteo the Evolutioonf Organisms
GenesE ncodingN ewP roteinCs anB eC reatedb y the
Recombinatioonf Exons
NeutraMl utationsO ftenS preadto BecomeF ixedin a Population,
with a Probabilittyh at Dependso n PopulationS ize
A GreatD ealC anB eL earnedfr omA nalyseosf theVariation
Among Humans
Summary
Problems
References
Chapter5 DNA ReplicationR, epaira, nd
Recombination
THEM AINTENANOCFDE N AS EQUENCES
MutationR atesA reE xtremelLyo w
LowM utationR atesA reN ecessarfoy r Lifea sW eK nowl t
Summory
DNA REPLICATIOMNE CHANISMS
Base-PairiUngn derlieDsN AR eplicatioann dD NAR epair
TheD NAR eplicatioFno rkl sA symmetrical
TheH ighF idelityo f DNAR eplicatioRn equireSs everaPl roofreading
Mechanisms
OnlyD NAR eplicatioinn the 5'-to-3'DirectioAnl lowsE fficienEt rror
Correction
A 5peciaNl ucleotide-PolymerizEinngz ymeS ynthesizeSsh ortR NA
PrimeMr oleculeosn t he LaggingS trand
SpeciaPl roteinHs elpt o OpenU pt he DNAD oubleH elixin Front
ofthe ReplicatioFno rk
A SlidingR ingH oldsa MovingD NAP olymerasoen tot he DNA
TheP roteinas t a ReplicatioFno rkC ooperatteo Forma Replication
Machine
A Strand-DirecteMdi smatchR epaiSr ystemR emoveRs eplication
ErrorsT hatE scapfer omt he ReplicatioMn achine
DNAT opoisomerasPesre venDt NAT anglingD uringR eplication
DNAR eplicatiolsnF undamentaSllyim ilairn Eucaryoteasn d
Bacteria
Summary
THEI NITIATIOANN D COMPLETIOONF DNA REPLICATION
IN CHROMOSOMES
DNAS ynthesBise ginas t ReplicatioOnr igins
BacteriaCl hromosomeTsy picallyH avea SingleO rigino f DNA
Reolication
EucaryotCich romosomeCso ntainM ultipleO riginso f Replication
In EucaryoteDsN AR eplicatioTna kesP laceD uringO nlyO neP art
of the cell cycle
DifferenRt egionos n the SameC hromosomRe eplicataet Distinct
Timesin SP hase
HighlyC ondenseCd hromatinR eplicateLsa teW, hileG enesin
LessC ondenseCd hromatinT endt o ReplicatEe arly
Well-DefineDdN AS equenceSse rvea sR eplicatioOn riginsin a
SimpleE ucaryoteth, e BuddingY east
A LargeM ultisubuniCt omplexB indsto EucaryotiOc riginso f
Reolication
TheM ammalianD NAS equenceTsh atS pecifyth e Initiationo f
ReplicatioHn aveB eenD ifficulto ldentify
NewN ucleosomeAsr eA ssembleBd ehindt he ReplicatioFno rk
TheM echanismosf EucaryotiCc hromosomDe uplicationE nsure
ThatP atternos f HistoneM odificationC anB eI nheriteo
TelomerasRee plicatetsh e Endso f Chromosomes
TelomereL engthl s Regulatebdy Cellsa ndO rganisms
Summary
DNA REPAIR
WithoutD NAR epairS, pontaneouDsN AD amageW ouldR apidly
ChangeD NAS equences
TheD NAD oubleH elixl s ReadilyR epaired
DNAD amageC anB eR emovedb y MoreThanO neP athway
CouplingD NAR epaitro TranscriptioEnn sureTsh att he Cell'sM ost
lmportantD NAl sE fficientlRy epaired
TheC hemistroy f the DNAB asesF acilitateDsa mageD etection
SpeciaDl NAP olymeraseAsr eU sedi n Emergencietos RepaiDr NA
Double-StranBdr eakAs reE fficientlRy epaired
DNAD amageD elaysP rogressioonf the CellC ycle
Summary
HOMOLOGOURSE COMBINATION
HomologouRs ecombinatioHna sM anyU sesin the Cell
HomologouRs ecombinatioHna sC ommonF eatureisn All Cells
DNAB ase-PairinGgu idesH omologouRs ecombination
TheR ecAP roteina nd its HomologsE nablea DNA5 ingleS trand
to Pairw ith a HomologouRs egiono f DNAD oubleH elix
BranchM igrationC anE itherE nlargeH etrodupleRx egionos r
ReleasNe ewlyS ynthesizeDdN Aa sa SingleS trand
HomologouRse combinatioCna nF lawlessRlye paiDr ouble-
StrandeBd reakisn DNA
CellsC arefullyR egulatteh e Useo f HomologouRs ecombination
in DNA Repair
HollidayJ unctionsA reO ftenF ormedD uringH omologous
RecombinatioEnv ents
MeioticR ecombinatioBne ginsw ith a programmedD ouble-
StrandB reak
HomologouRs ecombinatioOnf tenR esultisn GeneC onversron
MismatchP roofreadinPgr eventps romiscuouRs ecombinatron
BetweenT woP oorlyM atchedD NAS equences
Summary
TRANSPOSITIOANN D CONSERVATISVIET E-SPECIFIC
RECOMBINATION
FROM RNATO PROTEIN 366
An mRNAS equencles Decodedin Setso fThreeN ucleotide 367
IRNAM oleculeMs atchA minoA cidst o Codonsin mRNA 368
tRNAsA reC ovalentlMy odifiedB eforeT heyE xitf romt he Nucleus 369
SpecificE nzymeCs oupleE achA minoA cidt o ltsA ppropriateIR NA
Molecule
Editingb y RNAS ynthetaseEsn sureAs ccuracy
AminoA cidsA reA ddedt o the C-terminaEl ndo f a Growing
PolypeptidCe hain
TheR NAM essagels Decodedin Ribosomes
ElongationF actorsD riveT ranslatioFno rwarda nd lmprovelt s
Accuracy 377
TheR ibosomels a Ribozyme 379
NucleotideS equenceisn mRNAS ignaWl heret o StartP rotein
Synthesis 379
StopC odonsM arktheE ndo fTranslation 381
ProteinAs reM adeo n Polyribosomes 391
ThereA reM inorVariationins the StandardG eneticC ode 392
Inhibitorso f ProcaryotiPcr oteinS ynthesiAsr eU sefual s
Antibiotics
Accuraciyn TranslatioRn equiretsh e Expendituroef FreeE nergy
QualityC ontroMl echanismAsc tt o PrevenTtr anslatioonf Damaqed
mRNAs
SomeP roteinsB egint o FoldW hileS tillB eingS ynthesized
MoleculaCr haperoneHse lpG uidet he Foldingo f Mostp roteins
ExposedH ydrophobiRc egionsP rovideC ritica5l ignalsfo r protein
QualityC ontrol
TheP roteasomles a CompartmentalizePdr oteaswe ith
SequestereAdc tiveS ites
An ElaboratUe biquitin-ConjugatinSgy stemM arksP roteinfso r
Destruction
ManyP roteinAs reC ontrolledb y RegulateDd estruction
AbnormallyF oldedP roteinCs anA ggregateto CauseD estructive
Human Diseases 396
ThereA reM anyS tepsF romD NAt o Protein 3gg
Summory 3gg
THER NAW ORLDA NDT HEO RIGINSO F LIFE 4OO
LifeR equireSs toredI nformation 401
PolynucleotideCsa nB othS toreI nformationa ndC atalyze
ThroughT ranspositioMn,o bileG eneticE lementCs anI nsertl nto
Any DNA Sequence y7
DNA-OnlyTransposoMnosv eb y BothC ut-and-pasaten d Replicative
Mechanisms 317
SomeV irusesU sea TranspositioMne chanismto MoveT hemselves
intoH ostC ellC hromosomes 319
Retroviral-likRee trotransposoRnse semblRe etrovirusebsu, t Lacka
Protein Coat 320
A LargeF ractiono f the HumanG enomels C omoosedo f
NonretroviraRl etrotransposons 32,l
DifferenTt ransposabElel ementps redominatein Different
Organisms 322
GenomeS equenceRse veatlh e ApproximatTei mest hat
TransposabElel ementHs aveM oved 323
ConservativSei te-SpecifRice combinatioCna nR eversibly
RearrangDeN A 323
ConservativSei te-SpecifRice combinatioWn asD iscovereidn
Bacteriophag)e, n+
ConservativSei te-SpecifRice combinatioCna nB eU sedt o Turn
GenesO n or Off
Summary
Problems
References
Chapter 6 How Cells Read the Genome: From
DNA to Protein
FROMD NATOR NA
Portionso f DNAS equencAe reT ranscribeidn to RNA
TranscriptioPnr oduceRs NAC omplementartyo OneS trando f DNA
CellsP roduceS everaTl ypeso f RNA
SignalsE ncodedin DNAT ellR NAp olymerasWe heret o Starta nd
Stop
TranscriptioSnt arta nd StopS ignalsA reH eterogeneouins
NucleotideS equence
TranscriptioInn itiationin EucaryoteRse quireMs anyp roteins
RNAP olymeraslel R equireGs eneraTl ranscriptioFna ctors
Polymeraslel A lsoR equireAs ctivatorM, ediatora, ndC hromatin-
ModifyingP roteins
TranscriptioEnlo ngatioPnr oduceSsu perhelicTael nsioinn DNA
TranscriptioEnl ongationin EucaryotelsT ightlyC oupledto RNA
Processing
RNAC appingls t he FirstM odificationo f Eucaryotipcr e-mRNAs
RNAS plicingR emoveIsn tronS equencefsro m NewlyTranscribed
Pre-mRNAs
NucleotidSee quenceSsig naWl hereS plicinOg ccurs
RNAS plicingls Performedb y the Spliceosome
TheS pliceosomUes esA TPH ydrolysitso producea ComplexS eries
of RNA-RNAR earrangements
OtherP ropertieosf Pre-mRNaAn d lts SynthesiHs elpt o Explain
the Choiceo f ProperS pliceS ites
A Second5 eto f snRNPSsp licea SmallF ractiono f IntronS equences
in Animalas ndP lants
RNAS plicingS howsR emarkablpel asticity
Spliceosome-CatalyRzeNdA S plicingp robablyE volvedfr om
Self-SpliciMnge chanisms
RNA-ProcessiEnngz ymeGs eneratteh e 3, Endo f Eucaryotimc RNAs
MatureE ucaryotimc RNAsA reS electivelEyx portedfr omt ne
Nucleus
ManyN oncodingR NAsA reA lsoS ynthesizeadn d processeidn the
Nucleus
TheN ucleolulss a Ribosome-produciFnagc tory
TheN ucleusC ontainsa Varietyo f SubnucleaSrt ructures
Summarv
ChemicaRl eactions
A Pre-RNWA orldM ayP redateth e RNAW orld
Single-StrandReNd AM oleculeCsa nF oldi ntoH ighlyE laborate
Structures
Self-ReplicatinMgo leculeUs ndergoN aturaSl election
HowD id ProteinS ynthesiEs volve?
All Present-DaCye llsU seD NAa sT heirH ereditarMy aterial
Summary
Problems
References
Chapter 7 Control of Gene Expression
Pathwafyr om DNAt o RNAt o Protein
Summary
AN OVERVIEWO F GENEC ONTROL 4'11
TheD ifferenCt ellT ypeso f a MulticellulaOr rganismC ontainth e
SameD NA 411
DifferenCt ellT ypesS ynthesizDei fferenSt etso f proteins 412
ExternaSl ignalsC anC ausea Cellt o Changeth e Expressioonf
Its Genes 413
GeneE xpressioCna nB eR egulateadt Manyo fthe Stepsin the
DNA-BINDINMGO TIFISN G ENER EGULATOPRRYO TEINS 416
GeneR egulatorPy roteinWs ereD iscovereUd singB acterial
Genetics
TheO utsideo f the DNAH elixC anB eR eadb y proteins
ShortD NAS equenceAsr eF undamentaClo mponentosf Genetic
Switches
GeneR egulatorPy roteinCs ontainS tructuraMl otifsT hatC an
Read DNA Seouences
TheH elix-Turn-HelMixo tifl sO neo f the Simplesat nd Most
HomeodomaiPn roteinCs onstitutea SpeciaCl lasso f Helix-Turn-
Helix Proteins
ThereA reS everalTypeosf DNA-B|ndinZgi ncF ingerM otifs
p sheetsC anA lsoR ecognizDe NA
SomeP roteinsU seL oopsT hatE ntert he Majora nd MinorG roove
to RecognizDe NA
TheL eucineZ ipperM otifM ediatesB othD NAB indinga nd Protein
Dimerization
HeterodimerizatioEnx pandtsh e Repertoiroef DNAS equenceTsh at
GeneR egulatorPy roteinCs anR ecognize
TheH elix-Looo-HeliMx otifA lsoM ediatesD imerizatioann d DNA
Binding
It ls NotYetP ossiblteo Predictth e DNAS equenceRse cognized
by AllG eneR egulatorPy roteins
A Gel-MobilitSy hiftA ssayR eadilyD etectsS equence-Specific
DNA-BindinPgr oteins
DNAA ffinityC hromatographFya cilitatetsh e Purificatioonf
Sequence-SpecDifiNc A-BindinPgr oteins
TheD NAS equencRe ecognizebdy a GeneR egulatorPy rotein
CanB eD eterminedE xperimentally
PhylogenetiFco otprintingld entifiesD NAR egulatorSy equences
ThroughC omparativGe enomics
Chromatinlm munoprecipitatioldne ntifiesM anyo f the Sites
ThatG eneR egulatorPy roteinOs ccupyin LivingC ells
Summary
HOW GENETICS WITCHEWS ORK
TheT ryptophanR epressolsr a SimpleS witchT hatT urnsG enes
On and Off in Bacteria
TranscriptionAacl tivatorTs urnG enesO n
A TranscriptionAacl tivatoar nda TranscriptionRale pressor
Controtlh e LocO peron
DNAL oopingO ccursD uringB acteriaGl eneR egulation
BacteriUas eI nterchangeabRlNe AP olymerasSeu bunittso Help
RegulateG eneT ranscription
ComplexS witchesH aveE volvedto ControGl eneT ranscription
in Eucaryotes
A EucaryotiGc eneC ontroRl egionC onsistosf a PromotePr lus
RegulatorDy NAS equences
EucaryotiGc eneA ctivatorP roteinsP romoteth e Assembloy f RNA
Polymerasaen dt he GeneraTl ranscriptioFna ctoras t the
Startpoinot f Transcription
EucaryotiGc eneA ctivatoPr roteinAs lsoM odifyL ocaCl hromatin
Structure
GeneA ctivatoPr roteinWs orkS ynergistically
EucaryotiGc eneR epressoPrr oteinsC anI nhibitT ranscription
in VariousW ays
EucaryotiGc eneR egulatorPy roteinsO ftenB indD NA
Cooperatively
ComplexG eneticS witcheTs hatR egulateD rosophilDa evelopment
AreB uiltU pf romS malleMr odules
fhe DrosophilEav eG enel s Regulatebdy CombinatoriaClo ntrols
ComplexM ammalianG eneC ontroRl egionAs reA lsoC onstructed
from SimpleR egulatorMy odules
InsulatorAs reD NAS equenceTsh atP revenEt ucaryotiGc ene
RegulatorPy roteinfsr om InfluencingD istanGt enes
GeneS witcheRs apidlyE volve
Summary
THEM OLECULAGR ENETICM ECHANISMTSH ATC REATE
SPECIALIZECDE LLTYPES
DNAR earrangemenMtse diateP haseVariatioinn B acteria
A Seto f GeneR egulatorPy roteinsD etermineCs ellT ypei n a
BuddingY east
TwoP roteinsThaRt epresEs achO ther! SynthesiDs etermineth e
HeritableS tateo f BacteriophagLea mbda
SimpleG eneR egulatorCy ircuitsC anB eU sedt o MakeM emory
Devices
TranscriptionCailr cuitAs llowt he Cellt o CanyO ut LogicO perations
SynthetiBc iologyC reateNs ewD evicefsr omE xistingB iologicaPl arts
CircadiaCn locksA reB asedo n FeedbacLko opsi n GeneR egulation
A SingleG eneR egulatorPy roteinC anC oordinatteh e Expression
of a Set of Genes
Expressioonf a CriticaGl eneR egulatorPy roteinC anT rigger
the Expressioonf a WholeB atteryo f DownstreamG enes
CombinatoriaGl eneC ontroCl reateMs anyD ifferenCt ellTypes
in Eucaryotes
A SingleG eneR egulatorPy roteinC anT riggerth e Formation
of an EntireO rgan
TheP atterno f DNAM ethylationC anB eI nheritedW hen
VertebratCe ellsD ivide
Genomilcm printingls B asedo n DNAM ethylation
CG-Riclhs landsA reA ssociatewdi th ManyG enesin Mammals
EpigenetiMc echanismEsn surTe hatS tableP atternos f
GeneE xpressioCna nB eTransmittetdo DaughteCr ells
Chromosome-WidAelt erationisn ChromatinS tructure
Can Be Inherited
TheC ontrool f GeneE xpressioins I ntrinsicallNy oisy
Summary
POST-TRANSCPRTII ONALC ONTROLS
TranscriptioAnt tenuationC ausetsh e PrematurTee rmination
of Some RNA Molecules
RiboswitcheMsi ghtR epresenAtn cientF ormso f GeneC ontrol
AlternativeR NAS plicingC anP roduceD ifferenFt ormso f a
Proteinfr omt he SameG ene
TheD efinitiono f a GeneH asH adt o BeM odifiedS inceth e
Discoveroyf AlternativeR NAS plicing
SexD eterminationinD rosophilDo ependso n a Regulated
Serieso f RNAS plicingE vents
A Changein the Siteo f RNAT ranscripCt leavagaen d Poly-A
AdditionC anC hangeth e C-terminuosf a Protein
RNAE ditingC anC hangeth eM eaningo f theR NAM essage
RNAT ransporftr omt he NucleusC anB eR egulated
Somem RNAsA reL ocalizetdo SpecificR egionos f the Cytoplasm
The5 'and3 'UntranslateRde gionosf mRNACs ontrol
TheirT ranslation
TheP hosphorylatioonf an lnitiationF actorR egulatePsr otein
SynthesGisl obally
lnitiationa t AUGC odonsU pstreamo f theT ranslatioSnt art
CanR egulateE ucaryotiTcr anslatioInn itiation
InternaRl ibosomeE ntryS itesP rovideO pportunitiefso r
TranslatioCno ntrol
Changesin mRNAS tabilityC anR egulateG eneE xpression
CytoplasmiPco ly-AA dditionC anR egulateTranslation
SmalNl oncodinRg NAT ranscripRtse gulatMe anyA nimaal nd
PlanGt enes
RNAI nterferencles a CellD efenseM echanism
RNAI nterferencCea nD irectH eterochromatFino rmation
RNAl nterferencHe asB ecomea PowerfuEl xperimentTalo ol
Summory
Problems
References
Chapter8 ManipulatingP roteinsD, NA,a nd RNA
ISOLATINCGE LLASN DG ROWINTGH EMIN C ULTURE
CellsC anB el solatedfr om IntactTissues
CellsC anB eG rowni n Culture
EucaryotiCc ellL inesA rea WidelyU sedS ourceo f
HomogeneouCse lls
EmbryoniSc temC ellsC ouldR evolutionizMee dicine
SomaticC ellN ucleaTr ransplantatioMna yP rovidea Wayt o
GenerateP ersonalizeSdt emC ells
HybridomaC ellL inesA reF actorieTsh atP roduceM onoclonal
Antibodies
Summary
PURIFYINPGR OTEINS
CellsC anB eS eparateidn toT heirC omponenFt ractions 510
CellE xtractPs rovideA ccessiblSey stemtso StudyC ellF unctions 511
ProteinCs anB eS eparatebdy Chromatography 512
AffinityC hromatographEyx ploitsS pecificB indingS iteso n
Proteins 513
Genetically-EngineeTreadg sP rovidea n EasyW ayt o Purify proteins
PurifiedC ell-FreSey stemAs reR equiredfo r the preciseD issectioonf
MoleculaFru nctions
Summory
ANALYZINGP ROTEINS
ProteinCs anB eS eparatebdy SDSp olyacrylamide-Gel
Electrophoresis
SpecificP roteinCs anB eD etectedb y Blottingw ith Antibodies
MassS pectrometrPy rovideas HighlyS ensitivMe ethod
for ldentifyingU nknownp roteins
Two-DimensionSaelp aratioMne thodsa reE specialplyo werful
HydrodynamMice asuremenRtse veathl eS izea ndS hapeo f
a Proteinc omolex
Setso f InteractingP roteinCs anB el dentifiedb y Biochemical
Methods
Protein-ProteiInn teractionCs anA lsoB el dentifiedb y a
Two-HybriTd echniquein yeast
CombiningD ataD erivedfr om DifferentTechniquperso duces
ReliablPer otein-lnteractMioanD s
OpticaMl ethodsC anM onitorP roteinIn teractionisn RealTime
SomeT echniqueCsa nM onitorS ingleM olecules
ProteinF unctionC anB eS electivelDy isruptedw ith Small
Molecules
ProteinS tructureC anB eD eterminedU singX -RayD iffraction
NMRC anB eU sedt o Determinep roteinS tructurein Solutron
ProteinS equencaen dS tructurep rovideC luesA boutp rotein
Function
Summory
ANALYZINGA ND MANIPULATINDGN A
RestrictioNn ucleaseCsu tL argeD NAM oleculeisn to Fragments
GelE lectrophoresSise parateDs NAM oleculeos f DifferenSt izes
PurifieDd NAM oleculeCsa nB eS pecificalLlya belewd ith
Radioisotopeosr ChemicaMl arkersin yitro
NucleicA cidH ybridizatioRn eactionpsr ovidea SensitivWe ayo f
DetectingS pecificN ucleotideS equences
Northerna ndS outhernB lottingF acilitatHe ybridizatiown ith
ElectrophoreticaSlley parateNd ucleicA cidM olecules
GenesC anB eC lonedU singD NAL ibraries
TwoT ypeso f DNAL ibrarieSs erveD ifferenpt urooses
cDNAC loneCs ontainU ninterrupteCdo dingS equences
GenesC anB eS electivelAym plifiedb y pCR
CellsC anB eU sedA sF actorietso produceS oecificp roteins
Proteinas nd NucleicA cidsC anB eS ynthesizeDdi rectlyb y
ChemicaRl eactions
DNAC anB eR apidlSy equenced
NucleotideS equenceAsr eU sedt o predictt he AminoA cio
Sequenceosf Proteins
TheG enomeso f ManyO rganismHs aveB eenF ullyS equenceo
Summary
STUDYINGG ENEE XPRESSIOANN D FUNCTION
ClassicGale neticBse ginbs y Disruptinag C ellp rocesbsy Ranoom
Mutagenesis
GeneticS creenlsd entifyM utantsw ith SpecifiAc bnormalirres
MutationsC anC auseL osso r Gaino f proteinF unction
ComplementatioTne stsR eveaWl hetheTr woM utationsA re
in the SameG eneo r DifferenGt enes
GenesC anB eO rderedin Pathwaybsy EpistasAisn alysis
Genesld entifiedb y MutationsC anB eC loned
HumanG eneticPsr esent5sp eciapl roblemasn dS pecial
Opportunities
HumanG eneAs reI nheriteidn HaplotypBe locksW, hichC an
Aid in the Searchfo r MutationsThaCt auseD isease
ComplexT raitsA reI nfluencedb y MultipleG enes
ReversGe eneticsB eginsw ith a KnownG enea ndD etermines
WhichC ellP rocesseRse quirelt s Function
GenesC anB eR e-Engineereind S everaWl ays
EngineereGde nesC anB eI nsertedin tot he GermL ineo f
Many Organisms
AnimalCs anB eG eneticalAlylt ered
TransgeniPcl antsA rel mportantf or BothC ellB iologya nd
Agriculture
LargeC ollectionosf TaggedK nockoutPs rovidea Toolf or
Examinintgh eF unctioonf EveryG enein anO rganism
RNAI nterferencles a Simplea nd RapidW ayt o TestG eneF unction
ReporteGr enesa nd/ n SituH ybridizatioRn evealWheann o
Wherea Genel s Expressed
Expressioonf I ndividuaGl enesC anB eM easureUds ino
QuantitativRe T-PCR
Lipids in Cell Membranes
Phosphol ioidsS oontaneouslvF ormB i lavers
MicroarrayMs onitort he Expressioonf Thousandosf Genesa t
Chapter 9 Visualizing Cells
LOOKINGA TC ELLSIN T HEL IGHTM ICROSCOPE
TheL ightM icroscopCe anR esolveD etails0 .2p m Apart
LivingC ellsA reS eenC learlyin a Phase-Contraosrt a Differential-
In terference-ContraMsi tc roscooe
lmagesC anB eE nhanceadn dA nalyzebdy DigitaTl echniques
IntactTissueAsr eU suallyF ixeda ndS ectionedb eforeM icroscopy
SpecificM oleculeCs anB eL ocatedin Cellsb y Fluorescence
Microscopy
AntibodiesC anB eU sedt o DetectS pecificM olecules
lmagingo f ComplexThree-DimensiOobnjaelc tsls P ossible
with the OpticaMl icroscope
TheC onfocaMl icroscopPe roduceOs pticaSl ectionsb y Excluding
Out-of-FocuLsi ght 590
FluorescenPtr oteinCs anB eU sedt oTagI ndividuapl roteinsin
LivingC ellsa ndO rganisms 592
ProteinD ynamicCsa nB eF olloweidn LivingC ells 593
Light-EmittinIngd icatorCsa nM easurRe apidlCy hanging
Intracellullaorn C oncentrations 596
SeveraSl trategieAsr eA vailableb yW hichM embrane-lmpermeant
SubstanceCsa nB eI ntroducedin to Cells 597
LightC anB eU sedt o ManipulateM icroscopiOc bjectsA sW ell
As to lmageThem 598
SingleM oleculeCsa nB eV isualizebdy UsingT otaIl nternal
ReflectionF luorescencMei croscopy 5gg
IndividuaMl oleculeCsa nB eToucheadn dM ovedU singA tomic
ForceM icroscopy 600
MoleculeCs anB eL abeledw ith Radioisotopes 600
RadioisotopAerse U sedto TraceM oleculeisn Cellsa ndO rganisms6 02
Summary 603
LOOKINGA TC ELLSA ND MOLECULEISN T HEE LECTRON
MtcRoScoPE 604
TheE lectronM icroscopRe esolvetsh e FineS tructureo fthe Cell 604
BiologicaSlp ecimenRse quirSe peciaPl reparatiofonr t heE lectron
Microscope 605
SpecifiMc acromoleculCeasn B eL ocalizebdy lmmunogolEd lectron
Microscopy 606
lmageso f SurfaceCsa nB eO btainedb yS canninEgl ectron
Microscopy 607
MetalS hadowingA llowsS urfaceF eaturetso BeE xamineda t
HighR esolutiobny TransmissioEnle ctronM icroscopy 60g
NegativeS taininga ndC ryoelectroMn icroscopBy othA llow
Macromoleculetos BeV ieweda t HighR esolution 6l O
Multiplelm agesC anB eC ombinetdo IncreasRee solution 610
DifferenVt iewso f a SingleO bjectC anB eC ombinedto Givea
Three-DimensionRael construction
Summary
Problems
References
Chapter 10 Membrane Structure
THEL IPIDB ILAYER 617
PhosphoglycerSidpehsin, golipaidnsd,S teroAlsr et heM ajor
TheL ipidB ilayelrs a Two-DimensionFalul id
TheF luidityo f a LipidB ilayeDr ependso n ltsC omposition
DespiteT heirF luidityL, ipidB ilayerCs anF ormD omainso f
DifferenCt omp ositions
LipidD ropletsA reS urroundebdy a PhospholipiMd onolayer
TheA symmetryo f the LipidB ilayelrs Functionalllym portant
GlycolipidAs reF oundo n the Surfaceo f All PlasmaM embranes
Summary
MEMBRANEP ROTEINS
MembraneP roteinCs anB eA ssociatewd ith the LipidB ilayeirn
VariouWs ays
LipidA nchorsC ontrotlh e MembraneL ocalizatioonf Some
SignalinPgr oteins
In MostTransmembranPero teintsh e PolypeptidCe hainC rosses
the LipidB ilayeirn an o-HelicaCl onformation
TransmembrancerH elicesO ftenl nteracwt ith OneA nother
Somep BarrelFso rmL argeTransmembrCanhea nnels
ManyM embraneP roteinAs reG lycosylated
MembraneP roteinCs anB eS olubilizeadn d Purifiedin Detergents
Bacteriorhodopslisna Light-DrivePn rotonP umpT hatT raverses
the LipidB ilayear sS evens Helices
MembraneP roteinOs ftenF unctiona sL argeC omplexes
ManyM embraneP roteinsD iffusein the Planeo f the Membrane
CellsC anC onfineP roteinas nd Lipidst o SpecificD omainsW ithin
a Membrane
TheC orticaCl ytoskeletoGni vesM embraneMs echanicaSl trength
and RestricMt embraneP roteinD iffusion
Summary
Problems
References
Patch-ClamRpe cordingIn dicatesThaInt dividuaGl atedC hannels
Openi n an All-or-NothinFga shion 680
Voltage-GateCda tionC hannelAs reE volutionarialyn dS tructurally
Related 682
Transmittercatedlo n ChannelCs onverCt hemicaSl ignalsin to
ElectricaOl nesa t ChemicaSl ynapses 682
ChemicaSl ynapseCsa nB eE xcitatoroyr Inhibitory 684
TheA cetylcholinRe eceptorast the NeuromusculJaur nctionA re
Transmitter-GatCeda tionC hannels 684
TransmitterGateldo n ChannelAs reM ajorTargetfso r Psychoactive
Drugs 686
NeuromusculTarra nsmissioInv olvetsh e SequentiaAl ctivation
of FiveD ifferenSt etso f lonC hannels
SingleN euronsA reC omplexC omputationD evices
NeuronaCl omputationR equireas Combinationo f at Least
Three Kinds of K+ Channels
Long-TermPo tentiatio(nL TPi)n the MammalianH ippocampus
Dependso n Ca2+E ntryThroughN MDA-ReceptCorh annels
Summary
Problems
References
Chapte1r 2I ntracellulaCro mpartmenatsn d
ProteinS orting 695
THEC OMPARTMENTALIZAOTFIOC NE LLS 695
AllE ucaryoCtice llsH aveth eS ameB asiSc eto f Membrane-
EncloseOdr ganelles 695
EvolutionarOy riginsE xplainth eT opologicaRl elationshiposf
Organelles
ProteinCs anM oveB etweenC ompartmentisn DifferentWays
SignaSl equenceDsi rectP roteintso the CorrecCt ellA ddress
MostO rganelleCs annotB eC onstructeDd eN ovoT: heyR equire
Informationin the Organellelt self
Summary
THET RANSPOROT F MOLECULESB ETWEENT HE NUCLEUS
ANDTHE CYTOSOL
NucleaPr oreC omplexePs erforatteh e NucleaEr nvelope
NucleaLr ocalizatioSni gnalsD irectN ucleaPr roteintso the Nucleus
Nuclealrm portR eceptorBsi ndt o BothN ucleaLr ocalization
Signalasn dN PCP roteins
NucleaEr xporWt orksL ikeN uclealrm port,B uti n Reverse
TheR anG TPaslem posesD irectionalitoyn T ransporTt hrough
NPCs
TransportThrougNhP CsC anB eR egulatebdy Controlling
Accestso theT ransPorMt achinerY
DuringM itosisth e NucleaEr nvelopeD isassembles
Summary
THETRANsPOROT F PROTEINISN TOM ITOCHONDRIA
AND CHLOROPLASTS 713
Translocatioint o MitochondriDa ependso n SignaSl equences
and ProteinTranslocators 7'13
MitochondriaPl recursoPrr oteinAs rel mporteda sU nfolded
PolypeptidCeh ains 715
ATPH ydrolysiasn da MembraneP otentiaDl riveP roteinlm port
Intot heM atrixS pace 716
Bacteriaan dM itochondriUas eS imilaMr echanismtos lnsert
Porinsin tot heirO uterM embra2n 717
TransDorInt tot he InnerM itochondriaMl embranea nd
IntermembranSep aceO ccursV iaS everaRl outes 717
TwoS ignaSl equenceDsi rectP roteintso theT hylakoid
Chapter1 1 MembraneT ransporto f SmallM olecules
and the ElectricaPl ropertieso f Membranes 651
PRINCIPLEOSF MEMBRANETRANSPORT 651
Protein-FreLeip idB ilayerAs reH ighlyl mpermeablteo lons 652
ThereA reT woM ainC lasseosf MembraneT ransporPt roteins:
Transporterasn dC hannels 652
ActiveT ransporlts M ediatedb yT ransporterCso upledto an
EnergyS ource
Summary
TRANSPORTERASN D ACTIVEM EMBRANETRANSPORT
ActiveTranspoCrta nB eD rivenb y lon Gradients
Transporterins the PlasmaM embraneR egulateC ytosolipc H
An AsymmetriDc istributiono f Transporterins EpitheliaCl ells
Underlietsh eT ranscellulTara nsporot f Solutes
ThereA reT hreeC lasseosf ATP-DrivePnu mps
TheC a2+P umpl st he Best-UnderstooPd-t ypeA TPase
TheP lasmaM embraneP -typeN a+-KP+ umpE stablishethse
Na+G radienAt crossth e PlasmaM embrane
ABCT ransporterCso nstituteth e LargesFt amilyo f Membrane
TransoorPt roteins
Summary
IONC HANNELSA NDTHEE LECTRICAPLR OPERTIEOSF
MEMBRANES 667
lon ChannelAs rel on-Selectivaen d FluctuateB etweenO pena nd
closed States 667
TheM embraneP otentiailn AnimalC ellsD ependsM ainlyo n K+L eak
Channelasn dt he K+G radienAt crossth e PlasmaM embrane 669
TheR estingP otentiaDl ecaysO nlyS lowlyWhenth e Na+-KP+ ump
ls Stopped 669
TheT hree-DimensionSatlr uctureo f a BacteriaKl +C hanneSl hows
Howa n lonC hanneCl anW ork
AquaporinAs reP ermeablteo WaterB utl mpermeablteo lons
TheF unctiono fa NeuronD ependso n lts ElongatedS tructure
Voltage-GateCda tionC hannelGs enerateA ctionP otentialisn
ElectricalElyx citablCe ells
MyelinationIn creasetsh e Speeda nd Efficiencoyf ActionP otential
Propagatioinn NerveC ells
Membranien Chloroplasts
Summary
PEROXISOMES
PeroxisomeUss eM oleculaOr xygena nd HydrogenP eroxideto
PerformO xidativeR eactions
A ShortS ignaSl equencDe irectsth e lmporto f Proteinsin to
THEE NDOPLASMIRCE TICULUM 723
TheE Rl sS tructuralalyn dF unctionalDlyi verse 724
SignaSl equenceWs ereF irstD iscovereidn proteinslm oorteo
into the Rough ER 726
A Signal-RecognitiPona rticle(S RpD) irectsE RS ignaSl equences
to a SpecificR eceptoirn the RoughE RM embrane 727
TheP olypeptidCeh ainP asseTsh rougha nA queoups orei n the
Translocator 730
TranslocatioAnc rossth e ERM embraneD oesN ot AlwaysR equire
OngoingP olypeptidCeh ainE longation 731
In Single-PaTsrsa nsmembraPnreo teinas, S ingleIn ternaEl RS ignal
SequencRee mainisn theL ipidB ilayears a Membrane-spanning
o Helix 732
Combinationosf Start-Transfaenrd S top-TransfSeirg nalsD etermine
theT opologyo f MultipasTs ransmembranpero teins 734
TranslocatePdo lypeptidCe hainsF olda ndA ssemblein the Lumen
of theR oughE R n6
MostP roteinSs ynthesizeidn the RoughE RA reG lycosylatebdy
theA dditiono f a CommonN -LinkeOd ligosaccharide 736
OligosaccharidAerse U seda sT agsto Markt he Stateo f protein
Folding 738
lmproperlyF oldedP roteinAs reE xportedfr omt he ERa nd
Degradedin the Cytosol 739
MisfoldedP roteinsin the ERA ctivatea n Unfoldedp rotein
TRANSPORFTR OMT HE IRANSG OLGIN ETWORK
TO LYSOSOMES 779
LysosomeAsr et he PrincipaSl iteso f IntracellulaDri gestion 779
LysosomeAsr eH eterogeneous 780
Planta nd FungaVl acuoleAs reR emarkabVlye rsatilLey sosomes 781
MultipleP athwayDs eliverM aterialtso Lysosomes 792
A Mannose6 -PhosphatRe eceptoRr ecognizeLsy sosomaPlr oteins
in the lrons Golgi Network
TheM 6PR eceptoSr huttlesB etweenS pecificM embranes
A SignaPl atchin the HydrolasPe olypeptidCe hainP rovides
the Cue for M6P Addition
Defectsin the GlcNAcP hosphotransferaCsaeu sea Lysosomal
StoragDe iseasien Humans
SomeL ysosomeUsn dergoE xocytosis
Summary
TRANSPORITN TOT HEC ELLF ROMT HEP LASMA
MEMBRANEE:N DOCYTOSIS
SpecializePdh agocytiCc ellsC anI ngestL argeP articles
PinocytiVc esicleFso rmf rom CoatedP itsi n the PlasmaM emorane
Not All PinocytiVc esicleAsr eC lathrin-Coated
CellsU seR eceptor-MediatEedn docytostiso lmportS elected
ExtracellulMaar cromolecules
EndocytoseMd aterialTsh atA reN ot Retrievefdr om Endosomes
End Up in Lysosomes
SpecificP roteinAs reR etrievefdr om EarlyE ndosomeasn d
Returnedto the PlasmaM embrane
MultivesiculaBro diesF ormo n the Pathwatyo LateE ndosomes
TranscytosTisra nsferMs acromoleculeAsc rossE pithelial
Cell Sheets
EpitheliaCl ellsH aveT woD istinctE arlyE ndosomaCl ompartments
but a CommonL ateE ndosomaCl omoartment
Summory
TRANSPORFTR OMT HE IRANSG OLGIN ETWORK
TOT HEC ELLE XTERIORE:X OCYTOSIS
ManyP roteinas nd LipidsS eemt o BeC arriedA utomaticallv
fromt he GolgiA pparatutso the CellS urface
SecretorVy esicleBs udf rom thefuonsG olgiN etwork
ProteinAs reO ftenP roteolyticalPlyr ocesseDdu ringt he
Formationo f SecretorVy esicles
SecretorVy esicleWs aitN eart he PlasmaM embraneU ntil
Signaledto ReleasTeh eirC ontents
RegulatedE xocytosCisa nB ea LocalizeRd esponsoef the
PlasmMa embranaen dl tsU nderlyinCgy toplasm
SecretorVy esicleM embraneC omponentAs ree uicklyR emoved
fromt he PlasmaM embrane
SomeR egulateEd xocytosEisv entsS erveto Enlargeth e plasma
Membrane
PolarizeCd ellsD irectP roteinfsr omt he lransG olgiN etworkt o
theA ppropriatDeo maino f theP lasmMa embrane
DifferenSt trategieGs uideM embraneP roteinas nd LipidsS electively
to the CorrecPt lasmaM embraneD omains
SynaptiVc esicleCs anF ormD irectlyfr om EndocytiVc esicles
Chapter1 4 EnergyC onversionM: itochondria
and Chloroplasts 813
THE MITOCHONDRION 815
TheM itochondrioCno ntainasn O uterM embranea,n I nner
Membranea,n dT woI nternaCl ompartments 916
TheC itricA cidC ycleG enerateHs igh-EnergEyl ectrons 817
A ChemiosmotiPcr ocesCs onvertsO xidationE nergyin to ATp 917
NADHT ransferists Electrontso OxygenT hroughT hreeL arge
RespiratoEryn zymCe omplexes gl9
AsE lectronMs oveA longt he RespiratorCyh ainE, nergyls S tored
asa n ElectrochemicParlo tonG radienAt crossth e lnner
Resoonse
SomeM embraneP roteinAs cquirea CovalentlAy ttached
Glycosylphosphatidylino(GsiptolA)l nchor
TheE RA ssembleMs ostL ipidB ilayers
Summory
Problems
References
Chapter 13 Intracellular Vesicular Traffic
THEM OLECULAMRE CHANISMOSFM EMBRANE
TRANSPOARNTD T HEM AINTENANOCFE
COMPARTMENTDAIVLE RSITY
ThereA reV ariouTsy peosf C oateVde sicles
TheA ssembolyf a ClathriCn oaDt riveVse siclFeo rmation
NotA llC oatFs ormB asket-liSkter uctures
PhosphoinositMidaerskO rganellaensd M embranDeo marns
CytoplasmPirco teinRse gulatthee p inching-Oanffd U ncoarrng
of CoatedV esicles
MonomericG TPaseCso ntroCl oatA ssembly
NotA llTranspoVrte sicleAsr eS pherical
RabP roteinsG uideV esiclTe argeting
SNAREMse diateM embranFe usion
InteractingS NARENse edt o Bep riedA partB eforeTheCy an
FunctioAn gain
ViraFl usionP roteinasn dS NAREMsa yU seS imilaFr usion
Mechanisms 764
Summary 766
TRANSPORFTR OMT HEE RT HROUGHT HEG OLGI
APPARATUS 766
ProteinsL eaveth e ERi n COPII-CoatTerda nsporVt esicles 767
OnlyP roteinTs hatA rep roperlyF oldeda ndA ssembleCd anL eave
the ER 767
VesiculaTru bularC lusterMs ediateT ransporftr omt he ERt o the
Golgi Apparatus 768
TheR etrievaPl athwayto the ERU sesS ortingS ignals 769
ManyP roteinAs reS electivelRy etainedin the Compartmentisn
WhichT heyF unction 771
TheG olgiA pparatuCs onsistosf an OrderedS erieso f
Compartments 771
OligosaccharCidhea inAs reP rocesseind t heG olgAi pparatus 773
ProteoglycanAsr eA ssembleidn the GolgiA pparatus 775
Whatl st heP urposoef Glycosyfationt 776
TranspoTrth roughth eG olgAi pparatuMs ayO ccurb yV esicular
Transporot r CisternaMl aturation 777
GolgiM atrixP roteinsH elpO rganizeth e Stack 77g
Summory 77g
Membrane
TheP rotonG radien
TheP rotonG radienDt rivesC oupledT ransporAt crossth e Inner
Membrane 822
ProtonG radientPs roduceM osto f the Cell'sA TP 822
MitochondriMaa intaina HighA TP:ADRPa tioin Cells 823
A LargeN egativeV alueo f AGf or ATPH ydrolysiMs akesA TP
Usefutlo the Cell 824
ATPS ynthasCe anF unctionin Reversteo HydrolyzAe TPa nd
Pumo Hr 826
Summary 827
ELECTRON-TRANSPCOHRATI NSA NDT HEIRP ROTOI'
PUMPS 827
ProtonsA reU nusuallEy asyto Move 827
TheR edoxP otentialls a Measureo f ElectronA ffinities 828
EfectronTransfeRresl easLea rgeA mountso fEnergy 829
SpectroscopMice thodsld entifiedM anyE lectronC arrierisn the
RespiratorCyh ain 829
TheR espiratoCryh ainIn cludesThreLea rgeE nzymCe omplexes
Embeddeidn the InnerM embrane 831
An lron-CoppeCr enterin CytochromOe xidaseC atalyzeEsf ficient
02 Reduction 832
ElectronT ransferisn the InnerM itochondriaMl embraneA reM ediated
by ElectroTnu nnelindgu ringR andomC ollisions 834
A LargeD ropi n RedoxP otentiaAl crossE acho ftheThreeR espiratory
EnzymeC omplexePs rovidetsh e Energyfo r H+P umping 835
TheH +P umpingO ccurbs y DistincMt echanismins t heThreeM ajor
EnzymeC omplexes 835
H+l onophoreUs ncoupleE lectronT ransporftr omA TPS ynthesis 836
RespiratorCyo ntroNl ormallyR estrainEsl ectronF lowThrough
the Chain 837
NaturaUl ncouolerCs onvertth e Mitochondriain BrownF ati nto
Heat-GeneratinMga chines 838
TheM itochondrionP laysM anyC riticaRl olesin CellM etabolism 838
BacteriAal soE xploiCt hemiosmotMice chanismtos H arness
Energy 839
Summary 840
CHLOROPLASTASN D PHOTOSYNTHESIS 840
TheC hloroplaslst O neM embero f the PlastidF amilyo f
Organelles 841
ChloroplastRse semblMe itochondriaB utH avea n Extra
Compartment 842
ChloroplasCtsa ptureE nergfyr omS unlighat ndU sel t to Fix
Carbon 843
CarbonF ixationls C atalyzebdy RibuloseB isphosphate
Carboxylase 844
EachC O2M oleculeT hatl s FixedC onsumeTsh reeM olecules
ofATPa ndTwoM oleculeosf NADPH 845
CarbonF ixationin SomeP lantsls C ompartmentalizetod Facilitate
Growth at Low CO2 Concentrations 846
PhotosynthesDise pendso n the Photochemistroyf Chlorophyll
Molecules 847
A PhotochemicaRle actionC enterP lusa n AntennaC omplex
Form a Photosystem 848
In a ReactionC enterL, ightE nergyC apturedb y Chlorophyll
Createas StrongE lectronD onorf roma WeakO ne 849
NoncyclicP hotophosphorylatioPnro duceBs othN ADPHa ndA TP 850
ChloroplastCsa nM akeA TPb y CyclicP hotophosphorylation
WithouMt akingN ADPH 853
PhotosystemI sa nd ll HaveR elatedS tructuresa,n dA lsoR esemble
BacteriaPl hotosystems
TheP roton-MotivFeo rcels t he Samein Mitochondrian d
Chloroplasts
CarriePr roteinisn theC hloroplaIsnt nerM embranCe ontrol
MetaboliteE xchangwe ith the Cytosol
ChloroplastAsl soP erformO therC ruciaBl iosyntheses
Summary
THEG ENETICS YSTEMOSF MITOCHONDRIAAN D
PLASTIDS
Mitochondrian dC hloroplastCso ntainC ompleteG eneticS ystems
OrganellGe rowtha ndD ivisioDn eterminteh e Numbeor f
Mitochondraian dP lastidisn a Cell
Mitochondrian dC hloroplastHsa veD iverseG enomes 859
Mitochondrian dC hloroplastPsr obablyB othE volvedfr om
EndosymbiotBica cteria 859
MitochondriHa avea RelaxeCd odonU sagea ndC anH avea
VarianGt eneticC ode
AnimalM itochondriCa ontainth e SimplesGt eneticS ystemKs nown
SomeO rganelleG enesC ontainIn trons
TheC hloroplaGste nomeo f HighePr lantsC ontainAsb out
1 20 Genes
MitochondriGale nesA reI nheritebdy a Non-Mendelian
Mechanism
OrganellGe enesA reM aternallIyn heriteidn ManyO rganisms
PetiteM utantsin YeastDs emonstratteh e Overwhelming
lmportancoef theC ellN ucleufso r MitochondriBali ogenesis
Mitochondrian d PlastidCs ontainT issue-SpeciPfirco teintsh at
AreE ncodeidn theC ellN ucleus
Mitochondrilam portM osto fT heirL ipidsC; hloroplasMtsa ke
Most of Theirs
MitochondriMa ayC ontributeto the Agingo f Cellsa ndO rganisms
WhyD o Mitochondrian dC hloroplastHsa veT heirO wn Genetic
Systems?
Summary
THE EVOLUTIONO F ELECTRON-TRANSPOCRHTA INS
TheE arliesCt ellsP robablyU sedF ermentatiotno ProduceA TP
Electron-TransoCorhta insE nabledA naerobicB acteritao Use
NonfermentablMe oleculeass T heirM ajorS ourceo f Energy
ByP rovidinga n InexhaustiblSeo urceo f ReducingP ower,
PhotosynthetBica cteriOa vercamae MajorE volutionary
Obstacle
TheP hotosynthetEicl ectron-TranspCorhta inso f Cyanobacteria
ProducedA tmospheriOc xygena nd PermittedN ewL ife-Forms
Summary
Problems
References
Chapter 15 Mechanisms of Cell Communication 879
GENERAPL RINCIPLEOSF C ELLC OMMUNICATION 879
ExtracellulaSri gnaMl oleculeBs indt o SpecificR eceptors 880
ExtracellulaSri gnaMl oleculeCs anA ctO verE itherS horto r Long
Distances 881
GapJ unctionAsl lowN eighborinCge llsto ShareS ignaling
lnformation 884
EachC elll s Programmetdo Respondto SpecifiCc ombinationosf
ExtracellulSairg naMl olecule5 884
DifferenTt ypeso f CellsU suallyR espondD ifferentltyo the Same
ExtracelluSlairg naMl olecule 885
TheF ateo f SomeD evelopingC ellsD ependso nT heirP ositionin
MorphogenG radients 886
A CellC anA ltert he Concentratioonf an lntracellulaMr olecule
QuicklyO nlyl f the Lifetimeo f the Moleculels S hort 886
NitricO xideG asS ignalsb y DirectlyR egulatintgh e Activityo f
SpecificP roteinsIn sideth eTargeCt ell 887
NucleaRr eceptorAsr eL igand-ModulateGde neR egulatory
Proteins 889
TheT hreeL argesCt lasseosf Cell-SurfacRee ceptoPr roteinsA rel on-
Channel-CoupleGd-,P rotein-Coupleadn,d E nzyme-Coupled
Receptors 891
MostA ctivatedC ell-SurfacRee ceptorRs elayS ignalVs iaS mall
Moleculeasn da Networko f IntracellulaSri gnalingP roteins 893
ManyI ntracellulSairg nalinPgr oteinFsu nctioans M oleculaSrw itches
ThatA reA ctivatedb y Phosphorylatioonr GTPB inding 895
IntracellulaSri gnalingC omplexeEs nhancteh e SpeedE, fficiency,
and Specificitoyf the Response 897
ModularI nteractionD omainsM ediateln teractionBs etween
IntracellulaSri gnalingP roteins 897
CellsC anU seM ultipleM echanismtos ResponAdb ruptlyto
a GraduallIyn creasinCgo ncentratioonfa n ExtracellulSairg nal 899
IntracellulSairg nalinNg etworkUs suallMy akeU seo f
FeedbacLko ops
CellsC anA djustTheSire nsitivittoy a Signal
SIGNALINTGH ROUGGH- PROTEIN-COUCPLEELDLsURFACREE
CEPTO(RGSP CRAs)N DS MALL
INTRACELLUMLAERD IATORS
TrimeriGcP roteinRse laSy ignaflsro mG pCRs
SomeG ProteinsR egulateth e Productiono f CyclicA Mp
Cyclic-AMP-DependPernot teinK inase(p KAM) ediatesM osr
of the Effectso f CyclicA MP
SomeG ProteinAsc tivatAe n InositoPl hospholipSidig naling
Pathwayb y ActivatingP hospholipasCe- p
Ca2+F unctionass a UbiquitouIsn tracellulMare diator
TheF requencoyf Ca2+O scillationlsn fluenceas Cell! Response
Ca2+/Calmodulin-Dependperontte inK inase(sC aM-Kinases)
MediateM anyo f the Responsteos C a2+S ignalisn AnimaCl ells
SomeG ProteinsD irectlyR egulatelo n Channels
Smella ndV isionD ependo n GPCRTsh atR egulateC yclic-
Nucleotide-GatleodnC hannels
IntracellulaMr ediatorsa nd EnzymatiCc ascadeAsm plify
ExtracellulSairg nals
GPCRD esensitizatioDne pendso n Receptopr hosphorylation
Summory
SIGNALINGTH R OUGHE NZYME-COUPLECDE LL-SURFACE
RECEPTORS
ActivatedR eceptorTyrosinKein ase(sR TKsp)h osphorylate
Themselves
PhosphorylateTdy rosineosn RTKsS ervea sD ockingS itesfo r
IntracellulSairg nalinPgr oteins
Proteinws ith SH2D omainsB indt o phosphorylateTdy rosines
RasB elongsto a LargeS uperfamiloyf MonomericG Tpases
RTKAs ctivateR asV iaA daptorsa ndG EFsE: videncfer omt he
DevelopinDg rosophilEay e
RasA ctivateas M APK inasSe ignalinMg odule
ScaffoldP roteinsH elpP revenCt ross-TaBlke tweenp aralleMl Ap
KinasMe odules
RhoF amilyG TPaseFsu nctionallCy oupleC ell-SurfacRee ceptors
to the Cytoskeleton
Pl3 -KinasPer oduceLsi pidD ockingS itesin thep lasmaM emorane
TheP l-3-Kinase-ASkitg nalingP athwayS timulateAs nimalC ellsto
Survivea ndG row
TheD ownstreamS ignalingP athwayAs ctivatedB yR TKas ndG pCRs
Overlao
Tyrosine-Kinase-AssociRaetecde ptorDs ependo n Cytoplasmic
TyrosineK inases
CytokineR eceptorAsc tivateth e JAK-STASTi gnalingp athway,
Providinga FasTt rackto the Nucleus
ProteinT yrosineP hosphataseRse verseTyrosipnheo sphorylations
SignaPl roteinso f theT GFBS uperfamilAy ctT hroughR eceptor
Serine/ThreonKinien aseasn dS mads
Serine/Threonianned T yrosinep roteinK inaseAs reS tructurally
Related
BacteriaCl hemotaxiDs ependso n a Two-ComponenSti gnaling
PathwayA ctivatedb y Histidine-Kinase-AssociRateecde ptors
ReceptoMr ethylationls Responsibfloer Adaptationin Bacterial
Chemotaxis
Summory
SIGNALINGP ATHWAYDSE PENDENOTN REGULATED
PROTEOLYSOISF LATENTG ENER EGULATORPYR OTEINS
TheR eceptoPr roteinN otchl sa LatentG eneR egulatorpyr otein
Wnt ProteinsB indt o FrizzledR eceptorasn d Inhibitt he
Degradatioonf p-Catenin
HedgehoPg roteinBsi ndt o patchedR elievinlgts I nhibition
of Smoothened
ManyS tressfualn d InflammatorSy timulAi ctT hrougha n
NFrB-DependeSnitg nalinPga thway
Summory
SIGNALINGIN PLANTS
Multicellularaitnyd C ellC ommunicatioEnv olveIdn dependently
in Plantsa ndA nimals
ReceptoSr erine/ThreoninKein aseAs ret he LargesCt lasso f
Cell-SurfacRee ceptorisn Plants
EthyleneB locksth e Degradatioonf SpecificG eneR egulatory
Proteinsin the Nucleus 957
RegulatePd ositioninogf AuxinT ransporterPsa tternPs lantG rowth 959
PhytochromeDse tectR edL ight,a ndC ryptochromeDse tectB lue
Light
Summory
Problems
References
Chapter 1 6 The Cytoskeleton
THES ELF-AssEMBALYN D DYNAMICS TRUCTUROEF
CYTOSKELETAFLIL AMENTS 965
CytoskeletaFli lamentAs reD ynamica ndA daptable 966
TheC ytoskeletoCna nA lsoF ormS tableS tructures 969
EachT ypeo f CytoskeletaFli lamenlts C onstructefdro m Smaller
ProteinS ubunits 970
FilamentFs ormedfr om MultipleP rotofilamenHtsa ve
AdvantageouPsr operties 971
Nucleationls t he Rate-LimitinSgt epi n the Formationo f
a CytoskeletaPlo lymer 973
TheTubuliann dA ctinS ubunitAs ssemblHee ad-to-Tailto
CreateP olarF ilaments 973
Microtubuleasn dA ctinF ilamentHs aveT woD istinctE nds
ThatG rowa t DifferenRt ates 975
FilamenTtr eadmillinagn dD ynamicIn stabilitAyr eC onsequences
of NucleotideH ydrolysibsy Tubulina ndA ctin 976
Treadmillinagn d DynamicIn stabilitAy id RapidC ytoskeletal
Rearrangement 980
Tubulina ndA ctinH aveB eenH ighlyC onserveDdu ring
EucaryotiEc volution 982
IntermediatFe ilamenSt tructureD ependso n TheL ateral
Bundlinga ndT wistingo f CoiledC oils 983
IntermediaFteil amentlms partM echanicSalt abilittyo
AnimaCl ells 985
DrugsC anA lterF ilamenPt olymerization 987
BacteriaCle llO rganizatioann dC ellD ivisioDn ependo n
Homologso fthe EucaryotiCc ytoskeleton 999
Summary 991
HOWCELLSR EGULATETHEIRCYTOSKELFEITLAALM ENTS 992
A ProteinC omplexC ontainingyT ubulinN ucleateMs icrotubules 992
MicrotubuleEsm anatfero mt heC entrosomine A nimaCl ells 992
ActinF ilamentAs reO ftenN ucleateda t the PlasmaM embrane 996
TheM echanismof NucleationIn fluenceLsa rge-ScaFleil ament
Organization 999
ProteinTs hatB indt o the FreeS ubunitsM odifyF ilamenEt longation9 99
SeveringP roteinsR egulateth e Lengtha nd KineticB ehavioor f
ActinF ilamentasn dM icrotubules 1000
ProteinTs hatB indA longt he Sideso f FilamentCs anE itherS tabilize
or DestabilizeThem 1OO1
ProteinsThIantt eracwt ithF ilamenEt ndsC anD ramaticalClyh ange
FilamenDt ynamics 1OO2
DifferenKt indso f ProteinsA ltert he Propertieosf RapidlyG rowing
MicrotubulEen ds
FilamentAs reO rganizedin to Higher-OrdeSrt ructureisn Cells
IntermediatFe ilamentAs reC ross-Linkeadn d Bundledln to
Strong Arrays
Cross-LinkinPgr oteinws ith DistinctP ropertieOs rganizeD ifferent
Assemblieosf A ctinF ilaments 1006
Filamina nd SpectrinF ormA ctinF ilamenWt ebs l OOg
CytoskeletaEll ementMs akeM anyA ttachmenttso Membrane 1009
Summary l0l0
MOLECULARM OTORS
Actin-BaseMd otorP roteinAs reM emberso f the Mvosin
Superfamily
ThereA reT woT ypeso f MicrotubuleM otorP roteinsK: inesinasn d
Dyneins rc14
TheS tructuraSli milaritoyf Myosina ndK inesinIn dicateas
CommonE volutionaryOrigin 1015
MotorP roteinGs enerateF orceb y CouplingA TPH ydrolysitso
ConformationCahl anqes
MotorP roteinK ineticAs reA daptedt o CellF unctions 1020
MotorP roteinMs ediateth e IntracellulaTrr ansporot f Membrane-
Microtubule-DependeMnot torP roteinGs overnS pindle
Assemblay nd Function 1077
EncloseOdr ganelles TwoM echanismCso llaboratien the Assembloy f a BipolarM itotic
TheC ytoskeletoLno calizeSsp ecificR NAM olecules
CellsR egulateM otorP roteinF unction
Summary
THEC YTOSKELETOANN D CELLB EHAVIOR
Slidingo f Myosinll andA ctinF ilamentCs auseMs uscletso
Contract
A SuddenR isein CytosoliCc a2+C oncentratioInn itiatesM uscle
Contraction
HeartM usclels a PreciseElyn gineereMda chine
of the Actin Cytoskeleton
ExtracellulaSri gnalsC anA ctivateth eT hreeR hoP rotein
FamilyM embers
ExternaSl ignalsC anD ictateth e Directiono f CellM igration
Ciliaa nd FlagellaA reM otileS tructureBs uiltf rom Microtubules
and Dyneins 1031
Constructioonf the MitoticS pindleR equireMs icrotubule
Dynamicas ndt he Interactionosf ManyM otorP roteins
ManyC ellsC anC rawlA crossA SolidS ubstratum
ActinP olymerizatioDnr ivesP lasmaM embraneP rotrusion
CellA dhesiona ndT ractionA llowC ellsto PullT hemselves
Forward 1040
Memberso f the RhoP roteinF amilyC auseM ajorR earrangements
Soindle
CentrosomDe uplicationO ccursE arlyin the CellC ycle
M-CdkI nitiatesS pindleA ssembliyn Prophase
TheC ompletiono f SpindleA ssembliyn AnimalC ellsR equires
NucleaEr nvelopeB reakdown
MicrotubuleIn stabilityIn creaseGsr eatlyin Mitosis
MitoticC hromosomePsr omoteB ipolarS pindleA ssembly
KinetochoreAst tachS isteCr hromatidtso the Spindle
Bi-OrientatiolnsA chievedb yTriala nd Error
MultipleF orcesM oveC hromosomeosn the Spindle
TheA PC/CT riggersS ister-ChromatSide paratioann dt he
Completiono f Mitosis
UnattacheCd hromosomeBsl ockS ister-ChromatSide paration:
TheS pindleA ssemblCY heckPoint
ChromosomeSse gregatien AnaphasAe and B
Reproduction
Summory
CYTOKINESIS
Actina ndM yosinll in the ContractilRe ingG eneratteh e Forcefo r
Cytokinesis
SegregateCdh romosomeAsr eP ackageidn DaughterN ucleai t
Teloohase 1o9o
Meiosisls a SoeciaFl ormo f NucleaDr ivisionIn volvedin Sexual
CommunicatioBne tweenth e Microtubulea ndA ctinC ytoskeletons 10 93
CoordinateWs hole-CePll olarizatioann dL ocomotion 1046
TheC omplexM orphologicaSl pecializatioonf NeuronsD epends
on the Cytoskeleton
Summary
Problems
References
Chapter 17 The Cell Cycle
OVERVIEOWFT HEC ELCL YCLE
TheE ucaryotiCc ellC yclels D ividedi nto FourP hases
Cell-CyclCeo ntrols S imilarin All Eucaryotes
Cell-CyclCeo ntroCl anB eD issecteGd eneticallbyy Analysiosf
YeasMt utants
Cell-CyclCeo ntroCl anB eA nalyzedB iochemicalilny Animal
Embryos
Cell-CyclCeo ntroCl anB eS tudiedin CulturedM ammalianC ells
Cell-CyclPer ogressioCna nB eS tudiedin VariousW ays
Summary
THEC ELL-CYCLCEO NTROLS YSTEM
TheC ell-CyclCeo ntroSl ystemT riggersth e MajorE ventso f the
Cell Cycle 1060
TheC ell-CyclCeo ntroSl ystemD ependso n CyclicallAy ctivated
Cyclin-DependePnrt oteinK inase(sC dks) 1062
InhibitoryP hosphorylatioann dC dkI nhibitoryP roteins(C Kls)
CanS uppresCs dkA ctivity
TheC ell-CyclCeo ntroSl ystemD ependso n CyclicaPl roteolysis
Cell-CyclCeo ntroAl lsoD ependso n TranscriptionRale gulation
TheC ell-CyclCeo ntroSl ystemF unctionas sa Networko f
BiochemicaSlw itches
Summaty
5 PHASE
S-CdkIn itiatesD NAR eplicatioOn nceP erC ycle
ChromosomDe uplicationR equireDs uplicationo f Chromatin
Structure
CohesinHs elpH oldS isteCr hromatidTso gether
Summory
MITOSIS
M-CdkD rivesE ntryI ntoM itosis
DephosphorylatioAnc tivateMs -Cdka t the Onseto f Mitosis
CondensinH elpsC onfigureD uplicatedC hromosomefos r
Separation
TheM itoticS pindlels a Microtubule-BaseMda chine
LocaAl ctivationo f RhoAT riggersA ssemblay ndC ontractiono f the
ContractileR ing 1094
heM icrotubuleosf the MitoticS pindleD etermineth e Planeo f
AnimaCl ellD ivision
TheP hragmoplasGtu idesC ytokinesiisn HigherP lants
Membrane-EnclosOedrg anelleMs ustB eD istributedto Daughter
CellsD uringC ytokinesis
SomeC ellsR epositioTnh eirS pindleto DivideA symmetrically
MitosisC anO ccurW ithoutC ytokinesis
TheG 1P hasels a StableS tateo f Cdkl nactivity
Summary
CONTROLO F CELLD IVISIONA ND CELLG ROWTH
MitogensS timulateC ellD ivision
CellsC anD elayD ivisionb y Enteringa SpecializeNdo ndividing
AbnormaPl roliferatioSni gnalsC auseC ell-CyclAer resto r
ApoptosisE, xcepitn CanceCr ells
Organisma ndO rganG rowthD ependo n CellG rowth
ProliferatinCge llsU suallyC oordinatTeh eirG rowtha nd Division
NeighboringC ellsC ompetefo r ExtracellulaSri gnaPl roteins
AnimalsC ontrolTotaCl ellM assb y UnknownM echanisms
Summary
Problems
References
Chapter 18 APoPtosis
State 1 103
MitogensS timulateG r-Cdka ndG rlS-CdAk ctivities 11 03
DNAD amageB locksC ellD ivisionT: heD NAD amageR esponse 11 05
ManyH umanC ellsH avea Built-lnL imitatioonn theN umber
of TimesT heyC anD ivide 1oo7
ProgrammeCd ellD eathE liminateUs nwantedC ells 11 1 5
ApoptoticC ellsA reB iochemicalRlye cognizable 1117
ApoptosisD ependso n an IntracellulaPrr oteolytiCc ascade
Thatl s Mediatedb YC asPases
Cell-SurfacDee athR eceptorAsc tivateth e ExtrinsiPc athway
ofApoptosis 1 120
TheI ntrinsicP athwayo f ApoptosisD ependso n Mitochondria 1121
Bcf2P roteinsR egulateth e IntrinsicP athwayo f Apoptosis 1121
lAPsI nhibitC aspases 1124
ExtracellulaSru rvivaFl actorsIn hibitA poptosisin VariousW ays '1126
EitherE xcessivoer InsufficienAtp optosiCs anC ontributeto Disease1 1 2 7
Summary 1128
problems 1128
References
Chapter1 9 CellJ unctionsC, ellA dhesion,a nd
the ExtracellulaMr atrix
CADHERAINNSD C ELL-CEALDLH ESION
CadherinMse diateC a2+-DependCenetl l-CeAlld hesioinn
All Animals
TheC adherinS uperfamiliyn VertebrateIsn cludesH undredso f
DifferenPt roteinsIn, cludinMg anyw ithS ignaling
Fu nctions
CadherinMse diateH omophiliAcd hesion
5electiveC ell-CelAl dhesionE nableDs issociateVde rtebrare
Cellsto Reassembilnet oO rganizeTd issues
CadherinCs ontrotlh e SelectivAe ssortmenot f Cells
TwistR egulateEs pithelial-MesenchyIT mraan sitions
CateninsL inkC lassicaCla dherintso the ActinC ytoskeleton
AdherenJsu nctionCs oordinatteh eA ctin-BaseMdo tilityo f
AdjacenCt ells
DesmosomJeu nctionGs iveE pitheliMa echanicSalt renqth
Cell-CeJllu nctionSse ndS ignalisn tot heC ellI nterior
SelectinMs ediatTe ransienCte ll-CeAlld hesionisn the
Bloodstream
Memberosf thel mmunoglobul5inu perfamiolyf proteins
MediateC a2+-lndependCeenltl -CeAll dhesion
ManyTypeosf CellA dhesionM oleculeAs ct in paralletlo Create
a Synapse
ScaffoldP roteinOs rganizeJ unctionaCl omplexes
Summary
TIGHTJ UNCTIONASN DT HEO RGANIZATIOONF
EPITHELIA
TightJ unctionsF orma SeaBl etweenC ellsa nda FenceB etween
MembranDe omains
ScaffoldP roteinsin JunctionaCl omplexepsl aya Keyp artI n
the Controol f CellP roliferation
Cell-CellJunctioannsd t heB asaLl aminaG overnA oico-Basal
Polaritiyn Epithelia
A SeparatSei gnalinSgy stemC ontrolpsl anaCr ellp olarity
Summary
PASSAGEWAFYRSO MC ELLT O CELLG: ApJ UNCT|ONS
AND PLASMODESMATA
GapJ unctionCs oupleC ellsB othE lectricalalyn dM etabolically
A Gap-JunctioCno nnexolns M adeU po f SixT ransmembrane
ConnexiSn ubunits
GapJ unctionHs aveD iversFeu nctions
CellsC anR egulatteh eP ermeabiliotyfT heirG apJ unctions
In PlantsP, lasmodesmaptae rformM anyo f the SameF unctions
as Gap Junctions
Summary
THE BASAL LAMINA
BasaLl aminaUe nderliAe llE pitheliaan dS urrounSd ome
NonepitheliCael lTl ypes
Lamininls a PrimarCy omponenotf theB asaLl amina
Typel VC ollagenG ivesth e BasaLl aminaT ensileS trenoth
BasaLl aminaHe aveD iversFe unctions
Summary
INTEGRINASN D CELL-MATRAIXD HESION
IntegrinsA reT ransmembranHee terodimerTsh atL inkt o tne
Cytoskeleton
IntegrinsC anS witchB etweena n Activea nda n Inactive
Conformation
IntegrinD efectsA reR esponsibfloer ManyD ifferenGt enetic
Diseases
IntegrinCs lustetro FormS trongA dhesions
ExtracellulaMra trixA ttachmentAs ctT hroughI ntegrinsto
ControCl ellP roliferatioann dS urvival
IntegrinRs ecruiItn tracellulSairg nalinpgr oteinast Siteso f Cell-
SubstratumA dhesion
IntegrinsC anP roduceL ocalizeIdn tracellulaErf fects
Summory
THEE XTRACELLUMLAART RIOX FA NIMALC ONNECTIVE
TlsSuES 1178
TheE xtracellulaMra trixl s Madea ndO rientedb y the Cells
Withinl t j179
Glycosaminoglyc(aGnA GC) hainsO ccupyL argeA mountso f
Spacea ndF ormH ydrateGd els 1179
HyaluronaAnc tsa sa SpaceF illear nda Facilitatorf CellM igration
DuringT issueM orphogenesainsd R epair 11 80
ProteoglycanAsr eC omposedo f GAGC hainsC ovalentlLyi nked
to a Core Protein
ProteoglycanCsa nR egulatteh e Activitieso f SecretedP roterns
Cell-SurfacPer oteoglycanAsc ta sC o-Receptors
CollagenAs ret he MajorP roteinos f the ExtracellulaMra trix
CollagenC hainsU ndergoa Serieso f Post-Translational
Modifications
PropeptideAsr eC lippedO ff ProcollageAnf terl ts Secretion
to AllowA ssembloyf Fibrils
SecretedF ibril-AssociatCedo llagenHs elpO rganizeth e Fibrils
CellsH elpO rganizeth e CollagenF ibrilsT heyS ecreteb y
ExertingT ensiono n the Matrix
ElastinG ivesT issueTsh eirE lasticitv
Fibronectilns a n ExtracellulaPrr oteinT hatH elpsC ellsA ttach
to the Matrix 1191
TensionE xertedb y CellsR egulateAss semblyo f Fibronectin
Fibrils
FibronectiBni ndsto IntegrinsThrouagnh R GDM otif
CellsH avet o BeA blet o DegradeM atrixa, sW ella sM akei t
MatrixD egradatiolns Localizetdo the Vicinityo f Cells
Summary
THEP LANTC ELLW ALL
TheC ompositioonf the CellW allD ependso n the CellT ype
TheT ensileS trengtho f the CellW allA llowsP lantC ellsto
DevelopT urgorP ressure
TheP rimarCy elWl all sB uiltf romC ellulosMe icrofibrils
Interwovenw ith a Networko f PecticP olysaccharides
OrientedC ell-WaDll epositionC ontrolsp lantC ellG rowth
MicrotubuleOsr ienCt ell-WaDlle position
Summary
Problems
References
Chapter 20 Cancer
CANCEAR5A MICROEVOLUTIOPNRAORCYE SS
CanceCr ellsR eproducWe ithoutR estrainatn dC olonize
OtherT issues
MostC ancerDs erivefr oma SingleA bnormaCl ell
CanceCr ellsC ontainS omatiMc utations
A SingleM utationls N otE noughto CauseC ancer
CancerDse velopG raduallfyro mI ncreasingAlyb erranCt ells
CervicaCl ancerAs reP reventebdy EarlyD etection
TumorP rogressioIn volvesS uccessivReo undso f Random
InheritedC hangeF ollowedb y NaturaSl election
TheE pigenetiCc hangeTsh atA ccumulatien CanceCr ellsI nvolve
InheriteCd hromatiSnt ructureasn dD NAM ethylation
HumanC anceCr ellsA reG eneticalUlyn stable
CancerouGs rowthO ftenD ependso n DefectiveC ontrool f
CellD eathC, ellD ifferentiatioonr, Both
CanceCr ellsA reU suallyA lteredi n TheirR esponsetos DNA
Damagea ndO therF ormso f Stress
HumanC anceCr ellsE scapae B uilt-lnL imitt o Cellp roliferation
A SmalPl opulatioonf CanceSr temC ellsM aintainMs any
Tumors
HowD o CanceSr temC ellsA rise?
ToM etastasizMe,a lignanCt anceCr ellsM ustS urvivea nd
Proliferatien a ForeignE nvlronment
TumorsIn duceA ngiogenesis
TheT umorM icroenvironmenInt fluenceCs ancer
Development
ManyP ropertieTsy picallCy ontributeto CancerouGs rowth
THEP REVENTABCLEA U5E5O FC ANCER
ManyB, utN otA ll,C ancer-CausAingge ntsD amageD NA
TumorI nitiatorDs amageD NAT; umorP romoterDso N ot
Viruseasn dO therI nfectionCso ntributteo a Significant
Proportioonf HumanC ancers
ldentificatioonf CarcinogenRse vealWs aysto Avoid
Cancer
Summary
FINDINGT HEC ANCER-CRITICGAELN ES
Thel dentificatioonf Gain-of-Functioann d Loss-of-Function
MutationsR equireDs ifferenMt ethods
RetroviruseCsa nA cta sV ectorsfo r OncogeneTsh atA lter
Cell Behavior
DifferenSt earchefso r OncogeneHs aveC onvergeodn the
SameG ene-Ras
Studieosf RareH ereditarCya nceSr yndromeFsi rsltd entified
TumorS uppressGore nes
TumorS uopressGore neCs anA lsoB el dentifiefdr omS tudies
of Tumors
BothG enetiac ndE pigenetMice chanismCsa nI nactivatTeu mor
SuppressGore nes
GenesM utatedin CanceCr anB eM adeO veractivine Many
Ways
TheH untf orC ancerCriticGael nesC ontinues
Summary
THEM OLECULARBA SISO FC ANCER-CELBLE HAVIOR
Studieosf BothD evelopinEgm bryoasn dG enetically
EngineereMdi ceH aveH elpedto Uncovetrh e Functioonf
Cancer-CritiGcaeln es
ManyC ancer-CritiGcaeln esR egulatCee llP roliferation
DistincPt athwayMs ayM ediateth e Disregulationf C ell-Cycle
Progressioan dt heD isregulatioonf C elGl rowthin
CanceCr ells
Mutationisn GeneTs hatR egulatAep optosiAsl lowC anceCr ells
to SurvivWe henT heyS houldN ot
Mutationisn thep 53G eneA llowM anyC anceCr ellsto Survive
and ProliferatDe espiteD NAD amage
DNAT umoVr iruseBs lockth eA ctiono f KeyT umorS uppressor
Proteins
TheC hangeisn T umorC ellTs hatL eadto MetastasAisr eS till
Largelya Mystery
ColorectCala ncerEsv olveS lowlyViaa S uccessionf V isible
Changes
A FewK eyG eneticL esionAs reC ommont o a LargeF ractiono f
ColorectCala ncers
SomeC olorectCala ncerHsa veD efectisn DNAM ismatcRh epair
TheS tepso f TumorP rogressioCna nO ftenB eC orrelatewd ith
SDecifMicu tations
EachC aseo f Cancelrs C haracterizebdy ltsO wn Arrayo f Genetic
Lesions
Summary
CANCERTR EATMENPT:R ESENATN D FUTURE
TheS earcfho rC anceCr uresls D ifficulbt ut NotH opeless
TraditionalTherapEiexps loitth eG enetiIcn stabilitayn dL osso f
Cell-CycCleh eckpoinRte sponseins C anceCr ells
NewD rugsC anE xploitth eS pecifiCc auseo f aT umor'Gs enetic
Instability
GeneticIn stabilityH elpsC ancerBs ecomeP rogressiveMlyo re
Resistantot Therapies
NewT herapieAs reE mergingfr omO ur Knowledgeo f Cancer
Biology
SmalMl oleculeCsa nB eD esignetdo InhibitS pecifiOc ncogenic
Proteins
TumorB loodV esselAsr eL ogicaTl argetsfo r CanceTr herapy
ManyC ancerMs ayB eTreatabbley Enhancintgh e lmmune
ResponsAeg ainsat SpecifiTcu mor
TreatinPg atientwsi thS everaDl rugsS imultaneousHlay s
PotentiaAl dvantagefso r CanceTr herapy
GeneE xpressioPnr ofilinCg anH elpC lassifCya ncerisn to
ClinicallMy eaningfuSlu bgroup

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