Chapter 3 The nucleus（第1页）
Chapter3Thenucleus
Althoughthehelargestandmostahecell，theprocesseswithinithaveprovedrathermoredifficulttostudythahesurrounding。Thismayhavebeehediffiicalseparationofitsts。LargelyasaresultofimprovedteologyoverthelastdeowknowthatthehemostspatiallyanizedandprobablythemostdynamicallyactivepartoftheeheproduofDNA，RNAandtheassemblyofribosomesinvolvesamassivelevelofiiooplasmandalsotrepositioningoftheents。Weshalluclearstrutheoutsideinwards，beginningwiththebouweennud—thenuvelope。
Thenuvelopeseparatestheentsfromthe，alsatandmassivemoletergebetweewoents。Sowhydotothistroublewhenprokaryoteslikebacteriahavenyetreproducethemselvesatsugrates?Successfulastheyare，atleastintermsoferiasideredessentially‘oriies’。Theyhavereachedtheirlimitassimplesinglecells，despitereprodugprolifidretainingsuffieticvariabilitytotly（andunfortunately）produtibiotitstraialnumberanismsoisequatedwithsucbaeoutontop。versely，intermsofbiologiplexity，theyarealsothemostsimplealy‘primitive’anismso。Bacteriaalsoaretheoldestatsomefourbillionyears，andassuchprovidedtherawmaterialforallsubsequehelargeststepiionoflivingthihwastheswitprokaryotictoeukaryoticizatioheaofaaierialinsideanisolatihishasledtotheproliferationaionoflifeasweknowittoday。Justhowthenucleuswasacquiredisuain，butitrobablyasaresultofphagoallbacteriumbyalargerohesmallerbacteriumthen‘tookover’troleroneorendosymbiosisoccurredwiththepartitioningoftheDNAinsideamembrahoughcellbiologyisgenerallyitheinofmitodriaandchloroplastsbye，nosususexistsfinofthenucleus。
Engthegeofthecellwithinitsownenthasfosteredthediversityweseeinbothunicellularandmulticellulareukaryoticcreatures。Eaprodud150，000differeiacrossthevariousspecializedtissuesthroughoutthebody。Thisispossibleihefactthatweonlyhave23，600gehegeicmessagebemodifiediheertrans（thetransferofinformationfromDNAtoRNA），aheheadditionofsimplechemicalstructuressuchasfatsandsugars），thusiheoverallnumberofpossibleproteinproduparisobacteriumisprobablyMyagenitalium（fenitalia）whichhasarouheongutbacteriumEscherichiacolihas4，300gehesmallestfluvirus（whieedstohijackthemaeryofthecellsitioreproduceitself）hasbut11genes。
&ioentsandhasresultediicuchlargerandmoreplexinparisontoprokaryotes。ThecircularmoleAiatotheihecellmembravariouspointsandmaystretdthewholecell。Thisisfinefeh4。6millioidebasepairs（idesequehegehecaseforE。coli。Witha1000-foldihfortheDNAinhumancellshowever，agaspeeofaroundafewhundredbasepairsfromtheoverall3。1billionbasepairshastobeeasierwhentheDNAistratedwithintheherestriofDNAtothenueukaryotecellsalsoavoidsaerferehesophisticatedwsofthecytoskeletonandielles。Therearenosusinprokaryotes，wheretheDNAisshort（andcirdthereislittleifaructure。
Thenuvelopeandporeplexes
Thenuvelopesistsoftwodistines，theoutermostbeingformedbyendoplasmicreticulum，whichisseparatedfromtheinnernuclearmembranebyaperinuclearspace（Figure5a）。Theinnernuclearmembrahaworkoffibrousproteinswhiastruownasthenuclearlamina。Boththenuclearmembrahelamiarepieruplexes，whitroltheflintoandoutofthefromverysmallmoleculesassdirectlythroughthenuvelope。Therearearound5，000poreplexesdistributedoverthesurfaceofthenumammalianuplexesaremadefrom50proteins（nus），amolecularmatheuclearporeseerandouternuclearmembranes，andalshtcable-likeproteinsioplasm，aherfibresintothenuingastructureratherlikeabasket（Figure 7d，e）。Inboesofmoleculesattachtothefibresextendingoutwardsfromthepore，ahehroughthemembraofthebasketintothenucleus。
7。Thenucleus。（a）Sethroughanintaucleus，（b）surfaceview，
withtheinternalatinexposedbyremovalofpartoftheporeuvelope，and（uuucleoskeletonafterDNAremoval，（d），（e）nuclearporesviewedfromtheoutsideahenucleus，（f）leukaemiatainingdistortednuclei
Ascaled-upanalogyofporetrafficactivitywouldilengthofdraiheporeel）throughwhichamixtureoftennisballs，golfballs，andmarbleswouldpassinbothdiresatarateof1000journeyspersed。Theflowistrolledbynuproteinswhichprojetotheel，sahevariousmolethecorrectdire。
&eincargois‘tagged’byanamihatactslikealuggagelabeltoeheyfinishosideoftheheactualpassagethroughtheporerequiresattatof‘e’proteiiins，ahroughtheporebutarethenchoppedoffasthecargoexitstheporeaao。RibosomesareassembledfromRhenudproteihe），alygeeahighlevelardlessofotheroplasmige。InaHeLamillionribosomesareproducedeachday。Seventhousandareproducedeaute，eagaround80prtheproduofhalfamillionproteieioplasm。Theseproteiedintothearateof100perporeperminute，passing（amoraffic）threeribosomalsubunitsontheirwayoutoftheaindiseasesaredirectlyassociatedwithnuproteins。Inprimarybiliarycirrhosis，proteins（autoimmuibodies）areproducedthatattaus，eveopletecirrhosisoftheliver。
Althoughthenuvelopeclearlyseparatesnud，italsophysiksthem。Proteinsesprins，whitheinnernuclearmembrane，reachacrosstheperinuclearspace，passthroughtheouternuclearmembraendforsomedistahe，wheretheyattachtothecytoskeleton。Nesprinsaresomeestproteihisattaolewithintheiheoskeletalelements（whichthemselvesareliheplasmamembrathereisapotentialmedirethecellsurfacethroughtothenuiasyetunexplainedlinkage。
Thenuclearlamina
Thenuclearlaminawasinallyvisualizedironmicroscopeasafibrousmatrixontheiheinnerheseproteisresiststretdformthe‘high-tensilecables’，closelyrelatedtotheiefilameoskeleton。Thus，thenuclearlamiheentsfrommeicalstress，andalsoaionofthehecell，providiattothecytoskeletooplasm。Astructurecalledthee，whichisthemainmicrtreofthecell，isalsokeptclosetothenuclearsurfacebyattatstothenuclearlamihesemeis，thenuclearlaminaalsoplaysamajorroleintheanizatioehgeionandthepassageofgeiatiooplasm。Geleadtodisruptionofthenuvelopeandlamiinsevereces，termed‘hies’or‘lamihesareusuallyied，aregenerallyincurable，aremelyraremusculardystrophiditioyofgeiditifrommalfungbuildingbloyightmakethemappeartrivial，butmorelikely，theseargrequirementsofbuildingananismwithoutallthefullentofcorrectpartsislikelytostopdevelmuchfartherthanafewdivisioe。
&istituentsofthenucleus
AlthoughthehavebeenreizedbyAntonievanLeeuwehelate17thtury，itwasnotuntil1831thatitortedasaspecificstruorchidepidermalcellsbyaScottishbotaBrowerknnizing‘Brow’ofpollengrainsinwater）。In1879，WaltherFlemmihenucleusbrokedownintmentsatcelldivision，followedbyre-formatioscalledakehedaughtercells。Itwasnotuntil1902thatWalterSuttonandTheodorBoveriilylinkedesdirealiaahan’sworkwithfruitflies（Drosophila）atthestartofthe20thturyshowedspecificcharacterspositiohelengthofthees，followedbytherealizationbyOswaldAveryin1944thatthegeerialwasDNA。Someer，JamesWatsonandFrancisCrickshowedthestructureofDNAtobeadoublehelix，forwhichtheysharedtheNobelPrizein1962withMauris，whoselaboratoryhadprovidedtheevideledtothediscovery。RosalindFranklin，whoseX-raydiffraagesofDNAfromtheWilkinslabhadbeeoDNAstructure，dieded37in1958，andNobelPrizesarehumously。WatsonandCrickpublishedtheclassicdoublehelixmodelin1953。ThefihejigsawofDNAstructureroducedbyWatsoionthatthepairiidebases，adehymineaosionlyprovidedtherungsholdiingladderofDalsoprovidedacodeforaccuratereplidatemplateforproteinassembly。tiudyaethebasepairingrequiredfproteins，ahefual‘dogma’that‘DNAmakesRNAandRein’。ThediscoveryofDNAstructuremarkedanenormousadvanbiology，probablythemostsignifi’spubliof inofSpecies。
WehavealotofDNA
Ifthedouble-strandedDNAineaucleuswaslaidoutasasiwouldmeasurearoundoneandahalfmetresihegeiationitcarriesisstoredintheorderoffouridebases—e（e（G），adenine（A），a）—aloh。GroupsofthreebaseseniAeheamiT—phenylalanine）。AsinglegenemayrequirehuhousandsofbasestogeeasiermsoftheinformatithislengthofDNA，itwouldtake200telephooprihreebillionbasesequences。
Allthe23，600humangeintoaround2cmofourDNA，whichleaves98。5%uhiswasinallysideredtobe‘junk’Dermjunkisperhapsmoreiheignoranceofearlyreseardthus‘nong’（i。e。notgfenes）isabetterdes。AsitseemsuhecellshouldgotothetroubleofrepligmorethahsofitsDimeitdividesfornoreason，wewoulddobesttosiderthisvastmajorityofourDNAtohaveanunkhannofun。Atleastsomenon-Aislyimportanttothecell，asdamagerestrion-gregioobejustaseffectiveatgcelldeathasthatingregions。NonAspseudogeareomakeproteiheremainsofinformationaccumulatedoveraioime，whichmaybesilentformilliobereactivatedaransenon-AalmostlyrepresentstheincorporationofviralDNAfrompastiioed，individualsrarelypletelylosevirusDionarytimesscales，thesescnifits，estimatedat8%forthehumangenome。
&hemselvesareplexstructures，havingastartier）builtintothebeginningofeadainator）attheend。Amidthegsequehereareinterveningnon-gsequerons），whiovedbeforeuse。Ingeneral，ifaprimitiveanismhasapartie，thenanismsplexitywillanumberenesinproportioioiohissuggeststhatwithtime，geenduplidtheheirsequeely。
Hoackaged?
Toaodateoneandahalfmetresofdouble-strahinaspheriucleusroughlyohousandthofthislength，itisclearthattheDNAhastobepaafairlysophistier。Pagsuoleculemustalleobeaccessible，andalsoforthewholeoftheDobeduplicatedsothatexactbepassedtoeachdaughtercell。AtcelldivisioebloAwhichexistwithinthearenotvisibleasdistinctbodies，uherlevelsofdsuperg，aprocessdensation。Thisproducesthediseswhicharethefamiliarimageeer（Figure 8c，d，e）。Duringfinalesation，thenuvelopeisbrokendown，andtheesaredistributedtoeachdaughtercell（seeChapter4formoredetails）。heineachdaughtercell，duringwhichtherigidandrod-likeesappeartolosetheirindividualidentityastheydeseaotheoverallstructureofthedaughteruclei。Thequestionofwhereesgoinnon-dividing（interphase）nucleiwasauryaftertheirinitialdiscoverythankstoateiquecalledfluoressituhybridization（FISH），edbyJoeGallandMary-LouParduein1969。Arelatedteiquecalledepaintingiiplefluorestprobes，allowingindividualesthierphasenucleus。epaintingshowsthateaeoccupiesadistiorywithinthenucleus，usuallywithattatsatthenuclearlamina。Interphaseesoccupyabouthalfoftheinternalnuclearspace，therestbeingfilledbyahostofothernupos，suudCajalbodies（seelater）。Thetsofthenucleusarebynomeahereisatfiuxaofallnupohlongandshortdistances，whichrequiresenergy。
8。DNAandes。（a）NakedDNAandnuake‘beads’，（b）atihinthenucleus，（anes（knoe），（d）esduringfiion，and（e）humaaphasees
Althoughitis‘naked’inprokaryotes，Diccellsisalwaysassociatedwithothermoledispackagedviaaseriesofstages。HumanDNAisfirstbihgroupsofstructuralproteiohefirststageofpag，DNAbeesedtwidgroupsofeighthistooformastruownasanue，leadingtoa‘beadsappearance（Figure 8a）。AdjauestheachedtoeachotherbyaonecalledH1，inazig-zagfashiafibreteresihisfibreistheoasolenoidfiguration（ahollowtube30resier）calledatin。atiandardfiguratioeDNApag（Figure 8b），asintwoformscalledheteroatiiinismoredenselypackaged，produgdarkerstainiobeperipherallydistributedwithinthenucleus（Figure 7a）。MuchoftheDinhasshortidebasesequearerepeatedthousandsoftimes（repetitiveDNA）andmayhaveastructuralratherthaion，toanAwithinthenutrast，euatinismuchlesssedandained，andprisesalmostallofthegeicallyactivepartoftheDerphaseesundergofiionjustbeforedivisioiinfblogthelengthofthees，whibestaioprodusistentbandihislengthwiseseriesofsubdivisionsprovidesa‘roadmap’thathasallowedindividualgeelypositioonlyonspees，buttospecifisalohee。Duringfinalesatioinisfurtherlooped，folded，dsuperassivelyredugtheoverallDoapoihepagratioofDNAinaeatdivisionreaches10，000to1（Figure 8c，d，e）。Agoodanalogytoappreciatethisamazinganizatioakeaskippihelengthofafootballfieldandfolditintthofabouthalfaeologiceshaveshowofthehumanes（e1）hasDNAwith246millionbasepairs，anddisruptionsintheirsequencehavebeeoover350humandiseasesingdneurologiddevelopmentaldisorders。
iregenomehasbeensequesuspectthattheselvesmightbeelessrelevantbeindividual’sDNAalysed，paredroblemsdiagiallybyputer。ItisworthpointingoutthatatthetimeonlysevenindividualsohavehadtheirDheseincludeter，pioneerofDNAdeesWatson（fittingly），twoKoreans，aese，aYoruban（amemberofahniNigeria），andaleukaemiavictim。Thecostofsequehumangenomein2003wasaround$500millioreearer$250，000。Forsequengtobeafeasiblediagnostie，aethousanddollarsisthetarget，whichmaybeteologicallyfeasibleiure。However，themaihemediesisthatdiseasessucer，diabetes，orAlzheimer’sareinvariablycausedbymanyDNAvariations，makingitdifficulttoidesfiinostididtlylimitingtheideaofpersonalizedmediebasedonanindividualgehetimebeiheWelleFoundationhaveannouncedaprojecttosequenes，fromamixtureofhealthypeopleandthfromavarietyofmediditiastatistiifiparison。
Thenucleolus
&ebodieswithinthereizedbyFeliain1774andnamed‘nuucleoliarethelargestofthedistihinthenudeaucleustofive，clearlyvisiblebylightmicroscopywithoutneedforspecifig。Nucleoliareformedfromamixtureofproteinsandnucleicacids，whichareshowronmicroscopy（Figure 7c）taoa‘tripartite’iructureofafibrillartre，adensefibrillarpohegranularpo。Nucleoliaredevotedtotheprodues，aitestructurereflectsthethreeeventsthattakeplacethere:transalRer4），proalRNA，andribosomalassembly。TheDNArespoheseprocessesissituatedonfivedifferenthumanesatdivisionatsitesucleregions（NORs）。Theseregioherafterdivisiontoformthreeorfournucleoli，wheretheribosomalgeransdribosomalsubunitspartiallyassembled，readyforexportfromthehistratioransaery，prog，aooeallowsamazingratesofprodu—dividinghumancellsmaketenmillionribosomesihanaday，sothenucleolusisessentiallyaribosomefactory，withawouldhavebeentheenvyofHenryFord。
Beandsofribosomeprodu，thenucleolusisalsoremarkablyrespooaressthatacellmayexperie，oticstress，aysallucleolarstructure，asdoviraliionaarvatiooseewhetheracellishealthyorhenucleolusfirst。
Cajalbodies，snurposomes，andsplies
In1906，RamonyadridandPaviasharedtheNobelPrizefortheirworkoureofthenervoussystem。Golgidiscoveredtheapparatusorplexthattookhisname，whileddeaiothenucleolus，whichheinallycalledaccessorybodies，andweresubsequentlynamedcoiledbodiesbecauseoftheatureoftheirmainprotein，1999，JoeGallsuggestedtheyshouldbecalledCajalbodies。CajalbodiesalsobodiescalledGemsandGall’swoitledspliesandsnurposomes（similartocoiledbodiesbutrestriphibianoouclei），alliheprogofRNAintheertrans。Sainsmallnuclearriboeins（snRNPs，pronounurps’），andspliesaresiteswherespliAtakesplathelastfewyears，maranuclearbodieshavebeeified，althoughiisstilllimited。JusttomeherearePMLbodies（alsocalledKremerbodies），speckles，paraspedes。
theerior
Fromrelativelyretresearch，ithasbeeapparentthatfarfrombeioryforDNA，thenucleusisjustasvariedanddynamicastheintermsofdactivity。Thesegregatiooplasmbymembraoindividualanellesallowsroutinebiochemicalseparationandanalysis。Teasingoutdiffereherickier，astherearenosuch‘bordered’sub-ents，althoughthehighdensityofthenuititsisolationfromsfragmentedbyasohisstartingpoint，usingmassspee700humaeiifiedsofarinaEuropeancollaborationledbyAngusLamondatDuy。
Interphaseesocdhalfthetotalnue，aedfromeachotherbytheinterespace，whichisfilledwithnu，aviscousliquid，equivaleoplasmoutsidethenucleus。that，aswellashavingtheirown‘domains’，interphaseovearoundtheeriene-ries（whichhavemoreeuatinandcarrythemajorityofaes）tendtobefouralpartsofthenucleus，wheremosttransalactivitytakesplasequentlythegene-poores（whichhavemoreheteroatin）aremoreperipherallypositioned，aheihenuvelopewheretheproteinsofthenuclearlaminaprovideafibrousworkidealfortheangofents。Ifthenuclearlamihenthenormallyaiaightstrayintoatransallyactiveregionofthenudbeeinappropriatelyexpressed，ashappehediseasescalledlaminopathies，suchasDuemusculardystrophy。
Althougheleicroscopyhasproducedvastamountsofinformationsofthe，ithasbeeivelylesssuccessfulforthehisisduetotheintensepadfibrousheents，whichmakesitvirtuallyimpossibletofollowalengthofatinoveranydistahiioransmissioronmicroscopy。Addthesheersizeofthenuesthevolumeofamito）anditwouldrequire200–300serialsestobecut，colledphotographedataround100imagespersebeforeanythree-dimeioed，whichistlyask。Novelapproachessuchastheselectiveremovalofpossimplifythings。AfibrousstrubeseenbysgEMafterthebiochemicalremovalofDNAandatiworkoffibresrunningthroughthehickersesiscalledtherixofscaffold（Figure 7c）。Althoughthistypeofapproaitiallytroversialbecausetheextensivebiochemicalprotpreparationmightewstructures（artefacts）ratherthaheinalanization，theideaofafibrwthroughouttheerior（theon）isnoted。