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ThisstylisticdiagramshowsageneinrelationtothedoublehelixstructureofDNAandtoachromosome(right).ThechromosomeisXshapedbecauseitisdividing.Intronsareregionsoftenfoundineukaryotegenesthatareremovedinthesplicingprocess(aftertheDNAistranscribedintoRNA):Onlytheexonsencodetheprotein.Thediagramlabelsaregionofonly55orsobasesasagene.Inreality,mostgenesarehundredsoftimeslonger.

GeneFromWikipedia,thefreeencyclopedia

Ageneisthemolecularunitofheredityofalivingorganism.Itisusedextensivelybythescientificcommunityasanamegiventosomestretchesofdeoxyribonucleicacids(DNA)andribonucleicacids(RNA)thatcodeforapolypeptideorforanRNAchainthathasafunctionintheorganism.Livingbeingsdependongenes,astheyspecifyallproteinsandfunctionalRNAchains.Genesholdtheinformationtobuildandmaintainanorganism'scellsandpassgenetictraitstooffspring.Allorganismshavegenescorrespondingtovariousbiologicaltraits,someofwhichareinstantlyvisible,suchaseyecolorornumberoflimbs,andsomeofwhicharenot,suchasbloodtype,increasedriskforspecificdiseases,orthethousandsofbasicbiochemicalprocessesthatcompriselife.ThewordgeneisderivedfromtheGreekwordgenesismeaning"birth",orgenosmeaning"origin"(seepangenesis).

Amodernworkingdefinitionofageneis"alocatableregionofgenomicsequence,correspondingtoaunitofinheritance,whichisassociatedwithregulatoryregions,transcribedregions,andorotherfunctionalsequenceregions".[1][2]Colloquialusageofthetermgene(e.g.,"goodgenes","haircolorgene")mayactuallyrefertoanallele:ageneisthebasicinstructionasequenceofnucleicacids(DNAor,inthecaseofcertainvirusesRNA),whileanalleleisonevariantofthatgene.Thus,whenthemainstreampressrefersto"having"a"gene"foraspecifictrait,thisiscustomarilyinaccurate.Inmostcases,allpeoplewouldhaveageneforthetraitinquestion,althoughcertainpeoplewillhaveaspecificalleleofthatgene,whichresultsinthetraitvariant.Further,genescodeforproteins,whichmightresultinidentifiabletraits,butitisthegene(genotype),notthetrait(phenotype),whichisinherited.

Biggenesareaclassofgeneswhosenucleartranscriptspans500kb(1kb=1,000basepairs)ormoreofchromosomalDNA.Thelargestofthebiggenesisthegenefordystrophin,whichspans2.3Mb.ManybiggeneshavemodestlysizedmRNAstheexonsencodingtheseRNAstypicallyencompassabout1%ofthetotalchromosomalgeneregioninwhichtheyoccur.

Contents

1History2Mendelianinheritanceandclassicalgenetics3Physicaldefinitions



ThechemicalstructureofafourbasefragmentofaDNAdoublehelix.

GregorMendel

3.1RNAgenesandgenomesintheworld3.2Functionalstructureofagene3.3Chromosomes

4Geneexpression4.1Geneticcode4.2Transcription4.3Translation

5DNAreplicationandinheritance5.1Molecularinheritance

6Mutation7Genome

7.1Chromosomalorganization7.2Numberofgenes7.3Geneticandgenomicnomenclature7.4Essentialgenes

8Evolutionaryconceptofagene9Genetargetingandimplications10Changingconcept11Seealso12Notesandreferences13Bibliography14Externallinks

History

TheexistenceofgeneswasfirstimpliedfromtheworkofGregorMendel(18221884),who,betweentheyearsof1857to1864planted8000commonediblepeaplantsandstudiedandtabulatedtheinheritancepatternsinpeaplants(Pisum)trackinginheritanceoftraitsfromparenttooffspringanddescribingthesemathematicallyas2ncombinationswherenisthenumberofdifferingcharacteristicsintheoriginalpeas.Althoughhedidnotusethetermgene,heexplainedhisresultsintermsofinheritedcharacteristics.Thenotionofagene[3]isevolvingwiththescienceofgenetics,butbeganwhenMendelnoticedthatbiologicalvariationsareinheritedfromparentorgrandparentorganismsasspecific,discretetraitsandaretransmittedthusunalteredfromtheoriginalsource.PriortoMendel'swork,thedominanttheoryofhereditywasoneofblendinginheritance,pangenesis,whichsuggestedthateachparentcontributedfluidstothefertilisationprocess



andthatinmeiosisthetraitsoftheparentsblendedandmixedtoproducetheoffspring.AlthoughMendel'sworkwaslargelyunrecognizedafteritsfirstpublicationin1866,itwas'rediscovered'in1900bythreeEuropeanscientists,HugodeVries,CarlCorrens,andErichvonTschermak,whoclaimedtohavereachedsimilarconclusionsintheirownresearch.However,thesescientistswerenotyetawareoftheidentityofthe'discreteunits'onwhichgeneticmaterialresides.Thebiologicalentityresponsiblefordefiningtraitswaslatertermedagene,butthebiologicalbasisforinheritanceremainedunknownuntilDNAwasidentifiedasthegeneticmaterialinthe1940s.Mendelwasalsothefirsttoshowindependentassortment,thedistinctionbetweendominantandrecessivetraits,thedistinctionbetweenaheterozygoteandhomozygote,thephenomenonofdiscontinuinginheritanceandwhatwouldlaterbedescribedasgenotype(thegeneticmaterialofanorganism)andphenotype(thevisibletraitsofthatorganism)andtheconversionofoneformintoanotherwithinfewgenerations.

CharlesDarwinusedthetermgemmuletodescribeamicroscopicunitofinheritance,andwhatwouldlaterbecomeknownaschromosomeshadbeenobservedseparatingoutduringcelldivisionbyWilhelmHofmeisterasearlyas1848.Theideathatchromosomesarethecarriersofinheritancewasexpressedin1883byWilhelmRoux.Darwinalsocoinedthewordpangenesisby(1868).[4]ThewordpangenesisismadefromtheGreekwordspan(aprefixmeaning"whole","encompassing")andgenesis("birth")orgenos("origin").

Mendel'sconceptwasgivenanamebyHugodeVriesin1889,inhisbookIntracellularPangenesisalthoughprobablyunawareofMendel'sworkatthetime,hecoinedtheterm"pangen"for"thesmallestparticle[representing]onehereditarycharacteristic".[5]DanishbotanistWilhelmJohannsencoinedtheword"gene"("gen"inDanishandGerman)in1909todescribethefundamentalphysicalandfunctionalunitsofheredity,[6]whiletherelatedwordgeneticswasfirstusedbyWilliamBatesonin1905.[7]HederivedthewordfromdeVries'"pangen".Intheearly1900s,Mendel'sworkreceivedrenewedattentionfromscientists.In1910,ThomasHuntMorganshowedthatgenesresideonspecificchromosomes.Helatershowedthatgenesoccupyspecificlocationsonthechromosome.Withthisknowledge,MorganandhisstudentsbeganthefirstchromosomalmapofthefruitflyDrosophila.In1928,FrederickGriffithshowedthatgenescouldbetransferred.InwhatisnowknownasGriffith'sexperiment,injectionsintoamouseofadeadlystrainofbacteriathathadbeenheatkilledtransferredgeneticinformationtoasafestrainofthesamebacteria,killingthemouse.

Aseriesofsubsequentdiscoveriesledtotherealizationdecadeslaterthatchromosomeswithincellsarethecarriersofgeneticmaterial,andthattheyaremadeofDNA(deoxyribonucleicacid),apolymericmoleculefoundinallcellsonwhichthe'discreteunits'ofMendelianinheritanceareencoded.In1941,GeorgeWellsBeadleandEdwardLawrieTatumshowedthatmutationsingenescausederrorsinspecificstepsinmetabolicpathways.Thisshowedthatspecificgenescodeforspecificproteins,leadingtothe"onegene,oneenzyme"hypothesis.[7]OswaldAvery,ColinMunroMacLeod,andMaclynMcCartyshowedin1944thatDNAholdsthegene'sinformation.[8]In1952,RosalindFranklinandRaymondGoslingproducedastrikinglyclearxraydiffractionpatternindicatingahelicalform,andin1953,JamesD.WatsonandFrancisCrickdemonstratedthemolecularstructureofDNA.Together,thesediscoveriesestablishedthecentraldogmaofmolecularbiology,whichstatesthatproteinsaretranslatedfromRNAwhichistranscribedfromDNA.Thisdogmahassincebeenshowntohaveexceptions,suchasreversetranscriptioninretroviruses.



Crossingbetweentwopeaplantsheterozygousforpurple(B,dominant)andwhite(b,recessive)blossoms

In1972,WalterFiersandhisteamattheLaboratoryofMolecularBiologyoftheUniversityofGhent(Ghent,Belgium)werethefirsttodeterminethesequenceofagene:thegeneforBacteriophageMS2coatprotein.[9]RichardJ.RobertsandPhillipSharpdiscoveredin1977thatgenescanbesplitintosegments.Thisledtotheideathatonegenecanmakeseveralproteins.Recently(asof20032006),biologicalresultsletthenotionofgeneappearmoreslippery.Inparticular,genesdonotseemtositsidebysideonDNAlikediscretebeads.Instead,regionsoftheDNAproducingdistinctproteinsmayoverlap,sothattheideaemergesthat"genesareonelongcontinuum".[1]Itwasfirsthypothesizedin1986byWalterGilbertthatneitherDNAnorproteinwouldberequiredinsuchaprimitivesystemasthatofaveryearlystageoftheearthifRNAcouldperformassimplyacatalystandgeneticinformationstorageprocessor.

ThemodernstudyofgeneticsatthelevelofDNAisknownasmoleculargeneticsandthesynthesisofmoleculargeneticswithtraditionalDarwinianevolutionisknownasthemodernevolutionarysynthesis.

Mendelianinheritanceandclassicalgenetics

AccordingtothetheoryofMendelianinheritance,variationsinphenotypetheobservablephysicalandbehavioralcharacteristicsofanorganismaredueinparttovariationsingenotype,ortheorganism'sparticularsetofgenes,eachofwhichspecifiesaparticulartrait.Differentformsofagene,whichmaygiverisetodifferentphenotypes,areknownasalleles.OrganismssuchasthepeaplantsMendelworkedon,alongwithmanyplantsandanimals,havetwoallelesforeachtrait,oneinheritedfromeachparent.Allelesmaybedominantorrecessivedominantallelesgiverisetotheircorrespondingphenotypeswhenpairedwithanyotheralleleforthesametrait,whereasrecessiveallelesgiverisetotheircorrespondingphenotypeonlywhenpairedwithanothercopyofthesameallele.Forexample,iftheallelespecifyingtallstemsinpeaplantsisdominantovertheallelespecifyingshortstems,thenpeaplantsthatinheritonetallallelefromoneparentandoneshortallelefromtheotherparentwillalsohavetallstems.Mendel'sworkdemonstratedthatallelesassortindependentlyintheproductionofgametes,orgermcells,ensuringvariationinthenextgeneration.

Physicaldefinitions

RNAgenesandgenomesintheworld

Whenproteinsaremanufactured,thegeneisfirstcopiedintoRNAasanintermediateproduct.Inothercases,theRNAmoleculesaretheactualfunctionalproducts.Forexample,RNAsknownasribozymesarecapableofenzymaticfunction,andmicroRNAhasaregulatoryrole.TheDNAsequencesfromwhichsuchRNAsaretranscribedareknownasRNAgenes.

SomevirusesstoretheirentiregenomesintheformofRNA,andcontainnoDNAatall.BecausetheyuseRNAtostoregenes,theircellularhostsmaysynthesizetheirproteinsassoonastheyareinfectedandwithoutthedelayinwaitingfortranscription.Ontheotherhand,RNAretroviruses,suchasHIV,require



Diagramofthe"typical"eukaryoticproteincodinggene.PromotersandenhancersdeterminewhatportionsoftheDNAwillbetranscribedintotheprecursormRNA(premRNA).ThepremRNAisthensplicedintomessengerRNA(mRNA)whichislatertranslatedintoprotein.

thereversetranscriptionoftheirgenomefromRNAintoDNAbeforetheirproteinscanbesynthesized.In2006,FrenchresearcherscameacrossapuzzlingexampleofRNAmediatedinheritanceinmice.MicewithalossoffunctionmutationinthegeneKithavewhitetails.OffspringofthesemutantscanhavewhitetailsdespitehavingonlynormalKitgenes.TheresearchteamtracedthiseffectbacktomutatedKitRNA.[10]WhileRNAiscommonasgeneticstoragematerialinviruses,inmammalsinparticularRNAinheritancehasbeenobservedveryrarely.

Functionalstructureofagene

ThevastmajorityoflivingorganismsencodetheirgenesinlongstrandsofDNA(deoxyribonucleicacid).DNAconsistsofachainmadefromfourtypesofnucleotidesubunits,eachcomposedof:afivecarbonsugar(2'deoxyribose),aphosphategroup,andoneofthefourbasesadenine,cytosine,guanine,andthymine.ThemostcommonformofDNAinacellisinadoublehelixstructure,inwhichtwoindividualDNAstrandstwistaroundeachotherinarighthandedspiral.Inthisstructure,thebasepairingrulesspecifythatguaninepairswithcytosineandadeninepairswiththymine.Thebasepairingbetweenguanineandcytosineformsthreehydrogenbonds,whereasthebasepairingbetweenadenineandthymineformstwohydrogenbonds.Thetwostrandsinadoublehelixmustthereforebecomplementary,thatis,theirbasesmustalignsuchthattheadeninesofonestrandarepairedwiththethyminesoftheotherstrand,andsoon.

Duetothechemicalcompositionofthepentoseresiduesofthebases,DNAstrandshavedirectionality.OneendofaDNApolymercontainsanexposedhydroxylgrouponthedeoxyribosethisisknownasthe3'endofthemolecule.Theotherendcontainsanexposedphosphategroupthisisthe5'end.ThedirectionalityofDNAisvitallyimportanttomanycellularprocesses,sincedoublehelicesarenecessarilydirectional(astrandrunning5'3'pairswithacomplementarystrandrunning3'5'),andprocessessuchasDNAreplicationoccurinonlyonedirection.Allnucleicacidsynthesisinacelloccursinthe5'3'direction,becausenewmonomersareaddedviaadehydrationreactionthatusestheexposed3'hydroxylasanucleophile.

TheexpressionofgenesencodedinDNAbeginsbytranscribingthegeneintoRNA,asecondtypeofnucleicacidthatisverysimilartoDNA,butwhosemonomerscontainthesugarriboseratherthandeoxyribose.RNAalsocontainsthebaseuracilinplaceofthymine.RNAmoleculesarelessstablethanDNAandaretypicallysinglestranded.Genesthatencodeproteinsarecomposedofaseriesofthree



nucleotidesequencescalledcodons,whichserveasthewordsinthegeneticlanguage.Thegeneticcodespecifiesthecorrespondenceduringproteintranslationbetweencodonsandaminoacids.Thegeneticcodeisnearlythesameforallknownorganisms.

AllgeneshaveregulatoryregionsinadditiontoregionsthatexplicitlycodeforaproteinorRNAproduct.Aregulatoryregionsharedbyalmostallgenesisknownasthepromoter,whichprovidesapositionthatisrecognizedbythetranscriptionmachinerywhenageneisabouttobetranscribedandexpressed.Agenecanhavemorethanonepromoter,resultinginRNAsthatdifferinhowfartheyextendinthe5'end.[11]Althoughpromoterregionshaveaconsensussequencethatisthemostcommonsequenceatthisposition,somegeneshave"strong"promotersthatbindthetranscriptionmachinerywell,andothershave"weak"promotersthatbindpoorly.Theseweakpromotersusuallypermitalowerrateoftranscriptionthanthestrongpromoters,becausethetranscriptionmachinerybindstothemandinitiatestranscriptionlessfrequently.Otherpossibleregulatoryregionsincludeenhancers,whichcancompensateforaweakpromoter.Mostregulatoryregionsare"upstream"thatis,beforeortowardthe5'endofthetranscriptioninitiationsite.Eukaryoticpromoterregionsaremuchmorecomplexanddifficulttoidentifythanprokaryoticpromoters.

Manyprokaryoticgenesareorganizedintooperons,orgroupsofgeneswhoseproductshaverelatedfunctionsandwhicharetranscribedasaunit.Bycontrast,eukaryoticgenesaretranscribedonlyoneatatime,butmayincludelongstretchesofDNAcalledintronswhicharetranscribedbutnevertranslatedintoprotein(theyaresplicedoutbeforetranslation).Splicingcanalsooccurinprokaryoticgenes,butislesscommonthanineukaryotes.[12]

Chromosomes

Thetotalcomplementofgenesinanorganismorcellisknownasitsgenome,whichmaybestoredononeormorechromosomestheregionofthechromosomeatwhichaparticulargeneislocatediscalleditslocus.Achromosomeconsistsofasingle,verylongDNAhelixonwhichthousandsofgenesareencoded.Prokaryotesbacteriaandarchaeatypicallystoretheirgenomesonasinglelarge,circularchromosome,sometimessupplementedbyadditionalsmallcirclesofDNAcalledplasmids,whichusuallyencodeonlyafewgenesandareeasilytransferablebetweenindividuals.Forexample,thegenesforantibioticresistanceareusuallyencodedonbacterialplasmidsandcanbepassedbetweenindividualcells,eventhoseofdifferentspecies,viahorizontalgenetransfer.Althoughsomesimpleeukaryotesalsopossessplasmidswithsmallnumbersofgenes,themajorityofeukaryoticgenesarestoredonmultiplelinearchromosomes,whicharepackedwithinthenucleusincomplexwithstorageproteinscalledhistones.ThemannerinwhichDNAisstoredonthehistone,aswellaschemicalmodificationsofthehistoneitself,areregulatorymechanismsgoverningwhetheraparticularregionofDNAisaccessibleforgeneexpression.Theendsofeukaryoticchromosomesarecappedbylongstretchesofrepetitivesequencescalledtelomeres,whichdonotcodeforanygeneproductbutarepresenttopreventdegradationofcodingandregulatoryregionsduringDNAreplication.Thelengthofthetelomerestendstodecreaseeachtimethegenomeisreplicatedinpreparationforcelldivisionthelossoftelomereshasbeenproposedasanexplanationforcellularsenescence,orthelossoftheabilitytodivide,andbyextensionfortheagingprocessinorganisms.[13]

Whereasthechromosomesofprokaryotesarerelativelygenedense,thoseofeukaryotesoftencontainsocalled"junkDNA",orregionsofDNAthatservenoobviousfunction.SimplesinglecelledeukaryoteshaverelativelysmallamountsofsuchDNA,whereasthegenomesofcomplexmulticellularorganisms,



SchematicdiagramofasinglestrandedRNAmoleculeillustratingthepositionofthreebasecodons.

includinghumans,containanabsolutemajorityofDNAwithoutanidentifiedfunction.[14]Howeveritnowappearsthat,althoughproteincodingDNAmakesupbarely2%ofthehumangenome,about80%ofthebasesinthegenomemaybeexpressed,sotheterm"junkDNA"maybeamisnomer.[2]

Geneexpression

Inallorganisms,therearetwomajorstepsseparatingaproteincodinggenefromitsprotein:First,theDNAonwhichthegeneresidesmustbetranscribedfromDNAtomessengerRNA(mRNA)and,second,itmustbetranslatedfrommRNAtoprotein.RNAcodinggenesmuststillgothroughthefirststep,butarenottranslatedintoprotein.TheprocessofproducingabiologicallyfunctionalmoleculeofeitherRNAorproteiniscalledgeneexpression,andtheresultingmoleculeitselfiscalledageneproduct.

Geneticcode

Thegeneticcodeisthesetofrulesbywhichinformationencodedwithinageneistranslatedintoafunctionalprotein.EachgeneconsistsofaspecificsequenceofnucleotidesencodedinDNAorRNA.Thenucleotidebeingmadeupofasugar,aphosphatemoleculeandaspecificbase(adenine,thymine,cytosine,guanineorsometimesuracil[thymineisreplacedwithuracilinsomeviruses[15]])acorrespondencebetweennucleotides,thebasicbuildingblocksofgeneticmaterial,andaminoacids,thebasicbuildingblocksofproteins,mustbeestablishedforgenestobesuccessfullytranslatedintofunctionalproteins.Setsofthreenucleotides,knownascodons,eachcorrespondtoaspecificaminoacidortoasignalthreecodonsareknownas"stopcodons"and,insteadofspecifyinganewaminoacid,alertthetranslationmachinerythattheendofthegenehasbeenreached,justasaspecificsetof3bases,"AUG",knownasthe"startcodon",signifiesthegenetostarttranscribing.Thereare64possiblecodons(fourpossiblenucleotidesateachofthreepositions,hence43possiblecodons)andonly20standardaminoacidshencethecodeisredundantandmultiplecodonscanspecifythesameaminoacid.Thecorrespondencebetweencodonsandaminoacidsisnearlyuniversalamongallknownlivingorganisms.

Transcription

TheprocessofgenetictranscriptionproducesasinglestrandedRNAmoleculeknownasmessengerRNA,whosenucleotidesequenceiscomplementarytotheDNAfromwhichitwastranscribed.TheDNAstrandwhosesequencematchesthatoftheRNAisknownasthecodingstrandandthestrandfromwhichtheRNAwassynthesizedisthetemplatestrand.TranscriptionisperformedbyanenzymecalledanRNApolymerase,whichreadsthetemplatestrandinthe3'to5'directionandsynthesizestheRNAfrom5'to3'.Toinitiatetranscription,thepolymerasefirstrecognizesandbindsapromoterregionofthegene.Thusamajormechanismofgeneregulationistheblockingorsequesteringofthepromoterregion,eitherbytightbindingbyrepressormoleculesthatphysicallyblockthepolymerase,orbyorganizingtheDNAsothatthepromoterregionisnotaccessible.



Inprokaryotes,transcriptionoccursinthecytoplasmforverylongtranscripts,translationmaybeginatthe5'endoftheRNAwhilethe3'endisstillbeingtranscribed.Ineukaryotes,transcriptionnecessarilyoccursinthenucleus,wherethecell'sDNAissequesteredtheRNAmoleculeproducedbythepolymeraseisknownastheprimarytranscriptandmustundergoposttranscriptionalmodificationsbeforebeingexportedtothecytoplasmfortranslation.Thesplicingofintronspresentwithinthetranscribedregionisamodificationuniquetoeukaryotesalternativesplicingmechanismscanresultinmaturetranscriptsfromthesamegenehavingdifferentsequencesandthuscodingfordifferentproteins.Thisisamajorformofregulationineukaryoticcells.

Translation

TranslationistheprocessbywhichamaturemRNAmoleculeisusedasatemplateforsynthesizinganewprotein.Translationiscarriedoutbyribosomes,largecomplexesofRNAandproteinresponsibleforcarryingoutthechemicalreactionstoaddnewaminoacidstoagrowingpolypeptidechainbytheformationofpeptidebonds.Thegeneticcodeisreadthreenucleotidesatatime,inunitscalledcodons,viainteractionswithspecializedRNAmoleculescalledtransferRNA(tRNA).EachtRNAhasthreeunpairedbasesknownastheanticodonthatarecomplementarytothecodonitreadsthetRNAisalsocovalentlyattachedtotheaminoacidspecifiedbythecomplementarycodon.WhenthetRNAbindstoitscomplementarycodoninanmRNAstrand,theribosomeligatesitsaminoacidcargotothenewpolypeptidechain,whichissynthesizedfromaminoterminustocarboxylterminus.Duringandafteritssynthesis,thenewproteinmustfoldtoitsactivethreedimensionalstructurebeforeitcancarryoutitscellularfunction.

DNAreplicationandinheritance

Thegrowth,development,andreproductionoforganismsreliesoncelldivision,ortheprocessbywhichasinglecelldividesintotwousuallyidenticaldaughtercells.ThisrequiresfirstmakingaduplicatecopyofeverygeneinthegenomeinaprocesscalledDNAreplication.ThecopiesaremadebyspecializedenzymesknownasDNApolymerases,which"read"onestrandofthedoublehelicalDNA,knownasthetemplatestrand,andsynthesizeanewcomplementarystrand.BecausetheDNAdoublehelixisheldtogetherbybasepairing,thesequenceofonestrandcompletelyspecifiesthesequenceofitscomplementhenceonlyonestrandneedstobereadbytheenzymetoproduceafaithfulcopy.TheprocessofDNAreplicationissemiconservativethatis,thecopyofthegenomeinheritedbyeachdaughtercellcontainsoneoriginalandonenewlysynthesizedstrandofDNA.[16]

AfterDNAreplicationiscomplete,thecellmustphysicallyseparatethetwocopiesofthegenomeanddivideintotwodistinctmembraneboundcells.Inprokaryotesbacteriaandarchaeathisusuallyoccursviaarelativelysimpleprocesscalledbinaryfission,inwhicheachcirculargenomeattachestothecellmembraneandisseparatedintothedaughtercellsasthemembraneinvaginatestosplitthecytoplasmintotwomembraneboundportions.Binaryfissionisextremelyfastcomparedtotheratesofcelldivisionineukaryotes.EukaryoticcelldivisionisamorecomplexprocessknownasthecellcycleDNAreplicationoccursduringaphaseofthiscycleknownasSphase,whereastheprocessofsegregatingchromosomesandsplittingthecytoplasmoccursduringMphase.Inmanysinglecelledeukaryotessuchasyeast,reproductionbybuddingiscommon,whichresultsinasymmetricalportionsofcytoplasminthetwodaughtercells.

Molecularinheritance



Theduplicationandtransmissionofgeneticmaterialfromonegenerationofcellstothenextisthebasisformolecularinheritance,andthelinkbetweentheclassicalandmolecularpicturesofgenes.Organismsinheritthecharacteristicsoftheirparentsbecausethecellsoftheoffspringcontaincopiesofthegenesintheirparents'cells.Inasexuallyreproducingorganisms,theoffspringwillbeageneticcopyorcloneoftheparentorganism.Insexuallyreproducingorganisms,aspecializedformofcelldivisioncalledmeiosisproducescellscalledgametesorgermcellsthatarehaploid,orcontainonlyonecopyofeachgene.Thegametesproducedbyfemalesarecalledeggsorova,andthoseproducedbymalesarecalledsperm.Twogametesfusetoformafertilizedegg,asinglecellthatonceagainhasadiploidnumberofgeneseachwithonecopyfromthemotherandonecopyfromthefather.

Duringtheprocessofmeioticcelldivision,aneventcalledgeneticrecombinationorcrossingovercansometimesoccur,inwhichalengthofDNAononechromatidisswappedwithalengthofDNAonthecorrespondingsisterchromatid.Thishasnoeffectiftheallelesonthechromatidsarethesame,butresultsinreassortmentofotherwiselinkedallelesiftheyaredifferent.TheMendelianprincipleofindependentassortmentassertsthateachofaparent'stwogenesforeachtraitwillsortindependentlyintogameteswhichalleleanorganisminheritsforonetraitisunrelatedtowhichalleleitinheritsforanothertrait.Thisisinfactonlytrueforgenesthatdonotresideonthesamechromosome,orarelocatedveryfarfromoneanotheronthesamechromosome.Theclosertwogeneslieonthesamechromosome,themorecloselytheywillbeassociatedingametesandthemoreoftentheywillappeartogethergenesthatareverycloseareessentiallyneverseparatedbecauseitisextremelyunlikelythatacrossoverpointwilloccurbetweenthem.Thisisknownasgeneticlinkage.

Mutation

DNAreplicationisforthemostpartextremelyaccurate,withanerrorratepersiteofaround106to1010

ineukaryotes.[16](Althoughinprokaryotesandviruses,therateismuchhigher.)Rare,spontaneousalterationsinthebasesequenceofaparticulargenearisefromanumberofsources,suchaserrorsinDNAreplicationandtheaftermathofDNAdamage.Theseerrorsarecalledmutations.ThecellcontainsmanyDNArepairmechanismsforpreventingmutationsandmaintainingtheintegrityofthegenomehowever,insomecasessuchasbreaksinbothDNAstrandsofachromosomerepairingthephysicaldamagetothemoleculeisahigherprioritythanproducinganexactcopy.Duetothedegeneracyofthegeneticcode,somemutationsinproteincodinggenesaresilent,orproducenochangeintheaminoacidsequenceoftheproteinforwhichtheycodeforexample,thecodonsUCUandUCCbothcodeforserine,sotheUCmutationhasnoeffectontheprotein.Mutationsthatdohavephenotypiceffectsaremostoftenneutralordeleterioustotheorganism.Variantsmayconferbenefitstotheorganism'sfitnessitiscommonlythoughtthatmutationsmayproducebeneficialvariants.Themostcommonmutationsincludepointmutationsinwhichasinglecodonisreplaced,frameshiftmutationwhereasinglenucleotidebaseisinsertedordeletedfromtheDNAstrandsothatallbasesareshiftedover,silentmutationswhereasinglenucleotidebaseisreplacedbutwithoutcausingachangefortheaminoacidbeingcodedfor,andnonsensemutations,whereachangeinasinglenucleotidebasecausesacodontobeturnedintoastopcodonhenceterminatingtranscriptionatthispoint.

Mutationspropagatedtothenextgenerationleadtovariationswithinaspecies'population.Variantsofasinglegeneareknownasalleles,anddifferencesinallelesmaygiverisetodifferencesintraits.Althoughitisrareforthevariantsinasinglegenetohaveclearlydistinguishablephenotypiceffects,certainwelldefinedtraitsareinfactcontrolledbysinglegeneticloci.Agene'smostcommonalleleiscalledthewildtypeallele,andrareallelesarecalledmutants.However,thisdoesnotimplythatthewildtypealleleisthe



Theproteinencodingcomponentofthehumangenome,categorizedbyfunctionofeachgeneproduct,givenbothasnumberofgenesandaspercentageofallgenes.[17]

ancestorfromwhichthemutantsaredescended.Forthemostpart,thesemutationsarerecessiveandarephasedoutquickly.However,onoccasionthesemutationsappearasdominanttootheralleles,becomingpredominantandincreasingintheratetheyareseeninapopulation.

Genome

Chromosomalorganization

Thetotalcomplementofgenesinanorganismorcellisknownasitsgenome.Inprokaryotes,thevastmajorityofgenesarelocatedonasinglechromosomeofcircularDNA,whileeukaryotesusuallypossessmultipleindividuallinearDNAhelicespackedintodenseDNAproteincomplexescalledchromosomes.Genesthatappeartogetherononechromosomeofonespeciesmayappearonseparatechromosomesinanotherspecies.Manyspeciescarrymorethanonecopyoftheirgenomewithineachoftheirsomaticcells.Cellsororganismswithonlyonecopyofeachchromosomearecalledhaploidthosewithtwocopiesarecalleddiploidandthosewithmorethantwocopiesarecalledpolyploid.Thecopiesofgenesonthechromosomesarenotnecessarilyidentical.Insexuallyreproducingorganisms,onecopyisnormallyinheritedfromeachparent.

Numberofgenes

Earlyestimatesofthenumberofhumangenesthatusedexpressedsequencetagdataputitat50000100000.[18]Followingthesequencingofthehumangenomeandothergenomes,ithasbeenfoundthatratherfewgenes(~20000inhuman,mouseandfly,~13000inroundworm,>46,000inrice[19])encodealltheproteinsinanorganism.[20]Theseproteincodingsequencesmakeup12%ofthehumangenome.[21]Alargepartofthegenomeistranscribedhowever,tointrons,retrotransposonsandseeminglyalargearrayofnoncodingRNAs.[20][21]Totalnumberofproteins(theEarth'sproteome)isestimatedtobe5millionsequences.[22]

Geneticandgenomicnomenclature

GenenomenclaturehasbeenestablishedbytheHUGOGeneNomenclatureCommittee(HGNC)foreachknownhumangeneintheformofanapprovedgenenameandsymbol(shortformabbreviation).AllapprovedsymbolsarestoredintheHGNCDatabase(http://www.genenames.org/cgibin/hgnc_search.pl).



Eachsymbolisuniqueandeachgeneisonlygivenoneapprovedgenesymbol.Thisalsofacilitateselectronicdataretrievalfrompublications.Inpreferenceeachsymbolmaintainsparallelconstructionindifferentmembersofagenefamilyandcanbeusedinotherspecies,especiallythemouse.

Essentialgenes

Essentialgenesarethosegenesofanorganismthatarethoughttobecriticalforitssurvival.Surprisinglyfewgeneshavebeenshowntobeabsolutelyessentialforthesurvivalofbacteria,e.g.onlyabout10%ofthe~4,200genesofEscherichiacoli.

Evolutionaryconceptofagene

GeorgeC.Williamsfirstexplicitlyadvocatedthegenecentricviewofevolutioninhis1966bookAdaptationandNaturalSelection.Heproposedanevolutionaryconceptofgenetobeusedwhenwearetalkingaboutnaturalselectionfavoringsomegenes.Thedefinitionis:"thatwhichsegregatesandrecombineswithappreciablefrequency."Accordingtothisdefinition,evenanasexualgenomecouldbeconsideredagene,insofarthatithaveanappreciablepermanencythroughmanygenerations.

Thedifferenceis:themoleculargenetranscribesasaunit,andtheevolutionarygeneinheritsasaunit.

RichardDawkins'booksTheSelfishGene(1976)andTheExtendedPhenotype(1982)defendedtheideathatthegeneistheonlyreplicatorinlivingsystems.Thismeansthatonlygenestransmittheirstructurelargelyintactandarepotentiallyimmortalintheformofcopies.So,genesshouldbetheunitofselection.InRiverOutofEden,Dawkinsfurtherrefinedtheideaofgenecentricselectionbydescribinglifeasariverofcompatiblegenesflowingthroughgeologicaltime.Scoopupabucketofgenesfromtheriverofgenes,andwehaveanorganismservingastemporarybodiesorsurvivalmachines.Ariverofgenesmayforkintotwobranchesrepresentingtwononinterbreedingspeciesasaresultofgeographicalseparation.

Genetargetingandimplications

Genetargetingiscommonlyreferredtotechniquesforalteringordisruptingmousegenesandprovidesthemousemodelsforstudyingtherolesofindividualgenesinembryonicdevelopment,humandisorders,aginganddiseases.Themousemodels,whereoneormoreofitsgenesaredeactivatedormadeinoperable,arecalledknockoutmice.Sincethefirstreportsinwhichhomologousrecombinationamonghomologouschromosomesinembryonicstemcellswasusedtogenerategenetargetedmice,[23]genetargetinghasproventobeapowerfulmeansofpreciselymanipulatingthemammaliangenome,producingatleasttenthousandmutantmousestrainsanditisnowpossibletointroducemutationsthatcanbeactivatedatspecifictimepoints,orinspecificcellsororgans,bothduringdevelopmentandintheadultanimal.[24][25]

Genetargetingstrategieshavebeenexpandedtoallkindsofmodifications,includingpointmutations,isoformdeletions,mutantallelecorrection,largepiecesofchromosomalDNAinsertionanddeletion,tissuespecificdisruptioncombinedwithspatialandtemporalregulationandsoon.Itispredictedthattheabilitytogeneratemousemodelswithpredictablephenotypeswillhaveamajorimpactonstudiesofallphasesofdevelopment,immunology,neurobiology,oncology,physiology,metabolism,andhumandiseases.Genetargetingisalsointheoryapplicabletospeciesfromwhichtotipotentembryonicstemcellscanbeestablished,andthereforemayofferapotentialtotheimprovementofdomesticanimalsandplants.[25][26]



Changingconcept

Theconceptofthegenehaschangedconsiderably(seehistorysection).Fromtheoriginaldefinitionofa"unitofinheritance",thetermevolvedtomeanaDNAbasedunitthatcanexertitseffectsontheorganismthroughRNAorproteinproducts.Itwasalsopreviouslybelievedthatonegenemakesoneproteinthisconceptwasoverthrownbythediscoveryofalternativesplicingandtranssplicing.[7]

Thedefinitionofageneisstillchanging.ThefirstcasesofRNAbasedinheritancehavebeendiscoveredinmammals.[27]Evidenceisalsoaccumulatingthatthecontrolregionsofagenedonotnecessarilyhavetobeclosetothecodingsequenceonthelinearmoleculeorevenonthesamechromosome.Spilianakisandcolleaguesdiscoveredthatthepromoterregionoftheinterferongammageneonchromosome10andtheregulatoryregionsoftheT(H)2cytokinelocusonchromosome11comeintocloseproximityinthenucleuspossiblytobejointlyregulated.[28]Eventhecodingsequenceofageneitselfdoesn'thavetobeallonthesamechromosome:MarandeandBurgershowedthat,inthemitochondriaoftheprotistDiplonemapapillatum,"genesaresystematicallyfragmentedintosmallpiecesthatareencodedonseparatechromosomes,transcribedindividually,andthenconcatenatedintocontiguousmessengerRNAmolecules".[29]

Theconceptthatgenesareclearlydelimitedisalsobeingeroded.Thereisevidenceforfusedproteinsstemmingfromtwoadjacentgenesthatcanproducetwoseparateproteinproducts.Whileitisnotclearwhetherthesefusionproteinsarefunctional,thephenomenonismorefrequentthanpreviouslythought.[30]Evenmoregroundbreakingthanthediscoveryoffusedgenesistheobservationthatsomeproteinscanbecomposedofexonsfromfarawayregionsandevendifferentchromosomes.[2][31]Thisnewdatahasledtoanupdated,andprobablytentative,definitionofageneas"aunionofgenomicsequencesencodingacoherentsetofpotentiallyoverlappingfunctionalproducts".[7]Thisnewdefinitioncategorizesgenesbyfunctionalproducts,whethertheybeproteinsorRNA,ratherthanspecificDNAlociallregulatoryelementsofDNAarethereforeclassifiedasgeneassociatedregions.[7]

Seealso

CopynumbervariationDNAEpigeneticsFullgenomesequencingGenecentricviewofevolutionGenedosageGeneexpressionGenefamilyGenepatentGenepoolGeneredundancyGenetherapy



Notesandreferences

GeneticalgorithmGeneticengineeringGeneticsGenomicsListofgenepredictionsoftwareListofnotablegenesPopulationgeneticsPredictivemedicinePseudogene

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2. âbcElizabethPennisi(2007)."DNAStudyForcesRethinkofWhatItMeanstoBeaGene".Science316(5831):15561557.doi:10.1126/science.316.5831.1556(http://dx.doi.org/10.1126%2Fscience.316.5831.1556).PMID17569836(https://www.ncbi.nlm.nih.gov/pubmed/17569836).

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Externallinks

ComparativeToxicogenomicsDatabase(http://ctdbase.org/)DNAFromTheBeginningaprimerongenesandDNA(http://www.dnaftb.org/)GenesAndDNAIntroductiontogenesandDNAaimedatnonbiologist(http://www.bioinformaticstutorials.com/?p=6)EntrezGeneasearchabledatabaseofgenes(http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene)IDconverterconvertsgeneIDsbetweenpublicdatabases(http://idconverter.bioinfo.cnio.es/)iHOPInformationHyperlinkedoverProteins(http://www.ihopnet.org/UniPub/iHOP/)TranscriptomeBrowserGeneexpressionprofileanalysis(http://tagc.univmrs.fr/tbrowser)TheProteinNamingUtility,adatabasetoidentifyandcorrectdeficientgenenames(http://www.jcvi.org/pnutility)Genes(http://www.mdpi.com/journal/genes/)anOpenAccessjournalIMPC(InternationalMousePhenotypingConsortium)(http://www.mousephenotype.org/)EncyclopediaofmammaliangenefunctionGlobalGenesProject(http://www.globalgenes.org/)Leadingnonprofitorganizationsupportingpeoplelivingwithgeneticdiseases

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ENCODEthreadsExplorer(http://www.nature.com/encode/#/threads/characterizationofintergenicregionsandgenedefinition)Characterizationofintergenicregionsandgenedefinition.Nature(journal)

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