Biology Review1

8/6/2019 Biology Review1

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BiologyReview(bysomewikimaterial,EssentialCellBiology,andpersonaladds)

(Maytheforcebewithus)

1CentralDogmaofmolecularbiologyandimplications

DNAcontainsthecompletegeneticinformationthatdefines

thestructureandfunctionofanorganism.Proteinsare

formedusingthegeneticcodeoftheDNA.Threedifferent

processesareresponsiblefortheinheritanceofgenetic

informationandforitsconversionfromoneformto

another:1.Replication:adoublestrandednucleicacidisduplicatedtogiveidenticalcopies.Thisprocess

perpetuatesthegeneticinformation.

2.Transcription:aDNAsegmentthatconstitutesageneisreadandtranscribedintoasinglestrandedsequence

ofRNA.TheRNAmovesfromthenucleusintothe

cytoplasm.

3.Translation:theRNAsequenceistranslatedintoasequenceofaminoacidsastheproteinisformed.

Duringtranslation,theribosomereadsthreebases(a

codon)atatimefromtheRNAandtranslatestheminto

oneaminoacid

Ineucarioticcells,thesecondstep(transcription)is

necessarybecausethegeneticmaterialinthenucleusis

physicallyseparatedfromthesiteofproteinsynthesisinthe

cytoplasminthecell.Therefore,itisnotpossibletotranslateDNAdirectlyintoprotein,butanintermediarymustbe

madetocarrytheinformationfromonecompartmenttoan

other.


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Belowasimpledescriptionofprokaryoticandeukaryotic

cells


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Prokaryoticcells

Diagramofatypicalprokaryoticcell:

Theprokaryotecellissimpler,andthereforesmaller,thana

eukaryotecell,lackinganucleusandmostoftheother

organellesofeukaryotes.Therearetwokindsof

prokaryotes:bacteriaandarchaea;theseshareasimilar

structure.

Nuclearmaterialofprokaryoticcellconsistsofasingle

chromosomethatisindirectcontactwithcytoplasm.Here,theundefinednuclearregioninthecytoplasmiscalled

nucleoid.

Aprokaryoticcellhasthreearchitecturalregions:

Ontheoutside,flagellaandpiliprojectfromthecell's

surface.Thesearestructures(notpresentinall

prokaryotes)madeofproteinsthatfacilitatemovementand

communicationbetweencells;


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Enclosingthecellisthecellenvelopegenerallyconsisting

ofacellwallcoveringaplasmamembranethoughsome

bacteriaalsohaveafurthercoveringlayercalledacapsule.

Theenvelopegivesrigiditytothecellandseparatesthe

interiorofthecellfromitsenvironment,servingasa

protectivefilter.Thoughmostprokaryoteshaveacellwall,

thereareexceptionssuchasMycoplasma(bacteria)and

Thermoplasma(archaea).Thecellwallconsistsof

peptidoglycaninbacteria,andactsasanadditionalbarrier

againstexteriorforces.Italsopreventsthecellfrom

expandingandfinallybursting(cytolysis)fromosmotic

pressureagainstahypotonicenvironment.Someeukaryotecells(plantcellsandfungicells)alsohaveacellwall;

Insidethecellisthecytoplasmicregionthatcontainsthecell

genome(DNA)andribosomesandvarioussortsof

inclusions.Aprokaryoticchromosomeisusuallyacircular

molecule(anexceptionisthatofthebacteriumBorrelia

burgdorferi,whichcausesLymedisease).Thoughnot

forminganucleus,theDNAiscondensedinanucleoid.

ProkaryotescancarryextrachromosomalDNAelementscalledplasmids,whichareusuallycircular.Plasmidsenable

additionalfunctions,suchasantibioticresistance.


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Eukaryotic cells

Main article:Eukaryote

Diagramofatypicalanimal(eukaryotic)cell,showingsubcellularcomponents.

Organelles:

(1)nucleolus

(2)nucleus

(3)ribosome(4)vesicle

(5)roughendoplasmicreticulum (ER)

(6)Golgiapparatus

(7)Cytoskeleton

(8)smoothendoplasmicreticulum

(9)mitochondria

(10)vacuole

(11)cytoplasm

(12)lysosome

(13)centrioleswithincentrosome

Eukaryoticcellsareabout15timeswiderthanatypical

prokaryoteandcanbeasmuchas1000timesgreaterin

volume.Themajordifferencebetweenprokaryotesand

eukaryotesisthateukaryoticcellscontainmembrane-bound

compartmentsinwhichspecificmetabolicactivitiestake

place.Mostimportantamongtheseisacellnucleus,a

membrane-delineatedcompartmentthathousestheeukaryoticcell'sDNA.Thisnucleusgivestheeukaryoteits


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name,whichmeans"truenucleus."Otherdifferences

include:

4. Theplasmamembraneresemblesthatofprokaryotesinfunction,withminordifferencesinthesetup.Cellwallsmayormaynotbepresent.

5. TheeukaryoticDNAisorganizedinoneormorelinearmolecules,calledchromosomes,whichareassociated

withhistoneproteins.AllchromosomalDNAisstored

inthecellnucleus,separatedfromthecytoplasmbya

membrane.Someeukaryoticorganellessuchas

mitochondriaalsocontainsomeDNA.

6. Manyeukaryoticcellsareciliatedwithprimarycilia.Primaryciliaplayimportantrolesinchemosensation,

mechanosensation,andthermosensation.Ciliamay

thusbe"viewedassensorycellularantennaethat

coordinatealargenumberofcellularsignaling

pathways,sometimescouplingthesignalingtociliary

motilityoralternativelytocelldivisionand

differentiation."[7]

Eukaryotescanmoveusingmotileciliaorflagella.The

flagellaaremorecomplexthanthoseofprokaryotes.

DNAReplication(Sum)

Beforeacelldivides,itsDNAisreplicated(duplicated.)

BecausethetwostrandsofaDNAmoleculehave

complementarybasepairs,thenucleotidesequenceofeach

strandautomaticallysuppliestheinformationneededto

produceitspartner.IfthetwostrandsofaDNAmolecule

areseparated,eachcanbeusedasapatternortemplateto

produceacomplementarystrand.Eachtemplateandits

newcomplementtogetherthenformanewDNAdouble

helix,identicaltotheoriginal.Beforereplicationcan

occurs,thelengthoftheDNAdoublehelixabouttobe

copiedmustbeunwound.Inaddition,thetwostrands


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mustbeseparated,muchlikethetwosidesofazipper,by

breakingtheweakhydrogenbondsthatlinkthepaired

bases.OncetheDNAstrandshavebeenunwound,they

mustbeheldaparttoexposethebasessothatnew

nucleotidepartnerscanhydrogen-bondtothem.The

enzymeDNApolymerasethenmovesalongtheexposed

DNAstrand,joiningnewlyarrivednucleotidesintoanew

DNAstrandthatiscomplementarytothetemplate.

Eachcellcontainsafamilyofmorethanthirtyenzymesto

insuretheaccuratereplicationofDNA.

ThoughDNApolymerasecanelongateapolynucleotide

strandbyaddingnewnucleotides,itcannotstartastrand

fromscratchbecauseitcanonlybondnewnucleotidestoa

freesugar(3')endofanucleotidechain.DNApolymerase

requirestheassistanceofaprimer,apreviouslyexisting

shortstrandofDNA(orRNA)thatiscomplementarytothe

firstpartoftheDNAsegmentbeingcopied.Thissmall

strandofnucleotidesanneals(binds)bycomplementary

basepairingtothebeginningoftheareabeingcopied.With

theprimerinplace,DNApolymeraseisthenabletocontinue

addingtherestofthepairsofthesegmentuntilanew

doublestrandofDNAiscompleted.Primersareformed

fromfreenucleotidesinthecellbyenzymescalledDNA

primases.

Thatnucleotidescanbeaddedonlytothesugaror3'endofthegrowingcomplementarychainpresentsnoproblemfor

thesideoftheDNAchainopeningatitsphosphateor5'

end.Theprimerthatbindstothefirstfewexposedbases

willendwithasugar(3')wherethephosphateofanew

nucleotidecanbeattached.Fromthereon,DNApolymerase

cancontinuouslysynthesizethegrowingcomplementary

strand.ThisstrandofDNAiscalledtheleadingstrand.


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AdifferentchallengefacesDNApolymerasewhenthe

complementarysideoftheDNAmoleculebeginsunzipping

fromitssugar(3')towarditsphosphate(5')end.Aprimer

ofcomplementarymoleculesattachingtotheopeningendof

thischainwouldhaveaphosphatenotasugaratitsexposed

endsothatnewnucleotidescouldnotbejoined.Toget

aroundthisproblem,thisstrandissynthesizedinsmall

piecesbackwardfromtheoveralldirectionof

replication.Thisstrandiscalledthelaggingstrand.The

shortsegmentsofnewlyassembledDNAfromwhichthe

laggingstrandisbuiltarecalledOkazakifragments.As

replicationproceedsandnucleotidesareaddedtothe3'endoftheOkazakifragments,theycometomeeteachother.The

primerfragmentsarethenbootedoutbyenzymesand

replacedbyappropriateDNAnucleotides.Thewholething

isthenstitchedtogetherbyanotherenzymecalledDNA

ligase.


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BecausehumanDNAissoverylong(withupto80million

basepairsinachromosome)itunzipsatmultipleplaces

alongitslengthsothatthereplicationprocessisgoingon

simultaneouslyathundredsofplacesalongthelengthofthe

chain.Eventuallytheseareasruntogethertoforma

completechain.Inhumans,DNAiscopiedatabout50base

pairspersecond.Theprocesswouldtakeamonth(rather

thanthehouritactuallydoes)withoutthesemultipleplaces

onthechromosomewherereplicationcanbegin.DNA

polymerasemakesveryfewerrors,andmostofthosethat

aremadearequicklycorrectedbyDNApolymeraseand

otherenzymesthat"proofread"thenucleotidesaddedintothenewDNAstrand.Ifanewlyaddednucleotideisnot

complementarytotheoneonthetemplatestrand,these

enzymesremovethenucleotideandreplaceitwiththe

correctone.Withthissystem,acell'sDNAiscopiedwith

lessthanonemistakeinabillionnucleotides.Thisisequal

toapersoncopying100large(1000page)dictionariesword

forword,andsymbolforsymbol,withonlyoneerrorforthe

wholeprocess!

DNAReplicationineukaryotes:

DNAreplicationineukaryotesismuchmorecomplicated

thaninprokaryotes,althoughtherearemanysimilar

aspects.EukaryoticcellscanonlyinitiateDNAreplicationat

aspecificpointinthecellcycle,thebeginningofSphase.

(themaindifferenceisaboutthepreparingphaseinthecell

cycle,theG1phase,andsomespecializedproteinsmore

thanintheprokaryaworld)

Theeukaryoticchromosomesarecontainedwithinanucleusthatisboundedbyadouble-membrane

nuclearenvelope.

Herethenucleolusandthenuclearfibrousskeletoncantriggerandlocalizethegeneticactivities


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MedicalapplicationsofDNAReplication

***Registrationswerenotclearatall,soItriedtodigthe

webtofindthemainmedicalapplicationsofDNA

Replication,butIcanonlymakealist:

Forensicstudies Paternitytest Geneticalstudies(tolocalizethepartofthestrandthatruleanentiredisease)

Historyandanthropology(UsingDNAmeasurementtechniquestobetterunderstandourpasts)

Nanotechnology(usingDNAitselftodevelopinterestingnewphysicalconceptsinthenano-world)

GeneticEngineering(Usinganunderstandingofgenestomanipulatephysicalcharactertraits)

Transcriptionessentials

TranscriptionistheprocessbywhichaDNAtemplateiscopiedbyRNApolymerasetoproducea

complementarymoleculeofRNA

Itinvolvesfourstages:1.BindingofRNApolymerasetopromotersequencesin

theDNAtemplatestrand

2.InitiationofRNAsynthesis3.

ElongationofRNAchain4.Termination

Intheeukaryoticcellsismorecomplex,onemajordifferenceisthateukaryoticcellshavemultipleforms

ofRNApolymerasethatarespecializedfor

synthesizingdifferenttypesofRNA

ThethreenuclearRNApolymerasesrecognizedifferentfamiliesofDNApromoterseq.Theseeukaryoticpromotersareusuallyboundbytranscriptionfactors


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thatassociatewithRNA

polymeraseratherthanby

RNApolymeraseitself.

Idontwanttolosetimeontranscription,just

typetranscriptionanimationonyoutubetoget

aquicklookatthisprocess

Checkonthissiteforfurtherinfos:

http://users.rcn.com/jkimball.ma.ultranet/Bio

logyPages/T/Transcription.html


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MedicalApplicationsofTranscriptions

Proteinsynthesisiscriticaltothegrowthofcells;medicines

thatworkbykillingcellsoftentargetthisprocess.Amajority

ofantibioticsworkbydisruptingthetranslationprocess.

TetracyclineisanantibioticthatinhibitsthebindingoftRNA

totheassemblysite.Streptomycinworksbycausingthe

translationprocesstomakemoremistakesthanusualas

highasonemistakeforevery100aminoacids.Proteinswith

thismanyerrorsarenotcapableofperformingtheirtasks,

andthecells(inthiscase,bacteria)die.Streptomycinalso

inhibitstheinitiationofthesynthesisprocess.***Icouldntfindmore

TranslationProteinBiosynthesisEssentials

Duringtranslation,asmallribosomalsubunitattachestoa

mRNAmolecule.Atthesametime,aninitiatortRNA

moleculerecognizesandbindstoaspecificcodonsequence

onthesamemRNAmolecule.Alargeribosomalsubunitthen

joinsthenewlyformedcomplex.TheinitiatortRNAresides

inonebindingsiteoftheribosomecalledthePsite,leaving

thesecondbindingsite,theAsite,open.WhenanewtRNA

moleculerecognizesthenextcodonsequenceonthemRNA,

itattachestotheopenAbindingsite.Apeptidebondforms

connectingtheaminoacidattachedtothetRNAinthePsite

totheaminoacidattachedtothetRNAintheAbindingsite.


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AstheribosomemovesalongthemRNAmolecule,thetRNA

inthePsiteisreleasedandthetRNAintheAsiteis

translocatedtothePsite.TheAbindingsitebecomesvacant

againuntilanothertRNAthatrecognizesthenewmRNA

codontakestheopenposition.Thispatterncontinuesas

moleculesoftRNAarereleasedfromthecomplex,newtRNA

moleculesattach,andtheaminoacidchaingrows.The

ribosomewilltranslatethemRNAmoleculeuntilitreachesa

terminationcodononthemRNA.

***Watchavideo,itisaneasyprocess

HeresomemoreKey-featuresofthemechanism:

Translationinvolvesinitiation,elongationandterminationstages

Duringtheinitiationstage,initiationfactorstriggertheassemblyofmRNA,ribosomalsubunits,initiator

aminoacyltRNAintoninitiationcomplex

ChainelongationinvolvessequentialcyclesofaminoacyltRNAbinding,peptidebondformationandtranslocation,witheachcycledrivenbytheactionof

elongationfactors.Thenetresultisthataminoacyl

tRNAsaddtheiraminoacidstothegrowing

polypeptidechaininanorderspecifiedbythecodon

sequenceinmRNA

ChainterminationoccurswhenastopcodoninmRNAisrecognizedbyreleasefactors,whichcausesthe

mRNAandnewlyformedpolypeptidetobereleased

fromtheribosome

GTPbindingandhydrolysisarerequiredfortheactionofseveralinitiation,elongationandreleasefactors

Properfoldingofnewlyproducedpolypeptidechainsisassistedbymolecularchaperones.Abnormalitiesin

proteinfoldingcanleadtovarioushealthproblems,

includingAlzheimersdiseaseandmadcowdisease


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VirusGeneralities

Avirusisasmallinfectiousagentthatcanreplicateonly

insidethelivingcellsoforganisms.Mostvirusesaretoo

smalltobeseendirectlywithalightmicroscope.Viruses

infectalltypesoforganisms,fromanimalsandplantsto

bacteriaandarchaea.Sincetheinitialdiscoveryofthe

tobaccomosaicvirusbyMartinusBeijerinckin1898,about

5,000viruseshavebeendescribedindetail,althoughthere

aremillionsofdifferenttypes.Virusesarefoundinalmost

everyecosystemonEarthandarethemostabundanttypeof

biologicalentity.Thestudyofvirusesisknownasvirology,asub-specialityofmicrobiology.

Virusparticles(knownasvirions)consistoftwoorthree

parts:thegeneticmaterialmadefromeitherDNAorRNA,

longmoleculesthatcarrygeneticinformation;aproteincoat

thatprotectsthesegenes;andinsomecasesanenvelopeof

lipidsthatsurroundstheproteincoatwhentheyareoutside

acell.Theshapesofvirusesrangefromsimplehelicaland

icosahedralformstomorecomplexstructures.Theaveragevirusisaboutoneone-hundredththesizeoftheaverage

bacterium.

Theoriginsofvirusesintheevolutionaryhistoryoflifeare

unclear:somemayhaveevolvedfromplasmidspiecesof

DNAthatcanmovebetweencellswhileothersmayhave

evolvedfrombacteria.Inevolution,virusesareanimportant

meansofhorizontalgenetransfer,whichincreasesgenetic

diversity.Virusesspreadinmanyways;virusesinplantsareoften

transmittedfromplanttoplantbyinsectsthatfeedonthe

sapofplants,suchasaphids;virusesinanimalscanbe

carriedbyblood-suckinginsects.Thesedisease-bearing

organismsareknownasvectors.Influenzavirusesare

spreadbycoughingandsneezing.Norovirusandrotavirus,

commoncausesofviralgastroenteritis,aretransmittedby

thefaecal-oralrouteandarepassedfrompersontopersonbycontact,enteringthebodyinfoodorwater.HIVisoneof


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severalvirusestransmittedthroughsexualcontactandby

exposuretoinfectedblood.Therangeofhostcellsthata

viruscaninfectiscalledits"hostrange".Thiscanbenarrow

or,aswhenavirusiscapableofinfectingmanyspecies,

broad.

Viralinfectionsinanimalsprovokeanimmuneresponse

thatusuallyeliminatestheinfectingvirus.Immune

responsescanalsobeproducedbyvaccines,whichconferan

artificiallyacquiredimmunitytothespecificviralinfection.

However,somevirusesincludingthosecausingAIDSand

viralhepatitisevadetheseimmuneresponsesandresultin

chronicinfections.Antibioticshavenoeffectonviruses,butseveralantiviraldrugshavebeendeveloped.

Keyfeatures:

Structure:

Avirusparticle,alsoknownasavirion,isessentiallya

nucleicacid(DNAorRNA)enclosedinaproteinshellorcoat.Virusesareextremelysmall,approximately15-25

nanometersindiameter.

GeneticMaterial:

Virusesmayhavedouble-strandedDNA,double-stranded

RNA,single-strandedDNAorsingle-strandedRNA.Thetype

ofgeneticmaterialfoundinaparticularvirusdependsonthenatureandfunctionofthespecificvirus.Thegenetic

materialisnottypicallyexposedbutcoveredbyaprotein

coat.

Theviralgenomecanconsistofaverysmallnumberof

genesoruptohundredsofgenesdependingonthetypeof

virus.Notethatthegenomeistypicallyorganizedasalong

moleculethatisusuallystraightorcircular.


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Capsids

Theproteincoatthatenvelopesviralgeneticmaterialis

knownasacapsid.Acapsidiscomposedofproteinsubunits

calledcapsomeres.Capsidscanhaveseveralshapes:

polyhedral,rodorcomplex.Capsidsfunctiontoprotectthe

viralgeneticmaterialfromdamage.

Inadditiontotheproteincoat,someviruseshave

specializedstructures.Forexample,thefluvirushasa

membrane-likeenvelopearounditscapsid.Theenvelope

hasbothhostcellandviralcomponentsandassiststhevirusininfectingitshost.Capsidadditionsarealsofoundin

bacteriophages.Forexample,bacteriophagescanhavea

protein"tail"attachedtothecapsidthatisusedtoinfect

hostbacteria.

VirusReplication

Virusesareintracellularobligateparasiteswhichmeansthattheycannotreplicateorexpresstheirgeneswithoutthehelp

ofalivingcell.Asinglevirusparticle(virion)isinandof

itselfessentiallyinert.Itlacksneededcomponentsthatcells

havetoreproduce.Whenavirusinfectsacell,itmarshals

thecell'sribosomes,enzymesandmuchofthecellular

machinerytoreplicate.Unlikewhatwehaveseenincellular

replicationprocessessuchasmitosisandmeiosis,viral

replicationproducesmanyprogeny,thatwhencomplete,leavethehostcelltoinfectothercellsintheorganism.

Virusesmaycontaindouble-strandedDNA,double-stranded

RNA,single-strandedDNAorsingle-strandedRNA.Thetype

ofgeneticmaterialfoundinaparticularvirusdependson

thenatureandfunctionofthespecificvirus.Theexact

natureofwhathappensafterahostisinfectedvaries

dependingonthenatureofthevirus.Theprocessfor

double-strandedDNA,single-strandedDNA,double-strandedRNAandsingle-strandedRNAviralreplicationwill


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differ.Forexample,double-strandedDNAvirusestypically

mustenterthehostcell'snucleusbeforetheycanreplicate.

Single-strandedRNAviruseshowever,replicatemainlyin

thehostcell'scytoplasm.

Onceavirusinfectsitshostandtheviralprogeny

componentsareproducedbythehost'scellularmachinery,

theassemblyoftheviralcapsidisanon-enzymaticprocess.

Itisusuallyspontaneous.Virusestypicallycanonlyinfecta

limitednumberofhosts(alsoknownashostrange).The

"lockandkey"mechanismisthemostcommonexplanation

forthisrange.Certainproteinsonthevirusparticlemustfitcertainreceptorsitesontheparticularhost'scellsurface.

HowVirusesInfectCells

Thebasicprocessofviralinfectionandvirusreplication

occursin6mainsteps.

1.Adsorption-virusbindstothehostcell.2.Penetration-virusinjectsitsgenomeintohostcell.

3.ViralGenomeReplication-viralgenomereplicatesusingthehost'scellularmachinery.

4.Assembly-viralcomponentsandenzymesareproducedandbegintoassemble.

5.Maturation-viralcomponentsassembleandvirusesfullydevelop.

6.Release-newlyproducedvirusesareexpelledfromthehostcell.

Virusesmayinfectanytypeofcellincludinganimalcells,

plantcellsandbacterialcells.Toviewanexampleofthe

processofviralinfectionandvirusreplication,seeVirus

Replication:Bacteriophage.Youwilldiscoverhowa

bacteriophage,avirusthatinfectsbacteria,replicatesafterinfectingabacterialcell.


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AmendmentstotheCentralDogma

Icouldnotfindanythingaboutthis,theonlyinterestingandfaithfully

informationaboutthedogmaarethoseprocessesnotstatedbyitselfbutstill

trueintherealpractice:

ReversetranscriptionisthetransferofinformationfromRNAtoDNA(thereverseofnormal

transcription).

RNAreplicationisthecopyingofoneRNAtoanother.Manyvirusesreplicatethisway.

DirecttranslationfromDNAtoproteinhasbeen

demonstratedinacell-freesystem(i.e.inatesttube),

usingextractsfromE.colithatcontainedribosomes.

VariationinmethylationstatesofDNAcanaltergeneexpressionlevelssignificantly.

Prionsareproteinsthatpropagatethemselvesbymakingconformationalchangesinothermoleculesof

thesametypeofprotein.

ImsureIcouldnotreachtheendoftheentireworkthistimebutasthelast

one,IhopeitwouldbehelpfulforYouguys

Yourbelovedandtiredandcrazyandemotionalandcomplicatedandlazyand

excitedandstrangeandprettyandadorablecolleague,

AlessandroMotta

PS:itwillbemorecomplicatedthanwhatwecanthink,iftheresahellbelow.Weareallgonnago!

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