TheCentralDogma

m

RNAPolymerase

TheRibosome

• Note:Wewilllookmainlyatprokaryo=c(e.g.e.coli)processes.

• Someofthisisthesameineukaryotes,butthereareimportantdifferences.

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

DNA(Nota=ons)YouhavetosaywhichwaytheDNAgoes,usuallyfrom5’to3’.

AsinglestrandedDNA:

AdoublestrandedDNA:

Some=mes,wewritedsDNAbywri=ngonlyonestrand,sincetheotherisimplied,asingenebankdata.

5’-ATCCTGTAATGC-3’

5’-ATCCTGTAATGC-3’ |||||||||||| 3’-TAGGACATTACG-5’

Thedoublehelix

Minorgroove

Majorgroove

2nm10

basepairspertu

rn:3.4nm

Nucleo=des5’end 3’end

MoreDNA

DNAisstoredunderpressureinviruscapsids.This160,000bppieceofDNAexplodedfromwithinaT4bacteriophage.

E.Coligenome=4.6Mbp(onemolecule!)

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

DNAislong.

RNAisshort.

DNAisstable.

RNAsappearanddisappear.

DNAisdoublestranded.

RNAissinglestrandedandsomeBmesfoldsuponitselfinfunnyways.

DNAstoresinforma=on.

RNAdoesmanythings!

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

RNAistranscribedfromDNAtemplates

• TheregionthatexpressesanRNAiscalledagene.• MostmRNAsare3000bpor,usually,shorter.

triphoshpate

AlltypesofRNAaregeneratedthisway

mRNA

tRNA(e. coli has ~60 tRNA genes)

siRNA

microRNA

RibosomalRNA(e. coli has 7 copies of its rRNA genes so that it can produce a lot of ribosomes)

Transcrip,on

RNAisthecoolestmolecule.

Eukaryotes

Sometimes several mRNAs are copied in a row to produce a string of protein coding mRNAs.

RNAPolymerase(RNAP)

Theworkhorseoftranscrip=onisRNAP.

RNAPcatalyzestheforma=onofthephosphodiesterbondlinkingthenucleo=destogetherinRNA.

RNAPmovesatabout20nucleo=despersecond!

Somegenesaretranscribedfasterthanothers.

Ifthewrongnucleo=deisadded,RNAPbacksupandfixesitsmistakes!RNAPisaholoenzyme,consis=ngof4

proteinssubunitsandadetachablecofactorenzyme(σ‐cofactor).

StartsignalsarecodedinDNA

TTGACATTATAAT1‐10‐35

upstream

downstream

1.  RNAPslidesalongDNAwithouttranscribing.

2.  σ-factorbindstopromotor

3.  RNAPbindswithσ‐factorun=labout10basesaretranscribed.

4.  WhenyouwriteDNAprograms,thesearethethingsyouspecify!

Promotor

StopsignalsareencodedinDNA

• TerminatorsareAAAAAAsequencesprecededbyashortpalindrome.

• ThepalindromeformsahairpininthegrowingRNA.

• TheshapeofthehairpinedRNApopsRNAPoffthegeneandtranscrip=onstops!

…

…

Ar=st’sRendi=on(WEHI‐TV)

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

AminoAcids

Aminoacidscondensetoformchainscalledpolypep,des.

Amino

Oneof20residues

CarboxylGroup

nterminus

cterminus

The20AminoAcids

Eachonehasadifferentshape,charge,andhydrophobcity.

Bylinkingupsomeintoalongchain,youcanmakealidlemachine.

Weknowhowtomakesomekindsofmachinesthisway,butforthemostpartwedon’tknowmuchabouthowtodothisinaprincipledmanner.

TransferRNA(tRNA)

• EachaminoacidcanhaveseveraltRNAs,oneforeachcodonvaria=on.

• VarioustRNAsynthetasesandotherenzymesprovideapost‐transla=onalmodifica=onthataddstheaminoacid.

Proteinsgrowatthecarboxylgroup(C‐terminus)

C‐Terminus

RNAistranslatedtoprotein

• Each3nucleo=desequence,calledacodon,inmRNA(from5’to3’)codesforanaminoacid.

• Transla=onistheprocessofbuildingthecorrespondingproteinfromthiscode.

5’‐CUCAGCGUUACC‐3’

Leu

Ser

Val

Thr

Thestartandstopcodons

•  Transla=onstartswiththecodonAUG.– Soallproteinsstartwithmethionine.

•  Transla=onstopswithUAA,UAGorUGA.– Thesedonotcodeforaminoacids.

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

RibosomestranslatemRNAtoprotein

Thetwosubunitsoftheribosomeareseparateun=ltransla=onstarts.

Inbacteria,aribosomeprocesses20aminoacidspersecond.

Theribosomemakesonemistakeevery10000aminoacids

Theribosome(2/3RNA,1/3Protein)

Ar=st’sRendi=on(WEHI‐TV)

TheRNAWorldTherearethosewhobelievethatRNAwasthefirstautocataly=cmolecularsystem.

RNAcancleaveandligateitself.

RNAshavebeendesignedthatcantranscribeRNA.

Theribosomeismadealmosten=relyoutofRNA.

ProteinandDNAmayhavecomealonglater.Havingseparatemoleculesforinforma=onandstructuremayhavebeenevolu=onarilyadvantageous.

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

• Primarystructure:Thesequenceofaminoacids• Secondarystructure:Thelocalshape(helix,coilorsheet)• Ter=arystructure:Theglobal3Dshape• Quaternarystructure:Howproteinsformgroups

Proteins

Ballands=ck Structurecartoon Spacefilling

Proteinsformgroups

Hemoglobinconsistsoffourproteinsubunitsandfournon‐proteinironcontaininghemeunits.Itisself‐assembledinsidethecelloncethecomponentsarepresent.

ProteinscanbeEnzymesAnenzymeisaproteinsthatacceleratesachemicalreac=on,usuallyveryspecifically.

Proteinscanpumpsmallmolecules(2003NobelPrizetoPeterAgre)

A1nanosecondsimula=onofthe60,000atomaquaporin‐1waterchannelwithfullelectrosta=csandconstantpressureinasingleweek(SchultenGroup,UIUC).

Phospholipidmembrane

Aquaporintransmembranefour‐proteincomplex.

Proteinsareinvolvedwithsignaling

RNAandProteinAreDegraded

•  RNAisdegradedbyRibonucleases(Rnase)

•  ProteinisdegradedbyProteases

•  SomeRNAsandProteinsaremorestablethanothers.

•  Synthe=cBiologistscantunedegrada=onrates.

ImportantMoleculesDNA=DeoxyribonucleicacidAsequenceofA,T,CandG(deoxyribonucleo=des)

RNA=RibonucleicAcid(mRNA,tRNA,…)AsequenceofA,U,CandG(ribonucleo=des)

RNAPolymerase(RNAP)Transcribes(copies)DNAsegmentsintoRNA

AminoAcidsandTransferRNA(tRNA)Helpbuildproteins

TheRibosomeTranslatesmessengerRNA(mRNA)intoprotein

ProteinAsequenceofaminoacids

Inprokaryotes,everythinghappensatonce!

Genesareregulated

Generegula=on

Synthe=cbiology

Comingsoon

•  Proteinsregulatetheproduc=onofmRNAsbyeitherac=va=ngorrepressingtranscrip=on.

•  Amathema=caldescrip=onoftranscrip=onandregula=on.