NUCLEIC ACIDS: DNA AND RNA...Nucleic Acids are important for their roles in the storage, transfer...

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NUCLEIC ACIDS: DNA AND RNA HLeeYu Jsuico Junsay Department of Chemistry School of Science and Engineering Ateneo de Manila University 1

Transcript of NUCLEIC ACIDS: DNA AND RNA...Nucleic Acids are important for their roles in the storage, transfer...

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NUCLEICACIDS:DNAANDRNAHLeeYuJsuicoJunsay

DepartmentofChemistry

SchoolofScienceandEngineering

AteneodeManilaUniversity1

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BUILDINGBLOCKSOFNUCLEICACIDS

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NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

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NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

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 NucleusprimarilycontainstheDNA Smallamountsarealsofoundin:

• mitochondriaofeukaryotes• chloroplastsofplants

 PackingofDNA:• 2‐3meterslong• histones

 Gene=DNAsequencetranscribedtoRNA(maycodeforaproteinornot) genome=completecollecDonofhereditaryinformaDonofanorganism

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NucleicAcidsareimportantfortheirrolesinthestorage,transferandexpressionofgeneDcinformaDon.

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TYPESOFRNA

•mRNA‐MessengerRNA

•tRNA‐TransferRNA

•rRNA‐RibosomalRNA

•snRNA‐SmallnuclearRNA‐siRNA,miRNA,shRNA

2002Breakthroughoftheyear(RNAi)

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NucleicAcidsarelinearpolymers.

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Eachmonomerconsistsof:

1.asugar

2.aphosphate

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Thesugarcomponentsofnucleicacidsaredifferent.RiboseisusedforRNA,DeoxyriboseisusedorDNA.

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WHICHISMORESTABLE?

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Thenitrogenousbasescaneitherbeapurineorpyrimidine.

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Thenitrogenousbasescaneitherbeapurineorpyrimidine.

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ThesebaseshaveimportantcharacterisDcs

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1. keto–enoltautomerism

2. strongUVabsorbance

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12ThebaseSUBSTITUTEDfor1’‐OHgroupofthesugar

Thelinkingofasugarandanitrogenousbaseiscalledanucleoside.

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SubsDtuDngaphosphatetothe5’‐OHofthenucleosidecreatesnucleoDdes.

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PHOSPHATE

SUGAR

NITROGENOUSBASE

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SubsDtuDngaphosphatetothe5’‐OHofthenucleosidecreatesnucleoDdes.

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Morethanonephosphatemaybeadachedtothe5’‐OHgroup

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NucleoDdesareconnectedviathe3’‐OHofonenucleoDdetothephosphateatthe5’posiDonofanothernucleoDde

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WHICHISMORESTABLE?

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AshorthandnotaDonmaybeusedtodrawthenucleicacidsequence.Basesequencesarealsousedandwridenfrom5’to3’

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RECAP:1. DNAandRNAdiffersonthesugarused2. Thenitrogenousbasescanbepurine‐orpyrimidine‐based.

3. Nucleicacidshaveanacidpartandbasicparts‐  AtphysiologicalpH,phosphoricacidlosesitsprotons,therefore(–)charged

‐  Basesarenotyetprotonated,neutral4. Somepartsofthenucleicacidiscapableofhydrogenbonding

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3DSTRUCTUREOFDNA

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Thereareseverallevelsofstructure:

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1. PrimaryStructure–sequenceororderofthemonomers(inthiscase,thenucleoDdes)

2. SecondaryStructure–Localizedregionsoftheprimarysequencefoldedintoaregular,repeaDngstructuralelement

3. TerNaryStructure–InteracDngsecondarystructurestoformmoreintricate3Dshapes

4. QuaternaryStructure–associaDonofoneormorechainstoformacomplex

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Theroadtodiscoveryofthe3DstructureofDNA:

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MauriceWilkinsandRosalindFranklinnotedtherepeaDngstructuralunitfrompadernsderivedX‐raycrystallography.

LevineanalyzedDNAandascertainedthatitcontainsA,T,C,G.ChargraffrevealedthattheraDobetweenA:TandG:Cis1,possibilityofbasepairing.

RecogniDonthatthebasesareinketo‐form=hydrogenbondingispossible!

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Theroadtodiscoveryofthe3DstructureofDNA:

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WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoNdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

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Theroadtodiscoveryofthe3DstructureofDNA:

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WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoNdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

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Theroadtodiscoveryofthe3DstructureofDNA:

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Majorandminorgroovesarelinedwithsequence‐specificH‐bonding.

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Theroadtodiscoveryofthe3DstructureofDNA:

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WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecNon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

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Theroadtodiscoveryofthe3DstructureofDNA:

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WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracDons

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Theroadtodiscoveryofthe3DstructureofDNA:

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WatsonandCrick(1953)proposedthefollowingbasedonpreviousevidences:1.  Tworighthandedhelical,

polynucleoDdechainscoiledaroundanaxis,withtopographicalfeatures.

2.  TwostrandsrunoppositedirecDon(ANTI‐PARALLEL)

3.  Polarchargedbackboneisontheoutsideofthehelix,andhydrophobicorganicbasesareinside.

4.  Stabilizedbya.  HydrogenBondsb.  HydrophobicinteracNons

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Theroadtodiscoveryofthe3DstructureofDNA:

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TheDNAcanalsohavemanydoublehelicalforms

30A‐DNA B‐DNA Z‐DNA

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TheDNAcanalsohavemanydoublehelicalforms

31A‐DNA B‐DNA Z‐DNA

 A‐DNA:right‐handed,shortandbroad,2.3A,11bpperturn

 B‐DNA:right‐handed,longer,thinner,3.32A,10bpperturn

 Z‐DNA:lem‐handed,longest,thinnest,3.8A,12bpperturn

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PhysicalproperDesofDNAdetermineit’sabilitybiologicalacDvity

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DNAstrandsarecomplimentary–canserveastemplateofeachotherorsomethingelse…(informaDontransferandreplicaDon!)

Butbeforethat,H‐bondsmustbebroken!

ISTHISCHEMICALLYPOSSIBLEorLOGICAL?

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Yes,itispossible!

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DenaturaNon–heaDngofDNAtodisruptH‐bondsandseparatethestrands.Ataround85‐90°CcalledthemelDngtemperature(Tm).

Annealing–gradualcoolingofdenaturedDNAtoassociatethetwostrands

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WecanmonitorDNAdenaturaDonusingUV‐Visbecauseofhyperchromiceffect.

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Hyperchromiceffect–increaseofUVabsorbancewhenDNAisdenaturedduetoalteraDoninthearrangementoftheπelectronsinthearomaDcringsofthebases

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

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relaxedDNA

supercoiledDNA

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

37EnzymescalledTopoisomerasescreateorrelaxsupercoils

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.CircularDNAcanoccurassupercoils

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EnzymescalledTopoisomerasescreateorrelaxsupercoils

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.Theymayalsooccurasquadruplexes

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DNAinlivingorganismscanhavedifferentpossibleterDarystructures.Inhumans,theyarepackedaschromosomes

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3DSTRUCTUREOFRNA

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StructuraldifferencebetweenRNAandDNA:

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1. Sugar(Ribosevs.Deoxyribose)

2.  Uracilvs.Thymine

STERICCLASHES???

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StructuraldifferencebetweenRNAandDNA:

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1.  Sugar(Ribosevs.Deoxyribose)

2. Uracilvs.Thymine

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SinglestrandedRNAscanfoldintoloops,helicesorhairpinturns:

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GeneDcinformaDonfromDNAiscarriedbymessengerRNA(mRNA)totheribosomeforproteinsynthesis.

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AminoacidforproteinsarecarriedbytRNAsthatcontainmodifiednitrogenousbases

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Containsmodifiedbases

m1G=methylguanosinem2G=dimethylguanosineI=inosinem1I=methylinosineD=dihydrouridineΨ=pseudouridine

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RibosomalRNA(rRNA)containsstructuralfeaturessimilartotRNA

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SmallnuclearRNA(snRNA)helpsinmRNAprocessinginsidethenucleus(splicing,etc.).Theyareonlyfoundineukaryotes

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NUCLEICACIDCLEAVINGANDOTHERFORMSOFNUCLEICACIDS

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Nucleicacidscanbecleavedbyenzymescallednucleases.

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RestricNonenzymes(aspecificendonuclease)mayalsobeusedtocleavecircularDNAfrombacteria..

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Nucleicacidsformmanycomplexeswithproteins:virus,chromosomes,snRNP,Ribosomes,Ribonucleoproteinenzymes.

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OTHERINTERESTINGFACTS

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BOX10‐1containsinformaDonaboutpurinesandpyrimidines

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BOX10‐2talksaboutspecialRNAsesthatarebeingtestedasanD‐canceragents

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