nucleic acids: dna and rna...nucleic acids are important for their roles in the storage, transfer...
TRANSCRIPT
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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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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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