flow of genetic information

welcome molecular biology

1. Flow of genetic information
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2. Macromolecules
•Macromolecules:Verylargemoleculesthatmakemostofthe
structureofthebodymadeofsmallerpiecescalledmonomersthat
canbeassembledtoformavarietyofstructures.Alargechainof
monomersiscalledapolymer.
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3. Proteins
•Monomer:aminoacid(20)
•Polymer:proteinorpolypeptide
•Structurecentralcarbonatomwithhydrogen,amine,
carboxyl,&Rgroups
•Uses:structure,emergencyenergy
•Functionexpressionofgeneticinformation
•Examples:skin,insulin,enzymes
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4. Nucleic Acids
•Monomer: nucleotide (5)
•Polymer: nucleic acid
•Structure: 5-carbon sugar attachedto
nitrogen base and phosphate group
•Uses: stores genetic code
•Examples: DNA and RNA
•DNAstore genetic information .
•RNAprocess genetic information
•Proteinexpress of genetic information
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5. Nucleic acids (DNA and RNA)
•Nucleicacids,DNAandRNAarepolymersofnucleotideswhich
themselvesconsistofanitrogenousbase,apentosesugarand
phosphoricacid.Nucleicacidsareinvolvedinthestorageand
processingofgeneticinformation.
•Bases:ThebasesofDNAandRNAarearomaticrings(Fig.1).Adenine
(A)andguanine(G)arepurines,bicyclicstructureswhereascytosine
(C),thymine(T)anduracil(U)aremonocyclicpyrimidines.InRNA,the
thyminebaseisreplacedbyuracil.
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6. •NucleosidesAnucleosideconsistsofabasecovalentlybondedtothe1'-positionofa
pentosesugarmolecule.InRNAthesugarisriboseandthecompoundsare
ribonucleosides,ornucleosides,whereasinDNAitis2'-deoxyriboseandthenucleosides
arenamed2'-deoxyribonucleosides,orjustdeoxynucleosides.Base+sugar=nucleoside.
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7. Nucleotides:
•Nucleotidesarenucleosideswithoneormorephosphategroups
covalentlyboundtothe3'-,5'-or(inribonucleotides)the2'-position.If
thesugarisdeoxyribose,thenthecompoundsaretermed
deoxynucleotides(Fig.3)Inthecaseofthe5'-position,uptothree
phosphatesmaybeattached,toform,forexample,adenosine5'-
triphosphate,ordeoxyguanosine5'-triphosphate,commonly
abbreviatedtoATPanddGTPrespectively.Inthesameway,wehave
dCTP,UTPanddTTP(equivalenttoTTP).5'-Monoand-diphosphates
areabbreviatedas,forexample,AMPanddGDP.Nucleoside5'-
triphosphates(NTPs),ordeoxynucleoside5'-triphosphates(dNTPs)
arethebuildingblocksofthepolymericnucleicacids..Therepeatunit
ofaDNAorRNAchainishenceanucleotide.Base+sugar
+phosphate=nucleotide
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8. Properties of nucleic acids
•StabilityofnucleicacidsAlthoughitmightseemobviousthatDNAdouble
strandsandRNAstructuresarestabilizedbyhydrogenbonding,thisisnot
thecase.H-bondsdeterminethespecificityofthebasepairing,butthe
stabilityofanucleicacidhelixistheresultofhydrophobicanddipole–dipole
interactionsbetweenthestackedbasepairs.
•Effectofacid:Highlyacidicconditionsmayhydrolyzenucleicacidstotheir
components:bases,sugarandphosphate.Moderateacidcausesthe
hydrolysisofthepurinebaseglycosylicbondstoyieldapurinicacid.More
complexchemistryhasbeendevelopedtoremoveparticularbases,andis
thebasisofchemicalDNAsequencing.
Effectofalkali:HighpHdenaturesDNAandRNAbyalteringthetautomeric
stateofthebasesanddisruptingspecifichydrogenbonding.RNAisalso
susceptibletohydrolysisathighpH,byparticipationofthe2'-OHin
intramolecularcleavageofthephosphodiesterbackbone.
•Chemicaldenaturation:Somechemicals,suchasureaandformamide,
candenatureDNAandRNAatneutralpHbydisruptingthehydrophobic
forcesbetweenthestackedbases.
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9. Properties of nucleic acids
•Viscosity:DNAisverylongandthin,andDNAsolutionshaveahigh
viscosity.LongDNAmoleculesaresusceptibletocleavagebyshearingin
solution,thisprocesscanbeusedtogenerateDNAofaspecificaverage
length.
•UVabsorptionThearomaticbasesofnucleicacidsabsorblightwithamax
of260nm.
•Hypochromicity:Theextinctioncoefficientofnucleicacidbasesdepends
ontheirenvironment.Theabsorbanceofisolatednucleotidesisgreaterthan
thatofRNAandsinglestrandedDNA,whichisinturngreaterthanthatof
double-strandedDNA.Double-strandedDNAishypochromicwithrespectto
single-strandedDNA.
•Quantitationofnucleicacids:Theabsorbanceat260nmisusedto
determinetheconcentrationofnucleicacids.Ataconcentrationof1mgml
and1cmpathlength,double-strandedDNAhasA260=20.RNAand
single-strandedDNAhaveA260=25.ThevaluesforRNAandsingle-
strandedDNAdependonbasecompositionandsecondarystructure.
•PurityofDNATheA260/A280ratioofadouble-strandedDNAsamplecan
beusedtoassessitspurity.ForpureDNA,thevalueis1.8.Valuesabove
1.8suggestRNAcontaminationandthosebelow1.8suggestprotein
contamination.
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10. Properties of nucleic acids
•Thermaldenaturation:Increasedtemperaturecanbringaboutthe
denaturationofDNAandRNA.RNAdenaturesgraduallyonheating,but
double-strandedDNA‘melts’cooperativelytogivesinglestrandsatadefined
temperature,Tm,whichisafunctionoftheG+CcontentoftheDNA.
DenaturationmaybedetectedbythechangeinA260.
•RenaturationDNA:renaturesoncoolingbutwillonlyformfullydouble-
strandednativeDNAifthecoolingissufficientlyslowtoallowthe
complementarystrandstoanneal.
•IntercalatorsIntercalators,suchasethidiumbromide,bindtoDNAby
insertingthemselvesbetweenthebasepairs(intercalation),resultinginthe
localuntwistingoftheDNAhelix.IftheDNAisclosed-circular,thentherewill
beacorrespondingincreaseinwrithe.
•Closed-circularDNA:ManyDNAmoleculesincellsconsistofclosed-
circulardouble-strandedmolecules,forexamplebacterialplasmidsand
chromosomesandmanyviralDNAmolecules.Thismeansthatthetwo
complementarysinglestrandsareeachjoinedintocircles,5'to3',andare
twistedaroundoneanotherbythehelicalpathoftheDNA.Themoleculehas
nofreeends,andthetwosinglestrandsarelinkedtogetheranumberof
timescorrespondingtothenumberofdouble-helicalturnsinthemolecule.
Thisnumberisknownasthelinkingnumber(Lk).
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11. Properties of nucleic acids
•Supercoiling: Supercoiling is the coiling of the DNA axis upon itself, caused
by a change in the linking number from Lk°, the value for a relaxed closed
circle. Most natural DNA is negatively supercoiled, that is the DNA is
deformed in the direction of unwinding of the double helix.
• Supercoiling is biologically important for two reasons. First, a supercoiled
DNA molecule has a more
•compact shape than does its relaxed counterpart. Second, supercoiling may
hinder or favor the capacity of the double helix to unwind and thereby affects
the interactions between DNA and other molecules.
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12. Chromatin structure
•ChromatinThetotallengthofDNAinaeukaryoticcelldependsonthe
species,butitcanbethousandsoftimesasmuchasinaprokaryotic
genome,andismadeupofanumberofdiscretebodiescalled
chromosomes(46inhumans).TheDNAineachchromosomeisbelieved
tobeasinglelinearmolecule,whichcanbeuptoseveralcentimeterslong.
AllthisDNAmustbepackagedintothenucleus,aspaceofapproximately
thesamevolumeasabacterialcell;infact,intheirmosthighlycondensed
forms,thechromosomeshaveanenormouslyhighDNAconcentration.This
featofpackingisaccomplishedbytheformationofahighlyorganized
complexofDNAandprotein,knownaschromatin,anucleoprotein
complex.Morethan50%ofthemassofchromatinisprotein.
•HistonesThemajorproteincomponentsofchromatinarethehistones;
small,basic(positivelycharged)proteinswhichbindtightlytoDNA.There
arefourfamiliesofcorehistone,H2A,H2B,H3,H4,andafurtherfamily,H1,
whichhassomedifferentproperties,andadistinctrole.Individualspecies
haveanumberofvariantsofthedifferenthistoneproteins.
•NucleosomesThenucleosomecoreisthebasicunitofchromosome
structure,consistingofaproteinoctamercontainingtwoeachofthecore
histones,with146bpofDNA.
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13. Chromatin structure
•TheroleofH1:AsinglemoleculeofH1stabilizestheDNAatthepointat
whichitentersandleavesthenucleosomecore,andorganizestheDNA
betweennucleosomes.
•HigherorderstructureTheorganizationofchromatinatthehighestlevel
seemsrathersimilartothatofprokaryoticDNA.Electronmicrographsof
chromosomeswhichhavebeenstrippedoftheirhistoneproteinsshowa
loopeddomainstructure..Eventhesizeoftheloopsisapproximatelythe
same,uptoaround100kbofDNA,althoughtherearemanymoreloopsin
aeukaryoticchromosome.Theloopsareconstrainedbyinteractionwitha
proteincomplexknownasthenuclearmatrix.TheDNAintheloopsisin
theformof30nmfiber,andtheloopsformanarrayabout300nmacross.
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14. Eukaryotic chromosome structure
•Themitoticchromosome:Thefamiliarpictureofachromosome(Fig.1)
isactuallythatofitsmosthighlycondensedstateatmitosis.Asthe
daughterchromosomesarepulledapartbythemitoticspindleatcell
division,thefragilecentimeters-longchromosomalDNAwouldcertainlybe
sharedbytheforcesgenerated,wereitnotinthishighlycompactstate.
ThestructureinFig.1actuallyillustratestwoidenticalsisterchromatids,
theproductsofreplicationofasinglechromosome,joinedattheir
centromeres.Thetipsofthechromosomesarethetelomeres,whichare
alsotheendsoftheDNAmolecule;theDNAmapsinalinearfashion
alongthelengthofthechromosome,albeitinaveryconvolutedpath.The
structureofasectionofamitoticchromatidisshowninFig.1.The
chromosomalloopsfanoutfromacentralscaffoldornuclearmatrixregion
consistingofprotein.
ThecentromereThecentromereistheregionwherethetwochromatidsare
joinedandisalsothesiteofattachmenttothemitoticspindle,whichpulls
apartthesisterchromatidsatanaphase.Centromeresarecharacterized
byspecificshortDNAsequencesalthough,inmammaliancells,theremay
beaninvolvementofsatelliteDNA.
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15. Eukaryotic chromosome structure
•TelomeresTheendsofthelinearchromosomalDNAareprotectedfrom
degradationandgradualshorteningbythetelomeres,whichareshort
repeatingsequencessynthesizedbyaspecificenzyme,telomerase,
independentlyofnormalDNAreplication.
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•HistonevariantsandmodificationThecontrolofthedegreeof
condensationofchromatinoperates,atleastinpart,throughthechemical
modificationofhistoneproteins,whichchangestheirchargeduringthecell
cycle,orthroughtheuseofhistonevariantsinparticularcelltypesorduring
development.
•Functionofhistone
CoiltheDNAintoasmallervolumeforfittinginthenucleusofthecellinform
ofanucleosome
Regulationofgeneexpression
DNAdamagerepair
DNAreplicationandrecombination
heritableepigeneticregulation 15

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17. Gene, Genome and Proteome
•Gene:AspecificsequenceofnucleotidesinDNA(incellsandcertain
viruses),orinRNA(inotherviruses),thatencodesagivenpolypeptide
oranRNAmoleculewithabiosyntheticorcontrolfunction.
•Genome:totalDNAcomplementorthesumofallthegenesofan
organism.Itmaycompriseasinglechromosomeorbespreadacross
multiplechromosomes.Ineukaryotes,itcanbesubdividedintonuclear,
mitochondrialandchloroplastgenomes.
•Transcriptome:sumofalltheRNAtranscripts(mRNA)ofanorganism,
producedfromthegenomeatanygiventime.
•Proteome:sumofalltheproteinsofanorganism.Isusedbothto
describethetotalsetofproteinsencodedinthegenomeofacellandthe
varioussubsetsthatareexpressedfromthetranscriptomeatanyone
time.Theproteomeincludesallthevariousproductsencodedbyasingle
genethatmayresultfrommultipletranscripts
•Metabolome:sumofallsmallmolecules–aminoacids,nucleotides,
sugarsetc.–andalltheintermediatesthatexistwithinacellduringtheir
synthesisanddegradation. 17

18. The flow of genetic information
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DNA makes RNA makes protein =protein
synthesis
DNA makes DNA = DNA replication
DNA makes RNA = transcription
RNA makes protein= Translation
RNA makes DNA= Reverse transcription
RNA makes RNA= RNA replication
biologicalinformationmovesfromthe
genometoecologies(DNAtoRNAto
proteintobiomodulesornetworksto
cellstoorganstoindividualsto
populationsofindividualstoecologies)

19. Genome of Prokaryotes
•Theirgenomeisasingle,circularDNAmolecule.
•Theirgenomesizeisintheorderofafewmillionbasepairs
[0.6–8].
•Theirgenedensity(thenumberofgenesperbasepairsinthe
genome)isapproximatelyonegeneper1,000basepairs.
•Theirgenomeiscontainingfewuselessparts(70percentis
codingforproteins).
•Theirgenesaretranscribed(copiedintomessengerRNA)right
afteracontrolregioncalledapromoter.
•TheirMessengerRNA(mRNA)iscollinearwiththegenome
sequence.Inotherwords,genesareinasinglepiece,not
interruptedbynoncodingDNAsegment(calledintrons).
mRNAdoesn’tneedprocessing(splicing,polyadenylationand
capping).
•GeneoftenexhibitonemRNA(andprotein)form.
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20. Genome of Eukaryotes
•TheirgenomeconsistsofmultiplelinearpiecesofDNAcalled
chromosomes(uptoahundredmillionbasepairslong).
•Theirgenomesize(10–670,000millionbasepairs),especiallyfor
animals,plantsismuchbiggerthaninprokaryotes.
•Theirgenedensityismuchlowerthanthatforprokaryotes(onehuman
geneper100,000basepairs).
•Theirgenomeiscontainingmanyuselessparts(lessthan5percentof
thehumangenomecodeforproteins).
•Theirgenesaretranscribedrightafteracontrolregioncalledapromoter,
butsequenceelementslocatedfarawaycanhaveastronginfluenceon
thisprocess.
•GenesequencesarenotcollinearwiththefinalmessengerRNA(mRNA)
andproteinsequences.Onlysmallbits(theexons)areretainedinthe
maturemRNAthatencodesthefinalproduct.Inotherwords,mRNA
needprocessing(splicing,polyadenylationandcapping)
•GenesoftenexhibitmorethanonemRNA(andprotein)form. 20