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DNA:TheCodeofLife
• Thestructureandthefourgenomicletterscodeforalllivingorganisms
• Adenine,Guanine,Thymine,andCytosinewhichpairA-TandC-Goncomplimentarystrands.
• DNAhasadoublehelixstructurewhichcomposedof– sugarmolecule– phosphategroup– andabase(A,C,G,T)
• DNAalwaysreadsfrom5’ endto3’ endfortranscriptionreplication
DNA:TheCodeofLife
DNAReplication• DNAcanreplicateby
splitting,andrebuildingeachstrand.
• Notethattherebuildingofeachstrandusesslightlydifferentmechanismsduetothe5’ 3’ asymmetry,buteachdaughterstrandisanexactreplicaoftheoriginalstrand.
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html
Genotype/Phenotype
• Topreventconfusionbetweengenes(whichareinherited)anddevelopmentaloutcomes(whicharenot),geneticistsmakeadistinctionbetweenthegenotype andthephenotype ofanorganism– Genotype:completesetofgenesinheritedbyanindividual
– Phenotype:allaspectsoftheindividual’sphysiology,behavior,andecologicalrelationships
DNAtheGeneticsMakeup• Genesareinheritedandareexpressed
• genotype (geneticmakeup)
• phenotype (physicalexpression)
Ontheleft,istheeye’sphenotypesofgreenandblackeyegenes.
• Twoorganismswhosegenesdifferatonelocus aresaidtohavedifferentgenotypes.
• Alocus(lociforplural)isthespecificlocationofageneofaDNAsequenceonachromosome.
• AvariantoftheDNAsequenceatagivenlocationiscalledaallele.
• Theorderedlistoflociknownforaparticulargenomeiscalledageneticmap.
Diploidandpolyploid cellswhosechromosomeshavethesamealleleofagivengeneatsomelocusarecalledhomozygous,withrespecttothatgene(otherwise,itisheterzygous).
Thechromosomallocusofagenemightbewritten"6p21.3”• 6:chromosomenumber• p:positiononthe
chromosome’sshortarm(“p”)orlongarm(“q”)
• 21.3:thepositiononthearm:region2,band1,sub-band3.Thebandsarevisibleunderamicroscopewhenthechromosomeisstained.
• Pleiotropy: whenonegeneaffectsmanydifferenttraits.
• Polygenictraits:whenonetraitisgovernedbymultiplegenes,whichmaybeonthesamechromosomeorondifferentchromosomes.– Theadditiveeffectsofnumerousgenesonasinglephenotypecreateacontinuumofpossibleoutcomes.
– Polygenictraitsarealsomostsusceptibletoenvironmentalinfluences.
Pleiotropy inhumans:PhenylketonuriaA disorderthatiscausedbyadeficiencyoftheenzymephenylalaninehydroxylase,whichisnecessarytoconverttheessentialaminoacidphenylalaninetotyrosine.AdefectinthesinglegenethatcodesforthisenzymethereforeresultsinthemultiplephenotypesassociatedwithPKU,includingmentalretardation,eczema,andpigmentdefectsthatmakeaffectedindividualslighterskinned
PolygenicInheritanceinHumans• Height iscontrolledbypolygenesforskeletonheight,buttheir
effectmaybeaffectedbymalnutrition,injury,anddisease.• Weight,skincolor,andintelligence.• Birthdefects likeclubfoot,cleftpalate,orneuraltubedefectsare
alsotheresultofmultiplegeneinteractions.• Complexdiseasesandtraits haveatendencytohavelow
heritability(tendencytobeinherited)comparedtosinglegenedisorders(i.e.sickle-cellanemia,cysticfibrosis, PKU,Hemophelia,manyextremelyraregeneticdisorders).
Selection• Somegenesmaybesubjecttoselection,whereindividualswithadvantagesor“adaptive”traitstendtobemoresuccessfulthantheirpeersreproductively
• Whenthesetraitshaveageneticbasis,selectioncanincreasetheprevalenceofthosetraits,becausetheoffspringwillinheritthosetraits.Thismaycorrelatewiththeorganism'sabilitytosurviveinitsenvironment.
• Severaldifferentgenotypes(andpossiblyphenotypes)maythencoexistinapopulation.Inthiscase,theirgeneticdifferencesarecalledpolymorphisms.
GeneticMutation• Thesimplestisthepointmutationorsubstitution;here,asingle
nucleotideinthegenomeischanged(singlenucleotidepolymorphisms(SNPs))
• Othertypesofmutationsincludethefollowing:– Insertion. ApieceofDNAisinsertedintothegenomeatacertainposition
– Deletion. ApieceofDNAiscutfromthegenomeatacertainposition
– Inversion. ApieceofDNAiscut,flippedaroundandthenre-inserted,therebyconvertingitintoitscomplement
– Translocation. ApieceofDNAismovedtoadifferentposition.– Duplication. AcopyofapieceofDNAisinsertedintothegenome
MutationsandSelection
• Whilemutationscanbedetrimentaltotheaffectedindividual,theycanalsoinrarecasesbebeneficial;morefrequently,neutral.
• Oftenmutationshavenooranegligibleimpactonsurvivalandreproduction.
• Therebymutationscanincreasethegeneticdiversity ofapopulation,thatis,thenumberofpresentpolymorphisms.
• Incombinationwithselection,thisallowaspeciestoadapttochangingenvironmentalconditionsandtosurviveinthelongterm.
RawSequenceData• 4bases:A,C,G,T+other(i.e.N=any,R=GorA(purine),Y=Tor(pyrimidine))– kb(=kbp)=kilobasepairs=1,000bp–Mb=megabasepairs=1,000,000bp– Gb=gigabasepairs=1,000,000,000bp.
• Size:– E.Coli4.6Mbp(4,600,000)– Fish130Gbp (130,000,000,000)– Parisjaponica(Plant)150Gbp– Human3.2Gbp
Fasta File• AsequenceinFASTAformatbeginswithasingle-line
description,followedbylinesofsequencedata(fileextensionis.fa).
• Itisrecommendedthatalllinesoftextbeshorterthan80charactersinlength.
Fastq File• Typicallycontain4lines:
– Line1beginswitha'@'characterandisfollowedbyasequenceidentifierandanoptional description.
– Line2isthesequence.– Line3isthedelimiter‘+’,withanoptionaldescription.– Line4isthequalityscore.– fileextensionis.fq
@SEQ_IDGATTTGGGGTTCAAAGCTTCAAAGCTTCAAAGC+!''*((((***+))%%%++++++++!!!++***
GenesandProteins
• Onegeneencodesoneproteinandbeginswithstartcodon(e.g.ATG),theneachthreecodeoneaminoacid.Thenastopcodon(e.g.TGA)signifiesendofthegene.
• Inthemiddleofa(eukaryotic)gene,therearesegmentsthataresplicedoutduringtranscription.– Introns:segmentsthataresplicedout– Exons:segmentsthatarekept.
• Detectingtheintronsandexonsisataskforgenefinding.