Lecture2:BiologyBasicsContinued

CentralDogma

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

InverseComplementofDNA

WhatistheinversecomplementsequenceofTATAGCCCG?

InverseComplementofDNA

WhatistheinversecomplementsequenceofTATAGCCCG? CGGGCTATA

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.

Genotype/PhenotypePhenotype:

Blueeyes Browneyes

Genotype:

Recessive:bb Dominant:BborBB

• 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.

Genomics:- Assembly- Detectionofvariation- GWAS

RNA:- Geneexpression- Transcriptome assembly- Pathwayanalysis

Protein:- Massspectrometry- Structureprediction- Protein-Protein

interaction