BIOL1090

DNA&Chromosomes
Functionsofgeneticmaterial
genotypicfunctionisreplication:ParentalDNAseparatesandnewcomplementarystrands
synthesizecreatingtwoidenticaldaughterDNAmolecules
phenotypicfunctionisgeneexpression.Phenotypeisdefinedashowfunctionisreadfrom
expressinggene.Phenotypicfunction:howgenomeisusedexpressionofindividualgenegenes
silent/notatrighttimeswanttopassongenes(successorfailureaccordingtonatureifyoucan
passongenesornot)

evolutionaryfunctionismutation:populationvariationisthesubstrateonwhichnaturalselection
acts.Thereisvariationineverypopulation(spotsonladybugs).Therecanbeaninnocuousallele
butiftheenvironmentchangesandthealleleisfavouredthenitmaybecomeexpressed,andit
canevenmakeawholenewspeciesifenoughmutationandexpressionoccurs.

Myostatin:regulationofmusclemasssize.MET5notinallcells,onlyexpressedinonesthat
willbemuscle.
Cellskeepdividinguntiltheybecomemorespecialized

Genomesarenotdeterministic:genomescaninteractwiththeenvironmentsuchastheDaphnia
whichcaneitherbelongorshortdependingonthesituation.Daphniaonleftislongerandthus
harderforpredatorstoeatwhiletheoneontherighthadtheabsenceofpredatorsignalso
developedlookinglikeawaterflea.

AttheheartofgenesandgeneticsisDNA(Deoxyribonucleicacid),whichisapolymer.Consists
ofaphosphategroup,a5carbonsugar(2deoxyribose),andoneof4cyclicnitrogenousbases.

SingleareCandTandarepyrimidinewhiledoubleareAandGwhicharepurine.
Deoxythymidinemonophosphate(dTMP)
Deoxycytidinemonophosphate(dCMP)
Deoxyadenosinemonophosphate(dAMP)
Deoxyguanosinemonophosphate(dGMP)

PurineandPyrimidinenucleotidesinpolynucleotidechainsareconnectedbyphosphodiester
bonds.
DNAischemicallypolar,5endhasafreephosphategroupwhile3endhasafreehydroxyl
group

DNAisdoublestrandedandthestrandsareantiparallelso5endnextto3endofopposite
strand.Thedoublehelixisrighthanded,meaningstrandstwistclockwisewhenholdingitaway
fromyourbodyandlookingatit.

Strandsheldtogetherbyhydrogenbondsbetweenbasesonopposingstrandsandhydrophobic
interactionsbetweenstackedbases.LongerDNAismorestablesincemorebondsandmore
stabilizinghydrophobicinteractions.BasepairingisspecificandmediatedbyHbonds.
Opposingstrandsarecomplementary(AalwayswithTCalwayswithG)
CGmorestablethanATsinceCGhas3HbondswhileATonlyhas2Hbonds.

MostcommonformofDNAisBDNA,whileADNAalsoexists.ZDNAistheonewithleft
handedtwist.
ThereisaminorandmajorgrooveinDNA(thereisalternatingnarrowerandwiderpartsin
DNA).ThisisforproteinbindingtoDNAsinceitcanrecognizethedifferentgroovesandbind
whereneeded.
Eukaryoticchromosomesarecomposedofproteins,DNA,andRNA.
Almost2/3ofnucleusisDNAinchromatinform.Thereislotsofproteinwhicharecalled
histones,butalsononhistoneproteins
seeslide

FirstlevelofcondensationispackagingDNAasanegativesupercoilintonucleosomes,
producingan11nmfibre.Nucleosomecoreis146nucleotidepairsofDNAwrapped1and
turnsaroundanoctamerofhistones.ThelinkerDNAjoiningthesecoresisvaryinginlength
from8to114nucleotidepairs.

th
Corenucleosomemadeof8histones,4typesand2ofeach,2H2a,2H2b,2H3,2H4.9

histoneanchorsthenucleosome,histoneH1

Thesecondlevelofcondensationanadditionalfoldingorsupercoilingofthe11nmfibreto
producea30nmfibre.Drivenbynucleosomalinteractions.HistoneH1isinvolved.Thetwo
modelsdescribingthesubstructurearethesolenoidandthezigzagmodels.Seeslide24Lecture
1.Modelscanbedrawndifferentlydependingonhowtheyareviewedbutitisstillthesame
DNAinthe30nmfibre.ThesolenoidmodelisfavouredastohowDNAlooksinalivingcell.

Thethirdlevelofcondensationistheattachmentofthe30nmfibreatmanypositionstoa
(nonhistone)proteinscaffold.Inmetaphasethechromosomeusesthe30nmfibreasthebasic
structuralunitbecauseDNAisinitsmostcondensedform.Theproteinscaffoldletsthefibre
looptoreduceevenmorespace.Scaffoldthenturnsinhelixshapetocontinuereducingspace.

Prokaryoticchromosomesarealsohighlycompact,beingfoldedandsupercoiledreducingthe
originalcircularshapeandsizefrom350umto2um.
DNAfoundinmitochondriaandchloroplastsexistsincircularchromosomesthatresemblethose
ofprokaryotes(stillhascoiling).
(Righthandedhelixmeanslefthandedtwisttoformsupercoils).

Endosymbiotic:2differentorganismswhereonecelllivedinsidetheotherandthiseventually
evolvedineukaryoticcellsnowtheinsideorganismNEEDStheoutsideonetofunctionand
survive(evolvedintodedicatedorganelle).

Chromosomesendsareprotectedbytelomeres.Specializedsequenceofbasepairs
5
14T,01
A,18G
3
.OneexamplewouldbeTTAGGG.
Telomeresprovidethreeimportantfunctions:
1.ResistdegradationbyDNAsescellhasenzymesthatcandegradeDNAsuchasendonuclease
orexonuclease.
2.Preventfusionofchromosomalendsfreeendsofchromosomescanfusetogetherandthis
wouldwantthosemoleculestosticktogethersincephosphodiesterbondswillbeformedso
telomerespreventthisfusion.
3.FacilitatereplicationoftheendsofthelinearDNAEverytimecelldividesthechromosome
getsabitshorterandsincetelomereshavethousandsofrepeatstheyprovideabufferfortheloss
oftheDNAattheend.Telomeresgetshorterattheendofeverycelldivisionbuttheyarelong
enoughthatthisdoesnotmatter.
Telomerasekeepstelomereslong,butcancercellsalsohavethistokeepdividingandspreading

Anotherfeatureofchromosomesiscentromeres:thewaistwherethechromosomeconstricts.
Theyprovidethepointofattachmentofchromosomestomicrotubulesinthemitoticspindle.
Centromeresalsohavespecificbasepairsequence.ATsequenceshave2Hbondssomore
flexiblethanaveragesequencecanbendDNAmoretightly.
Yeastcentromeresare110120basepairs(bp)long.Threeessentialregions:regionsIandIIIare
conservedsequencesthatbindproteinsinvolvedinspindleattachment.
regionII~90bp,>90%A,T
Centromeresinmulticellulareukaryotesaremuchlargerandmorecomplex,eg500015000
copiesofthe171bpalphasatellitesequence.BindingsitesforaproteincalledCENP(relatedto
HistoneH3).

CellCycle&Mitosis

Mitosis
Cellularorganellesandcytoplasmiccontentsaredividedmoreorlessequallybetween
daughter
cells
.
TheendoplasmicreticulumandGolgicomplexarefragmentedatthetimeofdivisionand
reformedinthedaughtercells.
Mitochondriaandchloroplastsarerandomlydividedbetweendaughtercellshowever
chromosomesmustbeduplicatedexactlyanddistributedequallyandexactlytodaughtercells

StagesofCelldivision

CellcycleiscomposedofInterphaseandmitosis
InterphaseisbrokenintoG1,S,andG2phase
MitosisisbrokenupintoProphase,Metaphase,Anaphase,Telophaseandendswithcytokinesis.
MitosisisalsocalledtheMphaseinthecellcycle
G1phase(
Gap1)growth,cellularmetabolism
Sphase
(Synthesis)DNAreplication(chromosomeduplication)
G2phase
(Gap2)preparationformitosis
Mphase(
mitosis)chromosomalpasdedeuxandcytokinesis
Interphase
thetimebetweensuccessivemitoses(G1+S+G2)

**
notallcellsundergomitosissomeleaveduringG1andenter
G0
,theyaresaidtobe
quiescent.

**
noclockthatregulatescellcycletimingineukaryoticcells

Centrosome
cycleiswhenthe
centrioles
areduplicated,occursalongthecellcycle
Inanimalcells,thecentrosomesaremicrotubuleorganizingcentres(MTOCs)
negativeendofMTOCsgotowardscentrosomesandpositiveendsgoawayfromcentrosomes,
thisorientationiskey
Chromosomesduplicateatthestartofmitosis
Duplicatedchromosomesatmetaphasecondenseundertheinfluenceof
condensin

Cohesin
holdsstrandsofDNAtogetherduringinterphase,duringprophase
condensin
pinches
strandsofDNAformingloopsinthestrands,theseloopsarethenadheredtogetherbycohesin.
Seeslide10forpicture
n
=haploidchromosomenumber
c
=DNAcontent

Diploidmothercell(2n)(4c)DNAsynthesisandthendivides(Fission)Twodaughtercells
(2c)(2n)**theyareidenticaldiploidcells

Interphase
whenmitosisbeginseachchromosomehasbeenduplicated,producingsister
chromatidsjoinedatthecentromereby
cohesin
,the
centrosome
isduplicated

Prophase
initiationofspindleformation,condensationofduplicatedchromosomes,
fragmentationofERandGolgi,nucleolusdisappears,Nuclearmembranebreaksdown,spindle
microtubulesinvadethenuclearspace.

Prometaphase
chromosomalmicrotubulesattachtothe
kinetochores
,locatedontheouter
surfaceofcentromeres,chromosomesmovetowardstheequatorofthespindle.

Kinetochores
outerkinetochoremicrotubulebindingandmicrotubulemotoractivitysignal
transduction,innerkinetochorecentromerereplicationchromatininterfacekinetochore
formation.Positiveendofmicrotubuleswheresubunitsareaddedorlost.Otherendisnegative.

Metaphase
duplicatedchromosomesarealignedmidwaybetweenthespindlepoles,this
equatorialplaneiscalledthe
metaphaseplate
.
Anaphase
centromeressplitandchromatidsseparatechromosomesmovetowardsopposite
spindlepoles,spindlepolesmovefurtherapart.
Telophase
chromosomesclusteratoppositespindlepoles,chromosomesbecomedispersedand
decondense,nuclearenvelopeassemblesaroundchromosomes,GolgiandERreform,daughter
cellsformby
cytokinesis
Inplantcells,acellplateformsthescaffoldforanew,cellulosecontaining,cellwall

Meiosis&gametogenesis

n=numberofchromosomes=the
haploidstate
2nchromosomes=the
diploidstate
Homologues
similarchromosomesthataresimilartooneanotherbutnotidentical(sister
chromosomes)
Heterologues
chromosomesthatarenotidenticalorsimilar(chromosomesthatdonotbelong
tothesamepair)
Sexchromosomes
Specializedchromosomes,infemalehumansitisXXandinmalehumansit
isXY.

MeiosisI
(
Leptonema,Zygonema,Pachynema,Diplonema
)chromosomes,eachconsisting
oftwosisterchromatids,begintocondense.Homologouschromosomesbegintopair,

homologouschromosomesarefullypaired,homologouschromosomesseparate,exceptat
chiasmata

Pairingofhomologouschromosomesiscalled
synapsis
andisoftenfacilitatedbyformationofa
synaptonemalcomplex
composedoflateralelementsconnectedtoacentralelementby
transversefibers.
Whenhomologouschromosomesarefullypaired,pairedsisterchromatidsarecalled
Tetrads
whilepairedsisterchromosomesarecalled
Bivalents
.

Crossingoverinvolvesthebreakageofchromatidsandtheexchangeofthebrokenpieces
betweenhomologouschromosomes(nonsisterchromatids).Following
crossingover
,
homologouschromosomesstarttopullapart,butremainjoinedatthecrossoverjunctions
(called
chiasmata).

**Diplotenestagemaypersistfortheentirereproductivelifeoftheindividual(morethan40
yearsinfemalehumans)

CelldivisioninMeiosisIiscalled
reductiondivision

ProphaseI
:Pairedchromosomescondensefurtherandbecomeattachedtospindlefibers.
MetaphaseI:
Pairedchromosomesalignontheequatorialplaneinthecell.
AnaphaseI:
Homologouschromosomesdisjoinandmovetooppositepolesofthecell.
TelophaseI:
Chromosomemovementiscompletedandnewnucleibegintoform.
**
Chromosomedisjunction
occursbetweenmetaphaseIandanaphaseI
MeiosisI
producestwo
haploid
daughtercellsthataregeneticallyidentical

Meiosis:Diploid(2c,2n,meiocyte)DNAsynthesis4cDivision1Two2ccells
DivisionIIfourccells(theyarenonidenticalhaploid(n)cells).

MeiosisII
ProphaseII
:Chromosomes,eachconsistingoftwosisterchromatids,condenseandbecome
attachedtospindlefibers.
MetaphaseII:
Chromosomesalignontheequatorialplaneineachcell
AnaphaseII:
Sisterchromatidsdisjoinandmovetooppositepolesineachcell(
chromatid
disjunction
occurs)
TelophaseII:
Chromosomesdecondenseandnewnucleibegintoform.
Cytokinesis
:Thehaploiddaughtercellsareseparatedbycytoplasmicmembranes

KinetochorepositionchangesbetweenprophaseIandII

Spermatogenesis
Spermatogonia(2n)Mitosisoccursforseveralgenerationschromosomeduplicationleadsto
Primaryspermatocyte(2n)MeiosisISecondaryspermatocyte(n)MeiosisIIspermatids
attachedtospermatocyteswhichareinterconnectedbycytoplasmicbridgesfoursperm
cells(n)

Oogenesis
Oogonium(2n)
ChromosomeduplicationandpairingprimaryoocyteMeiosisIPrimary
oocytedividingFirstPolarbodyandSecondaryoocyte
FirstpolarbodymeiosisIIpolarbodydividingTwopolarbodies(n)
Secondaryoocytesecondaryoocytedividingpolarbody(n)andegg(n)
**MeiosisIbeginsinthefetalovarybutarrestsatProphaseI(atdiplonema)
**Forovulation,aneggmaturestometaphaseIIandisreleasedintothefallopiantube.Atthis
timeoffertilizationtheoocyteisstill
2c
andmeiosisIIiscompleted(expulsionofthesecond
polarbody)afterfertilization

Bakersyeastfateofahaploidcell
BakersyeastAsexualbuddingHaploidcellsofoppositematingtypesmating
DiploidzygoteMeiosissporulationAscuswithfourhaploidascosporesBakers
yeast

Sporophyte(diploid)
GAmetophyte(haploid)

Atruealternationofgenerationsinplants
SporophytemaleandfemalegermcellsMALEmeiosisleadstomicrosporeswhile
FEMALEmeiosisleadstomegasporesMegaandmicrosporesgothroughmitosisand
becomeMALEandFEMALEgametophytesgametesfertilizationzygote(zygote
microspore)MitosisSporophyte

ThebasicprinciplesofMendelianinheritance

ThebenefitsofMendelsexperimentalsystem:hispeaswerehighlyinbred.Becauseflower
structurepromotedselffertilizationtheythereforebredtrue.Egwhentwotallplantswere
crossed,theyonlyproducedtallprogeny.Mendelsexperimentsweredesignedsothathecould
studyonetraitatatime.

Monohybridcross(singletraitisfollowed).
Inageneticcross,theparentsarereferredtoastheparental(P)generation.Theiroffspring
representthefirstfilial(F1)generation.TheirgrandoffspringaretheF2generation,etc.
1.Tallanddwarfvarietiesarecrossfertilized.
2.Allthehybridprogenyaretall.
3.Thehybridprogenyareselffertilized.
4.Tallanddwarfplantsappearamongtheoffspringofthehybridsapproxinaratioof3tall:1
dwarf.Thisratiofoundforsevenothertraitstested.
Eachtraitappearedtobecontrolledbyaheritablefactorthatcameinoneoftwoforms:
dominantandrecessive.
Mendelsheritablefactor=gene
dominantandrecessiveforms=alleles
Homozygousbothallelesareidentical
Heterozygousthetwoallelesaredifferent

Centromerenotexactlyinthemiddleofachromosome,thereisashortorparmandalongorq
arm.Locus(pluralloci)isafixedpositiononachromosome.Ageneorallelewillbefoundon
thisposition.
Tallisdominantanddwarfisrecessivealleleinplants.

(1) Eachparentalhomozygoteproducesonekindofgamete.PgenerationTallDDxDwarf
ddproduceoneDgameteandonedgamete.
(2) TheF1heterozygotesproducetwokindsofgametesinequalproportions.F1generation
TallDdproducesoneDandonedgamete.
(3) SelffertilizationoftheF1heterozygotesyieldstallanddwarfoffspringina3:1ratio.
F2GENERATION(SELFFERTILIZATION)

TallDD

TallDd

TallDd

Dwarfdd

Phenotypes

Genotypes

Genotypicratio

Phenotypicratio

Tall

DD

add1to2toget3

Tall

Dd

Dwarf

dd

MendelsPrincipleofDominance:inaheterozygote,oneallelemayconcealthepresenceof
another.

MendelsPrincipleofSegregation:neitheralleleistypicallychangedbycoexistingwithotherin
aheterozygote.Twodifferentallelessegregatefromeachotherduringtheformationofgametes.
InAnaphaseIthehomologouschromosomesdisjoinandmovetooppositepolesofthecell.
Maternalalleleonepoleandpaternalalleletotheotherpole.

Dihybridcrossaretwotraitsinheritedindependently?

P
Yellow,roundxGreen,wrinkled

F1
Yellow,roundselffertilizes

F2
Yellow,round/Green,round/Yellow,wrinkled/Green,wrinkled
31510810132

Approx9:3:3:1ratio

Yellow,roundappeartobedominanttraits.
4PhenotypicclassesintheF2generationrepresentallpossiblecombinationsofthecolourand
texturetraits:2thatresembletheparentsplus2newtraitcombinations.Theratioofphenotype
classessuggestedtoMendelascenarioinwhicheachtraitwascontrolledbyadifferentgene,
eachsegregatingtwoalleles.

1.Eachparentalhomozygoteproducesonekindofgamete.
P
Yellow,round(GGWW)xGreen,wrinkled(ggww)
Gametes
GW/GW/GW/GW
gw/gw/gw/gw

2.TheF1heterozygotesproducefourkindsofgametesinequalproportions.GWxgw
F1
Yellow,roundwithGgWwandgametesareGW/Gw/gW/gw

MendelsPrincipleofIndependentAssortment:theallelesofdifferentgenesassort/segregate
independentlyofeachother.InAnaphaseIg/GandG/gmovetooppositepoleswhileW/w
andw/Walsomovetooppositepoles(homologouschromosomes).

3.SelffertilizationoftheF1heterozygotesyieldsfourphenotypesina9:3:3:1ratio

GW

Gw

gW

gw

GW

GGWW

GGWw

GgWW

GgWw

Gw

GGWw

GGww

GgWw

Ggww

gW

GgWW

GgWw

ggWW

ggWw

gw

GgWw

Ggww

ggWw

ggww

9Yellow,round:3Yellow,wrinkled:3Green,round:1Green,wrinkled(Wwisthesameas
WWsinceitresultsinbothbeingRound).

Pedigreesandhumangenetics

Fornonhumans,wecandeducethegenotypebybreeding

Sinceaheterozygotemayhavethesamephenotypeasthehomozygousdominant,atestcross
maybeperformedtodeterminetheindividual'sgenotype.
Inatestcross,theindividualofunknowngenotypemustbecrossedwithahomozygous
recessiveindividual.
eg.atestcrossinvolvingaplantofthegenotypeDDGgWwwouldinvolvecrossingthisplantto
onewiththegenotypeddggww.

Pedigreesshowtherelationshipsbetweenmembersofafamily.

Atraitislikelyshowingadominantmodeofinheritanceif:
everyaffectedindividualhasatleastoneaffectedparent
thetraitismanifestedinatleastoneindividualineverygenerationoncethetraitappears
(thespontaneousappearanceofadominantalleleisextremelyrare)

Atraitislikelyshowingarecessivemodeofinheritanceif:
thetraitsuddenlyappearsinapedigree
thetraitskipsageneration
Intheabsenceofevidencetothecontrary,assumethatunrelatedindividualsmarryingintothe
familydonotcarrytherecessiveallele

Humanfamiliesarerelativelysmall,thereforephenotypicratiosamongoffspringoftendeviate
significantlyfromMendelianexpectations.
Consideracouple,eachheterozygousforarecessiveallelethatcausesaseriousdiseasein
homozygousindividuals.Iftheyhavefourchildren,whatistheprobabilitythatexactlyoneis
affected?
5possibleoutcomesandmultiplewaysofarrivingatsomeofthem
1. 4U,0A{UUUU}
2. 3U,1A{AUUU,UAUU,UUAU,UUUA}
3. 2U,2A{UUAA,UAAU,AAUU,UAUA,AUAU,AUUA}
4. 1U,3A{UAAA,AUAA,AAUA,AAAU}
5. 0U,4A{AAAA}

Theprobabilityofallpossibleoutcomescanbecalculated:**Treateachbirthasindependent**
P(affected)=P(cc)=x=
P(Unaffected)=P(CC)+P(Cc)=+=
Unaffected

Affected
401x()x()x()x()=81/256
314x()x()x()x()=108/256
226x()x()x()x()=54/256
134x()x()x()x()=12/256
041x()x()x()x()=1/256

Foratotalnumberofnprogenywecancalculatethe
Binomialprobability
thatexactlyx
progenywillfallintooneclass,andyastheotherclassas:

xy
[n!]/[x!y!]p
q

wherethetwoclassesarePandQ,withprobabilitiesofoccurrenceofpandq.Sincethereare
onlytwoclassesp=1q
3 1
Solutiontopreviousproblem:[4!]/[3!1!]()
()
=4x(27/64)x()=108/256

1.
2.
3.
4.

Fromthepedigree,albinismappearstobearecessivetrait
Sisthereforehomozygousrecessivefora
Rhassiblingswithalbinism,sothereissomeriskthatRisacarrier(heterozygousAa)
TheriskofThavingalbinismthereforedependsontwofactors:theprobabilitythatRisa
carrierandtheprobabilitythatRtransmitstheAalleletoTifheis.
Amongtheoffspringwithoutalbinismareheterozygotes

RiskcalculationthatchildThasalbinism:
P
(aa)=P
(Aa)xP
(a)xP
(a)
T
R
R
S
=xx1
=2/6
=

Theabsenceofaphenotypedoesntnecessarilyreflecttheabsenceofacausativegenotype.A
dominanttraitlikenonpolypoidcolorectalcancerthatmaynotmanifestuntilafterreproductive
agemakesriskassessmentdifficult

*insertimageonpage19here:

Imustbeaheterozygotebecausehermotherishomozygousandthereforethechanceofher
passingontherecessivealleleisTheparentsofHmustbothbeheterozygoussincetheyhave
anaffecteddaughter,butarentthemselvesaffectedHthereforehasa2/3probabilityofbeinga
carrierand,ifheisacarrier,thechanceofhimpassingontherecessivealleleisThe
probabilitythatthechildwillhavethetraitisx2/3x=2/12=1/6

ExtraClassnotes:

Ifthemanwashomozygousdominantthenallofhisoffspringwouldhavethetraitsinceit
wouldbepassedon.

Affectedindividualscantbehomozygousdominantbecausetheoffspringarenotcarryingthe
traitandhavetolookatmother/father.

UisunaffectedandAisaffected

1x()x()x()x()sincethereisonlyoncombination
nextlinemultipliedby4sincethereisfourpossibleoutcomesthancanhappen
thirdlineistimes6sincethereissixpossibleoutcomes
etc
Get42%that1of4childrenwillhavecysticfibrosisifbothparentsheterozygous.

intheequationnisnumberofchildren(4),
xandyaretwooutcomes(xisunaffectedandyisaffectedinthiscase)
pischanceofbeingaffectedandqischanceofbeingunaffected

Recessivetraitsinceneitherparenthasit(forslidingaskingforriskthatRandSwillhavea
childwithalbinism)
RmightbeAabutmayalsobeAA
ChancesthatRisheterozygousisBECAUSEitdoesnothavealbinismsoitisnotitisin
fact

AllelicVariationandGeneFunction
Lecturenotes:

OutsideofMendelsmodel,thingsarenotsosimple
genesmay(andusually)havemorethan
2alleles
,differentallelesmayaffectthephenotypeindifferentways,Asinglegenemaycontrol
severaltraits,Multiplegenesmaycontrolasingletrait.

+
+
Mostcommonalleleisconsideredthe
wildtype
(designatedwithasuperscripted+,A
orc
)
anyallelefoundatappreciablefrequencies,atleast1%,inthepopulationiscalleda
polymorphism.Allotherallelesareconsideredmutant.

Recessivemutationsalmostinvolvealossoffunction
nullallele
(completelossoffunction),
hypomorphicallele
(partiallossoffunction).Lossoffunctionisusuallyrecessivebecausemost
gensonlyrequireonefunctionalcopyfornormal(wildtype)phenotype.

DifferentTypesofMutations

Dominantmutations
:caninvolvealossoffunctionORagainofgenefunction.
Lossoffunction
:forgenesinwhichonefunctionalcopyisnotenough,thisiscalled
haploinsufficiency
Dominantnegative
alossoffunctionmutationthatinterfereswiththenormalfunctionofthe
wtallele
Gainoffunction
enhancesthenormalfunctionofthegene

AntennapediamutationinDrosophilaisa
(dominant)gainoffunctionmutation
inthe
regulatoryregionoftheAntpgene

IncompleteDominance
Phenotypeoftheheterozygoteisinbetweenthetwophenotypesofthetwohomozygotes,one
alleleiseitherpartiallyorincompletelydominantovertheother.E.g.Redandwhiteflower
producingapinkflower.
precursor+polypeptideW(GeneW)product(redpigment)phenotype

RedWW2x
PinkWwx
Whiteww0

Codominance
Theheterozygoteexpressesphenotypeofbothhomozygotes,neitheralleleisdominant

DominanceHierarchy
Allelicseries
describesthe
dominancehierarchy
ofmultiplealleles
Example:
+ +ch +h
ch
chh
Wildtype(c
c,c
c,c
c
)>Lightchinchilla(c
c)>=Lightchinchillawithblacktips(c
c
)>
h
Himalayan(c
c).
+
ch
h
c
>c>=c
>c

A
B
ForallelicseriesforhumanbloodI
andI
arecodominantoveri

SingleGeneaffectingseveraltraits
Y
A
:adominantvisibleallelethatisalsoarecessivelethal.
Y +
+ +
Example:HeterozygousA
A
crossproduces1A
A
graybrown(agouti)rat,
Y +
Y Y
2A
A
yellowrat,and1A
A
embryoniclethal.

Multiplegenesaffectingasingletrait
GeneAPolypeptideAcombineswithPolypeptideB(fromGeneB)wildtypephenotype
Testingwhethertwoallelesthatconferaparticularphenotypeareinthesamegeneiscalleda
complementationtest
.
Example:Complementationtestforallelisminvolvingrecessiveeyecolourmutationsin
Drosophila.
Crossofcinnabar&scarletwhentheyaredifferentrecessiveallelesinthesamegenesincethey
onlyproducethesameoffspring.
Crossofcinnabar&scarletwhentheyarerecessiveallelesindifferentgenesproduceseveral
differentcombinations.
Bycrossinganewrecessivemutationwithseveraltestergenotypesyoucanproduceseveral
hybridphenotypes,fromtheonesthataremutantyoucanconcludethatthetestergenotypeand
newrecessivemutationarealleles.

substrate+Cinnabarprotein(fromcinnabargene)intermediate+scarletprotein(scarletgene)
brownpigmentred/brown(wf)eyes

Keypoints
Geneactionisaffectedbybiologicalandphysicalfactorsintheenvironment.
Twoormoregenesmayinfluenceatrait.
Ageneis
pleiotropic
ifitinfluencesmultipleaspectsofanindividualsphenotype.

Classnotes:
Mostgenesknownaremultifunctional

Wildtypehasnothingtodowithdominant/recessive,justshowsfrequency(itismostcommon)

1%isanarbitrarynumberforthefrequencyforwhichaalleleisconsideredpolymorphism

Polymorphismswereatonetimemutants

Exampleofnullalleleissomethingthatpreventsgenefrombeingtranscribed/proteintranscribed
butnottranslated=completelossoffunction

Exampleofhypomorphicalleleissomethinglikeanenzyme,itslowsdowntheprocessofan
enzyme.Notoptimal.

Mitf+/+has8whileMitf+/has4sinceithasonlyhalfthedominantallelebuttheamount
requiredisstillenoughtofunctionsufficiently.Oneofthegenesthatcouldleadtoalbinism./
wouldhavenofunctionforMitf.
Mitf+/Mhasproteinproteinbindingdomainbutdoesntpossesthereplicationdomain(many
ofthereplicatedproteinsareincomplete),Hastwocompletedproteins.Thisisadominant
negativemutation.


Flyhaslegsgrowingoutofheadanditisgainoffunction.Regulatorymutation(mostcommon)
sothethoraxthatproducesantennainsteadproduceslegs.

GeneWmakesproteinandthenenzymewhichmakespigmentthatisdepositedintopetalsof
flowers.WWmakes2xtheamountsofullyred,Wwmakes1xtheamountsopink,andww
makesnonesowhite.Incompletedominance.

BloodtypeMcontainsmostlyantiMserumwithverylittleantiNserum.BloodtypeMN
containsbothantiserumMandN.BloodTypeNcontainsmostlyantiserumN.Codominance.

Wildtypealleleisthemostdominantinthedominancehierarchy,andwillalwaysappearwild.

GeneAcanbysynthesizerandthenBistransportorbothcanbeusedtomakeenzymesandthen
makestuff.Sosinglephenotypewithmultiplegeneshasmanydifferentthingsthatthegenescan
do.

sc
Crossingcinnabarandscarletproducesc
c
whichleavesnowildtypeandonlymutant.So
cinnabarandscarletareonsamegene(nocomplementation).

CinnabarandscarletondifferentgenessoccSSandCCss.Allpossibleoutcomesleave
heterozygoussothemutationscomplimenteachotherandthusalltheoffspringarewildtype.
**Allornothingeffecteitheralltheoffspringarewildtypeoralltheoffspringaremutant.

Mutationsandtheireffects(shithappens)
Sidenotes:
Mutationshavetheabilitytoarise
spontaneously
asaresultofanerrorwithinDNA
synthesis.Sucherrorsincludetheinherentfallibilityofreplicationproteins,aswellasthe
incorporationofrareisoformsofthefournitrogenousbasesthathavehadtheirpairing
characteristicsaltered.

NitrogenousbasesofDNAexistintwoisoforms(
tautomers
)

CommonformofThymine(Ketoform)4thcarbonhasdoublebondtooxygenandnitrogenin
thethirdpositionwiththreehydrogensbondedtoit.Rareformofthymine(Enolform)Carbon
inthefourthpositionisnowbondedtoanalcoholgroupandnowthereisadoublebondbetween
thenitrogeninthethirdpositionandthecarboninthefourthposition.

CommonformofCytosine(Aminoform)Carboninthefourthpositionisbondedtoamino
functionalgroupanddoublebondedtothenitrogeninthethirdposition.RareformofCytosine(
Iminoform)Carboninthefourthpositionnowdoublebondedtoiminogroupandthenitrogen
inthethirdpositionisbondedtothreehydrogens(ammonium?).

CommonformofAdenine(Aminoform)Carboninpositionsixhasanaminofunctionalgroup
andisdoublebondedtothenitrogeninpositionone.RareformofAdenine(Iminoform)
Carboninpositionsixhasiminofunctionalgroupandisnolongerdoublebondedtothenitrogen
inpositionone.

CommonformofGuanine(Ketoform)Carboninpositionsixhasaketonefunctionalgroupand
issinglebondedtothenitrogeninpositionone.RareformofGuanine(Enolform)Carbonin
positionsixhasanalcoholfunctionalgroupandisdoublebondedtothenitrogeninpos
**Tautomersallowfornonregulatoryalteredbasepairing,i.e.CytosinetoAdenineand
ThyminetoGuanine.

IncorporationofrareisoformduringDNAreplicationleadstomutationinDNAsequence.
e.g.Rareenoltautomericformofguanine(G*)canleadtoamutantprogenybeingproduced
duringthesecondgeneration.

Somaticmutations
ofthiskindmayaffecttheindividualinwhichtheyoccurbutwillnotbe
passedontofutureprogeny.

Increaseinmutationswithinthep53codonleadstoincreasedrisksofdevelopingcancer,
howeverthefrequencyatwhichthesemutationsoccurcannotbepredicted.

Germlinemutationswillbeinherited(
mutationsthatoccurduringmeiosissuchasduring
oogenesisandspermatogenesis)

HotspotsforspontaneousmutationsduringDNAreplication
simplerepeatsrepeatofanucleotideAAAAAAAAAA
DirectrepeatofadinucleotideGCGCGCGC
DirectrepeatofatrinucleotideTACTACTACTAC
SymmetricalrepeatscomplementarybasepairingwithinDNAstrand(thiscreatesahairpin
loopwithintheDNA)
PalindromesGAATTC
CTTAAG

Mutationscanbe
induced
byexposuretochemicalmutagens

chemicalmutagenscanbedividedintotwogroups:
onlymutagenictoreplicatingDNA(e.g.baseanalogues,acridinedyes)
MutagenictobothreplicatingandnonreplicatingDNA(e.g.alkylatingagents)ethyl
methanesulphonate(EMS)

Mutationscanalsobe
induced
byexposuretoradiation,anywavelengthgreaterthanthevisible
spectrumgivesoffradiation.Cosmicraysgiveoffthemostradiation.
AdsorptionofUVenergybypyrimidinesresultsintheirdimerization.Twothyminebases
exposedtoUVlightcombinetogetherandformaThyminedimer(thedoublebondedcarbons
foundwithineachmoleculebondtotheopposingthyminesdoublebondedcarbons).
ThethyminedimercausesakinkwiththeDNAstrand

Eachaminoacidisspecifiedbyoneormore
codon
Therearenospacesbetweencodons,codonsareadjacent
Geneticcodeisnonoverlapping,eachnucleotideispartofonecodon
Thegeneticcodeisdegenerate,mostaminoacidsarespecifiedbymorethanonecodon
Thegeneticcodeis(nearly)universal,withminorexceptions,eachtriplet/codonhasthesame
meaninginallorganisms.

Singlebasemutations
AGA(Arginine)AGG(Arginine)silentmutation
AGA(Arginine)TGA(stop)nonsensemutation
AGA(Arginine)AAA(lysine)conservativemissensemutation
AGA(Arginine)AGT(serine)nonconservedmissensemutation

Singlebasechangesinthebetaglobingenecausessicklecellanemiathismutationcauses
abnormalaggregationofhemoglobinmolecules.

Acridinesintercalatebetweenadjacentbasepairsanddistortthedoublehelix,whenthese
moleculesreplicate,additionsanddeletionsofonetoafewbasepairsoccur.

Basepairinsertionanddeletioncancompletelychangethecodonsequence.

MutationscanalsobeinducedbyDNAitselftransposableelements
thiselementjumpsintothemiddleofagenecausinganelongatedmRNAproteinergoproducing
aninactivetruncatedpolypeptide.

Atleast15humaninheriteddisordersresultfrom
expandingtriplet/trinucleotiderepeats

usually<40copiesoftripletrepeatarestablyinherited,largernumbersofcopiesareunstable
andpronetoexpansion.E.g.FragileXsyndrome(CGG),Huntingtondisease(CAG)

Expandingtriplet/trinucleotiderepeat
diseasescanshowincreasedseverityand/orearlier
onsetfromonegenerationtothenext.Seeslide22forpicture

Lecturenotes
:DNApolymeraseisanimperfectprotein,itmakesmistakeswhencopyingDNA.

Tautomersinconstantmotionandgobackandforthbetweenconfigurationsbutspendmuch
moretimeinthenormalform.

AlteredbasepairingsuchasACandGT.

p53actsinbetweenG1andSphase,almostallcancershavemutationwiththisp53gene.Even
thoughthemutationrateisconstantacrossthisgene,therearecertainpositionthatwhenmutated
arelinkedtoincreasedriskofcancer.

Forsymmetricalrepeatsthesymmetricalrepeatshavethecomplementarybasepairsonthe
SAMEstrandofDNAsotheysometimesfusetogether.Itisinvertedsotheycanfusetogether.
ThyminedimersaretwoTsonthesamestrandandtheUVcancausecovalentbondsonthetwo
Tsmakingthemdimerizedandthusproducesakinkinthedoublehelix.

AAAsimilarchemicallytoAGAsohavesimilareffectsonproteinsoitisconservative
mutation,onlyaslightdifferencethatwonthaveamassiveimpactontheprotein.

AGTnotsimilartoAGA,theyaredifferentchemicallysoitisnonconservativeandthusthere
willbeadifferencetotheprotein.

Nonsensemutationseffectdependsonwherealongthestringofcodonsitappears.

betaglobincomestogetherinterricgrouptoformhemoglobin.

MissensemutationinDNAforbetaglobincancauseimproperfoldingthusnotallowingthe
hemoglobintoformproperly,thisleadstosicklecellanemiasincethehemoglobincannot
properlycarryoxygen.

FragileXisthemostcommonformofretardationinpeople

TherearemanywaystoloseproteinfunctionII,mutationsthataffect
noncodingregions
1)
topreventorreducetranscription.2)PreventtranslationmRNAisunstable,ribosomescant
bind,mutationofthestartcodon,nuclearexportofmRNAiscompromised.

MyotonicdystrophytypeICTGexpansionintheuntranslatedregion(UTR)ofanmRNA
transcribedfromchromosome19encodinganenzyme(kinase).

MyotonicdystrophytypeIICCTGexpansioninanintronofageneonchromosome3encoding
azincfingertranscriptionfactor.
*Inbothcases,themRNAmaybecometoolargeforefficientexporttothecytoplasm.

SexChromosomesandHeredity

Inclassnotes:

Sex
(

)chromosomesvarybetweendifferentspecies

BridgesaysXchromosomesfailtodisjoininanaphaseIduringmeiosis.Sofemalescanmake
haploidcellsthatretainBOTHXchromosomes.
Leftsideofchartonslide16isnormaloutcomeandthenrightsideistheexceptionaloutcome.
HegotXXXandXXYwhichledtowhiteeyedfemalesandXOredeyedmaleandYOmale
whichdies.*Ostandsfornulloxwhichmeanstherewasnochromosomegiventoitanditdies.
ThereforegeneforeyecolourisontheXchromosome.

1/16chancefor?tohavehemophilia.(slide22)

Fliesboostsotheyhave2Xchromosomes.
Mammalsinactive1X.
C.elegansreducefunctionofbothbyhalftogetoneX
thesemechanismsequalizethenumberofxchromosomes

Xinactivationisthemechanismbywhichweequalizegenedosageonthechromosome.Which
Xisdeactivatedisrandombetweenindividualsanditisrandomcellbycell.Heterozygous
pigmentcatshaveorangeorbrownpatchesoffurduetothedifferenceinwhichXalleleis
equalizedsinceonehasbrownfurandonehasorange(randomnessinXinactivation).

Barrbodiesusuallyonedgeofnucleus,associatedwithnuclearenvelope.Canhaveonebarr
bodyinXXfemaleoreven2barrbodiesinanXXXfemale.

GeneStructureandTranscription:
Lectureslidenotes:

LectureSlidenotes:ThetransferofinformationfromDNAtoproteinisatwostepprocessinall
organisms.
CentralDogma
DNA(gene)TranscriptionmRNATranslationProtein

Definition1:AgeneistranscribedregionofDNA

GeneencodeoneofseveraltypesofRNA
Transcription:GeneregionsofDNATranscriptionRNAtranscriptprocessingsnRNA
(goestospliceosomewhichaffectsRNA)orrRNAortRNAormRNAorPremiRNAexits
throughnuclearpore.

Translation:
PremiRNAdicermiRNAcleavageofmRNAORrepressionoftranslation
mRNARibosomeproductionofpolypeptidechains
tRNAtRNA
rRNARibosomalsubunits

RNAusesthepyrimidineuracilinsteadofthymineUracilisonlyinRNA(withrareexceptions),
CytosineisinbothRNAandDNA,ThymineisonlyinDNA(withrareexceptions)

InRNA:UsesaRibosesugarwhichcontainsahydroxylgroupattachedtothesecondcarbon
InDNA:Uses2Deoxyribose,thesecondcarbonisnotbondedtoahydroxylgroup.

GeneralfeaturesofRNAsynthesisfromaDNAtemplate
mRNAmirrorsthenontemplatestrandoftheDNAbutusesUracilintheplaceofThymine.
RNAissynthesizedina5to3directionlikeDNA.

TheDNAdoublehelixislocallyunwoundduringtranscriptionRNApolymerase

Classnotes:
EveryribosomehasmultiplerRNAsthatmakeit
miRNAregulatestranslation,itisextremelysmall(microhencemiprefix).

Templatestrandread3to5

Promoterine.coli(prokaryotes)isATATTA[10sequence]aswellasAACTGT[35sequence].
E.coliRNApolymeraserecognizestheseandstartstranscription.Localunwinding(transcription
bubble)atAdenineandthyminerichlocationofsequence.
ATtakeslessenergytounwindthanGCduetolesshydrogenbonds,thereforeitischosensince
itiseasiertounwind.

Inprokaryotes,genesarecloselyspacedandseveralcanbetranscribedonasingleRNA
moleculefromacommonpromoter.

Rhorequiredforsometerminationsequencesbuttheoneinhisexampleisrhoindependent
doesntneedrho.

AsRNAismadeitisfoldedintoahydrogenbondedhairpinloop.

Intronnottranscribed,theyaresplicedout.

Eukaryoteshavelongerpromoter.ThereisalsoaTATAbox.RNApolymeraseonceboundtoa
genewillstarttranscribingine.coliwithnoproblem.EukaryoticRNApolymerases(wehave
many)canbeboundatapromoterbutneedhelptostarttranscription.Thuspromoterin
eukaryoteshelpstopositionpolymerasebutalsorecruitsotherproteins(generaltranscription
factors)togetpolymerasetostartmakingRNA.

Itcanbehardtodeterminethepromoterineukaryotes,canbethousandsofbasepairs.Needto
doitexperimentallyattimes.

Poly(A)tailcanbemodifiedandaddsstabilitytothematerial