MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

Lecture13:
1)DuringariverboattripontheAmazonriver,youencounterasmalltribeofpeoplethathave
livedthereforhundredsofyears.Yourecurioushowisolatedtheyvebeenfromothertribesin
thearea,anddecidedtotakeawholegenomesequencingapproachtoidentifyunique
polymorphismstotheirtribe.(Notethatallsequencesinthefollowingproblemareoriented5>
3andarefromthesamestrand).
(A)AssemblethefollowingreadsfromtheAmazoniantribegenomeprojectintoa
contig.
Theremustbeatleast5basesthatmatchinorderfortworeadstobeconsidered
overlapping.Orderthegivenreadsintoacontig,andlistthereadnumbersinorder(for
example,#5>#6>#7).(2pts)
[3>1>2]
Read#1:
GATGCT
CGCCGTA
GGAGACG
Read#2:
GGAGACG
TTCAGCGA
TCCTG
Read#3:
CACGACAA
TCGGGC
GATGCT

(B)InadditiontothecontigyoufoundinA(ContigA),youalsoobtaintwomore
contigs:
ContigB:
TTGCGAGTCAAGCGTTCACGACAATC
GCCCGATC
ContigC:
TCGAATT
CGATTAGGGCGATTCCGTTAGATTCCCA
Nowyouwouldliketoassembleallthreeintoscaffolds,soyouuseadditionalpairedend
readswhichspanthecontigs,shownbelow:
Pairedendread#1:
TCCTG
GAATCG
.....Gap.....
CGCAT
TCGAATT
Pairedendread#2:

GCCCGATC
CTG
.....Gap.....
ACC
CACGACAA
Usingtheinformationabovefromthepairedendsequencing,assemblethethreecontigs
intoscaffolds.Listthecontigsinorder(forexample,G>E>F),andindicatewhich
pairedendreadconnectswhichcontigs.(4pts)
[B>PE#2>A>PE#1>C]

2)YouhavethreeDNAfragmentsthatare100bplong.Youdidpairedendsequencingand
belowistheresult
Fragment1:ACGCTCGTTATGCTAGCGTTATGTCGATTC
Fragment2:GAGGCGTTACGTCAAAGTCTATTGGCTAAA
Fragment3:TATTGGCTAAATCGAATAGGACGCTCGTTA
Youoverlappedtheseresultsanddiscoveredthatthefragmentspartiallyoverlap:
___________________________Fragment1

___________________________Fragment(i)
___________________________Fragment(ii)
a)Whatisfragment(i)andfragment(ii)?[2p]
Fragment(i)=Fragment3
Fragment(ii)=Fragment2

MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

b)Howmanycontigsandgapsdoesthisscaffoldhave?Forthisquestion,consider
singlereadswithnooverlapascontigs.(2pts)
Contigs:4,Gaps:3
c)Whatisthetotallengthofthescaffold?Showyourwork.(2pts)
100+100+1001110=279bp

3)RestrictionenzymescutDNAintofragmentsaccordingtosequence.Therestrictionenzyme
HpyCH4VcleavesatsequencesTG^CA(^indicateswherethecleavingoccurs).Howmany
timesdoesHpyCH4Vcleavethefollowingsequence?Pleasecircleorunderlinetherestriction
enzymesitesinthefollowingsequence[6points]
agtaagagaatta
tgca
gtgctgccataaccatgagtgataacactgcggccaacttacttctgacaacgatcggaggaccgaa
ggagctaaccgcttttt
tgca
caacatgggggatcatgtaactcgccttgatcgttgggaaccggagctgaatgaagccatacca
aacgacgagcgtgacaccacgatgcctgtagcaatggcaacaacgttgcgcaaactattaactggcgaactacttactctagctt
cccggcaacaattaatagactggatggaggcggataaagt
tgca
ggaccacttctgcgctcggcccttccggctggctggtttat
tgctgataaatctggagccggtgagcgtgggtctcgcggtatcat
tgca
gcactgg

4)Youdoyourpairedendsequencingofallthefragmentsforawholegenomesequencing
project,butyourcomputerfilebecomescorrupted.Thereadsareintact,butyounolongerknow
whichreadscorrespondtowhichfragmentallthepairing(pairedend)dataislost.
a. 2ptWillyoubeabletoassemblecontigswithyourremainingdata?Whyorwhy
not?
Yes,youstillhavereadsandcanoverlapthemtoformacontig
b. 2ptWillyoubeabletomakescaffolds?Whyorwhynot?
Nothinglargerthanacontigyoudonthavethepairedenddatathatlinks
contigstogetheranymore
c. 2pt.Thecomputertechniciansareabletorecoveradditionalsequencereadsthat
youdidntknowweremissingfromthatfile,buttheystilllackpairing
information.Someofthesenewreadspartiallyoverlapwithtwo
nonoverlappingreadsthatyouhadbefore.Howdoesthisaffectyouranswerstoa
andb?
Youllbeabletomakelongercontigs,butstillnoscaffolds

Lecture14,Mondaylecture:
5)Aftercompletingthesequencingofthe
Ornithorhynchusanatinus
(duckbilledplatypus)
genome,younextwanttoknowwhatportionsoftheplatypusgenomearetranscribed.Tofind
transcribedgeneswithinthegenome,youpurifymRNAsfromthreedifferenttissuetypes(brain,
blood,andliver).YouthensynthesizecDNAfromthismRNAaswascoveredinlecture,makea
cDNAlibraryfromeachtissue,thensequencetheendofeveryclone.Yourinitialsequencing
revealsthreehighlyexpressedplatypusgenes,whichyounameS,B,andM.YoufindcDNAs

MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

fromgeneSineverytissue,butonlyfindcDNAsfromgeneBinbraintissueandcDNAsfrom
geneMinblood.
(A)WhydoyounotfindcDNAsfromgenesBandMineverytissueyousampledfrom?
(3pts)
becausegeneBisonlyexpressedinthebrain/hasabrainspecific
promoter/enhancers/cisregulatoryelements,andgeneMisonlyexpressedinthe
blood/hasabloodspecificpromoter/enhancers/cisregulatoryelements

(B)ItturnsoutthatcDNAsofgeneSderivedfrombraintissuehaveexonsthatarenot
presentinthecDNAsofgeneSfromthebloodorliverlibraries.Howcouldyouexplain
thistissuespecificdifferenceinwhatexonsarepresentinthegeneScDNAs?(3pts)
splicingdifferencesbetweentissues

6)Youvedecidedtoundertakeatranscriptomeanalysis(studyingofallthemRNAsexpressed
inacell)ofbrainandhearttissue,focusingonmRNAsencodingcomponentsofvoltagegated
calciumchannels.
A. (1pt)WhichenzymewouldyouusetoconvertyourRNAstothecorrespondingcDNAs?
reversetranscriptase
B. (2pts)Ifthesamevoltagegatedcalciumchannelgenesareexpressedinbothbrainand
heart,beforeyoucollectsequencedatacanyoupredicthowmuchcDNAfromeachgene
willbefoundinbrainversushearttissue?Whyorwhynot?
no,becauseevenifthesamegenesaretranscribed,therelativenumberofRNAscould
varybetweentissuetypes
C. (3pts)Youdiscoverthatinboththebrainandheart,thereare
more
uniquetypesof
cDNAs(uniquetypemeaningdifferentsetsofgenomicsequencespresentinthecDNA)
correspondingtovoltagegatedcalciumchannelsthantherearegenes.Whatisapossible
explanationforthisdiscrepancy?Howdoesthisexplanationaccountforthediscrepancy?
alternativesplicing(differentexonsbeingincluded/excludedinthefinalmRNA)leadsto
multipleRNAtypesderivedfromthesamegene

7)Youvediscoveredanewtypeofbutterflythatlooksverysimilartothemonarchbutterfly.
Sincetheylooksosimilar,youreasontheymightsharesomegeneticfeatures.Hereisan
examplesequencefromgenomicDNAandcDNAfrombothbutterflies:
Newbutterfly:
genomicDNA
ATGCAGGAGCATAAATTCCGCAATTGGATTAGGATGCCCAGTATT
cDNA

ATGCAGGAGCAT
TGGATTAGG

Monarchbutterfly:
genomicDNA
ATGCAGGAGCATCCATGAGACAATTGGATTAGGTACTTAAGTATT
cDNA

ATGCAGGAGCAT
TGGATTAGC

A. (2pts)CircletheintronsanddrawboxesaroundtheexonsinthegenomicDNA

MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

regionsthatarepresentalsointhecDNAareexons,regionsthatarenotalso
presentinthecDNAareintrons
B. (2pts)Ifthisgenomicregionfromthenewbutterflywasthemostsimilarin
sequencetothisgenomicregionfrommonarchbutterflies(andviceversa),what
wordwouldyouusetodescribetherelationshipbetweenthesetwogenes?
orthologs
C. (2pts)Thereisapolymorphisminoneoftheexons.Whatkindofpolymorphism
isit?
ASNP(singlenucleotidepolymorphism)orsinglebasesubstitution

8)mRNAscannotbesequenceddirectlybydideoxy(Sanger)sequencing.
a.TomakecDNAfrommRNA,whatonekindofnucleicaciddoyouneed(inaddition
tothemRNA)andwhatoneenzymewouldyouneedtosynthesizethecDNA?(2pts)
Aprimer(oroligonucleotideorpolyTprimer),andreversetranscriptase
b.(2pt)IfyouputacDNAintoaplasmidandsequencedbothends,whattypeofreads
wouldyougenerate?
5and3ESTreads
c.(2pts)Asidefromlearningregionsofthegenomewheretranscriptionoccurs,what
elsecanyoulearnfromcomparingindividualESTsequencestothegenomicsequencein
caseswhereoneESTreadalignsperfectlytotwoblocksofgenomicsequence?
locationofintrons/exons

Lecture15:Wednesdaylecture:
9)Somepaternitytests,whichtestwhethersomeoneisthefatherofaparticularchild,workby
genotypingalargecollectionofSNPsfromboththepotentialfatherandthechild.
a. Onaverage,whatpercentofgenomewideSNPsonautosomes(nonsexchromosomes)
wouldbeidenticalbetweenaparentandtheiroffspring,andwhy?[3p]
50%.Becauseachildinheritshalfoftheirchromosomesfromeachparent,youwould
expectonaverage50%ofgenomewidegenotypestobeidentical.
b)WhywouldyouwanttogenotypemultipleSNPsinapaternitytest,andnotjusta
singleSNP?[3p]
ItwouldbewaytooeasyforasingleSNPtobethesamebetweentwoindividualsjust
bychanceorfromdistantrelatedness

10)YouaregiventheDNAsequenceatthesamelocusforafewindividuals:
PersonA

GGCCGCGT
G
CCCA
G
GGTATATT
T
GGTCAGTAT
G
GAATGGACT

PersonB

GGCCGCGT
G
CCCA
C
GGTATATT
T
GGTCAGTAT
C
GAATGGACT

PersonC

GGCCGCGT
C
CCCA
C
GGTATATT
A
GGTCAGTAT
G
GAATGGACT

MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

Person1

GGCCGCGT
G
CCCA
C
GGTATATT
T
GGTCAGTAT
C
GAATGGACT

Person2

GGCCGCGT
G
CCCA
G
GGTATATT
T
GGTCAGTAT
G
GAATGGACT

a. (2points)RankindividualsA,B,andCinorderofhowcloselytheyarerelatedtoPerson
1,basedontheabovesequences.
PersonBismostcloselyrelated,thenPersonA,thenPersonC
b. (2points)RankindividualsA,B,andCinorderofhowcloselytheyarerelatedtoPerson
2,basedontheabovesequences.
PersonAismostcloselyrelated,thenPersonB,thenPersonC
c. (2points)Whatdowecalltheboldedregions?Howdidyouusethemtoanswerpartsa
andb?
SNPs,morecloselyrelatedindividualssharemoreSNPs

Lecture16:Fridaylecture:
11)Transposableelements(indicatedbythearrowsoveryellowsegmentsbelow)cancause
deletions.Usingthefollowingdiagram,drawtheproducts(2pointseach)andthecrossover
intermediate(2points)fromtheaberrantrecombination.
Eithersinglestrandedcrossover>
deletion,ortwostrandedcrossover>deletion+duplication

12)Nonallelichomologousrecombinationoccursattworegionsofhomologoussequencethat
arentatallelicpositions.
a. (2pt)Ifthehomologoussequencesareonthesamedirectiononthesamestrand,what
outcomedoyouexpect?Whatis/aretheproduct(s)?
deletionplasmidwithdeletedsequence,chromosomemissingdeletedsequence
b.(2pt)Ifthehomologoussequencesareintheoppositedirectiononthesamestrand,what
outcomedoyouexpect?Whatis/aretheproduct(s)?
inversionthesequenceinbetweenwillbebackwards(inverted)
c.(2pt)Whatresultdoyouexpectfromnonallelichomologousrecombinationbetweentwo
strands?
deletionandaduplication

13)

MCB104Quiz2combinedanswerkey

(Differentsectionshaddifferentquestions.)

Theabovediagramshowssomepartsoftwohomologouschromosomes.Thesequencesi)andii)
areidentical.Whatarethetwononalleliccrossingovereventsthatcouldoccurinthese
chromosomes?Drawtheeventsspecifically.[3ptsperevent]
Deletion(crossingoverwithinonechromosomeorbetweentwochromosomes)
Duplication(crossingoverbetweentwochromosomes)
Seeslidesfordiagramsofcrossingoverevents