Ch.

21Genomics

I. Linkagemapping
A. Morganslabcollecteddatafromanumberofcrossesusingdifferentpairsof
markers
B. Foreachpairofmarkerstherewasacharacteristicfrequencyofrecombinant
types,butitwasdifferentfordifferentpairs
C. somepairsofmarkersshowedalowfrequencyofrecombinationandother
showedfrequenciescloserto50%
D. manypairsofmarkersshowedindependentassortmentincompleteagreement
withMendelssecondlaw
E. A.H.Sturtevant,asophomoreenteredMorganslabasanundergraduate
researcher
1. Helistenedtothediscussionsaboutthevariousfrequenciesof
recombinationthatweredisplayedbydifferentpairsofmarkersthatdid
notshowindependentassortment
2. onedayhecollectedallthedatafromthesecrossesofthistypeandtook
themhome
3. Hegotouthisalgebrabooksandstayedupmostofthenightintegrating
thisdataintothefirstgeneticmap
a) thedatafromthelabshowedthattheirwas5.9%chanceblack
andpurple.thereare2possiblelocationsforblackonthismap:to
theleftofpuprpleortotherightofpurple
b) thenextexperimentshoweda16.9%recombinationbetweenblack
andpurple.
II. Genomeannotation
A. aprocessofgenomeanalysistoassignfunctionstoeachsegmentofgenomic
sequencebyacombinationofcomputationalmeansandhumananalysis
B. currently,genomeannotationsalmostexclusivelyfocusonindividualgenesand
theirproducts[protein,RNA]
C. noncodingsequencesarelargelyignoredduetotechnicaldifficulties
D. Howdoesanannotationdifferfromagene
1. manyannotationsdescribedfeaturesthatconstituteagene
2. otherannotationsdonotdirectlycorrespondasinanSTSorsequence
overlap
E. requirespowerfulcomputers
F. Examples:
1. geneannotation
2. individualgeneanotation
3. annotationoflistsofgenes[Genegroups]
4. Gene/proteinnetworks
5. analysisofannotatedlists
6. analysisofnetworks
III. Bioinformatics
A. thecombinationofmolecularbiologyandcomputersciencetonavigatethrough
thetremendousamountsofdatawhichisproducedbygenomeprojectsof
differentspecies
B. computerprogramshavebeenwrittentoscanthesequencedatatolocategenes
C. basicruletheprograms:
1. startcodonATGstopcodonTAA,TAG,orTGA
D. computerwouldscanthesequencesofthatwouldfollowanyATGandfindthose
areaswherethenextstopcodonsoccurs
E. usingbioinformaticstofinddrugtargets
1. bylookingforgenesinamodelorganismthataresimilartohumangenes,
researcherscanlearnabouttheproteinthehumangeneencodesand
searchfordrugstoactonthem.
IV. Proteomics
A. largescalestudyofproteins,particularlytheirstructuresandfunctions
B. wordwascoinedtomakeananalogytogenomics.
C. proteomicsismuchmorecomplicatedthangenomics
D. genomeisratherconstantbuttheproteomediffersfromcelltocellandis
constantlychangingduetobiochemicalinteractionsandtheenviroment
E. anorganismwillhaveradicallydifferentproteinexpressionindifferentpartsofits
body
F. branchesofproteomics
1. proteinseparation
a) reliesontheabilitytoseparateacomplexmixturesothatindividual
proteinsaremoreeasilyprocessed
2. protienidentification
a) higherthroughputproteomicstechniquesarebasedonbased
spectrometry,peptidemassfingerprintingordenovarepeat
detectionssequencingbymassspectrometry
b) antibodybasedassayscanalsobeusedbutareuniquetoonly
oneprotein
3. proteinquantification
a) gelbasedmethods,differentialstainingofgelwithfluorescent
dyes[differencegelelectrophoresis]
b) canalsousegelfree,varioustaggingorchemicalmodification
suchasisotopecodedaffinitytags[ICATs]
4. proteinsequenceanalysis
a) searchingdatabasesforpossibleproteinorpeptidemathc,or
functionalalignmentofdomains,predictionoffunctionfrom
sequence,andevolutionaryrelationshipsofproteins
5. structuralproteomics
a) highthroughputdeterminationofproteinstructuresin3D
b) usexraycrystallographyandNMRspectroscopy
6. interactionproteomics
a) investigationofproteininteractionsontheatomic,molecular,and
cellularlevels
7. proteinmodification
a) modificationofproteinsusingphosphoproteomicsand
glycoproteomics
8. cellularproteomics
a) mapthelocationofproteinsandproteinproteininteractionduring
cellularevents
b) usexraytomographyandopticalfluorescencemicroscopy
G. thecompleteproteincontentofanorganismisitsproteome
V. Genomesize
A. asarule,themorecomplextheorganismthelargerthegenome
B. therearemanyanimalswithgenomesizestwoordersofmagnitudegreaterthan
humans
C. genomesizedoesnotappeartocorrelatewithanythingobvious
VI. CodingandnoncodingDNA
A. inprokaryotes,almostalloftheDNAcodesforprotein
B. ineukaryotes,mostoftheDNAdoesnotcodeforanything
C. 97%ofhumanDNAdoesnotcodeforproteinandissometimescalledjunkDNA
D. Intronsjunk
E. Exonsgenes
F. TandemlyrepetitiveDNA[satelliteDNA]
1. ashortsequenceofDNAthatisrepeatedmanytimes
2. GTTACGTTAGTTACGTTAGTTACGTTA
3. namedbecausetheyrepeatnexttooneanother[intandem]
4. alsocalledSatelliteDNAbecausewhentheDNAiscutupintosmall
pieces,thesesegmentshavedifferentdensitiesthantherestoftheDNA
5. whentheDNAiscentrifugeditformssatellitebandsnexttothemainDNA
bands
6. thisisusedinDNAfingerprinting
7. makesupabout10%to15%ofmammalianDNA
8. foundincentromeresandtelomeres
9. mostlikelyhasastructuralroleinchromosomes
10. importantintheseparationofSisterchromatidsincelldivision
11. telomereslocatedatendsofchromosomesandcanshortenwitheach
celldivision
12. theycontainthousandsofrepeatesofTTAGGG
G. TandemlyrepetitiveDNAanddisease
1. FragileXsyndrome
a) CGGisrepeatedhundredsoreventhousandsoftimescreatinga
fragileSiteontheXchromosome
b) Severementalretardation
c) Huntingtonsdisease
(1) CAGisrepeatedandcausesaproteintohavelong
stretchesoftheaminoacidGlutamine
(2) leadstoaneurologicdisorderthatresultsinearlydeath
H. interspersedrepetitiveDNA
1. accountsfor25%to40%ofmammalianDNA
2. NotfoundnexttoeachotherliketheTandemlyrepeatedDNA
3. scatteredrandomlythroughoutgenome
4. hundredstothousandsofbasepairslong
5. copiesaresimilarbutnotidenticaltoeachother
6. famousexample:Aluelements
a) 300basepairslong
b) canbetranscribedbuttheirexactfunctionisunknown
c) 5%ofhumangenome
I. pseudogenes
1. DNAsequencesthataresimilartorealgenesbutlacktheregulatory
sequencesnecessaryforgeneexpression[promoters]
J. transposonsandretrotransposons
1. interspersedrepetitivegenesthatarenotstablyintegratedintothe
genome
2. movefromplacetoplace
3. calledtransposonselementsortransposons
4. atransposonsusetransposasewhereasaretrotransposonusesreverse
transcriptase
5. sometimesresponsibleformessingupgoodgenes
K.