Post on 04-Feb-2021
ProteinSynthesisandGeneFinding
Day2
DNAAnalysis
• 23andMe• Personalizedmedicine• Geneticscreensfordisease• Etc.
BioCrashCourse:DNA
Photo51:X-raydiffractioncreatedbyRaymondGoslingunderthesupervisionofRosalindFranklinMay,1952
DoubleHelixStructure:WatsonandCrick
DNAandtheCentralDogma
TheblueprintsformakingalltheproteinsnecessaryforlifearecontainedwithinDNA.Or,moresuccinctly:DNAMakesRNA,RNAmakesProtein
ProteinsProteinsarechainsofAminoAcids
Aside:ProteinSecondaryStructurePrediction
Fold-it:agameifiedapproachtocomputingthisstructure
Goal:findthelowestenergyconfigurationofanaminoacidchain
Unfortunatelythisproblemishard!Howhardisit?Thishard:http://www.cs.berkeley.edu/~christos/hp.ps
https://www.youtube.com/watch?v=lGYJyur4FUA
ProteinogenicAminoAcids
http://en.wikipedia.org/wiki/Amino_acid
DNAandProteinSynthesis
• Stage1:anenzyme“decides”thatitistimetosynthesizeaprotein(epigenetics)
• Stage2:DNAisunzippedandpairedwithacomplementarystrandofRNA(transcription)
• Stage3:tRNAattachesaminoacidstocomplementarysegmentsofRNA(translation)
ProteinSynthesisDetailedExample
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Aside:The5’and3’areusefulwhentalkingaboutthedirectionalityofcertainprocessesrelatedtoproteinsynthesis.Morelater.
ProteinSynthesisStep1:TranscriptionInitiation
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
ATGisalsoknownasthestartcodon.Thisiswheretranscriptionstarts.
TemplateStrand
SenseStrand
ProteinSynthesisStep2:MessengerRNAAttaches
5’ – AGCA
3’ – TCGTTACAAGGACTACATTAA – 5’
ATGTTCCT
GATGTAAT
T – 3’
AUGUUCCUGAUGUAAUU – 3’
ThisnewstrandisknownasmessengerRNA
ProteinSynthesisStep3:MessengerRNABreaksAway
5’ - AUGUUCCUGAUGUAAUU – 3’
ProteinSynthesisStep4:AminoAcidChainForms
5’ - AUGUUCCUGAUGUAAUU – 3’
UAC
M
AAG
F
GAC
D
UAC
M
StopCodonKnownasanOpenReadingFrame(ORF)
ProteinSynthesisSomethingstoNotice
5’ - AUGUUCCUGAUGUAAUU – 3’
UAC
M
AAG
F
GAC
D
UAC
M
StopCodonAnotherStartCodon(NestedReadingFrame)
OutofframeStopcodon
DNACodonTable
Thiscodeisreadfrom5’to3’ontheDNAstrand
6ReadingFrames:ReadingFrame1
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
6ReadingFrames:ReadingFrame2
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
6ReadingFrames:ReadingFrame3
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
6ReadingFrames:ReadingFrame4
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
6ReadingFrames:ReadingFrame5
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
6ReadingFrames:ReadingFrame6
5’ – AGCAATGTTCCAGATGTAATT – 3’
3’ – TCGTTACAAGGTCTACATTAA – 5’
Codonsreadinthisdirection
Mini-Project:GeneFinder!
• Createapythonprogramthatperformsabinitiogenefindingby– DeterminingwhichDNAsegmentslikelycodeforproteins
– OutputtingtheaminoacidsequencescodedbytheseregionsofDNA
• Runtheseaminoacidsequencesthroughasearchenginetodeterminetheirfunction!
Ab-InitioGeneFindingStrategy
• Tell-talemarker:suspiciouslylongORFs• Suspiciousisdefinedasbeingimprobabletofindinnon-codingDNA
(partof)Nexttime
JoannePrattwillguestlectureonageneticsearchenginecalledBLAST(anditsuses)aswellastheroleofBLASTinstudyingpathogenesis.