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.