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PCROrienta(on: This shows the black molecule expanded at two levels of detail: Note:Coloredpens/ pencilswillbehelpful! 5’ 3’ 5’ 3’ Test Tube Eachcolorreactantinthetesttubeis expandedindetail,byappropriatecolor. (ColorisforthisacKvityonly.Inreality,allmoleculesarecolorless). Enzyme that can synthesize the black molecule at an optimal working temperature of 72°C Orienta(onQues(ons: 1.Foreach,writethetypeofmoleculeitisinasmuchdetailasyoucan.(Blackgivenasanexample): a.black:doublestrandedDNA b.red:___________________________ c.green:____________________d.blue:____________________e.gray:____________________ 2.Labelthe5'and3'endsofallnucleicacidstrandsinthemodel(exceptinthetesttube). 3.a.Arethegreenandbluemoleculescomplementarytoeachother?__________ b.Arethegreenandbluemoleculescomplementarytoapartoftheblackmolecule?______ c.Labelthepartsoftheblackmoleculethatarecomplementarytothegreenandblueones. DevelopedbyDrAmandaSchivell 95°C PCRModel1: a.Imaginethatthistesttubewasheateduptoabout95°C,atemperatureatwhichallhydrogen bondsarebroken.Whichofthefollowingbestrepresentswhattheblackmoleculewilllooklike? (CircleONE) b.95°Cisalmosthotenoughtoboilwater.WouldahumanDNApolymeraseenzymeremaininan acKveconfiguraKonatthistemperature?WhataboutaDNApolymerasefromE.coli? c.ThepolymeraseusedinmodernPCRisfromThermusaquaCcus,abacteriathatnormallylivesin hotsprings.Whydoesthismakesenseforaprocessthatincludesa95°Cstep? PCRModel4:AnotherarrangementofDNAstrandsisasshownbelow.Describeinwordsor drawingwhathappenstothesemoleculesat95°Cinthetesttube.Arrowheadsindicate3’ends. PCRModel7:Later,describewhathappensat95°Ctothenewmoleculesshownhere. DuringModels1,4and7: WereanyDNAstrandsdestroyed?_________ Wereanyhydrogenbondsbroken?_________ Wereanyhydrogenbondscreated?_________ WereanynewDNAstrandssynthesized?_________ DevelopedbyDrAmandaSchivell PCROrienta(on: This shows the black molecule expanded at two levels of detail: Note:Coloredpens/ pencilswillbehelpful! 5’ 3’ 5’ 3’ Test Tube Eachcolorreactantinthetesttubeis expandedindetail,byappropriatecolor. (ColorisforthisacKvityonly.Inreality,allmoleculesarecolorless). Enzyme that can synthesize the black molecule at an optimal working temperature of 72°C Orienta(onQues(ons: 1.Foreach,writethetypeofmoleculeitisinasmuchdetailasyoucan.(Blackgivenasanexample): a.black:doublestrandedDNA b.red:___________________________ c.green:____________________d.blue:____________________e.gray:____________________ 2.Labelthe5'and3'endsofallnucleicacidstrandsinthemodel(exceptinthetesttube). 3.a.Arethegreenandbluemoleculescomplementarytoeachother?__________ b.Arethegreenandbluemoleculescomplementarytoapartoftheblackmolecule?______ c.Labelthepartsoftheblackmoleculethatarecomplementarytothegreenandblueones. DevelopedbyDrAmandaSchivell 60°C PCRModel2: a.Imaginethatthetesttubewascooledtoabout60°C,atemperatureatwhichhydrogenbonds quicklyre-form.Green,blueandblackmoleculescanbindintwodisKnctways.Giventhatthere aremany,manyshortgreenandbluemolecules:Whichofthesetwobindingsismorelikely? Binding#1: Binding#2: PCRModel5:WhatisthemostlikelyconfiguraKonat60°Cofthemoleculesshownhere?Draw arrowstoshowbinding.Arrowheadsindicate3’ends.Remember:Therearelotsofgreenandblueprimers! PCRModel8:ShowwhereblueandgreenprimersbindasthereacKoncoolsto60°C. DuringModels2,5and8: WereanyDNAstrandsdestroyed?_________ Wereanyhydrogenbondsbroken?_________ Wereanyhydrogenbondscreated?_________ WereanynewDNAstrandssynthesized?_________ DevelopedbyDrAmandaSchivell PCROrienta(on: This shows the black molecule expanded at two levels of detail: Note:Coloredpens/ pencilswillbehelpful! 5’ 3’ 5’ 3’ Test Tube Eachcolorreactantinthetesttubeis expandedindetail,byappropriatecolor. (ColorisforthisacKvityonly.Inreality,allmoleculesarecolorless). Enzyme that can synthesize the black molecule at an optimal working temperature of 72°C Orienta(onQues(ons: 1.Foreach,writethetypeofmoleculeitisinasmuchdetailasyoucan.(Blackgivenasanexample): a.black:doublestrandedDNA b.red:___________________________ c.green:____________________d.blue:____________________e.gray:____________________ 2.Labelthe5'and3'endsofallnucleicacidstrandsinthemodel(exceptinthetesttube). 3.a.Arethegreenandbluemoleculescomplementarytoeachother?__________ b.Arethegreenandbluemoleculescomplementarytoapartoftheblackmolecule?______ c.Labelthepartsoftheblackmoleculethatarecomplementarytothegreenandblueones. DevelopedbyDrAmandaSchivell 72°C PCRModel3: a.Themoleculesshownarekeptat72°Cinthetesttube.Arrowheadsindicatethe3’endsofDNA strands.FillinthenucleoKdeseverywherethatpolymerasesareabletowork. PCRModel6:Later,thefollowingmoleculesinthetesttubeareagainbroughtto72°C. AllcolorsindicateDNA.Drawinthenewstrandsthatwillbebuiltbythepolymeraseinred. PCRModel9:Again,drawinthenewmoleculesbuiltat72°Cfromthisnewarrangementofmolecules. DuringModels3,6and9: WereanyDNAstrandsdestroyed?_________ Wereanyhydrogenbondsbroken?_________ Wereanyhydrogenbondscreated?_________ WereanynewDNAstrandssynthesized?_________ DevelopedbyDrAmandaSchivell
