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CU-Boulder IPHY 3060 - Section 1 Review

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Sec$on'1'review'1)##Your#Mar*an#probe#has#returned#a#soil#sample#to#Earth,#and#you#have#found#in#it#replica*ng#cells#that#have#all#the#same#biochemical#components#(proteins,#lipids,#DNA,#RNA,#etc.)#as#cells#found#on#Earth#(!).##Unfortunately,#your#path#to#a#Nobel#prize#is#blocked#by#skep*cs#who#think#your#sample#is#just#contaminated#with#cells#from#your#dirty#lab.##What#might#you#hope#to#discover#about#your#Mar*an#cells#that#would#make#a#convincing#case#they#were#not#from#Earth?#####Finding#that#the#Mar*an#cells#had#a#different#gene*c#code#would#be#preMy#convincing.##Demonstra*ng#that#the#Mar*an#cells#did#not#have#ribosomes#or#tRNAs#(or#had#an#RNA#genome)#would#also#be#strong#evidence.#2)#Although#cells#were#first#observed#back#in#the#1600's,#some#subScellular#organelles#were#not#discovered#un*l#the#1940's.##Why#do#you#think#it#took#so#long?######The#right#tools#(specifically#the#electron#microscope)#had#not#been#invented#to#see#subScellular#organelles.#3)#DiSdeoxynucleo*des##are#just#like#regular#DNA#nucleo*des,#but#they#lack#both#hydroxyl#groups#on#the#ribose#sugar.##What#do#you#think#would#happen#if#DNA#polymerase#inserted#a#dideoxynucleo*de#into#a#growing#DNA#chain?#####The#dideoxynucleo*de#would#be#incorporated#into#the#growing#chain#(it#has#the#5'#phosphate#group)#and#should#base#pair#properly,#but#no#new#nucleo*des#could#be#added#aZerwards#,#i.e.,#chain#termina*on.##(This#is#how#Sanger#DNA#sequencing#works).#4)##You#have#successfully#engineered#E.#coli#to#make#human#insulin#by#adding#a#transgene#that#has#an#E.#coli#promoter#and#the#coding#sequence#of#human#insulin.##You#try#to#generate#a#new#strain#which#would#make#a#lot#more#insulin#by#making#one#with#10#copies#of#the#transgene.##Although#your#gene*c#engineering#is#successful,#your#new#strain#doesn't#make#much#more#insulin.##What#do#you#think#could#have#gone#wrong?#####Producing#more#insulin#protein#means#you#will#need#more#rNTPs#to#make#more#mRNA,#more#ribosomes#and#tRNA#to#translate#the#insulin#mRNA,#and#more#amino#acids#to#make#more#protein.##In#theory,#any#of#these#could#be#limi*ng,#no#maMer#how#many#gene#copies#you#have.##Other#acceptable#answers#include#limi*ng#amounts#of#whatever#transcrip*on#factor#ac*vates#transcrip*on#of#the#transgene,#or#the#possibility#that#too#much#insulin#is#toxic#to#the#cells,#perhaps#because#it#cannot#all#be#folded#properly#leading#to#toxic#aggregates.#5)##Your#pa*ent#is#a#vic*m#of#a#Bulgarian#secret#police#assassina*on#aMempt,#and#has#just#been#injected#with#ricin.##In#despera*on,#you#inject#your#pa*ent#with#purified#ricin#"B"#chain,#which#saves#him.##Why#do#you#think#this#worked?#####Since#the#ricin#"B"#chain#does#not#have#the#toxic#ac*vity,#it#will#compete#with#the#injected#A+#B#ricin#for#binding#to#galactose#on#the#cell#surface.##This#should#be#protec*ve#by#displacing#binding#of#the#toxic#ricin#form.#6)##In#lab,#we#have#worked#with#C.#elegans#containing#transgenes#that#express#a#jellyfish#protein#(GFP).##Do#you#think#jellyfish#could#be#engineered#to#make#a#C.#elegans#protein?##Why#or#why#not?#####Because#all#life#(we#know#of)#uses#the#same#gene*c#code,#there#is#no#conceptual#reason#why#the#engineering#could#not#be#done#in#reverse.##Of#course,#your#transgene#would#need#to#use#promoter#sequences#that#func*on#in#jellyfish,#and#you#would#have#to#have#a#way#of#pudng#the#transgene#into#the#jellyfish#genome.#7)'There'is'evidence'that'use'of'an$bio$cs'pre dispose s'som e one'to'get'inflammatory'bowel'disease.''C an' you'propose'a'mechanism'by'which'this'may'happen?''An$bio$cs'kill'off'bacteria'indiscriminately,'so'taking'an$bio$cs''changes'the'gut'microbiome.''This'abrupt'change'in'the'microbiome'can'disrupt'the'balance'of'the'gut'immune'system'(e.g.,'allowing'new'microorganisms'to'grow),'leading'to'an'overFac$ve'immune'system'and'excessive'inflamma$on.'Key'Points'regarding'Dolly'experime nt'1)#The#informa*on#to#make#a#differentated#cell,#or#a#sheep,#is#largely#encoded#in#chromosomal#DNA.#2)##Different#subsets#of#chromosomal#genes#must#be#expressed#in##different#cell#types#or#embryonic#vs.#adult#cells.#3)##There#must#be#factors#in#the#oocyte#cytoplasm#that#overSride##(i.e.,#“reprogram”)#the#mammary#gland#cell#gene#expression#paMern#originally#present#in#the#nucleus#of#the#mammary#cell.#4)##SoZware#depends#on#computers#and#gene#expression#paMerns#depend#on#cellular#context.#Key points of today’s lecture: 1) There is a great diversity of cell types. 2) Our descriptions and understanding of cells are completely dependent on our available tools. 3) Cells have been on Earth for a long time. 4) Self-replication is a key defining feature of cells.Cells todayKey'Points'of'Today’s'Lecture'1)#DNA#replica*on#is#semiSconserva*ve#and#templateSbased.#2)##DNA#replica*on#requires#a#DNA#polymerase#and#a#mechanism#to#ini*ate#the#start#of#replica*on.#3)##DNA#polymerases#are#always#unidirec*onal#and#may#include#“proofreading”#capabili*es.##5)#PCR#is#DNA#replica*on#in#a#test#tube.#4)#Short#stretches#of#DNA#can#be#synthesized#chemically.#CORRECT'Replica$on'of'DNA'“proofreading”'by'DNA'polymerase'Polymerase'Chain'Reac$on'(PCR)'–'first'replica$on'cycle'Key'point'of'today’s'lecture'1)##DNA#makes#RNA#makes#protein#Key'points'of'today’s'lecture''1)##The#primary#sequence#of#a#protein#determines#its#3D#structure#(but#we#do#not#yet#know#how#to#do#this#computa*onally).#2)##Protein#folding#is#driven#by#the#distribu*on#of#polar#####and#nonpolar#amino#acids.#3)##Proteins#oZen#have#cataly*c#func*ons#due#to#their#ability##to#bind#and#properly#posi*on#substrates.#“Fear'of'water”'is'a'major'force'driving'protein'folding'“Fear'of'water”'is'a'major'force'driving'protein'folding'Single'proteins'oWen'link'up'to'form'mul$Fsubunit'complex'Key'points'of'today’s'lecture''1)##Proteins#are#oZen#composed#of#evolu*onarily#conserved########func*onal#domains.#2)##Proteins#are#not#sta*c#structures,#and#oZen#change#their#######structure#and#func*on#aZer#binding#small#regulatory#ligands.#3)##Proteins#are#oZen#modified#by#addi*on#of#chemical#groups#######added#to#the#side#chains#of#specific#amino#acids.##4)##Proper#protein#folding#is#aided#by#chaperone#proteins.#5)##Misfolded#proteins#can#cause#disease.#GTPFbinding'proteins'(“G”Fproteins)'cycle'on'and'off'(unless#they#are#stuck#“on”#because#they#have##a#muta*on#in#their#GTP#hydrolysis#domain)#Protein'ac$vity'is'also'commonly'regulated'by'phosphoryla$on'Cells'use'chaperone'protein'and'energy'from'ATP'to'correct'misfolded'pr ote


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CU-Boulder IPHY 3060 - Section 1 Review

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