PS#1#Due#10/8/14#In#Class# # # Name:__________________________________#Bi/Ch&110&Introduction&to&Biochemistry:&Problem&Set&1&1)&Protein&synthesis:&(33&points)&a)#Underline#or#circle#the#open#reading#fra m es#o n#the #follow ing #mR N A's.#(6 #po ints)### (i)#5'#J#UUUAGUGCCACCAUGUGGUGCUGUCCAAAUGGUUGAUGCUTUGUAAA#J#3'## (ii)#3'#J#AAUUACCAUCUUAUGCUCGUACUAUUGUGG AAUAGGAUUUGUUU#J# 5'#b)#Notice#Peptide#A:#(12#points)## N#J#Met#J#Cys#J#Val#J#Arg#J#Lys#J#Gln#J#Leu#J#Ser#J#Gln#J#Met#J#His#J#Ala#J#Ala#J#C## (i)#Identify#one#pos sib le#sequence#of#DNA#that#could#specify#this#polypeptide.## (ii)#indicate#the#5'#and#3 '#end s#on #you r#D NA #se qu en ce .# ## (iii)#Are#there#any#hydrophobic#amino#acids#in#this#peptide?#If#so,#list#them.#c)#What#is#the#maximum#numb er#of#unique#amino#acids#that#the#threeJbase#codon#system#allows?#Is#it#possible#for#organisms#to#use#a#twoJbase#codon#system?#Why?#(5#points)#d)#You#are#a#researcher#in#a#lab#amplifying#proteins#in#e#coli.#Suggest#two#way#to#increase#the#yield#of#your#protein#and#explain#how#your#method#would#work.#(10#points)#2)&Protein&Structure:&(34&points)&a)#Draw#two#amino#acids#that#have#distinct#chemical#properties,#describe#what#makes#them#unique,#and#then#draw#th e#m ec ha nism #(w ith#elec tron #pu shin g#arro w s)#to#form #a #pep tide#b on d#b etw e en#th em .#(15 #points)#b)#Secondary#structures.#(9#points)## (i)#Draw#a#diagra m #de pictin g#th e#alp ha #helix#a nd #beta #she et#se co nd ary #structu re s.##Indica te#the #N## and#C#termini.### (ii)#Explain#the#interm o lec ular#in terac tion s#tha t#stab ilize#the se #structu re s.#Us e#a#dia gra m #if#you ## would#like.### (iii)#f)#Which#of#these #common#seco nd a ry#struc ture s#is#freq ue ntly#u sed #to#sp an #m embranes?## Approximately#how#many#amino#acid#residues#would#be#required#for#this#structure#to#span#the## membrane?#c)#The#properties#of#amino#acids#are#altered,#depending#on#the#local#chemical#environment.#If#a#Lys#residue#is#presen t#on #the#su rface #of#a#p rote in,#wh at#w o uld #you #exp ect#th e#pK a#to #be#of#the#R#group#(ball#park),#and#how#would#this#be#reflected#in#the#structure.#How#would #the#p Ka#ch an ge #if#the#Lys#w as#b uried #in#the#hy d ro ph o b ic #co re #o f#th e #p ro te in ,#an d #h o w #would#the #st ru ct ur e#c h an g e ?#(10#points)#3)&Protein&Folding:&(33&points)&a)#What#are#some#methods#for#helping#a#protein#fold#correctly?#(6#points)#b)#The#protein#folding#funnel#depicts#the#thermodynamics#of#protein#folding.#Draw#a#cross#section#of#the#protein#folding#funnel#and#describe#what#the#opening,#local#minima#and#a bs o lu te #m in imum#rep re s en t. #(10#points)#c)#Draw#an #en erg y#diagram#depicting#the#relative#energy#states#of#the#folded#and#unfolded#state#for#the#transition#of#a#folded #to#un fo lded #state .#(7#po ints