Folded, Proteins are Marginally Stable Practice Problems Key

1.#For,the,following,statement,,circle,true,or,false.,If,false,,please,rephrase,as,a,true, statement,for,full,credit, , True,or,False:,Folded,proteins,are,marginally,stable,because,the,DG,of,unfolding, under,physiological,conditions,is,positive,and,the,hydrophobic,effect,favors, unfolding.,, Folded,proteins,are,marginally,stable,because….,hydrophobic,effect,favors,folding.#, , , , , 2.,a),Draw,the,structure,of,the,following,peptide:,LKYA,at,pH,7.0.,Note,any,charges,that,are, present.,, , , , ,, b),Identify,one,peptide,bond,on,your,peptide,diagram,by,drawing,a,box,around,it., c),What,is,the,net,charge,of,the,peptide,at,pH,7.0?,,,+1.0, d),Which,of,the,following,would,you,use,to,purify,this,protein?,Assume,you,want, the,protein,to,stick,to,the,column.,(Circle,one),Anion,Exchange,, Cation, Exchange,, , 3.,,You,discover,a,protein,that,consists,entirely,of,hydrophobic/non-polar,amino,acids.,, a),Which,amino,acids,might,be,found,in,the,protein?,(Circle,one),, i),lysine,and,histidine, ii),histidine,and,valine, iii),alanine,and,tryptophan, iv),tryptophan,and,glutamine, v),isoleucine,and,asparagine, vi),methionine,and,aspartic,acid, , , , 1 b),What,happens,thermodynamically,when,you,transfer,the,protein,from,a,nonpolar,solvent,into,an,aqueous,environment?,Circle,your,answer,for,each,term.,, , DG,is:,,,,,,,,,,,,,favorable,,,,,,,,,,,,,,,,,,unfavorable,,,,,,,,,,,,,,,,,,,,no,effect,, TDS,is:,,,,,,,,,,,favorable,,,,,,,,,,,,,,,,,,unfavorable,,,,,,,,,,,,,,,,,,,,no,effect , DH,is:,,,,,,,,,,,,,favorable,,,,,,,,,,,,,,,,,,unfavorable,,,,,,,,,,,,,,,,,,,,no,effect, # # 4.#,The,molecule,depicted,below,can,be,protonated,or,unprotonated.,The,population,of, molecules,at,pH,11,is,shown,below.,# , , A.,What,is,the,pKa,of,the,molecule?,,pH=____10_____, B.,The,R,group,of,which,amino,acid,has,this,same,pKa,and,charge,at,pH11,as,this,molecule?, lysine, C.,What,is,the,approximate,average,charge,of,the,molecules,in,this,population,at,pH,11?,, +0.1, , , , , , , , , , , , 2 5.,Select,the,one,answer,in,each,box,of,the,table,(4,answers,total),that,correctly,describes, the,structure,of,alpha,helices,or,beta,sheets.,, , structural#element# Alpha#helix# Beta#sheet# Hydrogen#bonds# exist#between#which# groups?# a),backbone,atoms, a),backbone,atoms, b),atoms,in,the,amino,acid,R, groups, b),atoms,in,the,amino,acid,R, groups, c),between,R-group,and, backbone,atoms, c),between,R-group,and, backbone,atoms, , , # What#best#describes# a),parallel,to,the,direction,of, the#relationship#of# the,helix, the#R#groups#relative# b),extending,inward,to,the, to#the#backbone?# center,of,the,helix, # c),extending,outward,away, from,the,center,of,the,helix, a),within,the,plane,of,the,sheet, b),above,and,below,the,plane,of, the,sheet, c),extending,inward,to,the,center, of,the,sheet, , , , A.,Amyloids,are,formed,by,the,association,multiple,copies,of,a,protein,with,each,other., Which,secondary,structural,element,is,found,in,amyloids?,Beta,sheets/beta,strands, B.,Why,is,the,other,type,of,secondary,structure,not,found,in,amyloids?,, Alpha-helices,interact,with,other,alpha-helices,through,the,side,chains,(R,groups),and, therefore,the,interaction,is,,sequence,specific,while,the,hydrogen,bonding,interactions,of, the,backbone,atoms,of,beta,sheets,is,non-specific.,All,,backbone,hydrogen,bonds,in,alphahelices,are,satisfied., # # # # # # # , 3 6.,If,the,Kd,of,ligand,,L,,binding,to,a,protein,,P,,is,10-5,and,the,[L],is,10-4,,what,is,the,ratio,of, [PL],to,[P]?,Select,one,answer., , a),0.01, b)0.1, , c),1, , d),10, , e),100, # # 7.,Given,the,peptide,Ser-Asp-Lys,,answer,the,following,questions, A.What,is,the,net,charge,of,the,peptide,at,pH,3?,Choose,the,closest,possible,choice.,, ,,,,a.,0, ,,,,b.,+1, ,,,,c.,-0.9, ,,,,d.-0.1, ,,,,e.,+0.1, ,,,,f.,+0.5, ,,,,, B.,Which,statement,best,describes,the,definition,of,pI,for,a,peptide?, , i.,the,charge,of,an,ionizable,group, , ii.,the,charge,of,the,peptide, , iii.,the,pH,of,the,peptide, ,,,, iv.,the,molecular,weight,of,the,peptide, ,,,,, v.,the,pH,at,which,an,ionizable,R,group,is,uncharged, ,,,,, vii.,the,pH,at,which,an,ionizable,group,is,half,protonated,, viii.,the,pH,at,which,a,molecule,has,zero,net,charge, ix.,the,pH,at,which,a,molecule,has,no,charged,residues, , , , , 8.,Briefly,explain,how,the,hydrophobic,effect,contributes,to,tertiary,protein,structure.,, , Tertiary,structure,is,the,overall,fold,of,a,protein.,Hydrophobic,residues,are,more,stable, interacting,with,each,other,instead,of,water,due,to,entropic,effects,of,ordering,the,cage,of, water,around,hydrophobic,groups.,Therefore,,hydrophobic,residues,are,often,found,on,the, inside,of,a,folded,protein,and,polar,residues,are,often,found,only,on,the,outside,of,a,folded, protein.,The,favorability,of,the,hydrophobic,residues,on,the,interior,of,the,protein, contributes,to,overcoming,the,unfavorable,entropy,in,folding,a,protein., , , , 4 , , 9.,The,figure,below,shows,segments,of,two,different,2D,gels.,Samples,on,the,left,are,taken, from,normal,colorectal,cells.,The,samples,on,the,right,are,from,cancerous,colorectal,cells, from,the,same,individual., , A.,Which,of,the,following,can,be,learned,or,estimated,about,a,protein,based,on,the,results, of,a,2D,gel?,Select,all,that,apply.,, , i.,size,(molecular,weight), , ii.,abundance, , iii.,charge, , iv.,sequence, , v.,pI, , vi.,solubility, , You,decide,to,investigate,these,proteins,further,and,perform,gel,filtration,(size,exclusion, chromatography),on,the,contents,of,colorectal,cancer,cells,from,the,patient,above., Analyzing,the,gel,filtration,results,,you,detect,three,distinct,fractions,or,peaks,of,protein, that,represent,the,proteins,in,spots,a-d.,, , B.,Why,are,there,only,three,peaks,detected,for,four,spots,on,the,2D,gel?,Select,one,answer.,, , i.,A,and,C,are,about,the,same,molecular,weight, , ii.,B,and,C,are,about,the,same,molecular,weight, , iii.,A,and,C,have,about,the,same,pI, , iv.,B,and,C,have,about,the,same,pI, , v.,A,and,D,have,the,same,net,charge, , vi.,B,and,D,bind,each,other,to,form,a,dimer, , 5 , , C.,On,the,plot,below,,draw,the,three,peaks,you,would,expect,to,see,as,a,result,of,gel, filtration.,Label,the,peaks,1,,2,,and,3,(from,left,to,right).,, , , D.,In,which,of,your,peaks,would,you,find,the,protein(s),that,corresponds,to,the,signal, labeled,“D”,in,the,2D,gel?,Circle,one.,,, , i.,Peak,1, , ii.,Peak,2, , iii.,Peak,3, # # # # # # # # # # # , 6 10.,Antibodies,are,proteins,that,can,bind,specifically,to,small,parts,of,other,proteins., Antibodies,are,important,tools,for,many,experiments.,You,are,comparing,two,different, antibodies,(Ab,1,and,Ab,2),for,use,in,an,ELISA,to,test,for,the,presence,of,a,viral,protein., Both,antibodies,bind,the,same,viral,protein,as,illustrated,below., , , , , , A.,Select,the,correct,word,or,symbol,(from,the,choices,in,parentheses),to,complete,each, statement.,,At,the,exact,moment,you,add,the,antibody,to,the,viral,protein,, , i.,the,,,,,(bound,,,,,or,,,,,,,free),state,is,favored, , ii.,DG,is,(<,,,or,,,,>,,,or,,,,,=,),0,,, , iii.,and,the,reaction,will,proceed,in,the,(forward,,,,,,or,,,,,,,,reverse),direction.,, , , You,measure,the,binding,of,each,antibody,1,(Ab1),and,antibody,2,(Ab2),to,the,viral,protein, and,obtain,the,following,data., C.,What,is,the,approximate,Kd,of,Ab2?, Circle,one.,, , i.,0.7, , ii.,0.35, , iii.,50, , iv.,150, , v.,300, , D.,Which,antibody,would,you,choose,for, the,ELISA,and,why?,, , Circle,one:,,,,,,Ab1,,,,,,,,,,,,,,,,,Ab2, Why?,Binds,tighter , , 7 , E.,You,choose,to,do,the,first,ELISA,experiment,at,a,ligand,concentration,1000x,higher,than, the,Kd.,What,will,be,the,ratio,of,bound,to,unbound,viral,proteins?,, , , , ,,,,,,,,,,,,,,,,,,,__1000____,bound:,__1____,unbound,,, , 11.,,You,are,studying,oxygen,utilization,by,an,organism,isolated,from,a,water, sample,collected,at,a,depth,of,3000,ft.,in,the,middle,of,the,Atlantic.,Based,on, genome,analysis,,you,identify,a,gene,with,40%,identity,to,sperm,whale,Hemoglobin, and,decide,to,name,it,Newoglobin,(Nb).,Newoglobin,is,expressed,at,low,levels,,but, you,wish,to,investigate,its,potential,role,as,an,oxygen,carrier,in,this,organism.,, , You,successfully,purify,Newoglobin,and,find,the,structure.,You,find,that,the,protein, is,made,mostly,of,alpha,helices,and,forms,the,“globin,fold”.,, , a),Which,location,on,the,Ramachandran,plot,represents,the,angles,adopted, by,the,amino,acids,that,form,the,right-handed,alpha,helices,of,the,globin, fold?,(Circle,your,answer),,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, ,,,, Correct,answer:,F,,, , , , , , , , , , , A,portion,of,the,sequence,that,forms,helix,E,(residues,96-113),is,shown,below:,, , ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,V,N,K,Y,A,G,E,S,H,C,Q,W,V,F,T,R,A,Y,,, , b),The,oxygen,of,which,amino,acid,(provide,one,letter,code),will,be, hydrogen,bonded,with,the,amide,proton,of,cysteine?,,Correct,Answer:,G, , , , , , 8 , Using,purified,Nb,,you,measure,oxygen,binding,and,the,resulting,curve,is,a,sigmoid, which,you,model,as,a,mixture,of,two,states:,the,oxy,R,state,and,deoxy,T,state:,, , f),Based,on,the,binding,curve,behavior,,what,can,you,conclude,about, Newoglobin?,(Circle,all,that,apply),, , i),Nb,binds,at,least,two,Oxygen,molecules,, , ii),Nb,binds,oxygen,cooperatively, , iii),Nb,must,be,a,tetramer, , iv),The,T,state,has,a,higher,affinity,for,oxygen,, , , , , , , , , , , , , , One,time,when,you,repeat,the,experiment,you,find,that,the,Nb,behaves,differently., You,realize,that,you,forgot,the,dialysis,step,at,the,end,of,the,purification.,You, hypothesize,that,a,small,molecule,normally,removed,in,the,dialysis,step,is,affecting, the,behavior,of,Nb,in,the,O2,binding,experiment., , , , , , , , , , , , 9 , The,data,are,shown,on,the,graph,below:, , , , , , , , , , , , , , , , ,, , , , g),Small,molecules,like,the,one,described,above,are,called…?,(Circle,one),, , i),side,chains, , ii),isoforms, , iii),allosteric,effectors, , iv),regulatory,subunits, , v),covalent,modifications, , vi),protoporphyrin,rings, h),Based,on,the,binding,curve,,the,presence,of,the,small,molecule,does, which,of,the,following?,(Circle,all,that,apply),, , i),favors,the,R,state, , ii),favors,the,T,state, , iii),increases,the,intrinsic,KR/T,, , iv),increases,the,affinity,of,Nb,for,oxygen,, , v),decreases,the,affinity,of,Nb,for,oxygen, , vi),eliminates,cooperativity, , v),increases,the,amount,of,oxygen,bound,at,20,torr, , vi),increases,the,amount,of,oxygen,bound,at,50,torr, , , 10