Spring'2011'BIBC'102'midterm' ' Name______Metaboloso)the)Great!______________'Hampton'Class'@'6:30' ' ID'#__________________411___________________________'' ' ' '1')) Good evening. This is the midterm and like we discussed, it has two purposes. The first is to solidify your knowledge of the basic and oft-used concepts and information covered in this test. The second is to discern how much you know. I have tried to make the test more about recognizing things than simply pulling them out of memory. There are a few cases where pulling out of memory is asked, but not many. My only advice is to read the whole question before you dive in, and to feel free to ask questions. That is why we are circulating around like sharks who must move to breath. Finally, please believe me when I say we are not about tricking you, fooling anyone, or trying to be all crafty-like. This is a very straightforward exam, and what we ask for is what we want. Period. Enjoy, to the extent that this is possible in a midterm… Summation Page 2 ___________(out of 10) Page 3 ___________(out of 9 ) Page 4 ___________(out of 15) Page 5 ___________(out of 18) Page 6 ___________(out of 16 ) Page 7 ___________(out of 12 ) Page 8 ___________(out of 15) Page 9 ___________(out of 5) Total ___________(out of 100) ))))))))))Spring'2011'BIBC'102'midterm' ' Name______Metaboloso)the)Great!______________'Hampton'Class'@'6:30' ' ID'#__________________411___________________________'' ' ' '2''1/4)(6)pts))To'the'right'is'the'classic'free'energy'reaction'coordinate,'showing'the'S'to'P'reaction'in'two'situations.'In'one'an'enzyme'is'present,'and'in'the'other,'there'is'no'enzyme.''1)Which'curve'(1'or'2)'best'represents'the'reaction'with'the'active'enzyme,'and'why?'(one'sentence):' The curve 2 represents the plus enzyme curve, because the activation energy,'ΔG‡ is lowered. '))2'An'excellent'if'somewhat'aggressive'student'comes'to'Dr.'R’s'door'and'says'“This'problem'is'incorrect,'because'the'curve'with'the'enzyme'should'have'P'with'a'lower'free'energy'than'without'the'enzyme!”'Let’s'think'about'that,'and'answer'the'following'questions:'' If'the'free'energy'of'P'alone'were'lowered,'would'the'S'to'P'rate'be'changed?'(one'sentence)''' That would not change the S to P rate, and would increase the P to S rate! 3'If'the'free'energy'of'P'alone'were'lowered,'what'would'happen'to'the'Keq?''' The Keq would change to a larger quantity''4'In'general,'what'is'the'effect'of'an'enzyme'on'the'forward'(S'to'P)'and'reverse'(P'to'S)'reactions?''' Enzymes cause the same multiplicative change for both forward and reverse reaction. Each changes by a factor ed/RT where d is the drop in activation energy. '''5/8))(4)pts))The)Ghost)of)Allostery'The'strangely'familiar'picture'shows'a'“generic”'linear'metabolic'pathway,'in'which'A'goes'to'F'by'5'enzyme'steps.'The'graph'is'an'enzyme'rate'plot'like'we'have'discussed'in'class.'The'rate'of'the'C'to'D'reaction'is'shown,'when'C'is'alone'in'the'reactin'(“c'alone),'and'when'two'different'allosteric'regulators'are'present'(curve'1'and'curve'2).''' '5)Which'curve'shows'the'effect'of'an'allosteric'activator'___2__''' '6'Which'curve'shows'the'effect'of'an'allosteric'inhibitor'__1___''7'High'concentrations'of'A'stimulate'the'pathway''' by'altering'Ecd.'Which'curve'describes'A’s'action?'___2___'')8'High'concentrations'of'F'turn'down'the'pathway'by''' altering'Ecd.'Which'curve'would'best'describe'F’s'action?'__1___'''Spring'2011'BIBC'102'midterm' ' Name______Metaboloso)the)Great!______________'Hampton'Class'@'6:30' ' ID'#__________________411___________________________'' ' ' '3')9/11)(9)pts)'This)just)in!'Last'week,'the'FDA'indicated'that'the'company'Vertex'has'promising'results'in'the'fight'against'hepatitis'C'virus'(currently'afflicting'something'like'1'in'35'people'on'Earth).'Vertex'developed'an'inhibitor,'named'telaprevir','of'the'enzyme'NS3aA4.'NS3aA4'is'a'serine'protease,'similar'to'chymotrypsin.'Here'is'a'description'of'NS3aA4'from'the'scientific'literature:'“The%HCV%NS3,4A%serine%protease%retains%some%highly%conserved%features%of%the%chymotrypsin%family,%such%as%spatial%location%of%the%catalytic%triad%of%His57,%Asp81,%and%Ser139,%as%well%as%the%positions%of%backbone%amides%of%Gly137%and%Ser139,%which%forms%the%oxyanion%hole.”%See…'what'you'are'learning'actually'has'some'use!'Answer'the'following'questions:'')9)(3pts)'For'the'three'catalytic'triad'amino'acids'His,'Asp'and'Ser,'write'the'one'letter'code,'and'ONE'SENTENCE'describing'what'that'amino'acid'does'in'the'action'of'chymostrypin:'''' HIS _H_ : His transfers protons from the serine OH or from the attacking H20 to allow acid base catalysis SER _S__: Serine OH performs the actual nucleophilic attack on the peptide bond, and acquires the covalent adduct of the remaining peptide chain ASP __D__: Aspartate provides charge neutralization to the His that gains a positive charge when it is transferring protons during the catalytic cycle '10)(2'pts))At'Vertex,'you'and'an'assistant'are'each'measuring'the'activity'of'NS3aA4'using'a'substrate'S.'You'each'are'using'the'exact'same'batch'of'the'NS3aA4.'You'perform'a'rate'analysis'using'a'1uM'concentration'of'the'enzyme,'but'your'assistant'performs'their'analysis'using'2uM'enzyme'concentration.'Which'measured'quantities'below'will'be'the'same'and'which'will'be'different'in'your'two'analyses.'In'each'space,'write'S'for'same,'or'D'for'different.'That'is'all.'No'numbers.''' Km'___ S'___'''''''Vmax'__ D'_____''''''''kcat'__ S'____'''''Half'maximal'[S]'__ S'____''11)(4'pts)'This'is'a'Lineweaver'Burke'plot'of'the'results'form'your'and'your'assistant’s'experiment'on'NS3aA4.''Which'is'your'curve'(A'or'B),'and'which'is'the'assistant’s'curve'(A'or'B)''''' Your'curve:''__ A'__'''''Assistant’s'curve:'__ B'___''' Write'the'algebraic'term'for'the''' X'intercept'of'a'Lineweavera'' Burke'plot:''''' ' ' ' ' X intercept = -1/Km ' 'Spring'2011'BIBC'102'midterm' ' Name______Metaboloso)the)Great!______________'Hampton'Class'@'6:30' ' ID'#__________________411___________________________'' ' '
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