page1 (of10) Name______Key to the City_______________BIBC102 Midterm 1 Fa 2005 Stu. ID#__________________________________Proteins and peptides (9 points)Behold, a license plate! It is from a custom classic car (ca.1940) on display at Simpson’s Nursery in Jamul, which hasmany plants and a remarkable collection of vehicles (gofigure…).1; 4 pts) Write the sequence of the peptide spelled out in the plate, using the three letter code(eg. a tripeptide of tryptophan would be TrpTrpTrp).Glu-Leu-Phe-Ile-Arg-Glu-Ala2) At physiological pH (7.0), what is the net charge of thispeptide? (note this only requires knowing the R groupson each amino acid) _(-1 +1 –1) = -1__3) Give a one sentence, general description of a prosthetic groupA cofactor is a non-peptide molecule that is associatedwith an and needed for its function4) Write the name of the prosthetic group that contains iron _heme5; 2 pts) Write the name of the type of protein secondary structure that is depicted in the littlepictures, using the space under each one __alpha helix____ ____beta sheet____page2 (of10) Name______Key to the City_______________BIBC102 Midterm 1 Fa 2005 Stu. ID#__________________________________who’re those jerks, lineweaver and burk?they took my curve and made a linethat takes some nerve so I’ll speak my mindthose foolish nerds be wastin’ your timecause the hyperbola is still sublimeEminem: The Slim Substrate LPFlipping M & M (8 points)You are analyzing three enzymes (A, B and C)that catalyze the same reaction. You determinethe velocity (V) at various substrateconcentrations (S), and plot the data using theLineweaver-Burk method, excoriated byEminem (see inset box). The resulting graph is shown on the right, with eachenzyme’s data indictated by letter.Answer the following questions.6) What does the horizontalaxis represent? _1/S__7) What does the verticalaxis represent? _____1/V ____8) Which enzyme hasthe highest Vmax? ____ C ______9) Which enzyme attains 50%Vmax at the lowestsubstrate concentration? ___ C ______10) A fourth isozyme has a curved lineweaver burke plot.Sketch what the S vs V plot for that enzyme will look like inthe space to the right.. (that is Randy’s crappy version of asigmoidal plot…)11) What can you say about the structure of this fourth enzyme?It is very likely to have quaternary structure, that is, multiple subunits12) (not Lineweaver-Burk related)Write the equation that defines kcat kcat = Vmax/[E]tot(Hint: this is not Km)13) What is the definition of kcat in English? That is, use a sentence to describe its physicalmeaning, as opposed to an equation.The kcat is the maximum rate that an individual enzymemolecule can produce product.page3 (of10) Name______Key to the City_______________BIBC102 Midterm 1 Fa 2005 Stu. ID#__________________________________321Three residues for the Enzyme-Kings… (8 points)The catalytic triad is a very common feature of many enzymes that hydrolyze chemical bonds.We focused on chymotrypsin in this class. Below are the three amino acids of thechymotrypsin catalytic triad.Name each amino acid, and in one sentence describe its function in the catalytic triad.14) name: __HISTIDINE___15) function in catalytic triad:This residue accepts and donatesprotons in the course of thenucleophilic attacks that occur duringthe catalytic cycle16) name: _ SERINE ___17) function in catalytic triad:The R group oxygen performs anucleophilic attack on the peptidebond, at the carbonyl carbon18) name: _ASPARTATE __19) function in catalytic triad:Stabilizes the protonated histidine thatparticipates in acceptin and donatingprotons during the catalytic cycle20; 2 pts) Some catalytic triads have the amino acid cysteine in place of one of the amino acidsabove. Which amino acid above (you can say 1, 2, or 3 if you don’t remember the name) wouldbe the logical one to be substituted by cysteine in these alternate triads? Why? (one sentence).Cysteine could work in place of serine, since the sulfer incysteine can similarly function as a nucleophile andsimilarly be assisted by the other triad members.page4 (of10) Name______Key to the City_______________BIBC102 Midterm 1 Fa 2005 Stu. ID#__________________________________+ ADP+ ATPPEPThe last step…(11 points)A recent article (Zanella et al. (2005) British Journal of Heamatology 130, 11-25) describes agenetic deficiency in red cell pyruvate kinase (PK). etc…21; 4 pts) Write the reaction catalyzed by PK. Include the structures and names of theglycolytic pathway molecules; include any cofactors or other substrates used or produced in thereaction.In cells that have a PK deficiency, there is a buildup of the substrate of thePK reaction, and a build up of 2 phosphoglycerate (2-PG) and 3 phosphoglycerate (3-PG).Let’s think about this.What are the two reactions that directly precede the PK reaction? Write each in the spaceprovided. No need for structures, just names like 3-PG, etc. Include all reactants and products.22) First (earlier) of the two reactions (here): 3PG 2PG23) Second of the two reactions (here): 2PG PEP + H2O24) So why do the two molecules mentioned above build up in this syndrome? (one sentence)The primary block causes buildup of PEP, which will slow andeventually stop the second reaction, causing buildup of 2PG, whichwill eventually do the same to the next reaction, causing buildup of3PG.PK is allosterically regulated. Two regulators of PK are fructose 1,6 bisphosphate and ATP.Predict how each affects the enzyme’s activity (inhibitor, activator) and say with one sentencewhy it makes sense.25; 2 pts) Fr1,6bP is an allosteric _ACTIVATOR_ of PK. This makes regulatory sensebecause: An excess of this molecule indicates a need forgreater glycolytic pathway activity26; 2 pts) ATP is an allosteric INHIBITOR _ of PK. This makes regulator sense because:When there is sufficient ATP, the further production of AcCoA is notneeded, and the pyruvate can instead be used for other things(anabolism).page5 (of10) Name______Key to the City_______________BIBC102 Midterm 1 Fa 2005 Stu. ID#__________________________________Thinking about drinking (8 points)Ingested ethanol is detoxified by the liver to harmless acetate. This occurs by a two reactionpathway, in which ethanol is converted into acetaldehye, and then acetaldehyde is convertedinto acetate.27; 2 pts) First, draw the structures of the three molecules. I have included ethanol. That levelof detail is fine ethanol acetaldehyde
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