Problem Set #4 (same as Second Midterm Exam Sample)

Problem Set#4 - BIOCHEMISTRY lOOB SECOND MIDTERM EXAM Winter 2004 page 1 Bogomolni Name Student number(last four digits Score 1(40pts 2(25pts

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Unformatted text preview: BIOCHEMISTRY lOOB SECOND MIDTERM EXAM February 19, 2004 Winter 2004 page 1 Bogomolni Name: Student number: (last four digits) Score: 1 (40pts) 2 (25pts) 3 (20pts) 4 (20pts) 5 (l0pts) 6 (10pts) 7 (25pts) T(150) 1—(40 pts). Indicate whether the following statements are true or false. If true briefly justify your answer. If false explain why and write a true statement that applies to the case. a) The three essential amino acid residues in the active site of chymotrypsin: histidine, serine and aspartate, fulfill the following roles during catalysis: i- The histidine facilitates the reaction by acting as an acid— base catalyst. ii- The serine residue acts as an electrophile during the reaction. iii- The aspartate residue initiates the deacylation step by a nucleophilic attack on the carbonyl carbon of the acyl intermediate. b) Both low and high pH are expected to decrease the rate of chymotripsin catalyzed peptide bond hydrolysis 0) Competitive inhibitors do not alter the Vmax of an enzyme catalyzed reaction. d) The most important factor in the lysozyrne mechanism is the stabilization of the substrate conformation that approaches the conformation of the the transition state. BIOCHEMISTRY lOOB SECOND MIDTERM EXAM February [9, 2004 Winter 2004 page 2 Name: Student number: (last four digits) 2- (25 pts) a) lOpts. On the basis of the following NAG (abbreviated as G) binding energies for lysozyme's sugar binding sites A through F, SITE Binding Energy (KcaUMole) A -2.0 B -3.5 C -5.0 D +4.0 E —2.5 F ~3.0 predict which positions will be occupied in the most prevalent complex with each of the following oligosaccharides. Assume that sites that can accommodate NAM (abbreviated as M) would have the same affinity for NAG and NAM). 1- GG 2— GM 3- GGGG 4- GGGM 5- GGMM b-lO pts. An analog of tetra-NAG containing -H in place of ~CH20H at C-5 of residue D binds to lysozyme much more strongly than does tetra-NAG. Propose a structural basis for this difference in binding affinity. BIOCHEMISTRY 100B SECOND IVHDTERM EXAIVI February 19, 2004 Winter 2004 page 3 Name: Student number: (last four digits) 3— 20 pts. Many irreversible inhibitors react quantitatively and stoichiometrically with specific groups of the enzyme they inactivate. This offers a convenient experimental method to determine if an enzyme has more than one catalytic site (or catalytic subunit) per molecule. Such an experiment follows: An enzyme of molecular weight 100,000 kD was completely inactivated when its only cystein residue(s) known to be located at the catalytic site reacted with iodoacetamide (MW 185 kD). It was found that 3.7 x 10'2 mg of iodoacetamide were required to completely inactivate 5 ml of a 1.0mg/ml solution of the enzyme. Calculate the number of active sites (or catalytic subunits) present in each enzyme molecule. BIOCHEMISTRY 100B SECOND MIDTERM EXAM February 19, 2004 Winter 2004 page 4 Name: Student number: (last four digits) 4— (20 pts). Complete the following diagram to indicate the first step in the catalysis of a peptide substrate by a serine type protease. Be sure to indicate all relevant nucleophilic attacks, charge states and stereochernistry. 5- 1.0 pts. HOW would the Eadie-Hofstee and the Hams-Woolf linearized plots look for the following cases: 1- Competitive inhibition 2- Pure non-competitive inhibition BIOCHEMISTRY 100B SECOND MIDTERM EXAM February 19, 2004 Winter 2004 page 5 Bogomolni Name: Student number: (last four digits) 6-10 pts TheKM ofa typical enzyme is 1 uM a- Calculate the concentration of substrate necessary to fill 30% of the active sites. b- A competitive inhibitor for this reaction has a K = 10 uM. Calculate the fraction of active sites occupied by substrate when this inhibitor is present at a concentration of 20 uM. What would be under those conditions the fi'action of enzyme occupied by inhibitor? What is the fi‘action of free enzyme? BIOCHEMISTRY 100B SECOND MIDTERM EXAM February 19, 2004 Winter 2004 page 6 Name: Student number: (last four digits) 7-25pts. An enzyme that exhibits Michaelis-Menten kinetics was studied and yielded the following data relating initial reaction rates with the given substrate concentrations. (Note: [5] (M) a) b) c) d) e) f) g) 1.00E-03 is equivalent scientific notation for 1.00 x 10'3): _ v (M sec-1) 1/[3] (1%") IN (Ml sec) v. (M sec") l/Vi(M'1 sec) 1.00E-03 1.58E-07 2.50E-03 3.61E—07 5.00E-03 6.31E-07 1.00E-02 1.01E-06 2.00E-02 1.44E-06 5.00E-02 1.94E-06 1.00E-01 2.20E-06 L A v a H .4. C is g E 29:15“ amo’ 5.9m” uno’ 14154 M“ una' 10:19 * is; M 2.91m“ mm 5 Using the graph (above right), plot the raw data b) Fill in the two empty columns in the table above for the "double reciprocal" form of the data, and plot using the above graph on the left . What is the value of Km for this enzyme? What is the value of Vm for this enzyme? If the enzyme concentration is 5.05 x 10‘9M what is the value of kw? If a competitive inhibitior having a zyme—inhibitor dissociation constant, K = 10'2 M, is added at a concentration of 1.5 x 10'2 M calculate the velocities in presence of inhibitor, V;, for the substrate concentrations giv in the table, and enter those values and their inverse in the last two columns. Plot in the same graph the data calculated for the reaction in the presence of this competitive inhibitor. tiflfl‘ : ...
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This note was uploaded on 04/07/2010 for the course BIOC 100B taught by Professor Sethrubin during the Winter '10 term at University of California, Santa Cruz.

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Problem Set#4 - BIOCHEMISTRY lOOB SECOND MIDTERM EXAM Winter 2004 page 1 Bogomolni Name Student number(last four digits Score 1(40pts 2(25pts

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