Student Biochemistry I Homework III Due 10/13/04 64 points total (48 points based on text; 16 points for Swiss-PDB viewer exercise)

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1 Biochemistry I Homework III Due 10/13/04 64 points total (48 points based on text; 16 points for Swiss-PDB viewer exercise) 1). 20 points total T or F; if false, provide a brief rationale as to why. Only charged amino acids play a role in a proteins active site. Both enzyme specificity and enzyme catalysis can be explained by the "induced-fit model" for substrate binding. Enzymes alter the amount of energy consumed (or liberated) in a reaction. Catalysts accelerate a reaction by increasing the G The steady state assumption in Michaelis-Menten kinetics states that the ES intermediate is consumed as rapidly as it is formed. A lower activation energy means the forward and reverse reactions both proceed at faster rates. Biological reactions can have molecularities up to 5. V max is reached when every enzyme is carrying out a chemical reaction. A large K m (10-1 M to 10-3 M) means that substrate binds tightly to enzyme. Affinity labels are an example of irreversible inhibitors.

2 2). (6 points) The curves below represent the effect of adding a positive allosteric effector or a negative allosteric effector to an enzymatic reaction. a). Identify on the plot which curve represents the effect of a positive allosteric effector and which curve represents the effect of a negative allosteric effector. b). How do positive and negative allosteric effectors exert their effect on an enzyme?

3 3). 9 points total Properties of an enzyme involved in prostaglandin synthesis. Prostaglandins are fatty acid derivatives that are responsible for producing fever and inflammation and its associated pain. The are derived from the 20-carbon fatty acid arachidonic acid in a reaction catalyzed by the enzyme prostaglandin endoperoxide synthase. This enzyme uses oxygen to convert arachidonic acid to PGG2, an immediate precursor to many different prostaglandins. The kinetic data are given below in columns 1 & 2 for the reaction catalyzed by prostaglandin endoperoxide synthase. Kinetic data were also collected in the presence of ibuprofen, an inhibitor of prostaglandin endoperoxide synthase. Ibuprofen inhibits the synthesis of protaglandins, thus aiding in reducing inflammation and pain. The data collected in the presence of ibuprofen are given in column 1 & 3. Analyze the data using a Lineweaver-Burke plot. What is the Vmax and Km of the enzyme in the absence of ibuprofen? What kind of inhibitor is ibuprofen? Why can't we use the direct plots of vo vs. [S] to determine Vmax and Km? (Attach plots for full credit). [Arachadonic Acid] mm Rate of formation of PGG 2 (mm/min) Rte of formation of PGG2 with 10 mg/ml ibuprofen present (mm/min)

4 4). 3 points For a one-substrate, enzyme catalyzed reaction, double-reciprocal plots (Lineweaver- Burke plots) were determined for three different enzyme concentrations. Which of the following three families of curves would expected to be obtained (circle the appropriate plot). Briefly explain your choice in terms of the definitions of Vmax and Km.

5 5). 4points Short answer (no more than 4 grammatically correct sentences) A). What is the difference between amino acid sequence and amino acid composition? B). What techniques would you use to determine amino acid sequence? Amino acid composition?

6 6). 10 points Predict the sequence of the peptide based on the given information. Partial credit (up to 3 points) will be given for correct partial analysis, so justify your reasons. Total credit! only if correct sequence given. a). Amino acid analysis of a heptapeptide gave the following results (in no particular order Asp Glu Leu Lys Met Tyr Trp NH 4 + Recall that certain amino acids are destroyed upon acid hydrolysis. b). Trypsin had no effect. c). The phenylthiohydantion released by Edman degradation was d). Chymotrypsin treatment yielded several products, including a dipeptide and a tetrapeptide. The amino acid composition of the tetrapeptide was Glx, Leu, Lys and met d). CNBr treatment yielded a tetrapeptide that had a net positive charge at ph 7 and a tripeptide that a a zero net charge at ph 7. e). Cleavage with Staph protease leaves a dipeptide and heptapeptide.

7 Homework III Swiss PDB Viewer Exercise 16 points total Download the structure 1IOZ from the Protein Data Bank Website. a). This is the H isozyme of lactate dehydrogenase. What is an isozyme? b). What is the source of this LDH? c). What class of enzymes does LDH belong? d). What is the cofactor in LDH? e). What reaction does LDH catalyze? f). What is the oligomeric state of this structure? g). Describe the secondary structural content of LDH: h). Describe the location of the NADH: i). Oxamate is a competitive inhibitor. What is a competitive inhibitor? This would affect which Michaelis-Menten parameter? j). Is the oxamate in H-bonding distance from NADH? k). What is the distance between the reactive NHs of the two molecules of NADH? l). The active site is comprised of residues What is the location of the active site? What is its structure? m). What H-bond(s) are formed between oxamate and the active site loop?

BIOCHEMISTRY I HOMEWORK III DUE 10/15/03 66 points total + 2 bonus points = 68 points possible Swiss-PDB Viewer Exercise Attached

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