Example Problem Set for CHEM106 Section 002 Test 2
If you can answer these problems, you will have no trouble at all with the material covered by the test. Remember: Answer what you are asked. Think about your answers. Look at your answers and ensure that they make sense.
1) Which amino acids are more likely to be on the surface of a protein? Why?
a) Trp or Q
b) V or Glycine
c) D or F
d) Thr or Pro
2) You are mutating amino acids in a protein to test predictions about which residues are important for a protein’s function. Which of each pair of amino acid substitutions listed below would you expect to disrupt protein structure the most? Explain.
a) Val replaced by Ala or Phe
b) Lys replaced by Asp or Arg
c) Gln replaced by Glu or Asn
d) Pro replaced by His or Arg
3) Under physiological conditions, polylysine assumes a random coil conformation. Under what conditions might it form an alpha-helix?
4) Draw the peptide ATLDRK
What is its net charge at pH 7.0? (Yes, you will have to go online or use your textbook to find sidechain pKa values)
5) Calculate the pKa of the weak acid HA if a solution containing 0.1M HA and 0.2M A- has a pH of 6.5
6) For an enzymatic reaction that follows Michaelis-Menton kinetics, what are the Km and Vm for the enzyme?
[S] (mM) / V0 (µM/sec)1 / 2.5
2 / 4.0
5 / 6.3
10 / 7.6
20 / 9.0
7) Give the primary structure of a Type II Reverse Turn.
8) An enzyme catalyzed reaction has a Km of 1mM and a Vm of 5 nM./sec. What is the reaction velocity when the substrate concentration is:
a) 0.25 mM
b) 1500 mM
c) 0.010 M
9) Determine the type of inhibition of an enzymatic reaction from the following data collected in the presence and absence of the inhibitor.
[S] (mM) / V0 (mM/min) / V0 with Inhibitor present (mM/min)1 / 1.3 / 0.8
2 / 2.0 / 1.2
4 / 2.8 / 1.7
8 / 3.6 / 2.2
12 / 4.0 / 2.4
10) Describe, give the advantage(s) of and give an example of an enzyme that uses the following enzymatic control mechanisms:
a) Phosphorylation
b) Feedback Inhibition
c) Production as a zymogen
11) What are the 2 primary secondary structural elements in proteins? List the distinguishing features of each.
12) What is a Ramachandran Plot? What does it tell you?
13) Draw the Lewis Structure of the following dipeptide: KW. Identify the Ramachandran angles of each amino acid in the peptide (I don’t want numbers, I want to see where you measure the angles).
14) Describe the changes to Km and Vm for the three primary types of reversible, Michaelis-Menton inhibition. Give a molecular basis for the changes.
15) If you accidentally drank ethylene glycol, what therapy would the physician likely prescribe and why is it successful?
16) Suppose you took 3g of ibuprofen and dissolved it in 2.0L of water. You then removed 50 mL of the solution and added it to 350 mL of water, mixed it and then removed 10 mL of the resulting solution and added it to 90 mL of water, what would the final concentration of ibuprofen be in the 2.0L solution? If ibuprofen was a weak, monoprotic acid (Ka = 1.7 x10-5) what would the pH be in the final 100 mL solution?
17) Draw the chemical structure of the following compounds:
a) 2-amino-3-methylpentanoic acid
b) 2,5-diamino-5-oxopentanoic acid
c) 2-amino-3-phenylpropanoic acid
d) 2-amino-3-hydroxypropanoic acid
18) What are the common names of each of the compounds in question 17?
19) What is a chaotrope? Give an example of one and what would happen to a protein if you were to add the chaotrope to a protein solution?
20) You have purified a new compound from marine algae that shows some effectiveness in the treatment of stomach cancer. The compound absorbs at 260 nm with a molar absorptivity (e) value of 26 mM-1cm-1. You isolate a new batch of the compound and measure the absorbance of the sample in a 1.0 cm pathlength cuvette at 260 nm. If the absorbance you measured was 0.443, what is the concentration of the compound in the new batch?