Biochemistry Exam II Fall 2003                                             Name_____________________________

a. Decrease in pH from pH 7.4 to 7.2

b. Increase in CO₂ from 2 to 6 torr

c. Decrease in the BPG concentration from 8 mM to 5 mM

d. Dissociation of the tetramer complex into separate monomer subunits

2. (15 points) Explain the following observations in terms of the environment of each amino acid.

a. A lysine in Acetoacetate decarboxylase has a pKa of 6.6

b. Tyr-9 in Glutathione S-transferase has a pKa of 8.1

c. Glutamate 35 in lysozyme has a pKa of 6.3.

3. (5 points) Describe the concept of "induced fit" and give a specific example.

4. (10 points) Avidin is a protein that is found in egg whites. It probably protects the developing chicks from bacterial infections by binding biotin. Biotin is essential for bacterial growth. Biotin is also an essential component of the human diet. When Rocky ate all of those raw eggs, he was putting himself at risk for a Biotin deficiency. If the Kd for avidin-biotin binding is 1 x 10 ^-15,

a. What concentration of biotin will 50% of all the binding sites be occupied?

b. What concentration of biotin will 20% of all the binding sites be occupied?

5. (12 points) For the following questions about hemoglobin mutations in the , chains consider the following:

Name of mutant Hb Residue number Amino acid substitution

Hb Chongqing 2(NA2) Leu->Arg

Hb Aztec 76(EF5) Met->Thr

Hb Iwata 87(F8) His->Arg

Hb Ann Arbor 80(F1) Leu->Arg

This information was taken from the following www site:http://globin.cse.psu.edu/globin/html/huisman/variants/alpha/

a. Which of the following mutations would you predict to be the most damaging to the function of hemoglobin? Why?

c. Which of the above mutations will result in a change in the pI of the protein. If there is a change in the pI, indicate whether the mutant chain has a higher or lower pI.

6. (10 points) Draw the structure for the following peptide. Then, calculate the pI for this peptide. Use pKa=8 for the amino terminus group and pKa =3.4 for the carboxy terminus group. You know all of the other pKa values for the R groups.

VPREW

7. (10 points) The following peptide was cleaved with chymotrypsin and the resulting peptides were separated by cation exchange chromatography. Give the sequences of the peptide and the order of elution for these peptides at pH 7 on an cation exchange column. For all of the peptides, the N terminus amino group pKa is 8 and the C terminus carboxyl pKa is 3.4.

VIGAELYKAGGRFISLHGA

8. (10 Points) Fully describe how the Edman degradation reaction works and how it is used. You do not have to draw exact structures.

9. (20 points) Compare and contrast the quaternary structures of collagen and keratin. Fully describe the secondary structures of each. What are they? Fully describe how the structure is related to the function of each protein.