Chem 251

Name:

Midterm Exam I

10/05/11
Note: This exam consists of five pages

1. [25 p] The tripeptide shown below is called Glutathione. This peptide plays an important role in the
purification of proteins.

a) Describe the method of purification in which this peptide is involved with on the order of three sentences.
Use drawings if helpful. Name two additional protein purification techniques (provide a brief description for
each).
b) Hydrolyze Glutathione and draw each of the three amino acids with its side chains. Which amino acids does
Glutathione consist of (give full name, three letter, and one letter abbreviations for each)?
c) Draw two equivalent Fischer projections of naturally occurring amino acids (Hint: the correct configuration
can be inferred from the drawing above). Abbreviate the side chain as R.
d) Glutathione contains both usual and unusual peptide bonds. Indicate which ones are usual and which ones are
unusual; explain.

2. [25 p]
a. Draw a mechanism showing how protein disulfide isomerase converts an inactive form of a protein,
containing disulfide bonds between residues I and IV, and residues II and III, into an active form containing
disulfide bonds between residues I and II, and residues III and IV.

III ----S - S---

II

IV ----S - S---- I
b. Migration of a protein in an electric field (electrophoresis) is a function of the protein's charge density, size,
and shape. Why do proteins migrate in an SDS-PAGE experiment exclusively as a function of protein size?
c. Briefly describe the structure and function of the GroEL/GroES system

3. [25 p]
a) Calculate the ionic strength of one molar solutions of NaCl and K3PO4.
b) Describe the phenomena of salting out and salting in. What solution from a) would a protein be expected to
be more soluble in?
c) The protein hemoglobin has a pI value of 7.1, whereas the protein lysozyme has a pI value of 11. Using an
increasing ionic strength gradient on a CM (carboxymethyl) cellulose column, which protein is going to elute
first? Explain.
d) The pKa values of the two carboxy groups of the amino acid Glutamate are quite different. Give approximate
values for them and explain their difference.

4. [25 p]
a) Estimate the ratio of folding times for a 6 residue folding nucleus, and a 20 residue folding nucleus according
to the Levintal back of the envelope calculation. To do so, remember that a peptide chain may explore
roughly 1013 conformations per second.
b) During the earliest stages of protein folding, the likelihood of appearance of beta sheets and alpha helices is
different. Which one is likely to appear first and why is that the case?
c) The drawing on page 5 (next page) shows a type two beta turn with two peptide bonds. The angles phi and
psi for these two peptide bonds are either positive, zero, or negative. Label the bonds with the appropriate type
of angle and indicate its magnitude (use the format i > 0, or k =0, where i and k indicate the residue number).