Exam II/BiochemistryI/2002/ Dr. Stone

1.  (5 points) Gas gangrene is caused by the anerobic bacteria, Clostridium perfringens. This bacteria causes massive tissue destruction. One of the enzymes that it secretes cleaves preferentially at the Y-Gly bond in the sequence -Pro-Y-Gly-Pro- where Y is most frequently a neutral amino acid. See the reaction below:

-P-Y-G-P- ---------> -P-Y-COO- + +NH3-G-P-

How does this enzyme contribute to the invasiveness of the bacterium in human tissues?

 

Why doesn’t the enzyme affect the bacteria itself?

 

 

 

2.  (15 points) Briefly describe all of the steps and reactions required for determining the sequence of a long peptide.

3.  (10 points) How does the Edman degradation method work for sequencing peptides. You don’t have to reproduce exact structures, just give the general idea of the reagents, conditions and what makes this process work.

4.  (5 points) The peptides, GAHKT and GVECT were put into the same well of a polyacrlyamide gel that had a pH gradient of 9-3 and thus the peptides were separated by isoelectric focusing. Draw a picture of the gel and label the bands for each peptide. (The peptides remain intact.)

5.  (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 for the carboxy terminus group. You know all of the other pKa values for the R groups.

GPREAF

6.  (5 points) Dr. Stone went to Detroit for graduate school, hence her basketball team was the Pistons. Please give the products for the following reactions:

 

PISTONSMAKETRYPLE--------Trypsin----------->

 

PISTONSMAKETRYPLE-------Pepsin-------------->

                                                                        

PISTONSMAKETRYPLE----------CNBr------------->

 

7.  (5 points) What would the elution order be for the following peptides at pH 7 on an anion exchange column. The N terminus amino group pKa is 8 and the C terminus carboxyl pKa is 3.

TIRAHPGAL

WELYIG

ATDNICLEF

 

8.  (10 points) Compare and contrast collagen and keratin. Fully describe the secondary structures of each. What are the quaternary structures of each? Fully describe how the structure is related to the function of each.