Chemistry 40: Elementary Biochemistry

General Instructions

1. This is a group activity. 
2. Answer the problems shown below use the previously given pKa table as reference.
3. Submit your answers in pdf/jpg formats only following the naming, Chem40_PS2_<Section>_<Group No.>
4. Only one submission per group is needed. 

Problems

1. The pKa of an acid is partly dependent on the environment of the acid. What will be the effect of the following environmental changes on the ability of the glutamate side chain to donate a proton?

1.1. a basic amino acid is brought into close proximity to glutamic side chain

1.2 asN or glN is brought into close proximity

1.3 the glutamic side chain is shifted from the outside of the protein to a nonpolar site inside the protein molecule

1.4. protein denaturation

2. For the following pentapeptides:

A.  Ser-Glu-Gly-His-Ala      B.  Gly-His-Ala-Glu-Ser

2.1. Compute their isoelectric pH (pI)

2.2. Do these peptides with same composition have different net charges at pH 7.0? 

2.3. Indicate their charges at pH 7.0

2.4. Would you expect the titration curves of the two peptides to differ? Why or why not?

3. A pentapeptide  was found to increase the rate of hydrolysis of fats in the adipose tissues to provide fatty acids as sources of energy.  The amino acid sequence  of this peptide was determined to be:  ALA-ARG-LYS-MET-SER

Hydrolysis of the three variants of the peptide, and analysis of their amino acid composition revealed the following changes:

                     Variants                  Amino Acid Replacement

                    Peptide 1                 Arg was replaced by Leu

                    Peptide 2                 Ala was replaced by Tyr

                    Peptide 3                 Arg was replaced by Glu

What will be the positions of these variant peptides compared with the normal peptide in an electrophoretic run at pH 7.0?

4. What is the basis for the separation of proteins by the following techniques?

4.1.  gel-filtration chromatography

4.2.  affinity chromatography

4.3.  ion-exchange chromatography

4.4.  reverse phase HPLC

5. A mixture containing aspartic, lysine, serine and tyrosine was subjected to gel electrophoresis at pH 7.0. Indicate the position of each amino acid in the gel.

6. A mixture contains lysine, leucine, and glutamic acid. These three amino acids were separated by  ion-exchange chromatography, using a cation-exchange resin at pH 3.5, and eluting  buffer at the same pH.

6.1. What is the order of elution of the three amino acids?

6.2. Will any other treatment be needed to elute one of these amino acids from the column?

Use the pKa table found here.