PROTEIN STRUCTURE/CHARACTERIZATION

1. To bind the iron atom to the protein. The porphyrin ring provides four of the coordination sites for the iron atom.

2. trp is a much bulkier and hydrophobic amino acid. Thus, trp may interrupt a regular repeating pattern that includes gly. trp may also disrupt the protein structure if the gly were a key residue in the center of the protein.

3. asp. asp has a pKa value for its side chain very close to 4.5. Thus, when using the H-H equation from week 1, the change in pH for a solution of asp ,as more acid or base is added, is very small (that is the definition of a good buffer.).

4. If Hb binds the oxygen more tightly, then the level of saturation would always be higher. The saturation curve would move up and left (as in the myoglobin graph).

5. The study of many proteins has shown that the percent of hydrophobic residues in any given protein does not change very much. Thus, when a protein is mixed with SDS, a similar number of SDS molecules/molecular weight of protein bind. The amount of SDS binding is constant--nearly all proteins become surrounded by a shell of SDS molecules. Note: There are exceptions to everything in biological systems, but this behavior is very common.

6. No, gel filtration chromatography is NOT an exact technique. In fact, since the column particles vary somewhat, even the separation of two proteins of MW 30,000 and 33,000 would be difficult. In practice, the elution from a gel filtration column extends over many ml of solution. If two proteins are similar in MW, then most of the elution will contain a mixture of the two proteins as they are both eluting over several ml.

7. Without an electric field, the proteins do not move through the gel. The polyacrylamide impedes movement and the proteins are stuck at the top.

8. The lack of vitamin C causes a reduced number of hydroxy-proline residues in the protein collagen. Without the hydroxy groups, fewer H-bonds form and the protein is weaker (lacking some weak interactions that hold it together).