A cysteine found in the interior of a protein can act as a base in a chemical reaction. Since the pH for living organisms is held constant near 7.3, what would have to happen to the pKa of the side chain (as a result of microenvironmental effects) to optimize cysteineâs ability to act as a base. Explain your answer.
A cysteine found in the interior of a protein can act as a base in a chemical reaction. Since the pH for living organisms is held constant near 7.3, what would have to happen to the pKa of the side chain (as a result of microenvironmental effects) to optimize cysteineâs ability to act as a base. Explain your answer.
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| Amino Acid | M.W. g/mol | pKa for side chain |
| Alanine | 89.1 | |
| Arginine | 174.2 | 12.48 |
| Asparagine | 132.1 | |
| Aspartate | 133.1 | 3.90 |
| Cysteine | 121.1 | 8.37 |
| Glycine | 75.0 | |
| Glutamate | 147.1 | 4.07 |
| Glutamine | 146.1 | |
| Histidine | 155.1 | 6.04 |
| Isoleucine | 131.2 | |
| Leucine | 131.2 | |
| Lysine | 146.2 | 10.54 |
| Methionine | 149.2 | |
| Proline | 115.1 | |
| Phenylalanine | 165.2 | |
| Serine | 105.1 | |
| Threonine | 119.1 | |
| Tryptophan | 204.2 | |
| Tyrosine | 181.2 | 10.46 |
| Valine | 117.1 |
Take a look at your pKa table for the amino acids. It turns out that when these side chains are in a protein, they can have very different pKa values. Explain the following observations:
a. In the enzyme medium chain acyl-CoA dehydrogenase (b-oxidation of fatty acids), E376 has a measured pKa ~ 8.0. It is found in a very hydrophobic environment. What could account for it elevated pKa?
b. For the enzyme aconitase (Krebbâs Cycle), a catalytic serine is known to have a pKa ~ 8. What kind of factors could account for this decrease in pKa?
