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?
| 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?
