MCDB 310 Lecture Notes - Lecture 3: Aromatic Amino Acids, Protein Purification, Deprotonation
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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?
Consider the peptide:
NH2-GAPAGPAGTGKTETTKDLAKSMALLCWFNCS-COOH
Table I. pK values of some amino acids
amino acid | pK of side chain or terminal group |
---|---|
Alanine (Ala or A) | uncharged |
Arginine (Arg or R) | 12.5 |
Asparagine (Asn or N) | uncharged |
Aspartic acid (Asp or D) | 3.9 |
Cysteine (Cys or C) | 8.3 |
Glutamic acid (Glu or E) | 4.3 |
Glycine (Gly or G) | uncharged |
Histidine (His or H) | 6.0 |
Leucine (Leu or L) | uncharged |
Lysine (Lys or K) | 10.8 |
Phenylalanine (Phe or F) | uncharged |
Serine (Ser or S) | uncharged |
Tryptophan (Trp or W) | uncharged |
Tyrosine (Tyr or Y) | 10.9 |
Valine (Val or V) | uncharged |
peptide N terminus | 7.8 |
peptide C terminus | 3.6 |
Using Table I above, determine the net charge of the peptide at pH9.
(the answer is not -1 or 1)