I understand that cysteine is ionizable but are the other amino acids also ionizable from the polar amino acids category? What is the exact formula for calculating pI for this group of aa's?
Isoelectric Point for Polar Amino acids
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This is my understanding, and anyone is free to correct me:
All amino acids are ionizable, due to the alpha amino group and the alpha carboxyl group. For those amino acids with side chains that are not electrically charged (which we can consider not ionizable), calculating the pI is as simple as averaging the pKa's of the alpha amino and carboxyl groups. Their pI's will be in the 5.5 neighborhood, as the pKa of the amino group is roughly 9 and the pKa of the carboxyl is roughly 2. Thus, (9+2)/2 = 5.5
The tricky part is when you calculate the pI of amino acids with electrically charged side chains. These will usually be given. For example, lysine's side chain pKa is around 10. So then we can think about the amino acid at different pH values. At a high pH, such as 10-11, we know that the alpha amino group and the side chain amino group will both be neutral while the alpha carboxyl is negative. The isoelectric point is where the molecule is neutral, so we need to find the point where the aminos each equal "half of a positive charge" to balance out the negative carboxyl. We can find this by averaging the pKas of the aminos: (9+10)/2 = 9.5. In actuality, the pI for lysine is listed as 9.74, but it's enough to get you into the ballpark.
As a further example, at a very low pH the alpha carboxyl and side chain carboxyl of glutamic acid will both be neutral while the alpha amino is positive. Thus we'll need to find the point where the carboxyls are both "half negative". The pKa of glutamic acid's side chain is around 4, so (4+2)/2 = 3. Glutamic acid's real pI is listed as 3.08.
Let me know if you have any other questions
All amino acids are ionizable, due to the alpha amino group and the alpha carboxyl group. For those amino acids with side chains that are not electrically charged (which we can consider not ionizable), calculating the pI is as simple as averaging the pKa's of the alpha amino and carboxyl groups. Their pI's will be in the 5.5 neighborhood, as the pKa of the amino group is roughly 9 and the pKa of the carboxyl is roughly 2. Thus, (9+2)/2 = 5.5
The tricky part is when you calculate the pI of amino acids with electrically charged side chains. These will usually be given. For example, lysine's side chain pKa is around 10. So then we can think about the amino acid at different pH values. At a high pH, such as 10-11, we know that the alpha amino group and the side chain amino group will both be neutral while the alpha carboxyl is negative. The isoelectric point is where the molecule is neutral, so we need to find the point where the aminos each equal "half of a positive charge" to balance out the negative carboxyl. We can find this by averaging the pKas of the aminos: (9+10)/2 = 9.5. In actuality, the pI for lysine is listed as 9.74, but it's enough to get you into the ballpark.
As a further example, at a very low pH the alpha carboxyl and side chain carboxyl of glutamic acid will both be neutral while the alpha amino is positive. Thus we'll need to find the point where the carboxyls are both "half negative". The pKa of glutamic acid's side chain is around 4, so (4+2)/2 = 3. Glutamic acid's real pI is listed as 3.08.
Let me know if you have any other questions
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Yes, this is a good answer! The easy way to think of this concept is, first, to figure out whether your AA is acidic, basic, or neutral (you should DEFINITELY have this memorized for the new MCAT). For neutral amino acids like glycine, average the two pKas. Acidic and basic amino acids, however, will have THREE pKas. For acidic AAs, like glutamic and aspartic acid, average the two LOWEST pKas (which correspond to the carboxy terminal and the side chain). For basic AAs, like lysine, average the two HIGHEST pKas (which correspond to the amino terminal and the side chain).
The most commonly made mistake by far happens when people average all three pKas for an acidic or basic AA. If you do this, you'll get an answer that is way too moderate. Like @hubristicphantasm said above, the actual pI of glutamic acid is a little bit greater than 3 - in other words, it's pretty low due to the acidity of the side chain. If you accidentally average all three pKas, you'll be able to spot your mistake because you'll start getting answers closer to 5 or 6 - which more closely resemble the pI of a neutral AA.
The most commonly made mistake by far happens when people average all three pKas for an acidic or basic AA. If you do this, you'll get an answer that is way too moderate. Like @hubristicphantasm said above, the actual pI of glutamic acid is a little bit greater than 3 - in other words, it's pretty low due to the acidity of the side chain. If you accidentally average all three pKas, you'll be able to spot your mistake because you'll start getting answers closer to 5 or 6 - which more closely resemble the pI of a neutral AA.
