Question

How do I calculate pI of an amino acid that contains a side chain with a charge? I have tried finding it online but I just get more confused.

Answer 1

for example, in histidine. Pka COOH: 1.80, Pka NH3: 9.33, pKa side chain: 6.04

Answer 2

well, there are tables online that contain the pI of all amino acids usually found in natural or artificial proteins. I expect that's not the answer you're looking for. :-)

the isoelectric point of a protein is calculated as the mean value of the pI of all amino acids. and the pI of one amino acid is the pH value where the amino acid has no charge.

take glutamate, for example. you have three possible groups that count into the pI: the two backbone ends (NH3+ and COO-), as well as the side chain end (COO-). the pKa values are: (N = 9,67; C = 2,19; R = 4,25)

now, you just take the two pKa values that are the strongest into account. this is due to the fact that the pKa of the amino terminus doesn't contribute to the oerall charge all that much: at pH values below 9, the amino group is always w/o charge. now, you calculate the mean value.

pI = (2,19 + 4,25) / 2 = 3,22

ta daa =)

questions?

Answer 3

for basic amino acids, you take the two highest pKa values. for acidic amino acids, you take the two lowest values into account.

Answer 4

is glutamate glutamic acid?

Answer 5

yes

Answer 6

But, aren't all amino groups positively charged at pH 9 or lower?

Answer 7

you are right, I explained that one wrong. the amino group will be positively charged (+1)

at pH 3.22, one of the acid groups will also be negatively charged (-1), so the net load is 0.

Answer 8

do you have additional questions?

Answer 9

I still don't understand how to determine the important ones that are taken into account.

Answer 10

well, you usually have two pKa values on one side of 7, and one on the other side. you take the group of two. :-)

example:

6.5 - 9.8 - 2.3

you take 6.5 and 2.3

10.5 - 9.8 - 2.3

you take 10.5 and 9.8

Answer 11

wait! I got it! thaaannkksss!! :) you take the pKa that changes from a neutral molecule to a negative one or to a positive one.

Answer 12

well, it's not QUITE that simple, but you are basically on the right path.

you take the mean value of the two that are close together, because that's how you ensure that one is chared and the other is not. the third one (Nh3+ or COO-) is always charged, so you get a net charge of 0.

only exception to the rule is histidine, because of the indole pKa of 6. here, you take 6 and 9 (NH3+) for pI calculation.