Calcualting Net charge of amino acid

[globy123]

How do you calculate the net charge on the amino acid alanine at pH of 8 if the following pK values are given:

alpha-amino group: 9
alpha-carboxyl group: 2

side chains with pK:

lysine 10
arginine 13
histidine 6
aspartate 3.8
glutamate 4

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[neutropos]

I think this is how you do it:

When the pH is above the pKa, that side chain or end group will be deprotonated, while it will be protonated if the pH is below the pKa.

So, the amino group will be protonated, with a +1 charge, and the carboxyl group will be deprotonated, with a -1 charge.

Doing the same for the side chains:

Lysine: +1
Arginine: +1
Histidine: 0
Aspartate: -1
Glutamate: -1

So, this protein should have a net charge of zero, as all the positive and negative charges cancel out.

I believe there is another way to do it, but I do not remember.

 

[globy123]

I think this is how you do it:

When the pH is above the pKa, that side chain or end group will be deprotonated, while it will be protonated if the pH is below the pKa.

So, the amino group will be protonated, with a +1 charge, and the carboxyl group will be deprotonated, with a -1 charge.

Doing the same for the side chains:

Lysine: +1
Arginine: +1
Histidine: 0
Aspartate: -1
Glutamate: -1

So, this protein should have a net charge of zero, as all the positive and negative charges cancel out.

I believe there is another way to do it, but I do not remember.

But the question is asking what is the charge of amino acid alanine and not what is the charge of the protein. Based on the information I gave you how would you calculate the net charge of alanine?

 

[BerkReviewTeach]

But the question is asking what is the charge of amino acid alanine and not what is the charge of the protein. Based on the information I gave you how would you calculate the net charge of alanine?

You'd start by drawing the structure onto a piece of paper. You might even add the pKa values next to the pertinent groups. You would then go to your TA for the class, and ask "how to you get the total charge on this molecule at a given pH?"

That's a really good way to deal with homework questions, because as you probably know from the user agreement you accepted to register here, you cannot ask homework questions.