NS FL 2 B/B Q 46

Post Reply
Apudhota1
Posts: 2
Joined: Wed Jul 24, 2019 12:19 pm

NS FL 2 B/B Q 46

Post by Apudhota1 » Wed Jul 24, 2019 12:32 pm

I thought we only use side chains in pka calculations for basic or acidic AA, why are we using the pka of cysteine side chain in this calculation?

Picture attached in word doc
Attachments
NS FL2 BB Q46.docx
(125.7 KiB) Downloaded 24 times
NS_Tutor_Mathias
Posts: 282
Joined: Sat Mar 30, 2019 8:39 pm

Re: NS FL 2 B/B Q 46

Post by NS_Tutor_Mathias » Wed Jul 24, 2019 1:48 pm

Any sidechain with a measurable pKa should be taken into account. The reasoning is simple: If you can get a measurable pKa, that's because it does deprotonate under somewhat reasonable conditions, therefore it does have a significant effect on the pKa of the AA.

Remember, the numerical value of the pKa is equal to the pH at which 50% of the species would be protonated and 50% not. So a pKa around 8 for the side chain suggests that the sidechain can reasonably lose its proton, and do so well before the terminal amine does.

My somewhat foolproof way of approaching these kinds of things conceptually is to just start at pH 1 or 0, assign charge to the molecule and then find where the molecule transitions from a net charge of +1 to 0.

In this case:

Code: Select all

pH = 0 -> charge  = +1 (COOH = 0, S-H = 0, R-NH3+ = +1)
pH = 4 -> charge =   0 (COOH = -1, S-H = 0, R-NH3+ = +1)
So we know that our isoelectric point should be between those two - or more specifically, halfway between the first and second pKa. From there on it is just 1/2(pKa1+pKa2) = pI = 5.xx

There are actually no real exceptions to this. One thing to be slightly wary of is that the commonly given pKa of the sidechain of histidine is that of it's conjugate acid, but that's about it as far as major warnings or exceptions go.
Apudhota1
Posts: 2
Joined: Wed Jul 24, 2019 12:19 pm

Re: NS FL 2 B/B Q 46

Post by Apudhota1 » Wed Jul 24, 2019 2:16 pm

Sounds good I was just going off the assumption that only use pka of side chains of acidic and basic amino acids. Thanks for the explanation
NS_Tutor_Mathias
Posts: 282
Joined: Sat Mar 30, 2019 8:39 pm

Re: NS FL 2 B/B Q 46

Post by NS_Tutor_Mathias » Wed Jul 24, 2019 2:25 pm

Apudhota1 wrote:
Wed Jul 24, 2019 2:16 pm
Sounds good I was just going off the assumption that only use pka of side chains of acidic and basic amino acids. Thanks for the explanation
Technically you are doing the same thing for the pI of glycine too. It's just that the proton that is it's entire R-group will have a pKa between 15-50. Since we go from +1 to 0 already just by deprotonating the carboxy terminus, the pI of glycine is found by 1/2(pKa1+pka2) - and that pKa, despite existing, would never be relevant.

To put it in an intuitive way: If something has a pKa way out of range, we just don't talk about it, because it will always, always be protonated under any conditions we care about (ph 0-15-ish).

On a side note, I do want to encourage you to work out the pKa of histidine by hand real quick :)
Post Reply