Determine PI of an aa?

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I was taking a TPR the other day and I came across this question:

Lysine is an amino acid with a basic side chain. Its isoelectric point would be closest?
a) 6
b) 7
c) 8
d) 12

Answer: [Highlight below]
C - Having a basic side chain increases an aa's PI value.

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Can someone please explain to me how they determined this? I know that PI = average of the pKa. Am I supposed to memorize the pka of the separate side chains of all the aa? or what..

Thanks!

The question states that the amino acid's side chain is basic, meaning the isoelectric point has to be >7, eliminating 2 answers. 12 would be a VERY high pH for an amino acid with just 1 basic side chain, and would be even higher just for that side chain's isoelectric point. The only feasible answer here is C.

Off the top of my head, I probably would have chosen D because to me a pI of 8 is too close to neutral :P

However, for the amino acids, I would just know that

"His Lies Arg Basic" Histidine, Lysine, Arginine
Asparatic Acid and Glutamic Acid are the only acids
VIP MALT Ph Glycine are nonpolar amino acids
The rest are polar

Basic amino acids should have a PI greater than 7, acidic ones less than 7, the rest around 7. Also, for your averaging comment, remember that you take the avg of pka1 and pka2 for most of the amino acids. HOWEVER for BASIC amino acids, its the average of pka2 and pka 3

Originally Posted by PanRoasted

The question states that the amino acid's side chain is basic, meaning the isoelectric point has to be >7, eliminating 2 answers. 12 would be a VERY high pH for an amino acid with just 1 basic side chain, and would be even higher just for that side chain's isoelectric point. The only feasible answer here is C.

Thank you PanRoasted, that was very clear!

Originally Posted by member232

Off the top of my head, I probably would have chosen D because to me a pI of 8 is too close to neutral :P

However, for the amino acids, I would just know that

"His Lies Arg Basic" Histidine, Lysine, Arginine
Asparatic Acid and Glutamic Acid are the only acids
VIP MALT Ph Glycine are nonpolar amino acids
The rest are polar

Basic amino acids should have a PI greater than 7, acidic ones less than 7, the rest around 7. Also, for your averaging comment, remember that you take the avg of pka1 and pka2 for most of the amino acids. HOWEVER for BASIC amino acids, its the average of pka2 and pka 3

Thanks! Your answer was very clear as well. I loved the pneumonics, I think I'm going to remember it that way.

Regarding your acknowledgement of my pKa averaging: could you elaborate on that a bit more please? I may have missed it but what do you mean its the average of pka2 and pka3? what's the difference between pka1 and pka2?

Gracias and merry christmas

Examples:

Glutamic Acid: this is going to have the carboxylic acid group (pka1), the acidic side group (pka2), and the amine group (pka3)

**the pka's are numbered in increasing order of magnitude so pka1 is the going to be the most acidic

Because the PI is the point where the AA exists as a zwitterion, you need to look at the two pka values that will make the AA neutral. If the pH is greater than pka1 but less than pka2, then you will have a -1 charge for the pka1 group, 0 charge for pka2, and +1 charge for amine group -- that will give you a netural amino acid (therefore you take the avg of pka1 and pka2)

NOW for a basic one.... take lysine
pka1= carboxylic acid, pka2 = basic side chain, pka3 = amine group

same thing applies here.... if the pH is greater than pka2 but less than pka3, you will have a - charge for pka1, 0 for pka2, and +1 for pka3.... a total 0 charge on teh molecule, ensuring a zwitterion, and thus allowing the average of pka2 and pka3.

*** disclaimer- the side group may be more acidic/basic than the carboxylic acid and amine group respectively, i was just trying to simplify it

Holy poop. They did NOT teach us that at TPR, nor did it in the accompanied book (to that extent). Thanks a ton!

For hydrophobic side chains, I always learned FAMILY VW: Phe, Ala, Met, Ile, Leu, Tyr, Val, Try
(actually, my mom and I came up with that when she took the Biochem GREs and I was in elementary school!)
Glycine and proline were special cases
LOVE His Lies Arg Basic!

the isoelectric point is the average of the two pKas from the amino acid.

I think member232's explanation is helpful in seeing the trends. Once you understand it, you just kind of know "oh, acidic AAs have pI < 7 and basic AAs have PI > 7" (TPR taught me to memorize those value, btw) and have fast answers to the further questions.

Thanks all!