pH's and pKa's question

[bondgirl]

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guys,
trying to make sense of ph's and pKa's:

I'm trying to figure out what ionic species predominates at pH of 4, 8, and 11 of the following amino acids:

alanine: I found the pKa number to be 2.35. Does this mean that Alanine has the same structure and charges throughout 4,8,11 pH's as it does at neutral ph?

lysine: at pH 4, does lysine have a COO- instead of a COOH?

Aspartate: is the side group COOH protonated at ph 4? And at pH 11, is the NH3 still NH3?


Then there are buffer isues:
at pH 5, is phosphoric acid a better bufer or succinic acid.
Succinic acid has pKa's of 4.21 and 5.64. I think this woudl be better than phosphoric acid- am I right? and how do I think of it instead of just being intuitive?

Also - is HEPES or Tris a better buffer at pH 7.5?

 

[heifetz]

Well the first part of your question deals with the isolelectric point. If you consider the amino acids (AA) isoelectric point this is the pH where if you raise or lower the pH from this set value the AA will overall become + or - charged. General rule:
if you add base AA --> (-)
if you add acid AA --> (+)

Normally the AA is neutral with a positive charge on the nitrogen and a negative charge on the singly bonded oxygen. So if you add H+ or acid it attaches to the negatively charged oxygen and overall the AA is positive. Add OH- or base and it attacks one of the hydrogens bonded to the nitrogen giving a water molecule and changing the nitrogen from + to neutral because it went from 4 bonds to 3 bonds giving the AA a negative overall charge.

With buffers i'm not sure but i do know that buffers work best when made with weak acid and its conjugate base. To make a buffered soln you would pick the acid whose pKa is closest to the pH at which you want to buffer the soln. well hope this helps 😉

 

[ashkan33]

i'm not 100% sure, but what pka is implying is that if the pH was above the pka, then that species would exist predominantly in its base form(not completely tho). if the pka=pH, the [HA]=[A-]. does this help???

 

[Aptamer]

Ideally, at 25 C and 0.1M, both HEPES and Tris are ideal buffers for a pH of 7.5. Tris has an ideal buffer range of 7.2-7.8, and HEPES has a range of 6.8-8.0. So...which one should you use??? Depends on what you want to suspend...for DNA...I use Tris-HCl pH=8, and for enzymes, I use HEPES. What's the difference??? Not much...HEPES is ideal for freezing of enzymes because it resists temperature induced changes in Kd better than Tris. You can use either unless you have a compelling reason to use one over the other. Any other opinions from lab rats?

 

[cafe ahnan]

Hi bondgirl:

this is how i learned it.
at pH < pKa, you are adding more acid [H+] and therefore the species will be protonated.
at pH > pKa, you are adding more base [OH-] and therefore species will be deprotonated.
for the nonpolar AA's (GAVLIMPFW), you don't need to worry about the sidechains, just the N- & C- termini.

For the amino acids, remember that the NH3+ has a pKa~9.5 and the COO- has a pKa~2.

Alanine has a nonpolar sidechain -CH3, therfore it has the same structure across the pH ranges (but if it has free N- or C- termini, you will have to account for those).

Lysine is basic w/ sidechain pKa=10.5, therefore at physiological pH, it carries a positive charge. at pH4 > pKa~2 of carboxyl end ==> COO- instead of COOH; pH4 < pKa~9.5 of amino end so it will be protonated; similarly, at pH4 < pKa=10.5 of sidechain, the sidechain will remain protnated.

Aspartate has an acidic sidechain w/ sidechain pKa of 3.9, therefore at phys pH, it carries a negative charge. At pH4, both the sidechain beta-carboxyl and the alpha carboxyl will be COO-, the amino will be protonated NH3+. At pH11, both carboxyls will still be COO-, but the amino will be NH2 (neutral).

Hope this helps.