ph and pI concept

[dudewheresmymd]

Can someone explain the comparison of ph and pI? In biochem, we learned if ph>pkA bases are neutral and acids are (-) and if ph < pkA acids are neutral and bases are (+) but how does one compare ph and pI and calculate pI? I know it's the average of pka1+pka2, but what if the MCAT asks us histidine or lysine or aspartic acid etc.?

Thanks!

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[TheJourney]

As far as calculating the pI for a basic or acidic amino acid you would average the highest or lowest pKa values, respectively.
For example, for Lysine you would do (9 + 11)/2. <-- The two highest pkA values.
For Aspartic acid you would do (3+ 4)/2. <-- The two lowest pKA values.
I assumed the R group pkA for Lysine to be 11 and the R group pkA for Aspartic acid to be 4 in these calculations.

 

[tdod]

The pI is just the pH at which the net charge of the amino acid is zero.

 

[dudewheresmymd]

As far as calculating the pI for a basic or acidic amino acid you would average the highest or lowest pKa values, respectively.
For example, for Lysine you would do (9 + 11)/2. <-- The two highest pkA values.
For Aspartic acid you would do (3+ 4)/2. <-- The two lowest pKA values.
I assumed the R group pkA for Lysine to be 11 and the R group pkA for Aspartic acid to be 4 in these calculations.

The pI is just the pH at which the net charge of the amino acid is zero. Usually, the pI is just the average pH of the acidic/basic side chains.

if ph>pI does that mean the amino acid (regardless of hydrophilic/hydrophobic/acidic/basicc nature) will always be (-) charged and move to the (+) charged anode?

 

[tdod]

nvm

 

[tdod]

if ph>pI does that mean the amino acid (regardless of hydrophilic/hydrophobic/acidic/basicc nature) will always be (-) charged and move to the (+) charged anode?

i described it incorrect. its the average of the side chain and the similar terminal group. the basic idea is the same though, the pI is just the pH at which there is no net charge.

 

[dudewheresmymd]

As far as calculating the pI for a basic or acidic amino acid you would average the highest or lowest pKa values, respectively.
For example, for Lysine you would do (9 + 11)/2. <-- The two highest pkA values.
For Aspartic acid you would do (3+ 4)/2. <-- The two lowest pKA values.
I assumed the R group pkA for Lysine to be 11 and the R group pkA for Aspartic acid to be 4 in these calculations.

so for aspartic acid and glutamic acid pi = pka1+pka2/2, pi < 7

and for histidine, arginine, lysine pi = pka2+pka3/2, and pi > 7?

 

[TheJourney]

so for aspartic acid and glutamic acid pi = pka1+pka2/2, pi < 7

and for histidine, arginine, lysine pi = pka2+pka3/2, and pi > 7?

Hey, sorry man hadn't been on for a while since I took "the beast."
But, yes you are right the pI should be (will be) below 7 for acids and more than 7 for bases.
Also noteworthy, for the bases you listed lysine and arginine will probably be around 10/11, but histidine's pI will be more around 8 if I remember correctly. Although, still more than 7 it's somewhat significantly lower than arginine and lysine's.

 

[dudewheresmymd]

Hey, sorry man hadn't been on for a while since I took "the beast."
But, yes you are right the pI should be (will be) below 7 for acids and more than 7 for bases.
Also noteworthy, for the bases you listed lysine and arginine will probably be around 10/11, but histidine's pI will be more around 8 if I remember correctly. Although, still more than 7 it's somewhat significantly lower than arginine and lysine's.

thanks man. and for acidic amino acids, at ph> pi the charge would be -2 and for basic amino acids if ph > pi, the charge would be -1 right?

 

[TheJourney]

thanks man. and for acidic amino acids, at ph> pi the charge would be -2 and for basic amino acids if ph > pi, the charge would be -1 right?

Umm, no not necessarily. When generalizing we can say that that's true for basic amino acids, but I can also think of cases when pH > pI and the charge is 0. And I would not even make that generalization for acidic amino acids.
Here are tow examples:

Lysine is a basic amino acid, the R group has a pKa of 10.5, by using the pI formula I calculate its pI to be 9.8.
If the pH > than pI, let's say 11, then yes the charge is -1.
If the pH > than pI, let's say 10, the charge is 0 this time. <--- Try to understand why this case applies for any number between 9.8 - 10.5 and hence why this would probably be less frequently observed.

Aspartic acid has an R group with pKA 3.90 and I calculate its pI to be 2.95.
If the pH > than pI, let's say 11, then yes the charge is -2.
If the pH > than pI, let's say 8, the charge is -1. <-- This applies for any pH between 2.95 - 9.90.

Numbers taken from: http://academics.keene.edu/rblatchly/Chem220/hand/npaa/aawpka.htm

Edit: This can be a tricky concept, I don't think the MCAT requires anything more than a basic understanding of it. What helped me a lot, especially for titration curves, is knowing that basic amino acids will always start at +2 and acidic ones will start at +1, which you seem to already know based on your question. After knowing that for many questions testing this topic my thought process would be, ok Lysine is basic so it's +2 originally and they're asking for charge at pH 10, at pH 4 the carboxyl group will be deprotonated so the charge is now +1, then at pH 10 the amino group will be deprotonated so the charge is now 0, the R group probably won't be fully deprotonated until like pH 11 in which case the charge would be -1. Therefore pH 10 = charge of 0.

I really hope I didn't make a mistake and screw you up more lol. Good luck!

 

[Czarcasm]

thanks man. and for acidic amino acids, at ph> pi the charge would be -2 and for basic amino acids if ph > pi, the charge would be -1 right?

1. Acid amino acids have 2 acidic groups (R group, C-terminus) and 1 basic group (N-terminus).
Neutral amino acids have 1 acidic group (C-terminus) and 1 basic group (N-terminus).
Basic amino acids have 1 acidic group (C-terminus) and 2 basic groups (R group, NH3).

2. COOH (Protonated form) vs. COO- (Unprotonated form) 0 to -1
NH4+ (Protonated form) vs. NH3 (Unprotonated form); +1 to 0

3. Isoelectric point is the point at which the aa exists as a zwitterion (neutral overall charge).

4. If you recall from HH equation, when the pH is above pKa, the acid exists in its conjugate base form.

These 4 pieces of information will help you answer any question asked about pI and pH. Rather than memorizing random scenarios, I recall these facts above and manipulate what would happen in a given scenario. The best way to approach these types of problems is to find the pH, and then look at all the pKa's below it (all will be deprotonated), while those with pKa's above pH will be in protonated form. Consider what deprotonated/protonated tells you (ie. charge), and from there, calculate the overall charge.

If instead, you're only told the pH is above or below pI, well then consider which amino acid you're looking at. If it's a basic amino acid, assuming we're well above both pKa's (for the basic groups), then both would be neutral and the charge would be -1. You'd apply the same understanding to acidic or neutral aa. They could really get tricky with it and really test your understanding, but because this is more on the biochem side (more advanced), I can only see them asking very general questions to test your basic understanding. TBR will mislead you to think otherwise though. A more likely scenario is the charge of a neutral amino acid when pH is above pI, since you don't have two worry about two close pKa values.

It sounds more complicated than it is, but it's fairly straightforward.