Isoelectric point: part deux

[SaintJude]

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What is the isoelectric point of aspartic acid?

The values explained.

1st column : name
2nd column: pKA of COOH group
3rd column: pKa of NH3+ group
4th column: pKa of R group
5th column: molecular weight
6th column: description of R group


Good question from Kaplan. Don't completely understand it yet.

 

[MedPR]

~2.

Edit: oops, a little less than 3. Good thing I can do math! It's just (pka1+pka2)/2

 

[SaintJude]

Right, so that's wrong. Got it wrong too.

It's actually exactly 3. B/c it is the average of the pKas of the COOH and Rgroup. To be honest, I'm still musing over the answer so can't entirely explain it...Anyone understand why?

 

[MedPR]

Right, so that's wrong. Got it wrong too.

It's actually exactly 3. B/c it is the average of the pKas of the COOH and Rgroup. To be honest, I'm still musing over the answer so can't entirely explain it...Anyone understand why?

Yea it's exactly 3. I was using the values I have in my head, not the values in your table.

2.1+3.9=6

6/2 = exactly 3.

Isoelectric point is the average of the pKa values that take the amino acid from +1 to neutral and from neutral to -1.

If the C-terminal is 2.1, the sidechain is 3.9, and the N-terminal is 9.8, the first proton to be lost is the C-terminal (pKa=2.1) which takes aspartic acid from +1 to neutral. Then the next proton to be lost is from the sidechain (pKa=3.9), which takes the neutral aspartic acid to -1. So you average 2.1 and 3.9 and get 3.

 

[SaintJude]

the first proton to be lost is the C-terminal (pKa=2.1) which takes aspartic acid from +1 to neutral. Then the next proton to be lost is from the sidechain (pKa=3.9), which takes the neutral aspartic acid to -1. So you average 2.1 and 3.9 and get 3.

Values in your head??? 😱 Anyway, whatever works for you.


How do you know that the aspartic acid starts with a positive charge?

 

[MedPR]

Values in your head??? 😱 Anyway, whatever works for you.


How do you know that the aspartic acid starts with a positive charge?

It's just the method TBR teaches.

Assume a low pH so everything is protonated. Then figure out which pKa's correspond to the zwitterion.

 

[SaintJude]

Ok, cool-I'm too close to test date to question this further lol. Makes sense.

 

[MedPR]

Ok, cool-I'm too close to test date to question this further lol. Makes sense.

April 5?

 

[SaintJude]

No, but I have one more questions

This is lysine at ph 7. How do you know which amino group will be deprotonated first? The one with lower pKa?

 

[oxytiger]

Asp, as the name suggests, is acidic....so you just take the sum of the 2 lowest pKa's and average them.

the explanation above is good too.

for basic amino acids, you take the two highest pkas...and for neutral you take the lowest and highest pkas.

 

[oxytiger]

No, but I have one more questions

This is lysine at ph 7. How do you know which amino group will be deprotonated first? The one with lower pKa?

yes the lowest pKa is always deprotonated first and its always at the COOH group in the mcat....someone correct me if im wrong

 

[SaintJude]

what would you say the pI for lysine is?

And so the COOH gets deprotonated and then the NH3? the top or the bottom NH3?

 

[oxytiger]

pI of lysine would be around 10.

well i was wrong....its the carboxillic group first and then the R group...which is the top NH3. r group = (CH2)4 -NH3


so the shortcut is this....

neutral: pka(NH3)+pka(COOH)

acidic: pka(COOH) +pka(R)

basic: pka(NH3)+ pka(R)

and average those numbers

 

[SaintJude]

You are confusing me. Can you explain how you find the pI and the rationale behind it? (And please not just a general rule...)

 

[oxytiger]

You are confusing me. Can you explain how you find the pI and the rationale behind it? (And please not just a general rule...)

well depending on the amino acid' you want to find the pKa's that match with the neutral,basic, or acidic coditions.

so basically if you want to find the pI of an acidic aa, you have to take the pKa's of hydrogens that get depronated first. so its first at the COOH group, and then the R group's H's.

if you want to get a basic amino acid's pKa...you have to get the NH3 (non R group) and the R group's pKas...and both of their pKas are usually really high, thus making the pI higher than that of the acidic and neutral forms.

 

[SaintJude]

Why would the two NH3 get deprotonated first?

if you want to get a basic amino acid's pKa...you have to get the NH3 (non R group) and the R group's pKas

I see your "shortcut" but I'm asking 'why'?

 

[oxytiger]

Why would the two NH3 get deprotonated first?

there are two different NH3 groups. One that's part of the R group and one that defines an amino acid. the amino acid has this config NH3-CRH-COOH

 

[MedPR]

No, but I have one more questions

This is lysine at ph 7. How do you know which amino group will be deprotonated first? The one with lower pKa?

lower pKa = more acidic = donates its proton more readily = first to get deprotonated.

Since the other guy is confusing you, I'll offer my explanation.

At pH = 1, lysine is protonated in three places; the side chain, n-terminal, and c-terminal.

This means it has a +2 charge (the c-terminal is neutral when it is protonated).

When it loses its first proton (pKa1) it drops to +1 overall charge. Next proton (pKa2) drops it to a neutral charge. Next proton (pKa3) drops it to a -1 charge. Remember how the pI is just the pH where the zwitterion is predominant? And remember how the zwitterion is when the amino acid has a neutral (0) charge? The pI is just the average of the two pKa values that directly create the zwitterion. So for lysine it is (pKa2+pKa3)/2. So the pI of lysine is (9.18+10.79)/2

So for lysine:

pKa1 is the c-terminal
pKa2 is the n-terminal
pKa3 is the side chain

The shortcut is that for the basic amino acids (histidine, arginine, lysine) the pI is (pKa2+pKa3)/2. And for all other amino acids it is (pKa1+pKa2)/2

 

[MedPR]

In case you're wondering, the technique outlined above works for finding the pI of a protein as well, provided you know the pKa's all the amino acids in the primary structure of that protein.

Set pH = 1, count how many charges you have (don't forget about the n-terminus being +1), then sequentially deprotonate it until you get to the zwitterion. Then average the pKa values the zwitterion is sandwiched between and that is the pI if your protein.

 

[SaintJude]

yeah, i get it now. I think it's a very good strategy to start by assuming a low pH and that all groups are fully protonated.

Edit: With that assumption in mind, I also get now why basic amino acids have a net positive charge at physiological pH of 7.4. Thanks!

 

[MedPR]

yeah, i get it now. I think it's a very good strategy to start by assuming a low pH and that all groups are fully protonated.

Yea, it's such a good and simple (and seemingly exceptionless) strategy that I don't even care to think about why it works.