another question in TBR biology - pI

[batista_123]

this is on page 329, #2. in case we have differetneditions, its asking which one has a higher pI, valine or Glutamate. I just dont understand the explanation.
this is what i did:
for valine, at pH 0, everything is protonated, so it has a net charge of +1.
at pH 3, the COOH has been completely deprotonated, the total charge is 0.
so the pI for valine must be 3.

for gluatamate, at pH 0, everything is protonated, so net charge is +1.
at pH 3, the COOH has been deprotonated, but the side chain is still protonated, so the net charge is 0. so its pI must also be 3.

any ideas? any help?

---

Members don't see this ad.

 

[Will Hunting]

this is on page 329, #2. in case we have differetneditions, its asking which one has a higher pI, valine or Glutamate. I just dont understand the explanation.
this is what i did:
for valine, at pH 0, everything is protonated, so it has a net charge of +1.
at pH 3, the COOH has been completely deprotonated, the total charge is 0.
so the pI for valine must be 3.

for gluatamate, at pH 0, everything is protonated, so net charge is +1.
at pH 3, the COOH has been deprotonated, but the side chain is still protonated, so the net charge is 0. so its pI must also be 3.

any ideas? any help?

Glutamate has a lower pI. Why? Valine is neutral. Glutamate has a polar group a carboxyl. So, this means that it will have a negative charge. So, treat it like an acid versus a neutral amino acid. Acidic amino acids have lower pIs. You HAVE to account for the negative on the OH of the carboxyl which isn't present on the valine.

Your logic was only partially correct. You must remember to think of the WHOLE protein. You forgot that the first hydroxyl lost is the carboxyl terminus H. The second is the glutamate in this case. so the pka 1 and 2 are carboxyl. In Hbs, the first is the carboxyl and the next is the amino. In reality it isn't the case but since they're the same every where else you can simplify it to this.

So, then the hbs must have a higher pI.

 

[batista_123]

Glutamate has a lower pI. Why? Valine is neutral. Glutamate has a polar group a carboxyl. So, this means that it will have a negative charge. So, treat it like an acid versus a neutral amino acid. Acidic amino acids have lower pIs. You HAVE to account for the negative on the OH of the carboxyl which isn't present on the valine.

Your logic was only partially correct. You must remember to think of the WHOLE protein. You forgot that the first hydroxyl lost is the carboxyl terminus H. The second is the glutamate in this case. so the pka 1 and 2 are carboxyl. In Hbs, the first is the carboxyl and the next is the amino. In reality it isn't the case but since they're the same every where else you can simplify it to this.

So, then the hbs must have a higher pI.

hey will hunting,
i dont understand what you mean when you say "You HAVE to account for the negative on the OH of the carboxyl which isn't present on the valine. "

what negative charge? the COOH side chain pka is 4.4, so at pH=3, it is protonated and therefore neutral.

 

[Will Hunting]

hey will hunting,
i dont understand what you mean when you say "You HAVE to account for the negative on the OH of the carboxyl which isn't present on the valine. "

what negative charge? the COOH side chain pka is 4.4, so at pH=3, it is protonated and therefore neutral.

Listen, you have an extra hydrogen to account for in Hbs that you don't have in Hba. They can't have the same pI. At a pH of three three they are both neutral. However, what is the question asking? It's asking what is the pI. The pI is when the the charge is 0. Think about batista. If you had a valine amino acid, what would it's pI be? it would the the pka of the carboxyl terminal and the pka of the amino terminyl. Here you use pka 1 and pka 2 of 2 and 9 for an average of 5.5.

Now, what about the pka of glutamate? You use pka 1 and pka 2 as well. However, you're going to use the carboxyl terminal OH pka of 2 and the side chain pka of 4.4. Do you see, so your pI will be average of 2 and 4.4 which is 3.3. You need to realize that the first one lost is the carboxyl terminal and then the amino in neutral compounds. In acidic compounds the second one lost is another O-H group thus lowering the pI. pH of 3 is irrelevant. At that pH they have the same charge. However, many amino acids have the same charge at a certain pH. It doesn't mean that they have the same pI.

HTH

 

[Will Hunting]

this is on page 329, #2. in case we have differetneditions, its asking which one has a higher pI, valine or Glutamate. I just dont understand the explanation.
this is what i did:
for valine, at pH 0, everything is protonated, so it has a net charge of +1.
at pH 3, the COOH has been completely deprotonated, the total charge is 0.
so the pI for valine must be 3.

for gluatamate, at pH 0, everything is protonated, so net charge is +1.
at pH 3, the COOH has been deprotonated, but the side chain is still protonated, so the net charge is 0. so its pI must also be 3.

any ideas? any help?

I see why you're confused. Look, the pI for Valine is not 3. You made a huge gaffe. The pI for acidic compounds is generally less than 5.5. The Pi from neutral compounds is 5.5-6.5. The pI for bases is generally greater than 7.5. The pI for valine is about (2+9)/2= 5.5. The pI is the range from which it goes to 0. pI is the average from where the charge goes from +1 to 0 to -1. You only did from 1 to 0.

At pH 0 everything is protonated. So, we have a +1 charge.
at pH2. The carboxyl terminal O-H is 50% deprotonated. So, it has a -.5 charge. The amino terminal has a +1 charge. The overall charge is +.5. At ph 3, the carboxyl terminal O-H is 2 +log(10 O-H)/1*HA for a value of 3. So, the fraction deprotonated is 10/11 so the charge is now -.91 on the carboxyl and NOT 0. The amino is still protonated so the overall charge is +.09.

Remember, the henderson halsebach is a ratio. At pka1=pH the ratio is 1:1. At a pH of 1 greater than pka the ratio is 10:1 (base to acid). It takes a pH of 2 above the pka for it to be close to fully deprotonated 100-1. So, this is why your assumption of neutrality was incorrect.