isoelectric points kicking my ass

[thebillsfan]

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i understand pI, or i think i do, and then i come across a pI passage and realize i dont. time to figure it out for real.

i know that pI is the pH when an amino acid is neutral, that is, in zwitterion form

if an AA has an acidic side chain, then the pI is the avg of the pKas of the two acidic groups. if an AA has a basic side chain, then its the avg of the pKas of the two basic groups. based on this, what if you were just given pKbs? how would you calculate the pI from that? or could you? also, WHY is it the avg of the two pKas? I don't understand that qualitatively.

thanks.

 

[RogueUnicorn]

i understand pI, or i think i do, and then i come across a pI passage and realize i dont. time to figure it out for real.

i know that pI is the pH when an amino acid is neutral, that is, in zwitterion form

if an AA has an acidic side chain, then the pI is the avg of the pKas of the two acidic groups. if an AA has a basic side chain, then its the avg of the pKas of the two basic groups. based on this, what if you were just given pKbs? how would you calculate the pI from that? or could you? also, WHY is it the avg of the two pKas? I don't understand that qualitatively.

thanks.

to explain why it's the avg of the two pkas would be quite labor intensive. you can try to work it out yourself as a good learning experience. think how the charge of the amino acid changes as you shift the pH and protons are lost/gained as influenced by the pKa.

 

[thebillsfan]

to explain why it's the avg of the two pkas would be quite labor intensive. you can try to work it out yourself as a good learning experience. think how the charge of the amino acid changes as you shift the pH and protons are lost/gained as influenced by the pKa.

okay, what about the pKb thing? is that feasible? also...i'm confused as to how electrophoresis relates to isoelectric focusing. in electrophoresis, is the cathode always positive? is the pH gradient increasing towards the cathode or anode in pI focusing? I'd reason that the h ion concentration is getting larger as the pH decreases, so that means it's more positive. Thus I would expect a lower pH at the anode, assuming the anode is the negative electrode in electrophoresis. am i right?

 

[thebillsfan]

also bleargh are you a teacher for kaplan?

 

[RogueUnicorn]

also bleargh are you a teacher for kaplan?

yes.

re: pkb, i need to think about it...

edit: if they're reporting a pKb of the UNCHARGED basic AA side chain, then the Kb = (Ka)^-1

 

[thebillsfan]

you mean the side chain is uncharged or the whole AA is uncharged? also, since when does the kb*ka=1? that's what youre implying with that equation ( i think)

 

[RogueUnicorn]

you mean the side chain is uncharged or the whole AA is uncharged? also, since when does the kb*ka=1? that's what youre implying with that equation ( i think)

R + H --> RH+ for Kb

RH+ --> R + H for Ka

given this relationship Ka*Kb=1 is a necessity

 

[thebillsfan]

R + H --> RH+ for Kb

RH+ --> R + H for Ka

given this relationship Ka*Kb=1 is a necessity

alright, that was a stupid question on my part. however, i do know that the ka relates to the kb of its conjugate base. if youre telling me that i need to use the kb of the UNCHARGED side chain, well, then youd be saying that the ka of the uncharged (which is what is always given) is related to its own kb by the equation ka*kb=1. this isnt exactly what i learned.

 

[RogueUnicorn]

alright, that was a stupid question on my part. however, i do know that the ka relates to the kb of its conjugate base. if youre telling me that i need to use the kb of the UNCHARGED side chain, well, then youd be saying that the ka of the uncharged (which is what is always given) is related to its own kb by the equation ka*kb=1. this isnt exactly what i learned.

the ka of an uncharged basic sidechain doesn't exist... the N atom is not going to become negatively charged.

 

[Hemichordate]

I thought Ka*Kb = Kw (10^-14)

 

[RogueUnicorn]

I thought Ka*Kb = Kw (10^-14)

it is. the way i defined it only applies to the specific way in which i defined the two reactions

 

[RogueUnicorn]

on second thought, my premise is flawed.. it should be

R + H2O --> RH + OH-

in which case the Kb is in fact Kw/Ka

thanks hemichordate