polypeptide charge calculation

[jazzmetal]

Hi, I'm having trouble understanding AAMC's answer to #51 from the ChemPhys Section Bank pack.
The question involves calculating the net charge on a polypeptide:
HIPAGEATEKALRGD
This is at pH 7.
I calculated a net charge of 0, figuring that H is positively charged at pH 7, so there are three positively charged peptides (H, K and R) and three negatively charged (E, E and D).
AAMC says this polypeptide has a charge of –1.
What am I missing?
Any hints would be appreciated!

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[theonlytycrane]

The net charge should be -1. See @Phoodie's reply below.

 

[Phoodie]

H: +1
K: +1
R: +1
E: -1
E: -1
D: -2

The overall charge is -1.

 

[theonlytycrane]

H: +1
K: +1
R: +1
E: -1
E: -1
D: -2

The overall charge is -1.

Where does -2 come from?

 

[Phoodie]

Where does -2 come from?

A -1 charge comes from the deprotonated side chain and a second -1 charge comes from the deprotonated carboxyl group.

 

[theonlytycrane]

A -1 charge comes from the deprotonated side chain and a second -1 charge comes from the deprotonated carboxyl group.

The C-terminus -1 cancels with the N-terminus +1

 

[Phoodie]

The C-terminus -1 cancels with the N-terminus +1

I didn't want to give a detailed response since OP only asked for hints but here goes:

• H: N-terminus contributes a +1 charge; side chain contributes no charge
• K: Side chain contributes a +1 charge
• R: Side chain contributes a +1 charge
• E: Side chain contributes a -1 charge
• E: Side chain contributes a -1 charge
• D: C-terminus contributes a -1 charge; side chain contributes a -1 charge

 

[theonlytycrane]

Thanks for the clarification @Phoodie. I mistakenly had the R group on His at +1

 

[Phoodie]

Thanks for the clarification @Phoodie. I mistakenly had the R group on His at +1

No problem!

 

[jazzmetal]

Thanks everyone! Especially Phoodie for the detailed answer. So I should consider the H side-chain neutral at physiological pH - yes? Even though in reality, a greater proportion of His molecules would still be protonated than not, right? Because the pKa is just under 7?

 

[sakhir]

Histidine side group pKa is around 6.10. So I think is safe to assume that at pH of 7 it will be neutral.

 

[Wolfpack93]

Thanks everyone! Especially Phoodie for the detailed answer. So I should consider the H side-chain neutral at physiological pH - yes? Even though in reality, a greater proportion of His molecules would still be protonated than not, right? Because the pKa is just under 7?

A greater proportion would be deprotonated at a pH > pKa. Henderson hasselbach equation

 

[flyingeagle]

I didn't want to give a detailed response since OP only asked for hints but here goes:

• H: N-terminus contributes a +1 charge; side chain contributes no charge
• K: Side chain contributes a +1 charge
• R: Side chain contributes a +1 charge
• E: Side chain contributes a -1 charge
• E: Side chain contributes a -1 charge
• D: C-terminus contributes a -1 charge; side chain contributes a -1 charge

Why is Aspartic acid's C-terminus contributing a -1 whereas Glutamatic Acid's is not? Aren't they almost exactly the same molecule?

EDIT: nevermind, just realized it's because it's on the end of the chain

 

[NextStepTutor_3]

Just a note about the histidine issue - remember, when pH = pKa of a particular group, half of those molecules are already deprotonated at that group. So, if histidine's side chain pKa is around 6.11, half of the histidine molecules will have deprotonated side chains at pH 6.11, and significantly more than that at pH = 7. If you tested this out with the H-H equation, you'd see that the concentration of deprotonated histidine would be almost ten times that of protonated His under the conditions described. But you can avoid doing all this and generally assume that His is deprotonated at pH 7 (and certainly at pH 7.4).

 

[jazzmetal]

Just a note about the histidine issue - remember, when pH = pKa of a particular group, half of those molecules are already deprotonated at that group. So, if histidine's side chain pKa is around 6.11, half of the histidine molecules will have deprotonated side chains at pH 6.11, and significantly more than that at pH = 7. If you tested this out with the H-H equation, you'd see that the concentration of deprotonated histidine would be almost ten times that of protonated His under the conditions described. But you can avoid doing all this and generally assume that His is deprotonated at pH 7 (and certainly at pH 7.4).

Very helpful, thanks!