Threonine: It's proton doesn't count?

[justadream]

TBR page 185:

Why doesn’t the Threonine count as an amino acid that contains a site from which a proton may be lost (it’s R-group contains an OH group)?

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[t5Nitro]

TBR page 185:

Why doesn’t the Threonine count as an amino acid that contains a site from which a proton may be lost (it’s R-group contains an OH group)?

You just need to recognize the values of those with a listed pKa value in the side chain column. The pKa value is so high that you don't see it listed.

 

[justadream]

@t5Nitro

It's not listed (I even looked online) so I guess it's not relevant?

I just assumed it would be since TBR says to assume the pH = 1 conditions (pretty strong acid I thought)

 

[t5Nitro]

@t5Nitro

It's not listed (I even looked online) so I guess it's not relevant?

I just assumed it would be since TBR says to assume the pH = 1 conditions (pretty strong acid I thought)

It is not relevant, and that's why you never see the pKa value listed for that amino acid. What are you referring to with pH = 1 conditions? When you're removing protons, you always want to start at pH = 1 conditions, and then you look for the first proton that will be removed. The carboxyl group will lose its proton first, always. The N-terminus will lose its proton second or third or fourth or whatever, depending on the side chain pKa values. But if threonine is that side chain, then you ignore it.

 

[justadream]

@t5Nitro

I read about this in TBR page 185 (TBR Ochem Book II) where they do an example where they tell you to "assume the protein exists at pH = 1"

 

[t5Nitro]

@t5Nitro

I read about this in TBR page 185 (TBR Ochem Book II) where they do an example where they tell you to "assume the protein exists at pH = 1"

Hmm, I'm not sure then. I opened my old TBR book to check, but the version you have must be different. There are two examples on that page in my copy, but neither of them talk about this.

 

[Chrisz]

In order to be considered as acid or base, at pH 7.4, it has either be deprotonated or protonated respectively. Does alcohol satisfy either conditions? No. It has a pKa of that around 15 and pKb around 13.

 

[justadream]

@Chrisz

Well TBR was talking about at pH = 1.

I guess that doesn't change anything though because at pH =1, the alcohol (with pKa = 15) is protonated (not deprotonaed)

 

[Chrisz]

@Chrisz

Well TBR was talking about at pH = 1.

I guess that doesn't change anything though because at pH =1, the alcohol (with pKa = 15) is protonated (not deprotonaed)

I probably wrote to fast and did not express my idea clearly. The pKa of alcohol is 15, it is very close to water in structure. that is why it has a pKa very close to water. By the same reasoning, since the protonated form of water, the hydronium ion, has pKa of around -2 or -3, protonate alcohol should be close enough to it and also have a pKa around that range. pKa of this low, would you expect alcohol to be protonated at pH 7.4. Sorry, I did not sleep last night, so i wrote it down very recklessly

 

[justadream]

@Chrisz

I hope you'll excuse my ignorance here but is there a reason to consider the pKa of protonated alcohol (as in, like -OH2+)?

For example, from what I gather, TBR considers the OH of aspartic acid to count as a site from which a proton may be lost because:

pKa of the side chain of aspartic acid = 3.88. Since we're at pH = 1, the aspartic acid is protonated here.


Similarly, with the alcohol of Threonine, shouldn't we just consider the pKa of the side chain (which is an alcohol) of Threonine - and NOT the protonated alcohol?

Using this logic, at pH = 1 and if the pKa of the alcohol is 15, then the alcohol is unprotonated at pH = 1 and WOULDNT be considered as a site from which a proton may be lost.



Does this logic work?

 

[Chrisz]

Just went to the test book, you asking why it can not be deprotonated. It, of course can not be deprotonated. The starting charge at pH=1, you have total charge of +3. And your purpose is to make this polypeptide neutral, so you only have to deprotonate 3 H+ from the polypeptide to make the overall charge =0. So the equivalence point should be between (pka3+pka4)/2.=5. So how you gonna be able to deprotonate alcolhol, pKa=15, at pH=5

 

[Chrisz]

@Chrisz

I hope you'll excuse my ignorance here but is there a reason to consider the pKa of protonated alcohol (as in, like -OH2+)?

For example, from what I gather, TBR considers the OH of aspartic acid to count as a site from which a proton may be lost because:

pKa of the side chain of aspartic acid = 3.88. Since we're at pH = 1, the aspartic acid is protonated here.


Similarly, with the alcohol of Threonine, shouldn't we just consider the pKa of the side chain (which is an alcohol) of Threonine - and NOT the protonated alcohol?

Using this logic, at pH = 1 and if the pKa of the alcohol is 15, then the alcohol is unprotonated at pH = 1 and WOULDNT be considered as a site from which a proton may be lost.



Does this logic work?

Asparic acid has a carboxylic group, not an alcohol group. It has pKa of around 2.0. It can be easily deprotonated at a pH slightly higher than this pKa. Based on our calculated pH=5. asparic acid is deprotonated for sure, actually deprotonated very early in the process.

 

[Chrisz]

For clarification, just ignore the the protonation of alcohol. I was really tired this morning. I misunderstood your quesstion. I thought you were asking why alcohol can not be protonated. However, I believe it is a good chance for you to learn little bit more from the reasoning above, even though not specifically related to what you ask for