TBR Amino Acid Structure

This forum made possible through the generous support of SDN members, donors, and sponsors. Thank you.

nomdeplume1234

Full Member
7+ Year Member
Joined
Mar 18, 2015
Messages
270
Reaction score
133
Can someone explain to me why TBR books represent amino acids with the amino terminal group (NH3 +) and in other books like TPR they are represented as (NH2)? I'm a little confused by the differences. For example, in TBR Alanine is represented by Nh3(+)CHCH3COO(-) while in TPR Alanine is represented by NH2CHCH3COOH

Members don't see this ad.
 
It depends on the pH of whatever solvent/solution it's in.
Example: Amino acid (AA) Alanine (Ala) is in the blood, which has a pH of around 7.4. Alanine has no R-functional groups, so it just has the amino group and carboxyl group, pka values are 9 and 2.5.

Since pH = 7.4, that amino group will still have its proton. pka of amino group = 9 and pH of blood = 7.4, pH < pka so stays protonated (or exists as NH3+).
But, since the carboxyl group usually has a proton whenever the pH is lower than 2.5, in a solution/solvent with a pH > 2.5, the carboxyl will lose that proton. In this case with a pH of 7.4, the carboxyl terminus will be deprotonated, giving it a negative charge (COO-). Total charge of Ala is neutral at pH = 7.4 (called zwitterion) since you have a protonated amino terminus and deprotonated carboxyl terminus.
At pH of something greater than 9, pH > pka of amino terminus so it will deprotonate that amino group's proton, giving that amino terminus no charge now (exists as NH2). Total charge of Ala is -1 since the carboxyl terminus will also be deprotonated.

zwitterion-ph.gif
 
  • Like
Reactions: 1 user
pka of amino group = 9

Thank you for the response. I am a little unclear on the meaning of the amino group having a pka of a particular value. I associate pka with strength of acid and would like to know how to link the concept with the amino and carbonyl terminal.
So what does it mean when someone states that the amino group has a pka of 9?
 
It means that it is positively charged at a pH below 9 and neutral above 9. This is because the pka describes the acidity of the third proton, which gives the amino group it's positive charge. So when the solution is more basic than the amino group, it is deprotonated and neutral. When the solution is more acidic than the amino group, the amino group stays protonated and positively charged.

If a acid group has a pka of 4, then below pH 4 it is neutral and above pH 4 it is negatively charged.
 
  • Like
Reactions: 1 user
Members don't see this ad :)
Thank you for the response. I am a little unclear on the meaning of the amino group having a pka of a particular value. I associate pka with strength of acid and would like to know how to link the concept with the amino and carbonyl terminal.
So what does it mean when someone states that the amino group has a pka of 9?
Think of pka as a general concept for "how easy is it to take that H off that atom?"
Ex: H3PO4 (http://www2.ucdsb.on.ca/tiss/stretton/database/polyprotic_acids.htm)
We have 3 H's so we can take off those 3 H's so we'll have 3 pka values.
1st time to take off an H is easy, since the PO4 says 'oh that's fine, I have 2 more H's'.
2nd time to take off an H is harder since PO4 says 'hm, sure but I'll only have 1 left'.
3rd H is the hardest since it's the last H PO4 has.
Hence, the pka values increase. Remember, low pka = high Ka which means easy to take H off compared to a higher pka = lower Ka.

In terms of charge, after you take off the 1st H from H3PO4, it has a negative charge of -1, so it wants to keep all of its H's to 'balance' out that -1 charge.
2nd H taken off => HPO4^-2 so it has a negative charge of -2, so it really wants to keep the last H since opposite charges attract, which helps to balance out that -2 charge.
Same for 3rd H.
 
  • Like
Reactions: 1 user
Think of pka as a general concept for "how easy is it to take that H off that atom?"
Thank you for the explanation. I'm still working on gaining intuition with these relationships (increasing Ka means decreasing pka means easier to take off H).

My understanding so far is: the amino acid has two sides. On one side is the there is the amino (Nh2) group and on the other is the carboxyl (COOH) group.
The Pka for the amino group is usually around 9 and for the carboxyl group it is around 2.

The fluid inside the body is around ph of 7 so if we think of an amino acid sitting around in the body fluid:
then the amino will have a positive charge (Nh3+) because H+ ions are falling from the sky so it might as well take an extra one. Meanwhile the Carboxyl group has a pka of 2 (This is where I’m having trouble with the reasoning…)

somehow the pka value of 2 means that the carboxyl group will exist in the deprotonated form? because the ph is 7 but its pka is 2?

I’m guessing the answer has to do with the Henderson-Hasselbalch equation because I know the pH and the pka. Maybe my lack of intuition is in the math portion (logarithms). somehow the equation gives me the ratio..

but based on your explanation harder it gets to strip the H the the higher the pka value, so a low pka value would mean it is relatively easy to strip the H.
 
Thank you for the explanation. I'm still working on gaining intuition with these relationships (increasing Ka means decreasing pka means easier to take off H).

My understanding so far is: the amino acid has two sides. On one side is the there is the amino (Nh2) group and on the other is the carboxyl (COOH) group.
The Pka for the amino group is usually around 9 and for the carboxyl group it is around 2.

The fluid inside the body is around ph of 7 so if we think of an amino acid sitting around in the body fluid:
then the amino will have a positive charge (Nh3+) because H+ ions are falling from the sky so it might as well take an extra one. Meanwhile the Carboxyl group has a pka of 2 (This is where I’m having trouble with the reasoning…).

Yes, correct. Also, think of the fact that low pH means lots of H+ around OR not enough bases, like OH-, to take away protons/Hs from molecules/atoms. High pH = low [H]/high [OH] (or low concentration of protons/high concentration of bases)

somehow the pka value of 2 means that the carboxyl group will exist in the deprotonated form? because the ph is 7 but its pka is 2?

I’m guessing the answer has to do with the Henderson-Hasselbalch equation because I know the pH and the pka. Maybe my lack of intuition is in the math portion (logarithms). somehow the equation gives me the ratio..

but based on your explanation harder it gets to strip the H the the higher the pka value, so a low pka value would mean it is relatively easy to strip the H.

Think of the AA sitting in a solution with bases all around it, like NaOH. The base (OH-) will abstract the proton if there is enough base in the solution to take the H off of the carboxyl. See relevant thread http://forums.studentdoctor.net/threads/question-about-acids-at-low-ph-and-pka.540028/#post-6859540
Maybe this analogy works, but say you have 2 lolipops (your pka is 2, lolipops = Hs/protons). When there are more than 2 bullies (bases/OH-), they take away your lolipops (H+/protons). When there are less than 2 bullies, they can't take them away, so you keep your lolipops. When pka = pH (or when there are exactly 2 bullies), you're at the half-equivalence point, or when the concentration of carboxyls with H's = concentration of carboxyls without H's. Analogy-wise, this would be you lose 1 lolipop, but still have 1. (I think this analogy works..)
 
  • Like
Reactions: 1 user
Top