AAMC 10, BS #143 - pH of an amino acid???

[SephirothXR]

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"Alanine has two pKa values: one at 2.35 and one at 9.87. At what pH would alanine exist in the form shown below"


The diagram is a carbon bonded to 4 things: A methyl (CH3) group, an amine (NH2), a hydrogen, and a carboxylate ion (COO- ).

A)Less than 2.35
B)Between 2.35 and 6.11
C)Between 6.11 and 9.87
D)Above 9.87

My interpretation was that an amino acid has an N and C terminus, an NH2 and a COOH group. With just one of its protons gone, it should have reached the 1st pKa value, and thus have been over 2.35. The answer was actually D, which implies to me that somehow there have been two deprotonations. Anyone wish to elaborate?

 

[SeminoleVesicle]

"Alanine has two pKa values: one at 2.35 and one at 9.87. At what pH would alanine exist in the form shown below"


The diagram is a carbon bonded to 4 things: A methyl (CH3) group, an amine (NH2), a hydrogen, and a carboxylate ion (COO- ).

A)Less than 2.35
B)Between 2.35 and 6.11
C)Between 6.11 and 9.87
D)Above 9.87

My interpretation was that an amino acid has an N and C terminus, an NH2 and a COOH group. With just one of its protons gone, it should have reached the 1st pKa value, and thus have been over 2.35. The answer was actually D, which implies to me that somehow there have been two deprotonations. Anyone wish to elaborate?

I'm assuming you haven't taken biochemistry yet. The carboxylic acid group is generally deprotonated at pH=2.2 and the amino group is deprotonated at pH=9.6. These are numbers worth remembering. The Henderson-Hasselbach equation will also be your friend in this situation. Review amino acids in your books.

 

[SephirothXR]

This is probably what I'm not understanding here: is the NH2 the normal group? Thinking of a deprotonation to a NH- doesn't seem right at all. My thinking was that the COOH lost a hydrogen but that the NH2, which is what I usually see as the normal amine group on an amino acid, remained untouched. Is it supposed to be NH3+ at low pH or something?

 

[gunj122]

functional groups like NH2 and COOH are protonated when the pH is below the pKa. the pKa for the NH2 group is approx 9.87 while the COOH group its 2.35.

so if the pH is below 2.35, both functional groups will be protonated: it'll be NH3+ and COOH. as you get more basic and pass these "checkpoints" or pKa values, hydrogens will fall off.

 

[Arctangent]

This is probably what I'm not understanding here: is the NH2 the normal group? Thinking of a deprotonation to a NH- doesn't seem right at all. My thinking was that the COOH lost a hydrogen but that the NH2, which is what I usually see as the normal amine group on an amino acid, remained untouched. Is it supposed to be NH3+ at low pH or something?

You're right, in that R-NH2 is the "normal group" in that it is the deprotonated form. The protonated form will be R-NH3+, so you are also correct in that at low pH all the way to pH 9.6, the R-NH3+ form will exist. As for the rest of your analysis, you got that the R-COOH lost a hydrogen to become its acetate form. So just adjust what you know about amine groups and their protonated and deprotonated forms, and you should be good to go on this question.

 

[SephirothXR]

Got it now, thanks! Biochemistry would definitely help but I'm not investing time to look over that (more importance on practice)

 

[Mantis Toboggin]

Hey I have a quick question here.. I'm pretty confused as to how this works.

So R-NH2 exists as R-NH3(+) until 9.87 pH. After 9.87, does it become R-NH2 or R-NH (-)? What about AT pH 9.87?

Similarly, does the COOH group exist as COOH2+ or COOH until 2.35? The acetate ion suggests that it exists as COOH.


I get the fact that if pH<pka, you add a proton, and if pH>pka you take away a proton.

However what are our "starting points," so to speak.

A "normal" amino acid (as displayed in texts and such) has a R group, NH2, COOH, and H.

I feel like this is a lot more simple than what I think it is-- brain is struggling though.

 

[liveoak]

don't feel bad that it's hard to wrap your brain around. acid and base stuff is difficult.

think of it this way.

at a ridiculously low pH, the solution is PACKED with h+ protons. thus, it doesn't need any from the side chains, and you are left with COOH, and NH3+.

now, at a pH value of 2.3 (the pKa of COOH), the COOH begins to concede it's proton and now 1/2 is COOH, and 1/2 is COO-. At around 3.3, the COOH is totally deprotanated and now exists solely as COO-

the same happens for NH3+, except it occurs at a much higher pH

 

[salim271]

Hey I have a quick question here.. I'm pretty confused as to how this works.

So R-NH2 exists as R-NH3(+) until 9.87 pH. After 9.87, does it become R-NH2 or R-NH (-)? What about AT pH 9.87?

Similarly, does the COOH group exist as COOH2+ or COOH until 2.35? The acetate ion suggests that it exists as COOH.


I get the fact that if pH<pka, you add a proton, and if pH>pka you take away a proton.

However what are our "starting points," so to speak.

A "normal" amino acid (as displayed in texts and such) has a R group, NH2, COOH, and H.

I feel like this is a lot more simple than what I think it is-- brain is struggling though.

It is more simple than you're making it. No matter what they're bound to, carboxylic acids and amines behave as such. At physiological pH (assume about 7 for simplicity) the amino acid exists in a zwitterion form, the carboxylic acid is COO-, the amine is NH3+.

If the pH gets lowered far enough, NOTHING will happen to the NH3+ its already bound up with a proton, but the COO will become COOH. Similarly if the pH rises from 7, nothing will happen to the COO, its already lost its proton, but the NH3+ will lose its extra proton to the basic solution. It will NEVER become NH-. Similarly, you will never see COOH2. For the exact pH numbers where these changes take place, look at the pKas.

With R groups that have acid/base properties, use their pKas to determine when they will pickup/lose a proton.

Once you get this concept down its like riding a bike, I remember struggling with it too in ochem 2. I dont think my teacher had to go into as much detail as he did about biological molecules, but it definitely gave me a leg up when I took biochem and the MCAT.