[Sever]

I'm studying for the MCAT after being removed from chemistry for a couple of years and just want to verify that I am or not thinking things through correctly.

Looking at Glycine, for example, if it were set in a solution with a pH of 7, you would expect the carboxyl group (pKa = 2.34) to be deprotonated leaving behind a negative charge while the ammonium ion (pKa = 9.60) to be protonated giving it a positive charge.

If it were put in a hypothetical solution with a pH of 1, both groups would be deprotonated protonated; whereas the opposite would be true if it were a pH of 14 in which both groups would be protonated deprotonated.

For something like aspartate being one of 5 AA's with an additional pKa on the R group (pKa1 = 1.88, pKa2 = 9.60, pKa3 = 3.65) in a solution with a pH of 7, you would see both the 1st and 3rd groups deprotonated and the 2nd group protonated which is why it is usually just called aspartic acid rather than aspartate in vivo.

The reason I'm double-checking myself is that the book I'm using to review shows the structures of all the AA's with the amino group as NH2 and the carboxyl group as COOH. At what sort of pH would you expect to see this then? Or is it showing these two this way, making a neutral compound, because it is a zwitterion

[AWK]

If it were put in a hypothetical solution with a pH of 1, both groups would be deprotonated; whereas the opposite would be true if it were a pH of 14 in which both groups would be protonated.

?
http://faculty.une.edu/com/courses/bionut/distbio/obj-512/Chap6-titration-aspartate.html

[Babcock_Hall]

Some textbooks and journal articles draw the neutral forms of the amino acids, even though in neutral solution the zwitterion predominates, as you have shown via your arguments about pK_a.  There are legitimate reasons for doing so in certain circumstances.  The side chains can be a little trickier, but I agree with you that the side-chain of aspartate is mainly deprotonated at neutral pH.