Ionization of Amino Acids

All amino acids are have a neutral net charge at physiological pH (7.4).
The carboxyl and amino groups and any other ionizable groups determine charge.
Each amino acid has 2 or 3 pKa values (7 amino acids have side chains that are ionizable)
(see Table 3.2). This complicates the basic titration curve, so that there are 3 inflection
points rather than 2.
At a given pH, amino acids have different net charges.
Can use titration curves for amino acids to show ionizable groups.
The isoelectric point (pI) is the pH at which the amino acid has no net charge
= zwitterion.
If pH > pI, amino acid would be negatively charged.
If pH < pI, amino acid would be positively charged.
If pH = pI, amino acid would have no charge.
Can use Henderson-Hasselbalch equation to calculate the fraction of group ionized at a
given pH.
a carboxyl group pKa 1.8-2.5
a amino group pKa 8.7-10.7
If pH< pKa, a greater amount of the group is protonated (NH3
+ or COOH)
If pH > pKa, there is a greater ionization and a greater amount of unprotonated or anion
form (NH2 or COO-).
If pH = pKa, then [conjugate base] =[weak acid].
For the ionization of the carboxyl group of alanine,
pH = pKa + log [conjugate base]
[weak acid]
7 = 2.4 + log [RCOO-]
[RCOOH]
4.6 = log [RCOO-]
[RCOOH]
39810:1 meaning the anion predominates greatly (almost all COOH groups are
ionized).
For the ionization of the amino group of alanine,
7 = 9.9 + log [NH2] -NH3
+ ---> NH2 = H+
[NH3
+]
4
-2.9 = log [NH2]
[NH3
+]
0.001:1 or 1 in 1000 molecules (undissociated group predominates)
At pI of 6.15, there is no net charge (all of the carboxyl groups are unprotonated, and none
of the amino group is unprotonated).
pI = (pKa1 + pKa2)/2
For R groups that are ionizable, the pI is not simply the average!!!
Peptide Bonds
The primary structure of a protein is the linear sequence of amino acids that are covalently
bonded to form a polypeptide chain.
Formed by condensation reaction in which a molecule of water is removed.
Each amino acid residue is called by replacing -ine or -ate with -yl
glycine ---> glycyl
The peptide bond is a planar bond with no rotation around C-N axis. If is also in the trans
form. Will talk about the consequences later.