Important Point #1: the amino acids in proteins are alpha-amino acids.

Each ionizable group has a characteristic and independent pK_a.

Each amino acid has a characteristic pH where it is isoionic. This is the isoelectric point (pI). For the simple, diprotic amino acids (e.g. Gly or Ala) it is a simple average of the individual pK_a values. For amino acids with charged R-groups, you need to take the average of the pK_a values on either side of the neutral form of the molecule. As the pH increases above the pI, the net charge becomes more negative. As the pH decreases below the pI, the net charge becomes more positive.

Important Point #3: Amino acids in cells and proteins are generally in the L-form. However, the peptidoglycan in bacterial cell walls contain some D-amino acids. Review enantiomers [local].

You should know the structures of the amino acids for this class:

Glycine (not optically active), Alanine, Serine, Cysteine (thiol pK_a ~ 8.5), Threonine (-OH pK_a ~ 13), Valine, Leucine, Methionine, Isoleucine, Proline (an immino acid), Phenylalanine, Tyrosine (hydroxylated phe, pK_a ~10.5), Tryptophan, Asparagine, Glutamine, Aspartate (four carbons, pK_a ~4), Glutamate (five Carbons, pK_a ~ 4.25), Lysine (epsilon amino pK_a ~ 10.5), Arginine (CCCNCN+N pK_a ~ 12.5), and Histidine (CCCNCN in ring pK_a ~ 6).

Also, there are two abbreviation systems for amino acids, three letters and one letter. In this course, you should know the three letter code.

Amino acid structures

• Site #1 [local]
• Site #2 [local]
• Site #3 for RasMol or Chime viewers.

See jmol: alanine

See jmol: arginine

See jmol: asparagine

See jmol: aspartate

See jmol: cysteine

See jmol: glutamate

See jmol: glutamine

See jmol: glycine

See jmol: histidine

See jmol: isoleucine

See jmol: leucine

See jmol: lysine

See jmol: methionine

See jmol: phenylalanine

See jmol: proline

See jmol: serine

See jmol: threonine

See jmol: tryptophan

See jmol: tyrosine

See jmol: valine

The 21st amino acid that is coded for in mRNA and found occasionally in proteins is Selenocysteine [local]. There are some additional amino acids that are found in a few proteins (e.g. hydroxyproline) produced by post-translational modifications. Some of the amino acids in a protein are covalently modified as part of a signaling pathway (e.g. phosphorylated) or to localize them to a membrane (e.g. myristilated or prenylated).

Since amino acids have multiple functional groups that can deprotonate (diprotic, triprotic), they have titration curves more complex than monoprotic acids. Given the above pK_a values for the functional groups, you need to develop the skill of predicting what the titration curve (pH vs. equivalents NaOH added) will look like for each of the amino acids.

Things to look for in amino acid titrations:

• The half-equivalent values (e.g. 0.5, 1.5, 2.5) define the pK_a and maximum buffering for each functional group.
• 90% of the buffering occurs within one pH value of the pK_a.
• There should be minimal buffering at the whole equivalent values (e.g. 1.0, 2.0).
• The pH will jump after sufficient equivalents are added to completely neutralize (deprotonate) the amino acid.

Resource for practice titrations: Simulated titration of amino acids

Start with the first category to simulate titration of one amino acid at a time. Do glycine and then do alanine. Notice that they are practically identical because the molecules are so similar. Leucine and Isoleucine add aliphatic side-chains, but they don't affect the pK_a values of the amino and carboxyl. Phenylalanine does affect these pK_a values. Now examine triprotic amino acids. Notice that it takes three equivalents of base to deprotonate the functional groups.

Return to the index page and select the third option to be able to compare the simulated titration curves of two amino acids at once. Repeat the above process of comparing similar and different amino acids. Attempt to understand the process so that you will be able to guess from a titration curve the identity of an amino acid.

Essential amino acids for humans: His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val. We lack the enzymes to produce these amino acids and must have them included in the proteins of our diet.