Amino Acids

 The 20 naturally occurring amino acids are built on a common theme.
A free amino acid has the general structure shown in Fig. 1 with an amino group, NH2, at one end and a carboxyl group, COOH, at the other.
 
 Each goup is attached to an alpha carbon.  Also attached to the alpha carbon is a H atom and an R group (side chain) (Fig. 1).  The R group is the only thing that varies from one amino acid to another (Fig. 2).

Since the central alpha carbon is asymmetrical there are two possible isomers which are mirror images of each other (Fig. 3)  Biological systems use the L isomer.

 When amino acids are dissolved in water, the amino and carboxyl groups act as bases and acids respectively as shown in Fig. 4.  Therefore, amino acids are considered to be Zwitterionic (possessing both - and + charge) and amphoteric (able to act as an acid or as a base)

 Amino acids can act as buffers (resistant to pH change) in a pH range which is + or - 1 pH unit from their pKa values (pKa = -log Keq for acid dissociation).

The point on a titration curve, as shown in Fig. 4, where the amino acid has an equal number of positive and negative charges called the isolelectric point because such molecules when placed in an electric field will be unable to migrate to either the anode or cathode.  The pH at which the isolelectric point occurs is called the pI.

Amino acids fall into four groups:

NON-POLAR NEUTRAL

 The NON-POLAR NEUTRAL amino acids are HYDROPHOBIC (water-repelling).

There are 10 amino acids with hydrophobic side chains. They tend to interact with one another and with other hydrophobic groups and would be expected to be located within the interior of a protein or in membranes. Typically they have primarily C and Hs in the R group.

 The simplest of course is glycine, which has a single H as its side group:

 alanine, valine, leucine, and isoleucine have hydrocarbon chains consisting of up to 4 carbon atoms.

 Proline also contains a hydrocarbon side chain but it forms a ringed structure:
As a result, a proline residue disrupts the usual organization of the backbone of a polypeptide chain, causing a sharp transition in the direction of the chain. The presence of proline, therefore, interrupts the formation of any regular repeating structure.

 The side chains of cysteine and methionine contain sulfur atoms. Methionine is very hydrophobic, cysteine is less so.  Even though both contain sulfur atoms, only cysteine can form disulfide bonds.

 Phenylalanine and tryptophan both have side chains containing very hydrophobic aromatic rings.  These amino acids can participate in ring stacking.

BASIC

 Three amino acids have basic R-groups:
  lysine, arginine, and histidine

 Addition of a hydrogen ion converts the free (second) amino group of lysine or arginine to the positively charged form NH3+. A proton can similarly be added to the histidine ring making it positively charged.

Important point: charge of the side group will depend upon the pH of the surrounding solution.

 Lysine and arginine exist in the + charged form within the cell  (pH 6-8).

 Histidine can be either uncharged or charged at physiological pH so it frequently plays an active role in enzymatic reactions involving the exchange of H ions.

 The basic amino acids are polar and hydrophilic and, therefore, would normally be found on the outer surface of a protein.

 Two amino acids have acidic R-groups: aspartic acid and glutamic acid.

 Because the R-group carboxyl  can lose a hydrogen ion to exist in the negatively charged form O=C-O-. Both exist in - charged form within the cell. These amino acids are also polar and hydrophilic and, therefore, would be found on the outer surface of a protein.

 Five amino acids are classified as POLAR Like the basic and acidic amino acids, the polar amino acids are hydrophilic and able to hydrogen bond with water.

Three are considered alcohols and have OH groups in their side chains: serine, threonine, and tyrosine.

 Two have polar amide groups [ O=C-NH2]: asparagine and glutamine. The amide bonds are very similar to those found in peptide bonds.