Amino Acid Structure

Proteins start out life as a bunch of amino acids linked together in a headto-tail fashion—the primary sequence. Methylene groups (–CH2–) may be important, but keeping track of them on an individual basis is just too much to ask. Organize the amino acids based on the functional group of the side chain.Remember a few of the amino acids by functional groups. The rest are hydrophobic.

1.HYDROPHILIC (POLAR):-

CHARGED POLAR:-

• Acidic (–COO) and basic (–NH3) amino acidside chains have a charge at neutral pH and strongly “prefer” to be on the exterior, exposed to water, rather than in the interior of the protein.The acidic amino acids, Asp and Glu, are really bases (proton acceptors). Lys, Arg, and His are considered basic amino acids, even though they have a proton at neutral pH. The same argument applies: Lys, Arg, and His are such good bases that they have already picked up a proton at neutral pH.

• Charged groups are usually found on the surface of proteins. It is very difficult to remove a charged residue from the surface of a protein and place it in the hydrophobic interior, where the dielectric constant is low. This is termed a salt bridge.

NEUTRAL POLAR:-  

•  These side chains are uncharged, but they have groups (–OH, –SH, NH, C“O) that can hydrogen-bond to water. In an unfolded protein, these residues are hydrogen-bonded to water. They prefer to be exposed to water, but if they are found in the protein interior they are hydrogen-bonded to other polar groups.

2.HYDROPHOBIC (APOLAR):-

•  Hydrocarbons do not have many groups that can participate in the hydrogen-bonding network of water. They’re greasy and prefer to be on the interior of proteins . Note that a couple of the aromatics, Tyr and Trp, have O and N, and Met has an S, but these amino acids are still pretty hydrophobic. The hydrophobic nature usually dominates; however, the O, N, and S atoms often participate in hydrogen bonds in the interior of the protein.