Amino Acids and Proteins: Protein Structure

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While aspartic acid and glutamic acid release their protons to become negatively charged in normal human physiologic conditions, lysine and arginine gain protons in solution to become positively charged. Histidine is unique because it can form either basic or acidic side chains since the pKa of the compound is close to the pH of the body. As the pH begins to exceed the pKa of the molecule, the equilibrium between its neutral and acidic forms begins to favor the acidic form (deprotonated form) of the amino acid side chain. In other words, a proton is more likely to be released into solution. In the case of histidine, a proton can be released to expose a basic NH2 group when the pH rises above its pKa (6). However, histidine can become positively charged under conditions where the pH falls below 6. Because histidine is able to act as an acid or a base in relatively neutral conditions, it is found in the active sites of many enzymes that require a certain pH to catalyze reactions.

Polar and Non-Polar Amino Acids

Amino acids can be polar or non-polar. Polar amino acids have R groups that do not ionize in solution but are quite soluble in water due to their polar character. They are also known as hydrophilic, or "water loving" amino acids. These include serine, threonine, asparagine, glutamine, tyrosine, and cysteine. The nonpolar amino acids include glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine and tryptophan. Nonpolar amino acids are soluble in nonpolar environments such as cell membranes and are called hydrophobic molecules because of their "water fearing" properties.

Bonding in Amino Acids

Amino acids are linked to one another by peptide bonds. The carboxylic acid terminus of one amino acid joins to the amino group of another amino acid while releasing a molecule of water in the process of forming the bond.

Multiple amino acids joined by peptide bonds are called polypeptides. Because many of the hormones secreted by the body contain only a few amino acids they are commonly referred to as peptide hormones. In contrast, proteins contain thousands of peptide bonds and form complex shapes and crevices.

Due to the special dumbell shape electron density that the carbonyl group (C=O) and the nitrogen atom have in the C-N bond, electrons can become delocalized (spread out). Since these types of bonds are much stronger than regular covalent bonds, they are not able to rotate about their axis like regular bonds. This creates a rigid and planar peptide unit, limiting the number of conformations a polypeptide can adopt.

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