Proteins are one of the primary constituents of living matter. They consist of long chains of amino acids, which are bonded together by peptide linkages and thus called polypeptides. There are about 20 amino acids, and the atoms most prevalent in these are carbon, hydrogen, oxygen, nitrogen, and sulfur. Each amino acid contains a carboxylic acid end and an amino end. At a pH of 6-7 (the body's pH is 7.3) the amino end is protonated, while the carboxylic end remains an anion; this is called a zwitterion. Some amino acids cannot be synthesized by the body and must be obtained from food; these are arginine, histidine, isoleucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The simplest amino acid, glycine, is shown below.

A peptide bond occurs when the carboxylic acid end of one amino acid bonds with the amino end of another. The result is a huge chain, whose molecular weight ranges from 5000 to 1,000,000. The carbonyl group and the nitrogen and hydrogens around the peptide bond, as well as the two carbon atoms to which the amino and carbonyl groups are bonded, lie in a plane. The negative charge of electrons is delocalized around the entire peptide bond, a phenomenon called resonance, and both the carbonyl and the carbon-nitrogen bonds possess double-bond character. Because the carbon-nitrogen bond is partially a double-bond, there can be no free rotation around it.
The order of the linear linkages between amino acids in a protein is called its primary structure. However, the molecule itself bends and assumes a certain conformation, called its secondary structure. Such a common conformation is the alpha-helix, proposed in 1951 by Linus Pauling and R. Corey, as illustartated here. This chain forms a right-handed coil, having 3.7 amino acids per full turn. Hydrogen bonding exists between the hydrogen bonded to the nitrogen and the carbonyl group of the amino acid four units down the chain, granting the structure rigidity and stability. Several alpha-helixes can coil around each other to give strands that are held together by disulfide bridges, such as in the proteins called alpha-keratins.

A larger image of this protein.

Proteins also can exist as pleated sheets, or beta-keratins. In these, hydrogen bonding exists between adjacent chains, as they lie side by side. Another conformation is the collagen, or fibrous protein; this is a triple helix of polypeptides, each of which is a left-handed helix. An illustration of the subunit of a protein with five disulfide bonds is shown above. A larger image of this protein.

When several polypeptide units are associated with each other and with other simpler molecules such as sugars, inorganic residues, or coenzymes, the protein is said to possess a quaternary structure. The function of the protein relies of both the order of amino acids and the "topography" of its surface; each factor is equally important. This interdependence of the basic units with the overall form exemplifies a theme of our seminar's architectonic, which is the importance of the parts and the whole as a single function. A porcine insulin protein structure is illustrated above. A larger image of this protein.

Allison Smith '99.

Return to the Architectonic

May 25, 1996.