Information on protein composition. Proteins are chain-like polymers of small subunits. The chain links of proteins are amino acids. Proteins contain twenty different amino acids. Each amino acid has an amino group (NH3+) a carboxyl group (COO-) a hydrogen atom (H) and a side chain. The only difference between any two amino acids is in their two different side chains. Therefore it is the arrangement of amino acids, with their distinct side chains that gives each protein its unique character. The amino acids join together in proteins via peptide bonds. This gives rise to the name polypeptide for a chain of amino acids. A protein can be composed of one or more polypeptides.
A polypeptide chain has polarity. The dipeptide (two amino acids linked together) has a free amino group at its left end. This is the amino terminus or N-terminus. It also has a free carboxyl group at its right end, which is the carboxyl terminus or C-terminus.
The linear order of amino acids constitutes a protein’s primary structure. The way these amino acids interact with their neighbors gives a protein its secondary structure. The a-helix is a common form of secondary structure. It results from hydrogen bonding among near-neighbor amino acids. Another common secondary structure found in proteins is the B-pleated sheet. This involves extended protein chains, packed side by side, that interact by hydrogen bonding. The packing of the chains next to each other creates the sheet appearance. A third example of secondary structure is simply a turn. Such turn connect the a-helices and B-pleated sheet elements in a protein.
The total three dimensional shape of a polypeptide is its tertiary structure. Examples of tertiary structure of a protein are its spherical or globular shape as in myoglobin. The highest level of protein structure is its quaternary structure. This is the way two or more individual polypeptides fit together in a complex protein. It has long been assumed that a proteins amino acid sequence determines all of its higher levels of structure, much as the linear sequence of letters in a word. However, this is an oversimplification. Most proteins cannot fold properly by themselves outside their normal cellular environment. Some cellular factors besides the protein itself seem to be required in these cases, and folding often must occur during synthesis of a polypeptide.
What forces hold a protein in its proper shape? Some of these are covalent bonds, but most are non-covalent. The principal covalent bonds within and between polypeptides are disulfide (S-S) bonds between cysteines. The non-covalent bonds are primarily hydrophobic and hydrogen bonds. Predictably, hydrophilic amino acids cluster together in the interior of a polypeptide, or at the interface between polypeptides, so they can avoid contact with water. Hydrophobic interactions play a major role in tertiary and quaternary structures of proteins.