Question

Describe the four categories of amino acid side chains. What types of interactions are the members of each of these categories likely to make? Now describe and explain the four levels of protein structure, giving a specific example of each an how amino acids are involved.

Answer 1

The amino acids are classified into four categories on the basis of the polarity of their side chains. The side chains of the amino acids exhibit different polarities, from nonpolar and hydrophobic to polar and hydrophilic:

(1) Amino acids with non-polar, aliphatic side chains: The side chains of the amino acids in this group are non-polar and hydrophobic. The side chains of alanine, valine, leucine and isoleucine tend to cluster together in the proteins. This stabilizes the protein structures by hydrophobic interactions. Glycine has a very simple structure and with a very small side chain, it does not contribute much to the hydrophobic interactions. Methionine has a non-polar, thio-ether side chain. Proline has an aliphatic side chain with a cyclic structure that reduces the structural flexibilty of the polypeptides containing proline.

(2) Amino acids with aromatic side chains: The side chains of phenylalanine, tyrosine and tryptophan are aromatic and non-polar. These amino acids contribute to the hydrophobic interactions within the proteins.

(3) Amino acids with polar, uncharged side chains: The side chains of serine, threonine, cysteine, asparagine and glutamine are hydrophilic in nature as they contain fuctional groups that can from hydrogen bonds with water. The polarity of serine and theronine is due to the presence of the hydroxyl group in their side chains, that of cysteine due to presence of sulfhydryl group and that of asparagine and glutamine due to their amide groups.

(4) Amino acids with charged side chains: The side chains of some amino acids are either positively or negatively-charged. The positively-charged amino acids are lysine, arginine and histidine while the negatively-charged ones are glutamate and aspartate. Lysine has a second primary amino group in its aliphatic chain, arginine has a positively-charged guanidino group and histidine has an imidazole group. On the other hand, glutamate and aspartate have a negatively-charged carboxyl group in their side chains.

The four levels of protein structure are as follows:

(1) Primary structure: It is the sequence of amino acid residues in a polypeptide chain linked by the covalent bonds, such as peptide bonds and disulfide bonds. The amino acid residues are linked together by peptide bonds to form the peptide chains. The peptide bond formation is an example of condensation reaction. It is formed by removing a molecule of water from the carboxyl group of one amino acid and the amino group of the other. Thus, the amino acids are joined with these peptide bonds that produces the primary structure of a protein.

(2) Secondary structure: It is the particularly stable arrangements of the amino acid residues to produce recurring structural patterns. There are two types of secodary structures: alpha helices and beta-sheets. In the alpha helix, the polypeptide backbone is held around an imaginary longitudinal axis through the middle of the helix, and the side chains of the amino acid residues protrude outward from the backbone of the alpha helix. Each helical turn includes 3.6 amino acid residues and about one-fourth of all amino acid residues in polypeptides are found in alpha helices. On the other hand, beta-sheet is a more extended conformation of the polypeptide chains. In a beta-sheet, the backbone of the polypeptide chain is extended into a zigzag rather than a helical structure. It is stabilized by hydrogen bonds formed between adjacent segments of polypeptide chain. The side chains of adjacent amino acids protrude from the zigzag structure in opposite directions.

(3) Tertiary structure: It describes the three-dimensional folding of a polypeptide chain. It includes longer-range aspects of amino acid sequence. Amino acids that are present far away part in a polypeptide sequence and that reside in different types of secondary structure may interact within the completely folded structure of a protein. The location of bends in the polypeptide chain and the direction and angle of these bends are determined by the number and location of specific bend-producing residues, such as proline, threonine, serine, and glycine.

(4) Quarternary structure: When a protein contains two or more polypeptide chains, then the spatial arrangement of the chains is referred to as the quarternary structure. One good example is hemoglobin, which is an assembly of four globular proteins.