Question

Describe primary, secondary, tertiary, and quaternary structure and differentiate among the structures based on

• Stabilization by intramolecular covalent bonds
• Stabilization by hydrogen bonds
• Stabilization by hydrophobic effect
• Function in binding ligand
• Regulation of function by allostery

Answer 1

Solution

Primary structure

• The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain.
• For example, the hormone insulin has two polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown here is cow insulin, although its structure is similar to that of human insulin.)
• Each chain has its own set of amino acids, assembled in a particular order. For instance, the sequence of the A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, and is different from the sequence of the B chain.

Secondary structure

• The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. (The backbone just refers to the polypeptide chain apart from the R groups – so all we mean here is that secondary structure does not involve R group atoms.)
• The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another.
• Ionic bonding, hydrogen bonding etc.

Tertiary structure

• The overall three-dimensional structure of a polypeptide is called its tertiary structure.
• The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein.
• R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces – basically, the whole gamut of non-covalent bonds.
• For example, R groups with like charges repel one another, while those with opposite charges can form an ionic bond.
• Similarly, polar R groups can form hydrogen bonds and other dipole-dipole interactions. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.
• Salt bridges, disulphide bond hydrogen bonding etc.

Quaternary structure

• Many proteins are made up of a single polypeptide chain and have only three levels of structure (the ones we’ve just discussed).
• However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure.
• Hydrophobic interaction and hydrogen bonding