Question

Describe all types of associations (hydrophobic interactions, ionic interactions, etc.)
that lead to stabilization of tertiary structure. Be detailedin your descriptions. Indicate how
eachof these associations can be lost due to denaturation. Give an example of a denaturation
cause (high temperature, change in pH, salt, or chemical) that results in the loss of eachtype of
association.

Answer 1

As the secondary structure becomes established due to the primary structure, a polypeptide folds and refolds upon itself to assume a complex three-dimensional shape called the protein tertiary structure. Tertiary structure is the overall shape of a polypeptide. Tertiary structure results from the interactions between the side chains (R groups) of the various amino acids^.This three dimensional structure is due to intramolecular interactions (covalent bonds, hydrogen bonds, ionic bonds, and Van Der Waals interactions) between the side groups along the polypeptide chain. Its domain typically contains 300 – 400 amino acids, and it adopts a stable tertiary structure when it is isolated from their parent protein. As a polypeptide folds into its functional shape, amino acids that have hydrophobic side chains tend to end up clustered at the core of the protein so that they are out of contact with water Covalent bonds called disulfide bridges can also affect the shape of a protein. Disulfide Bridges form where two amino acids containing sulfhydryl groups on their side chains are brought close together by how the protein is folding. For some proteins, such as ribonuclease, the tertiary structure is the final structure of a functional protein. Other proteins are composed of two or more polypeptides and adopt a quaternary structure.

Protein denaturation: is the loss of native conformations of tertiary structure. Denaturing proteins experience either the destruction of disruption of internal tertiary or secondary structure. Denaturation however, does not break the peptide bond between adjacent amino acids, thus not affecting the primary structure of the protein. Denaturation however, will interfere the normal alpha-helix and beta sheets in a protein which ultimately distort its 3D shape.

Denaturation causes the disruption of hydrogen bonding between close proximity amino acids, thus interfering a protein's secondary and tertiary structure. In tertiary structure there are four types of bonding interactions between "side chains" including: hydrogen bonding, ionic bridges, disulfide bonds, and hydrophobic intermolecular interactions. In other words, there are several different conditions to denature the conformation of a protein.

Conditions that denature proteins:

1. Extreme pH (pH < 4 or pH > 9) : alters H-bonding

2. Heat (temp >70oC): thermal effect, disrupts weak forces of non-covalent bonds

3. Detergents or organic solvents : disrupts hydrophobic interaction

4. Chaotropic agents (high concentrations) : e.g., urea and guanidinium chloride