IMAT 2018 Q24 [HIV Virus]

The enzyme HIV-1 protease is produced by the HIV virus.

The enzyme is formed from two identical chains of 99 amino acids. In each chain, amino acids 25, 26 and 27 in the sequence form part of the active site.

Which levels of structure control the shape of the active site of the HIV protease?

A. primary, secondary and tertiary only
B. primary, secondary, tertiary and quaternary.
C. primary and quaternary only
D. secondary and tertiary only
E. quaternary only

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Primary Structure: the specific sequence/order of amino acids (for example A-T-G-C: A must be first, followed by T, and so on).

Secondary: Hydrogen bonds in the amino acid sequence modify the shape and therefore the interactions between the amino acids. Results in alpha helices or beta pleated sheets.
Mediated by hydrogen bonding (between the peptide backbone) and Van der Waals forces (both attraction and repulsion, increasing with increasing size of protein)

Tertiary: 3D shape as a result of side chain interactions of the amino acids.
Mediated by Hydrogen bonding, Disulfide bonding, Ionic bonding, and hydrophobic interactions

Quarternary: overall protein structure of 2 or more polypeptides. Can also include non-polypeptides (ex. heme group in hemoglobin).
Mediated by (same interactions as tertiary structure): Hydrogen bonding, Disulfide bonding, Ionic bonding, and hydrophobic interactions.

Now looking at the question, we are told that we have 2 chains of amino acids that are forming the enzyme (since it is formed by 2 chains, we know it has a quaternary structure and the interaction between these two chains can have an effect on the active site. We are also told that the active site is located at specific numbers within the chain, meaning the order matters and primary structure will be involved. The last two structures we haven’t mentioned are tertiary and secondary structures, and although they may not have anything that can specifically show their use in the text, we need to know that these two structures play key roles in the 3D shape of these polypeptides and how they assemble, therefore we cannot forget to include them. The 3D shape will influence how the active site is orientated and shaped, so we can confirm that secondary and tertiary will also play a role.

\fcolorbox{red}{grey!30}{As a result, B is correct, as all protein structures play a role.}