2 Biochemistry MC Questions - Protein Structure, Enzymes

[Atu]

1. A substrate molecule may be bound to the active site of an enzyme by all of the following EXCEPT
A. Hydrogen Bonds
B. Peptide Bonds
C. Ionic Bonds
D. Van der Waals Interactions
E. Hydrophobic Interactions

2. Which of the following components is the most important in determining the 3-D structure of Hemoglobin?
A. Quaternary Structure
B. Tertiary Structure
C. Secondary Structure
D. Primary Structure
E. Number of Disulfide Bonds

For question 1, I'm between Peptide (B) and Van der Waals Interactions (D). For 2, I'm between Quaternary (A) and Primary (D).

 

[Atu]

For question 1, my sources indicate that hydrogen, Ionic, and Hydrophobic interactions all play a role, but don't mention peptide or van der Waals at all. I'm thinking that maybe peptide bonding is present, as it involves proteins (the enzyme); therefore, the answer is van der Waals. However, van der Waals can also be present, because it is a weak interaction between "close" molecules.

For Question 2, I know that Hemoglobin consists of 4 subunits (thus Quaternary Structure); however primary structure determines shape of proteins...

 

[Borek]

Hint: enzyme and the substance that attaches to the active site are two different (separate) molecules.

 

[Atu]

Hint: enzyme and the substance that attaches to the active site are two different (separate) molecules.

That would imply that Peptide bonds are not present in active site binding, as it would form a completely new molecule, correct?

However, according to my textbook, sometimes an active site directly participates in a chemical reaction by having the R-group bond covalently to the substrate. And since a peptide bond is a covalent bond, I don't know...

 

[epenguin]

That would imply that Peptide bonds are not present in active site binding, as it would form a completely new molecule, correct?

However, according to my textbook, sometimes an active site directly participates in a chemical reaction by having the R-group bond covalently to the substrate. And since a peptide bond is a covalent bond, I don't know...

A peptide bond is a covalent bond, but not every covalent bond is a peptide bond! And what actually is meant by an R-group? - is it part of a peptide bond?

I suggest you flip the pages forward in your book to where some enzymatic mechanisms are treated to see what is meant by 'participates in a chemical reaction by having the R-group bond covalently to the substrate' in some examples showing what is meant by this straightforward idea rather than be content with this vague general description or be drawn into essentially verbal quizzes.