Problem #1

Match the interaction or bond on top with all the appropriate characteristics on the bottom.

(a) Ionic (electrostatic) interaction         (b) Hydrogen bond

(c) van der Waals interaction                 (d) Hydrophobic interaction

(1) Requires nonpolar species

(2) Involves charged species only

(3) Requires polar or charged species

(4) Involves either O and H or N and H atoms

(5) Involves polarizable atoms

(6) Is also called a salt bridge

(7) Exists only in water

(8) Is optimal at the van der Waals contact distance

(9) Is weakened in water

Answer (a) 2,6,9          (b) 3,4              (c) 5,8              (d) 1,7

2.  Proteins are large biomolecules which often bind to other molecules, often smaller but not necessarily. Binding occurs in a pocket in the enzyme and often water is excluded from the site as binding occurs. Suppose that at the binding site, a negatively charged small molecule interacts with a positively charged atom of the enzyme.

a.) Using Coulomb’s equation, how would binding be affected if water were present? How about if water were excluded?

Answer: If water were present, the dielectric constant would be large and the electrostatic interaction would be lessened which, in turn, would weaken binding. If water were excluded, the opposite would be the case.

b.) Suppose that binding occurs at some distance x. What would the affect on binding be if some atom in the pocket prevented close approach of the charged atoms (ions) and kept them at a distance of 3x?

Answer: According to Coulomb’s equation, the strength of an electrostatic interaction should diminish with the square of the distance. Thus, the strength of the attractive force would lessen by a factor of 9.