BIOLOGY 285 Study Guide - Quiz Guide: Nuclear Membrane, Ionic Bonding, Protein Folding
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Published on 16 Nov 2020
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Michelle Shang
Bio 285
Please type your responses and submit in hard copy.
Question 1: Protein/Ligand Interactions
In analyzing differences between star squash players and armchair warriors, you have discovered a
protein that only exists in star squash players. You design substrates that will bind to the “star
protein”. Keep in mind that substrates (small molecules or proteins) bind to other proteins using very
similar types of bonds/interactions as used in protein folding.
A. Give the name for the strongest intermolecular interaction between the substrate and the following
amino acids on the star protein. Choose from ionic bond, covalent bond, hydrogen bond and van der
Waals forces.
Amino Acid
Strongest Interaction
i.) Val
Van der Waals
ii.) Glu
Hydrogen bond
iii.) Asp
Ionic bond
iv.) Ala
Hydrogen bond
B. You make the following additional substrates (substrate 2 and substrate 3):
(i) Does the interaction between the Ala of the star protein and the substrate change with substrate 2
as compared to substrate 1 (note that the SH group is not quite as polar as the OH group)?
Yes, because sulfur is unable to form hydrogen bonds with the side chain on Alanine.
(ii) Does the type of interaction between the Glu of the star protein and the substrate change with
substrate 3 as compared to substrate 1?
No, because the Glutamic acid the nitrogen in the ammonia can also form a hydrogen bond
with the side chain.
iii) Which substrate would you expect binds the most tightly to the star protein? Why?
Substrate 1 will be the tightest bond because it has an oxygen forming a hydrogen between Glutamic
acid instead of the nitrogen from substrate 3. Compared to substrate 2, substrate one will form a