Practice Problems for Biochemistry, Session 4: Proteins, Levels of Structure, Non-

Covalent Forces
Question 1

You have discovered a new enzyme, enzyme E, which breaks down proteins by cleaving peptide bonds after
tyrosine or phenylalanine.

a) Enzyme E is the product of gene G that encodes a protein with the molecular weight of 50 kilodaltons (50 kD).
When you purify enzyme E, you obtain a single type of polypeptide of 50 kD. However, active enzyme E has a
molecular weight of 250 kilodaltons (250 kD), not 50 kD.

i) Why might active purified enzyme E be larger than the product encoded by gene G?

ii) Define primary, secondary, tertiary, and quaternary structure.

iii) Is the primary structure of the 50 kD protein the same or different than the primary structure of the 250
kD protein? Explain briefly.

iv) Is the tertiary structure of the 50 kD protein the same or different than the tertiary structure of the 250
kD protein? Explain briefly.

v) Is the quaternary structure of the 50 kD protein the same or different than the quaternary structure of
the 250 kD protein? Explain breifly.

b) You test enzyme E activity on a large protein substrate. This substrate is not cleaved by enzyme E. You then
treat the substrate with DTT (a compound that disrupts disulfide bonds) and test the enzyme E activity again.
This time the substrate is cleaved by enzyme E.
Why was enzyme E able to cleave the protein substrate only after the substrate was treated with DTT?
Question 2

For the first pair of amino acids listed below, draw the two amino acids with the side chains interacting and list the
strongest type of interaction that can occur between the side chain groups. For the remaining pairs, simply list the
strongest type of interaction that occurs between the side chain groups. Choose from covalent bonds, hydrogen
bonds, ionic bonds, or van der Waals interactions.
i) tyrosine, asparagine

ii) cysteine, cysteine

Question 3

In analyzing differences between drug resistant fungi and drug sensitive fungi, you have discovered a protein that
exists only in the drug resistant fungi. You named this the Resist protein and design substrates that you hope will
bind to it.

CH 3
Val CH 3

CH 3

HO substrate 1
Glu

+ OH
H N
3

Asp Ala

star protein
Resist protein

a) Give the name for the strongest intermolecular interaction between substrate 1 as shown and the side chains
of following amino acids on the Resist protein. Choose from ionic bond, covalent bond, hydrogen bond, and van
der Waals forces.

Amino Acid Strongest interaction

b) You make the following additional substrates .

Val CH 3
CH 3
What is the strongest interaction that
CH 3 now exists between the Ala of the
What is the strongest interaction that
Resist protein
now exists and substrate
between the ala of 2?
the star
Glu HO substrate 2
protein and substrate 2?

van der Waals

star protein
Resist protein

Val CH 3
CH 3

CH 3
What is the strongest interaction that
Val CH 3 now exists between the ala of the star
Glu HO CH 3
substrate 2
proteinWhat is the strongest
and substrate 2? interaction that
CH 3 now exists between the Glu of the
What
van derisprotein
Resist the strongest
Waals
______________________________ interaction
and substrate 3? that
H 3N + + SH
substrate 3 now exists between the glu of the star
Glu NH
Asp 3 Ala protein and substrate 3?
ionic
______________________________
star protein
H3 N ++ OH

Asp Ala

star protein
Resist protein

c) Which substrate would you expect to bind the most tightly to the Resist protein?
substrate 1 substrate 2 substrate 3

Explain why you made this choice.

7.01SC Fundamentals of Biology

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