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03-131 Genes, Drugs, and Disease
Problem Set 3
Solution Key
1. (10 pts, 10 min) The diagram on the left shows a small 12 residue
protein in its unfolded state (top) and its low-energy folded state
(bottom). Each circle represents an amino acid and the black circles are
non-polar residues. The mainchain is the red line.
a) Why is this state low in energy [Hint – where are the non-polar
residues]?
b) Draw the lowest energy form for the following protein. Does its
“structure” differ from the first protein?
This structure buries the non-polar residues and so it is more
stable than other possibilities. Note that the chain is folded in an
“S” shaped structure as opposed to the curl structure for the
structure on the top of the page.
Key Concept: The folded structure of the protein (and its
function) depends on the order of amino acids.
A
2. (6 pts, 15 min) Rituximab is a drug that is used to treat certain types of
cancer (you should use web resources to answer this question).
a) What is rituximab? A small organic molecule, or something else?
It is an antibody.
b) Briefly describe how Rituximab works as a drug (be sure to cite your sources).
It binds to a protein on the surface of B-cells, causing their death. Some cancers
involve the uncontrolled growth of B-cells.
3. (5 pts, 5 min) A rare genetic disease results in an individual who has no T-helper cells. Will such a person
be able to produce antibodies to fight disease? Justify your answer.
No, because T-helper cells are required to promote B-cells to develop into antibody
secreting plasma cells.
Please view Jmol-a to answer the following two questions:
4. (5 pts, 5 min) The enzyme that is shown is ribonuclease, an enzyme that is released by your pancreas to
digest RNA contained in your food. The product of the digestion is nucleotide bases, which your body
can utilize to make RNA and DNA.
a) How many α-helices does this enzyme have? (Click on the button marked ‘a’) (yes this is a simple
question).
The helices are the red helical structures – there are three.
5. (8 pts, 20 min)The “wild-type” sequence refers to the sequence of a protein that is found in most
organisms. A mutation is a change in the genetic code for a protein that results in a change in the amino
acid sequence. A point mutant involves the change of one amino acid. A genetic disease may occur if
the mutation leads to a non-functional protein.
This question involves the valine at position 108 in the polypeptide chain. You may find it useful to click
on button ‘5’ before answering the following questions. The two surfaces that you can place on the
structure (+/- 108 Surf & +/- Packing) may also be helpful.
i) A mutation changes the valine at position 108 in ribonuclease to Alanine. How do you think this will
affect the stability of the protein? Will the alanine containing protein be more or less stable than the
wild-type? Briefly justify your answer with reference to the forces/interactions that stabilize folded
proteins. You can use the button labeled Ala108 to see what Alanine at position 108 would look like.
The valine residue sits in a nice pocket that is formed by the rest of the non-polar
residues in the core of the protein – optimizing van der Waals interaction.
Alanine is smaller than valine, so it will not fit as well and there will be a gap between the
alanine sidechain and the rest of the pocket – reducing van der Walls and making the
protein less stable. You can understand this by thinking of the energy balance between
the unfolded state and the folded state. The unfolded state is stabilized by the
disorder of the protein chain. The folded state for the valine containing protein is
stabilized by van der Waals, the hydrophobic effect and hydrogen bonds. The van der
03-131 Genes, Drugs, and Disease
Waals interaction would be
missing in the alanine
containing mutation, causing
the protein to unfold.
ii) A person has a mutation in the
DNA that codes for their
ribonuclease enzyme. This
mutation converts Valine 108 to
alanine. Based on your answer
to part i), what disease condition
might exist in this person?
Problem Set 3
Wild-type (Valine)
Solution Key
Mutant (Alanine)
Chain
Disorder
Hydroph
vdW
Hydroph
Chain
Disorder
H-Bond
H-Bond
Unfolded
Folded
Unfolded
Folded
Unfolded proteins are not functional. Therefore this person would not have any
ribonuclease and would not be able to use nucleotides from their diet. No worries
though, we can make our own, but we would have to work a little harder.
Please view Jmol-b to answer the following question:
6. (10 points, 20 min) This Jmol page contains the structure of a complex between
an immunoglobulin (antibody) and cocaine. The chemical structure of cocaine
is shown on the right. Only the very top part of the immunoglobulin (Fv region)
is shown on the Jmol page.
a) Describe the general location of the binding pocket (area) for cocaine. Is it found predominately on the
light chain, heavy chain, or both? (2 pts)
It is sandwiched between the two chains (interacting with the hypervariable loops.
b)
i) Describe the energetics of the interaction between Tryptophan33H and the bound cocaine. Your
answer should discuss what stabilizes the bound cocaine, e.g. H-bonds, electrostatics, van der
Waals, or the hydrophobic effect. (4 pts)
ii) Describe the interaction(s) between Tyrosine32L and the bound cocaine. Your answer should
discuss what stabilizes the bound cocaine, e.g. H-bonds, electrostatics, van der Waals, or the
hydrophobic effect (4 pts).
You want to consider if any of the following interactions occur between the bound antigen
(cocaine) and the antibody:
H-bonds: Are donors and acceptors present in the appropriate location?
Van der Waals: Is there close contact between the antigen and the amino acid side chains
from the antibody.
Hydrophobic effect: Are there non-polar surfaces that would lead to the release of ordered
water when the antigen binds?
Electrostatics: Are there complementary (opposite) charges on the antigen and the antibody?
In general, there will always be van der Waals due to shape complementarity, and then one or
more of the other three.
vdW
For this particular antibody-antigen complex:
 Tyr32L on the light chain forms an H-bond hydroph
with cocaine, and also has van der Waals
interactions and a hydrophobic interaction with
the methyl group on cocaine.
 Tryptophan 33 on the heavy chain is in close
contact with the phenyl ring on cocaine,
showing van der Waals and the hydrophobic
effect.
H-bond
hydroph
vdW
Cocaine
In summary; The bound cocaine is stabilized
Residues from Antibody
by hydrogen bonding, van der Waals and the
hydrophobic effect. Cocaine has no ionizable groups, so it will not be charged and
therefore electrostatic interactions are not important here.