Biochemistry - Problem set 1
January 11, 2016
Problem Set 1: Due Monday Jan 18 by 3:30 - DH 1321 (Tara), MI 246A (Rule) Total time required ~45 min.
Calculate – use a formula to give quantitative answers.
Sketch - you need not calculate the curve, just try to reproduce its general features. However, take care in
representing certain 'landmarks', such as inflection points, etc. Fully label the axis with units and scale.
Problem Set Collaboration: Groups of 2-4 students can hand in collaborative problem sets; place all names on the
top right of the first page. Group members should be able to solve all the problems to prepare for the exams. Of
course, the work produced by one group is expected to independent of other groups/individuals.
1. (5 points, 5 min) Rank, from highest to lowest, the hydrogen bond strength of the following groups; assume the Hbond acceptor is the carbonyl (C=O) group. a) -N-H b) -O-H c) –S-H d) -C-H. Briefly justify your answer.
[Hint: A table of electronegativities may be helpful, see lecture 2 notes].
2. (6 pts, 15 min) Use the dry lab to determine the energy released due to hydrogen bond formation as a function of
the distance between the two electronegative atoms.
i) Plot the energy versus distance for distances from 2.75A to 5A.
ii) What distance gives the lowest energy?
iii) Why does your plot have regions of unfavorable (positive) energy?
3. (9 points, 15 min) The structure shown to the right is that of the amino acid asparagine.
The “sidechain atoms” are indicated in bold. You will need to look at a table of amino
acid structures to answer parts of this problem (see OLI lecture 5).
a) Which other amino acid is most similar to asparagine? In what ways does it differ, in
what ways is it similar? (2 pts)
b) What is the name of the functional group on the sidechain? (1 pt)
c) Do you expect asparagine to be more, or less, soluble in water than leucine? Why? (2 pt)
d) Estimate, to the nearest 5 Å (i.e. your answer should be a multiple of 5), the diameter of a sphere that would
contain the sidechain of a single asparagine molecule. In other words, how big is the sidechain of a single amino
acid? (Note, a single C-C bond is 1.54 Å, 1Å=10-10 meters) (1pt).
e) Add any protons that may be missing from this structure (1 pts).
f) Then add two H2O molecules to your drawing as indicated below. Clearly label the water that donates a H-bond
with 'donor' and the one that accepts an H-bond as 'acceptor' (2 pts).
One H2O that donates a H-bond to the side-chain of asparagine.
One H2O that accepts a H-bond from the side-chain of asparagine.
[Draw the waters as "H-O-H", with approximate bond angles and bond lengths.]
4. (5 pts, 10 min) Open the Jmol page associated with this problem set.
a) Which amino acid has this functional group as part of its structure (1 pt)?
b) State whether the compound shown in Jmol is polar or non-polar (or both);briefly justifying your answer(2 pts).
c) Identify all of the hydrogen bond donors or acceptors on this molecule; provide a sketch showing a water
molecule forming a hydrogen bond to the compound (2 pts).
5. (4 pts, 5 min) What is the most stable form of Mg? Is it ionized and if so what is its charge? Briefly justify your
answer.
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possible, you may choose to sign the following release, which will allow your graded assignments/exams/etc. to be
distributed via placing a small number in a separate folder, for pickup during class periods. In so doing, you
understand that this allows the potential that other students will see your graded work. If you choose not to sign this
release, your graded materials can be obtained directly from Dr. Rule or during recitation.
THE RELEASE STATEMENT [Please return with your completed homework assignment.]
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