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Biochemistry - Problem set 1
August 22, 2016
Problem Set 1: Solution Key
1. (5 points, 5 min) Rank, from highest to lowest, the hydrogen bond strength of the following groups; assume the H-bond
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].
Energy (kJ/mole)
Since the energy of a hydrogen bond is mostly (90%) due to electrostatic interactions between the partial
positive charge on the hydrogen and the partial negative change on the acceptor, the electronegativity of the
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atoms should be a good predictor of the strength. Since the acceptor
Hydrogen Bond Energy
50
is the same (C=O) we only need to consider the donor. The order of
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40
hydrogen bond strength (most energy released when the bond is
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30
formed) follows the electronegativity: OH, NH, SH, CH. The CH would
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20
be very weak, such that it generally would not be considered to form
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H-bonds.
10
5
2. (6 pts, 15 min) Use the dry lab to determine the energy released due to hydrogen
0
-5 2.6
bond formation as a function of the distance between the two electronegative
3
3.4 3.8 4.2 4.6
-10
atoms.
-15
-20
i) Plot the energy versus distance for distances from 2.75A to 5A. See right.
-25
ii) What distance gives the lowest energy? ~3.2 A, with an energy of -20
Distance (A)
kJ/mol.
iii) Why does your plot have regions of unfavorable (positive) energy? This is due to repulsion between the electron
clouds as the atoms are brought too close together. In this case it would be the electron on the hydrogen
being forced into the electrons of the acceptor.
3. (9 points, 15 min) The structure shown to the right is that of the amino acid
Acceptor
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)
 Glutamine has the same functional group, but one additional
donor
carbon.
 Aspartic acid has the amide group replaced by a carboxylate.
b) What is the name of the functional group on the sidechain? (1 pt)
Amide
c) Do you expect asparagine to be more, or less, soluble in water than leucine?
Why? (2 pt) Asparagine would be much more soluble than leucine,
because it has a polar amide group. The equivalent group in leucine is non-polar.
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-10
C bond is 1.54 Å, 1Å=10 meters) (1pt). A sphere with a diameter of ~5A would enclose this amino acid.
e) Add any protons that may be missing from this structure (1 pts). Carbon forms four bonds, and nitrogen three,
missing bonds are made up by adding H.
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.]
See above diagram for answer, note that the amide nitrogen on the sidechain does not accept a
hydrogen bond. To understand this consider the difference in the molecular orbitals between
a amino group and an amide.
The nitrogen in the amino group is sp3 hybridized and one of the orbitals is full (lone pair), these
electrons can accept a hydrogen bond.
Biochemistry - Problem set 1
August 22, 2016
The nitrogen in the amide group is sp2 hybridized, because it is planer. The pz orbital contains
two electrons, however those electrons are delocalized over the entire amide group and
therefore are not available to form a significant hydrogen bond.
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)? Tryptophan
b) State whether this compound is polar or non-polar (or both); briefly justifying your
N
answer (2 pts). It is both, the larger 6 membered ring could participate in non- Hydrogen
H
Bond
polar interactions while the NH group on the five-membered ring is polar.
c) Identify all of the hydrogen bond donors or acceptors on this molecule; provide a sketch
O H
showing a water molecule forming a hydrogen bond to the compound (2 pts).
H
The N-H group will only donate a hydrogen bond. The molecular orbitals on the
N are the same as in the amide group, sp2 hybridized. The lonepair electrons in the p z orbital are
delocalized and would not be available to accept a hydrogen bond. The same is true about the NH group in a
peptide bond.
5. (4 pts) What is the most stable form of Mg? Is it ionized and if so what is its charge? Briefly justify your answer.
Mg+2 is the most stable form – if it loses two electrons it has a full shell which will effectively screen the
nuclear charge. Because the nuclear charge is screened, the next two electrons are weakly bound and thus
Mg+2 can be easily formed from the parent metal ion.