BCHM 461_0101

Name______________________________________ 1

March 1, 2011
Dr. Paul Paukstelis

Exam 1

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#2_______/30
#3_______/60
#4_______/60
#5_______/20
Total:

/200

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BCHM 461_0101

Name______________________________________ 2

March 1, 2011
Dr. Paul Paukstelis

Exam 1
(200 points)

1)(30 points) Acid-Base Chemistry

A)(10 points) Which buffer from the table would you choose for an experiment to be done at pH 6
and which at pH 8? Explain briefly how you decided AND fill in the table the buffer pH range for each
weak acid.
ACID
Acetic acid
MES.H+
HEPES.H+
CAPSO.

pKa
4.7
6.1
7.5
9.6

Buffer Range

B)(20 points) Calculate the pH of the buffer of a solution of 0.02 M acetic acid and 0.04 M acetate.
How much of a 1 M solution of HCl must you add to 100 mL of the above mentioned solution to lower
the pH to 4.5? Write down the Henderson-Hasselbach equation. Ignore volume change of the
solution.

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 3

2) (30 points) Bioenergetics.

Given: [R= 8.315 J/mol . K] Consider the reaction at standard temperature:
glucose-1-P
glucose-6-P
Keq=21
A)(5 points) Is the concentration of glucose-6-P equal, higher or lower than that of glucose-1-P at
equilibrium? Justify your answer using the expression for Keq.

B)(6 points) What is G' for the reaction? Write down the equation used in the calculations and the
units in your answer.

C)(10 points) If the concentrations of glucose-6-P and glucose-1-P are 100 M and 1 M,
respectively, what is G at 25 C? Write down the equation used in the calculations and the units in
your answer. Under this condition is the reaction endergonic or exergonic?

D)(5 points) Why are G' and G different?

E)(4 points) Briefly describe two ways unfavorable reactions can be forced to proceed in the
forward direction.

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 4

3)(60 points) Peptide Chemistry, Sequencing, and Chemical Structure

You are working with a peptide of 16 residues. You are instructed to find the sequence of this
peptide. All sequences are written N-terminus to C-terminus. Use one letter abbreviations unless
otherwise noted.
A)(18 points) You perform a trypsin digestion on a peptide and determine there are three peptide
fragments: QAR, TDAMLMFNAK, CAT. Based on this information write down the two possible
correct sequences for the peptide using three-letter abbreviations. In one sentence describe how
you arrived at your answer.

B)(5 points) You perform chymotrypsin digestion on your starting peptide sample. This yields two
peptide fragments: NAKCAT, QARTDAMLMF. Based on this information, what is the actual
sequence of your peptide?

C)(7 points) If you were to treat your starting peptide with cyanogen bromide, how many peptide
fragments would you have? Write down the sequences of these fragments.

D)(30 points) You determine conditions under which cyanogen bromide treatment is only 50%
efficient (only cuts half the sites). Under these conditions you perform a triple digest using trypsin,
chymotrypsin, and cyanogen bromide simultaneously. You detect four different peptides that are
three residues in length. Write down these three peptides and draw the chemical structure of the
most hydrophobic peptide (draw all four residues linked through peptide bonds, use N, C, O for
respective atoms, indicate all charges). Indicate the N- and C-terminus, and assume no chemical
changes from the cleavage reaction. You can use the space on the next page.

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 5

4)(60 points) Nucleic Acids

A) (20 points) In the image below, draw the chemical reaction catalyzed by DNA polymerase by
which DNA is replicated. Please use arrows to clearly indicate electron-pushing, label the nucleophile,
the leaving group, and show required ions (both positive and negative).

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 6

B)(10 points) You have two solutions, A and B, with the same concentration of the same DNA
molecule. Their absorbance at 260 nm are 1.0 and 0.6, respectively. What can you tell about the
physical state of the DNA in these two solutions? What is the name of this phenomenon and why is it
observed? What might have been done to these samples to observe this result?

C) (20 points) For the following figure on the lines provided: 1. identify the nucleotide (base) with a
single letter, 2. identify the atom number of the given atom, 3. identify the sugar pucker. In the box
provided, draw the complementary nucleobase (with valences) base paired to the nucleobase in
panel 3.

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 7

D) (10 points) On the line provided, write out the sequence (5' to 3') for the nucleic acid molecule in
the following image.

5) (20 points) Putting concepts together. These are not trick questions. I am interested in seeing
how much you understand about the chemical properties of these polymers.
Consider four peptides:
Peptide-1: QVSALKATR; Peptide-2: WFLAWSVVY; Peptide-3:
ERDAGSDAA
and two RNA molecules:
RNA-1: 5'-AGUAAGAACGUAA; RNA-2: 5'-GGUUCAAAGAACC

KRANRKKRH;

Peptide-4:

A) (6 points) Order the peptides from most hydrophobic to least hydrophobic (e.g. Peptide-1,
Peptide-2, Peptide-3, Peptide-4)

B) (7 points) Which peptide do you expect is most likely to interact with the RNA molecules? Which
is least likely? Why?

BCHM 461_0101

March 1, 2011
Dr. Paul Paukstelis

Name______________________________________ 8

C) (7 points) You find that Peptide-2 interacts strongly with RNA-1 but does not interact with RNA-2.
Provide a short explanation for why this might be.