BIOL/CHEM 3361 Biochemistry I Spring 2020

(and BIOL 6352)

PROBLEM SET 1

Due: Tuesday Feb. 4, 2019 at 5:00 pm in the metal collection box in the hall outside FO
3.606.
Problem sets MUST contain a COVER SHEET that includes your:

Ø Name
Ø Net ID (e.g. xyz000000)
Ø Section Number (001 for Marsh/Spiro, 002 for Taylor)
Ø Total number of pages submitted, including the cover sheet

Please also write your name on EACH page.

NO late problem sets will be accepted.

For full credit, all steps to the solutions of the following problems must be shown.

PLEASE put the questions in order from 1 – 7.

You may work together on the problems, but YOU MAY NOT COPY FROM ONE ANOTHER
OR PLAGIARIZE FROM EXTERNAL SOURCES. Failure to maintain these standards may
result in a referral for academic dishonesty to the Office of Community Standards and Conduct.
Your answers must be written, must show your own math steps, and must be IN YOUR OWN
WORDS.

For these problems, assume an activity coefficient of 1 for all substances and no effect of ionic
strength. Eliminate terms in quadratic solutions for [H+] only if the weak acid is dissociated < 5%.
Reported pKa values can vary depending on the conditions under which they were measured;
therefore, in solving the following problems use the pKa values given with the problems.

Round your answers to two or three significant figures, as appropriate.

1. Acids & Bases

a. What is the pH of 100 mL of a 50 mM HNO3 solution?

b. What is the pH of 100 mL of a 50 mM solution of benzoic acid (pKa = 4.2)?

c. How do you know if you need to use the quadratic equation for weak acid problems? (Or, how
do you know that the “x is small assumption” is correct?) Why does this work?

d. What is the pH after 100 mL of a 50 mM HNO3 solution is added to 70 mL of a 50 mM NaOH

solution?

e. What is the pH of 100 mL of a 50 mM solution of benzoic acid is added to 70 mL of a 50 mM

NaOH solution?
f. Show the derivation for pH + pOH = 14, starting from the definition of Kw. Be sure to include
a sentence on where the number 14 comes from.

g. Does pH + pOH = 14 work at all temperatures? Why or why not? What should happen to this
value as the temperature increases?

2. Buffers
Tris is a commonly used as a component of biological buffers (pKa = 8.1), typically made by
adding HCl to obtain the desired pH. It is used in TAE and TBE buffers, and its image is below.
It is the amine group that is typically protonated at low pH.

a. What is the pH of a 100 mM solution of Tris?

b. What is the ratio of protonated to unprotonated Tris when the pH = 7.2?

c. How much water, 1M HCl and 1M Tris would you need to combine to make 100 mL of a 100
mM Tris-HCl buffer at a pH of 7.2?

d. Let us assume you made the buffer above (2c) at 23°C. You need to use it in an experiment in
the cold room, at 4°C. Over lunch, your friend tells you that Tris-HCl is notoriously temperature
sensitive. Assuming a raise in pH of 0.03 units per degree Celsius when the temperature is
lowered, how much 1M HCl or 1M NaOH (please specify which you would use) do you need to
adjust so that your buffer is still at a pH of 7.2 at the colder temperature?

3. Utilizing pH to get concentrations

a. What is the concentration of a 75 mL solution of benzoic acid with a pH of 3.9? (pKa = 4.2)

b. If the current ocean pH is 8.1, what is the most likely ratio of H2CO3/HCO3-/CO32- present?
pKa1 = 6.4; pKa2 = 10.3

c. One proposed solution to ocean acidification is to, essentially, add a base back to the ocean. If
we were to try to change the pH of the Atlantic Ocean (roughly 3 x 1020 L) to 8.2, how many
grams of NaOH would we have to add if there is a 2.3 mM carbonic acid buffer current at a pH
of 8.1? (Assume any volume change is negligible).
4. Equilibrium
A dehydrogenase has the following reaction:
NAD+ + H2 + substrateà product + NADH + H+ DG° = -17.2 kJ mol-1

a. Given the following concentrations for the above reaction (which is reversible), which
direction will the reaction proceed? Show your work.
[NAD+] = 5mM [H2] = 10mM [substrate] = 0.5 µM
[NADH] = 0.5mM + -5
[H ] = 1 x 10 M [product] = 0.01 µM

b. What is the value of Keq for the reaction above?

c. What is DG°’ and Keq’ for the reaction above? Justify your answer/show your work.

5. A reaction is temperature sensitive, as shown below.

AàB+C

Temp o C Keq
10 3.0 x 10-15
20 6.8 x 10-15
30 1.5 x 10-14
40 3.0 x 10-14
a. Using excel, make a Van’t Hoff plot. Include a table showing any results from calculations.
Also include trend line, and best fit equation on the plot.

b. Use the information to determine ∆ Ho' and ∆So'

c. Is this reaction entropically or enthalpically driven? Explain your reasoning.

6. Amino acids and pH

a. Draw the amino acid glutamate, showing the two dominate forms at a pH of 5.

b. What fraction of each species drawn above will be present at that same pH?

c. For the peptide glycine – arginine – glutamate – alanine – threonine, write the three letter and
one letter abbreviations

d. Calculate the pI of this peptide

e. Draw this peptide, with all groups properly protonated or deprotonated at a pH of 6.

7. Given the list of proteins below, answer the questions that follow.
Ovalbumin (chicken), monomeric, 42.7 kDa, pI = 4.6
Lysozyme (chicken), monomeric, 14.1 kDa, pI = 11.0
Myoglobin (horse), monomeric, 17.0 kDa , pI = 7.0
Hemoglobin (human), tetrameric, 64.0 kDa , pI = 7.1

a. What order would these proteins elute off of a size exclusion column?
b. What order would you expect these to run (from the lowest on the gel to the highest) on an
SDS-PAGE?
c. What order would these proteins elute off of with a DEAE column with a buffer solution with
a pH = 3.7?
d. What order would these proteins elute off of with a CM column with a buffer solution with a
pH = 11.5?
e. What method would you use to separate myoglobin from lysozyme? Explain your reasoning.