CELL 4010-6010 Assignment1

This assignment is due at 5 pm on Monday, September 14 at 5 pm. Late papers will not be
accepted. Directions below must be followed or points will be lost.
You may work with a group of no more than four people including you. Please submit one
paper for the group. All participants in the group must be listed. This list should appear on the first
page of your paper and should be on the left hand side of the paper on the first page under the heading.
Working together means that you work as a group to solve the problem, not that one person copies
anothers work. If you work in a group, you will submit one paper and by submitting the paper each
member is affirming that all persons list contributed to the paper. Dividing the questions among
group members and then copying each others answers is considered plagiarism. You are not
required to work in a group and you may submit your own paper. You may use any resource but you must
include who or what you used except for me, the TAs and the textbook. Including ideas or information
from any resource without proper citation violates the student honor code and is plagiarism. Presenting
another persons thoughts and ideas as your own is plagiarism. If you use outside sources be sure
you use your own words to incorporate this into your answers. You must cite these outside sources.
Even material from websites with no clear author must be cited. Plagiarism is also copying
information at of textbooks, websites and others old assignments or exams without indicating
where you got the material. Plagiarism in this class will not be tolerated.
All references should be in the style of the Journal of Biological Chemistry for all assignments.
In JBC, references are listed at the end of the paper and are numbered in chronological order as they
appear in the paper. The number of the reference should appear in the paper where it is cited. The
following are examples of the JBC style:
Journals: MacDonald, G. M., Steenhuis, J. J., and Barry, B. A. (1995) A difference Fourier transform
infrared spectroscopic study of chlorophyll oxidation in hydroxylamine-treated photosystem II. J. Biol.
Chem.270, 84208428
Books: Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual,
2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Website: Give author, if known, the title of the article, the website, the URL and the date accessed.
Example:
_____, Protein Domain, Wikipedia, http://en.wikipedia.org/wiki/Protein_domain, 1/20/14
All assignments must be completed on 8 X 11 paper, preferable white. Put your name(s) and
course section on the top right hand corner of the first page. The paper may be typed or handwritten or a
combination. The assignment should not be done in green, red, pink or similar colors of ink. Black ink
and /or pencil are preferred for handwritten papers. Clearly indicate which problem you are answering
and write your name(s) on each page. Please write large enough and clearly enough that your paper can
be read. If we cant read it, we will assume the answer is wrong. Typed papers are appreciated. You
must show your work on problems to receive complete credit. You may submit your assignment
electronically by e-mailing it to Dr. Hopkins as either a Word or PDF file. You may also submit it to Dr.
Hopkins in class or in her office or by placing it in the file outside her door. Do not use you cell phone to
send your assignment as a picture as those tend to be unreadable and produce huge files that are difficult
to download. Remember, anything that we cant read is wrong.

1. The highly pathogenic anaerobic bacterium Clostridium perfringens is responsible for gas
gangrene, a condition where animal tissue is destroyed. This bacterium secretes an enzyme that
efficiently catalyzes the hydrolysis of a specific peptide bond as show below:
-X-Gly-Pro-Y- + H2O -X-COO- + +H3N-Gly-Pro-Ywhere X and Y are any of the 20 common amino acids.
How does the secretion of this enzyme contribute to the invasiveness of this bacterium? Why
does this enzyme not affect the bacterium itself?
2. Which set of binding data is likely to represent cooperative ligand binding to an oligomeric
protein? Explain how you reached the conclusion.
a) [Ligand] (mM)
Y
b) [Ligand] (mM)
Y
0.1
0.3
0.2
0.1
0.2
0.5
0.3
0.3
0.4
0.7
0.4
0.6
0.7
0.9
0.6
0.8
3. Determine the net charge of the predominant form of peptide Asp-Pro-Cys-Glu in solution at
the following pH:
a. pH 1.0
b. pH 3.0
c. pH 6.0
d. pH 11.0
4. Using the data below, hand construct a Lineweaver-Burk plot and determine the K M and vmax
for the enzyme.
[S] (mmol/L)
v(mol/L/min)
1.25
1.67
2.50
5.00
10.00

1.72
2.04
2.63
3.33
4.17

5. A few hours after death of an animal, the corpse will stiffen as a result of continued
contraction of the muscle tissue (this state is called rigor mortis). This phenomenon is the result
of loss of ATP production in the muscle tissues.
a) Describe why this is the case based on what you have learned about myosin-actin reaction
cycle.
b) The Ca2+ transporter in sarcomeres that keeps the [Ca 2+] ~ 10-7 M requires ATP in order to
drive Ca2+ ions across the sarcoplasmic reticulum. How would a loss in this Ca 2+ transport
function result in the initiation of rigor mortis?
c) Rigor mortis is maximal at ~12 hrs after death and by 72 hours is no longer observed. Propose
an explanation for the disappearance of rigor mortis.

6. What is the pH of the following buffer mixtures?

a) 100 ml of 1 M acetic acid plus 100 ml of 0.5 M sodium acetic
b) 250 ml of 0.3 M phosphoric acid plus 250 ml of 0.8 M KH2PO4
7. What is the molecular basis for the observation that the overall charge on a protein becomes
increasing positive as the pH decreases and increasingly negative as the pH increases?