Name_________________________________________
Section_________
7.012 Problem Set 3
Stardate 7.012.10.4.00 Personal Log of Chief Medical Officer on the USS Hackerprise
Upon return from a mission to Europa, your fellow crew member, Noslen, becomes very ill. You
screen Noslen for signs of infection and find that he is harboring an alien virus.
Question 1
a) You discover that this virus carries nucleic acids, proteins and lipids. You also find that this
virus can infect E. coli cells making it easy to study in the laboratory.
i) You grow this virus with one of the following radioisotopes: 32P, 3H , or 35S.
Which of the viral macromolecules will be labeled with 32P?
Which of the viral macromolecules will be labeled with 3H?
Which of the viral macromolecules will be labeled with 35S?
ii) You analyze the nucleic acid and find the following.
What nucleic acid is the virus carrying. Why?
b) Because this is an alien virus, you want to determine which of the macromolecules (nucleic
acids, proteins and lipids) is the hereditary material. Explain how you would do this?
Question 2
a) The Vulcan scientist Crixon examines DNA replication to determine if it is similar to DNA
replication on earth. She constructs an in vitro system for DNA replication.
i) What are four components she should include in her system?
ii) Prior to replication, all the template DNA is labeled with 15N. Where is nitrogen
found in DNA?
iii) She repeats the Meselson-Stahl experiments. On the diagram below, draw the
results expected at each round for both conservative and semi-conservative replication.
Question 2, continued
b) You have invented a Nanoscopic Imager that allows you to examine an origin of DNA
replication. The computer returns the following picture. From this origin, replication is
occurring on both strands and the two forks are moving away from each other.
i) Label the 3’ and 5’ ends of the five DNA strands shown. Indicate which particular
strands are Okazaki fragments.
ii) What enzyme is required at C in the diagram above?
iii) To which site (A or B or both) can the primer, 5'-CAAGG-3' bind to initiate
replication?
iv) For each site chosen (in iii), what is the direction of elongation (left or right) of the
daughter DNA strand?
v) For each site chosen (in iii), is DNA synthesis performed in a continuous or a
discontinuous fashion relative to the nearest replication fork?
c) More human crew members on the USS Hackerprise began to feel sick from the viral
infection. While pondering this medical crisis, you notice that none of the Vulcan crew
members are ill. When you talk with Crixon, your Vulcan colleague, she is intrigued and gives
you a sample of Vulcan cells. So, you decide to mix the virus with the Vulcan cells and follow
the infection cycle in the Vulcan blood cells. When you analyze the Vulcan cells, you notice
that Vulcan DNA is highly modified with methyl groups on certain bases, and there is a
peculiar nuclease in Vulcan cells that disassembles regular, unmodified DNA. Can you
propose a model to explain the Vulcan immunity?
Question 3
Your preliminary characterization of this new virus is going well. You discover that this virus
has 1 chromosome, and you pinpoint a segment of DNA that you believe gives the virus its
ability to infect. Starfleet medical wants you to cut out that DNA segment and place it into a
vector to send to the Medical Research Facility at Omega Prime. Shown below is a schematic
of the desired viral gene fragment and some flanking DNA.
a) Shown below are the set of restriction enzymes (Purves, pp.312-315) present in your
freezer. Listed next to the enzyme name is its sequence specificity (from 5’ to 3’) and an arrow
marks the location where the enzyme cuts.
i) Circle the enzyme(s) that CANNOT cut the DNA fragment shown above.
ii) Place a check next to the enzyme(s) that leave blunt ends.
iii) Star the enzyme(s) that would leave overhanging ends after cutting.
Sna B I
TACGTA
Afa I
GTAC
Eco R I GAATTC
Sal I
GTCGAC
iv) What single enzyme could you use to remove the gene from the viral DNA?
v) Which pair of different enzymes could you use?
Question 3, continued
b) You want to insert the fragment into the vector shown below.
i) What enzyme(s) would you use to cut out the desired fragment from viral DNA?
ii) What enzyme(s) would you use to cut the vector DNA?
c) Say you use a single enzyme to cut both the vector and the fragment.
i) After ligation of the fragment and the vector, how many sites for that enzyme will
the resulting DNA have?
ii) How many possible DNA molecules can result from this kind of ligation?
d) You pass your wonderful instructions detailed above to a Ferengi Lab Technician. The
Ferengi bungles the experiment and uses only the enzyme SnaB I cut the vector DNA, and
uses only Afa I to cut the fragment from the viral DNA. He then ligates the cut fragment into
the cut vector.
i) Can you fix this mess by cutting the fragment back out with SnaB I? Explain why or
why not.
ii) Can you fix this mess by cutting the fragment back out with Afa I? Explain why or
why not.
Question 4
Starfleet Medical finally receives your vector, but they are having a lot trouble transcribing the
DNA vector with the fragment. In their reaction tube, they have the standard RNA synthesis
buffer, the vector DNA with fragment, DNA polymerase, and the nucleotide triphosphates
ATP, GTP, TTP, and CTP.
a) You think, “Of Course!”, and immediately send them a package containing
_____________________ and ___________________ which should allow them to successfully
synthesize RNA from the DNA vector containing the fragment.
b) You figure that the scientists at Starfleet Medical are meatheads, and will probably need the
components to synthesize protein from the RNA that they can now finally make. What three
major components do you need to send to Starfleet Medical so they can synthesize protein
from the viral RNA?
c) Meanwhile, back on the USS Hackeprise, you develop a nucleotide analog called Ketracell
Indigo which you use as a treatment against this virus. Ketracell Indigo fits into the catalytic
center of the viral RNA Polymerase and prevents the viral RNA Polymerase from binding
DNA. What effect will Ketracell Indigo have on viral transcription?
d) Your Ferengi technician suggests using Furomytin. Furomytin is a molecule that looks like
an amino acid-charged tRNA. It binds in the A site of ribosomes and causes premature
termination of protein synthesis. Which do you believe is a better drug against this infection?
Explain why.
And the epilogue to this story….
Not only do you cure your crew members, but you have been recognized for saving half the lives
on the USS Hackerprise. Starfleet awards you the Bashir Prize in Biology and Medicine, the
highest scientific honor given, and a holiday is created in your name. Starfleet Science Academy
gives you a professorship, where you continue to write problem sets to torture students at the
Academy. You end up living long and prospering. The End.