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Final Exam, 2007
It's up to you how final!
The final exam will be Monday, May 7 from 1-3 PM in room 3109 CEBS. Your lab group should develop an answer to the question below and be ready to turn it in at the beginning of the exam period. Your group will also present a poster on the results of your second experiment. You will be expected to evaluate each others work as presented on the posters, so come prepared to do so. - Enjoy
Problem 1.
Disclaimer: The situations given below are purely fiction. Any resemblence to real persons or situations are purely coincidental.
The following is an interactive mini-test from the spy thriller by U.R. Theere, entitled, "Trojan Horse". Answer the questions in italics, solve the mystery and save the world!
After graduating you are recruited by the CIA to work in their molecular biology section. The CIA tracks a number of extremist and terrorist groups but the elitist group called the Silver Spoon has been of special concern lately. Their goal is to bring themselves to power and rule all nations under a single world order. Agents have found that one Silver Spoon member, code named OJ, has been actively contracting work through GenCorp, a world leader in DNA/Protein synthesis and recombinant DNA work. GenCorp has made a large protein for him that appears to have no biological activity and he has recently sent an RNA to be subcloned. Your first assignment is to join GenCorp and discover what OJ is getting GenCorp to make for him and why.
What a great assignment! GenCorp is the top paying biotech company in the world. It is located on a tropical island outside the jurisdiction of all governments. Their employees are hired on five year contracts that are renewed after four years. Once on the island they can have no contact with the outside world. If after four years they decide not to renew their contract, they are isolated to less sensitive work for the last year until their contract expires and they leave. The island is a paradise with every conceivable form of recreation but at the same time it is a information fortress that allows only orders to come and go. GenCorp does nearly any kind of biotech work for those who are willing to pay. GenCorp markets several products such as Grower, a growth hormone coveted by athletic types; Clotter, a blood clotting agent for hemophiliacs; and DiaSafe, a liposome delivered system for proteins that prevent diarrhea and is commonly used by international travelers and diplomats.
Once in the lab at GenCorp you search for any files on the company computer network relating to orders or correspondence with the Silver Spoon agent OJ. You discover the original order for the large useless protein that he had made. The order simply said. "Translate sequence Trojan.seq and return.", signed OJ. You quickly look up file Trojan.seq in the Orders folder and translate it to see if you can get a clue. As you look at the amino acid sequence and set the display grouping to one, the letters seem to swim together and a clue appears. Using this clue you find the referenced file in the Orders folder. The sequence has no apparent meaning and translation does not help. You decide to compare it to other database sequences in the GenBank using the Blast Search. As the matches to the sequence appear on the screen, fear grips you with knowledge of the potential destruction that faces the world. A close examination of the matches shows that an additional sequence has been added to the potentially deadly sequence. You wonder why, would this additional sequence keep the deadly sequence from functioning? If so, what would activate the deadly sequence? What roll will the product DiaSafe play in this scheme and how could one use a commercial product for espionage without killing everyone?
A short time later another order comes in from agent OJ. This one also requests
that a translation be done on the file Helen.seq. You find Helen.seq in the
Orders folder and translate the sequence, looking for a new message. As
you read the new amino acid sequence another clue is discovered. You
again look up the file referred to in the message and compare it to the Orders
folder as before to see what it matches. As the matches begin to appear
on the screen you realize how the devious plan will be "executed" .
. . it is now time to leave!
You had pre-arranged to maintain simple contact with the CIA by sending messages
through the gel patterns generated by restriction digests. Each week a CIA
agent from the company called Cut'N Go (the RFLP equivalent of Toys'R Us)
would send samples to be digested and the migration information would be returned. You
put your message telling which of the pre-arranged exit plans you will use
the following week into the file RFLP1500050707, the number indicating the
time and date of departure. You prepare and wait, hoping that you have
not missed any clues (Use the RFLP file to determine how and when you
will leave the island).
Questions for Problem 1
Below is a summary of the questions found in question 1 that must be answered for the scenario above. Write brief answers to each and submit them at the beginning of the final exam period.
-- enjoy!
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