Molecular Biology Test #2 1998

Spring 1998 Molecular Biology Exam #2 - Real Data

Figures cannot be reproduced on the web version due to copy right restrictions - see originals on reserve in library.

There is no time limit on this test, though I have tried to design one that you should be able to complete within 2.5 hours, except for typing. You are not allowed to use your notes, or any books, nor are you allowed to discuss the test with anyone until noon Monday March 23, 1998. EXAMS ARE DUE AT 8:30 ON MONDAY, March 23. You must use the web as indicated on question #7 and only for #7. The answers to the questions must be typed on a separate sheet of paper unless the question specifically says to write the answer in the space provided. If you do not write your answers on the appropriate pages, I may not find them unless you have indicated where the answers are.

Please do not write or type your name on any page other than this cover page. Staple all your pages (INCLUDING THE TEST PAGES) together when finished with the exam.

Name (please print here):

Write out the full pledge and sign:

How long did this exam take you to complete (excluding typing)?

8 pts.

1) Figures 1 and 2 show the results when a receptor on the plasma membrane of mammalian cells (FcRII) interacts with its ligand (IgG). There are 2 naturally occuring alleles of FcRII (B1 and B2), and one engineered allele (Tail-) that has had its cytoplasmic tail deleted completely. Figure 1 is provided to give you some background information.

Interpret the data from figure 2.

8 pts.

2) A recent discovery was made about individuals who are resistant to the onset of AIDS after they have been infected with HIV. As we all know, there is genetic variation in the population and this included coding as well as non-coding portions of the genome. Some individuals have a chemokine (short protein used in cell to cell communications) that has an altered 3' UT region. In these individuals, the amount of chemokine is higher than in people who do not have the altered 3' UT region.

A. Formulate an hypothesis to explain what is being observed.

B. Devise an experiment to test your hypothesis.

8 pts.

3) As you can see in figure 3, you can now buy RNA blots all ready to probe from companies like Clonetech.

A. What assumption have the experimenters made with this figure? What control would you like to see?

B. Let's assume that the proper controls have been performed, interpret figure 3.

7 pts.

4) Figure 4 was published in Cell . Interpret the results.

7 pts.

5) Interpret figure 5B. Ignore the lines below the graph marked 1, 2, 3.

7 pts.

6) Figure 6 shows a family pedigree and an agarose gel. Interpret these results if an open symbol means wild-type, a spot in the middle means carrier genotype, and a black shape means diseased status for this recessive disease.

10 pts.

7) For this question, I want you to show off your computer skills that might be required of you for a job as a lab tech. You may use the web to figure out how to do this, including this site <http://bio.davidson.edu/Biology/Courses/Molbio/NIHsearch.htm>, but you may choose your favorite way.

A. You work in a lab that studies Okazaki fragments.

Find the RasMol image for Taq DNA polymerase and put it on your web page so that I can

click on it from your main page.

B. You work for Monsanto and have obtained a peptide sequence (IEESQFAIVVFSENY) from a plant

protein. Search Genbank and tell me two things.

1) What is the name of the full-length protein and what species did it come from?

2) Are there any proteins from other species that have a high degree of sequence similarity. Explain

your answer. (You might want to cut and paste some of your Genbank information to support your

answer.)

10 pts.

8) Figure 7 deals with a protein called Fgf5 that is involved in the growth of hair. A mutant strain of mice exists that has had this gene mutated so that normal Fgf5 protein is not made (recessive mutation).

A. Interpret the results from figure 7.

B. Given what you have learned in figure 7, hypothesize how the mutant phenotype can be very long hair

compared to wild-type.

Questions 9 - 11 are related questions on the same topic. You might want to look at all 3 questions before answering any of them.

8 pts.

9) Figure shows two immunofluorescence micrographs from a familiar lab (see title and authors). Interpret the results from figure 8 if you know that p58 is a protein that is located in the salvage compartment.

8 pts.

10) Figure 9 shows some experiments with lysozyme with modified carboxyl-termini. Three constructs were made that terminate in either KDEL, HDEL, or DDEL. Interpret these results.

8 pts.

11) What do we learn new about ERD2 from figure 10 if you know that GalT is a protein that is found in the Golgi compartment. (By the way, did you realize that the Golgi body was discovered 100 years ago in 1898?!)

9 pts.

12) Briefly answer these lab questions:

A) Tell me how you would make a 0.5% agarose gel that has a volume of 60 ml, is made of 0.5X TBE

(you have 1 L of 5X TBE) and the MW of agarose is 89.

B) What is calf intestine alkaline phosphatase used for (outside a calf, that is)?

C) What is the function of phenol/chloroform in a DNA prep?

2 pts.

13) What unit of measure is used for the molecular weight of proteins? (This is a give-me question to bring the total up to 100 pts.)

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