Test 3 Practice Questions

1.  A. What is the product of human gene FLT3?

B.  Name one disease associated with FLT3.  State the primary reference and evidence.

C.  State one function associated with FLT3.  State the primary reference and evidence.

D.  What kind of mutation in FLT3 is associated with disease?  Explain how this mutation can occur, in terms of DNA replication.

2.  A. What is the product of human gene BRCA2?

B. In what tissues is BRCA2 expressed?  State reference and technique.

C.  How does BRCA2 relate to male breast cancer?  Describe the evidence.

D.  What kind of molecular function is known for BRCA2?

E.  What is the role of BRCA2 in DNA repair?  What kind of DNA repair is mediated by BRCA2, and why is it important?

F.  State one example of a particular class of mutation of BRCA2, and how it impacts phenotype.

3.  A.  What is the produce of human gene TP53?  What is believed to be the specific role of its protein product in cell division?

B. What can we learn about TP53 from transgenic mice?  State reference. 

C. State one example of a point mutation.  Explain the result of the mutation for the gene sequence, and for the phenotype of the organism.  State reference.

D.  How does LSD1 interact with the product of TP53?  State reference.

E.  Explain how a HOX binding site may interact with the TP53 gene product during carcinogenesis.

F.  What is the chromosome location of TP53?  What is its protein sequence? 

G.  How does its protein sequence relate to sequences of other organisms?  What other organisms have orthologs?  (BLAST  Reference Proteins)  What is the most distant organism showing a possible ortholog?  What kind of organism is this, and how does it relate to humans?

H. View the DNA sequence.  How many exons does the gene have?  What gene lies immediately to the left (lower kilobase number) of TP53?  What is the function of this neighbor gene?

4.  Explain based on a specific figure in the research paper:

A. How was it shown that Argonaute is essential for mouse development?  What were the experimental conditions and controls?

B.  What is “slicer” activity, and what evidence support the role of Ago2 as a “slicer”?

C.  Explain an experiment that showed that Ago2 catalyzes cleavage of a siRNA, but not Ago1 or Ago3.

5. Explain with a diagram how the leading and lagging strands of DNA are replicated simultaneously by the replisome.

6. Explain the mechanism of a mutation causes by (a) water (hydrolysis); (b) oxidation; (c) alkylation; (d) a mistake by DNA pol III; (e) UV radiation; (f) X radiation; (g) acridine; (g) base tautomerization.

7.  For each mutation mechanism in question 5, explain how the mutation might be (a) reverted or repaired accurately (b) repaired inaccurately. 

8.  Based on what we know now, why might it be possible to clone a mammoth or a Neanderthal, but not a dinosaur?

9.  Explain the role of DNA recombination in DNA repair.  Include molecular details.

10.  Explain how to identify an enhancer sequence and establish its role in development.  Include experiments from genomics, biochemistry, and genetics (transgenic animals).

11.  Explain “exaptation” of a DNA sequence.  Propose a science fiction scenario in which the genome of HIV (human immunodeficiency virus) gets incorporated into a human genome and undergoes exaptation.

12.  In Santangelo et al: When in evolutionary history did the first nPE2 evolve?  Explain the evidence, referring to figures.

13.  What was the structure of the original retroposon ancestral to nPE2?  What other enhancers appear to have evolved from this retroposon?  Refer to figures.