1. How do retroviruses such as HIV differ from LTR-type retrotransposons?

2. Why is it important for transposons to regulate the frequency at which they transpose?

3. Given that modern-day strains of corn, widely grown in Illinois, contain thousands of copies of Ds elements, why are these lines so genetically stable?

4. In your studies of IS elements of E. coli, you have identified a unique element. This IS, called IS42, is non-autonomous and requires IS5 in the same cell in order to transpose. You observe that insertions of IS42 into the lacZ gene of the lac operon are mutagenic on lacZ, but do not exert polarity on the downstream genes, lacY and lacA. You sequence the transposon and find that:

A. It produces 7 bp target-site duplications.

B. It is 119 nucleotides in length including its 12 bp IR elements.

C. It does not contain any transcriptional termination signals or stop codons in any reading register in either DNA strand..

How is it that this IS element can transpose?

5. Describe three roles of the poly dA sequence located at the 3' ends of non-LTR, poly-A containing retrotransposons.

6. In replicative transposition in which the transposon moves from one replicon to another, how is the cointegrate intermediate (the fused replicons) that is produced during transposition converted back to the two replicons?

7. You know the mechanism by which a transposon can move from one site in a DNA molecule to another site in the same molecule or to a site on a different DNA molecule IN THE CELL. But how can a bacterial transposon move from one cell to another?

8. Target site duplications are seen at the sites of transpositon of bacterial transposons and both LTR and non-LTR type eukaryotic retrotransposons. How do these duplications arise and what do they suggest in terms of mechanisms of transpositon?