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1.A bacterial operon contains all of the following features except:

a. multiple transcription start sites
b. multiple cistrons
c. multiple ribosome binding sites
d. multiple genes encoding enzymes involved in a related function

2. Which of the following types of DNA will reanneal at the fastest rate?

a. single copy DNA
b. moderately repeated DNA interspersed throughout the genome
c. short sequences repeated in tandem arrays
d. mobile DNA elements

3. Which of the following statements about minisatellite DNA is true?

a. it is present at only a single site in the genome
b. it consists of repeating units of 15 to 100 basepairs
c. it exists in tandem arrays approximately 100 kilobases in length
d. it is located on extrachromosomal DNA molecules

4. All of the following statements about transposons are true except:

a. they move via RNA intermediates
b. they include DNA that encodes transposase
c. they often contain a drug resistance gene
d. they contain insertion sequences

5. All of the following steps are performed by the enzyme transposase during nonreplicative transposition of bacterial insertion sequences except:

a. excision of the IS element from the donor DNA molecule
b. introduction of staggered cuts into the target DNA molecule
c. ligation of the IS element to the target DNA
d. synthesis of DNA to fill in the single stranded gaps

6. Describe the difference between a pseudogene and a processed pseudogene.

Pseudogenes are genes that have the same apparent exon-intron structure as functional genes, but sequence drift during evolution has rendered them nonfunctional because they terminante translation or mRNA processing [or transcription] is somehow blocked. Whereas processed pseudogenes seem to be retrotransposed copies of spliced and polyadenylated mRNA. They lack introns and don't have flanking sequences. These inserted segments generally contain multiple mutations, which might have happened since their mRNA's were first reverse transcribed and randomly integrated into the genome.

NOTE: one of the "flanking sequences" that a processed pseudogene lacks is a promoter--anything upstream of the transcription start site of the original gene will not be retrotransposed, since it will not be part of the mRNA. Transcriptional initiation is therefore very likely to be blocked.

7. (2 pts) What characteristics of a DNA sequence would suggest that it is a transposon? How could you distinguish a transposon from an IS element?

A transposon consists of a DNA coding sequence that encodes a functional gene, commonly encoding a type of antibiotic resistance, flanked on either side by an IS element. The IS elements flanking the transposon have sequences that encode transposase as well as sequences that are inverted repeats and short direct repeats. However, the inverted repeats closest to the antibiotic resistance gene have acquired mutations that do not allow them to be recognized by transposase. Thus, when transposition occurs, the entire transposon element is excised from the chromosome, along with the antibiotic resistance gene. An IS element by itself does not have funcitonal genes other than the ones required for transposition. They also only have two copies of the inverted repeat sequences, while a transposon has four (albeit two mutated sequences.)

8. (2 pts) How could you determine whether a newly-described mobile genetic element was a transposon or a retrotransposon? Describe an experiment that could address this question. Include the results you would expect to obtain in each case.

To determine whether a mobile element is a transposon or a retrotransposon I would attempt to verify whether or not the element was transposed with the help of an RNA intermediate. One method would be to insert a foreign intron into the sequence in question. Then, after transposition, I could observe whether or not the transposed DNA sequence still contained said intron. If the intron was absent after transposition I would conclude that the original sequence had indeed been transcribed into an mRNA intermediate, which had then been spliced, thus losing the inserted intron before being reverse transcribed back into dsDNA and inserted into the host DNA. The presence of introns in the final transposed element would tell me that the mobile element most likely transposed directly as DNA.

NOTE: Putting either a transposon or a retrotransposon under the control of a strong promoter will increase transposition. A transposon carries a gene encoding transposase, and transcription and translation of this gene is required for transposition, unless an external source of transposase enzyme is provided. Thus neither a requirement for transcription nor a response to overexpression distinguishes one type of mobile element from the other.

Your textbook does describe an experiment in which a Ty element was cloned after a GAL-inducible promoter and an increase in transposition followed a shift from glucose to galactose. By itself, though, this experiment does not demonstrate that Ty is a retrotransposon. It is the following experiment (i.e. removal of an intron upon transposition) that demonstrates this.

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