GENE 3200 Exam 5 EOC Chp. 18

13) What are some differences between class I and class II transposable elements?

1) Class 1 TE's: -are replicative (type of transposition in which a copy of a transposable element moves to a new site while the original copy remains at the old site; increases the number of copies of the transposable element.) -"copy-and-paste" -TE's can move around a genome & inc. the TE copy number 2) Class 2 TE's: -are nonreplicative (type of transposition in which a transposable element excises from an old site and moves to a new site, resulting in no net increase in the number of copies of the transposable element.) -"cut-and-paste" -TE's can move around genome but they don't increase their copy number Pg. 544 online (table 18.4)

9) What general characteristics are found in many transposable elements?

1) Flanking direct repeat -generated when a transposable element inserts into DNA. -short, directly repeated sequence produced on either side of a transposable element when the element inserts into DNA. -are not a part of the transposable element and do not travel with it. -created when staggered cuts are made in the target DNA. 2) Terminal inverted repeat -sequences found at both ends of a transposable element that are inverted complements of one another.

15) List at least three different types of DNA repair and briefly explain how each is carried out.

1) Mismatch repair -incorrectly paired bases are detected and corrected by mismatch-repair enzymes. -the mismatch-repair system corrects small unpaired loops in the DNA -enzymes cut out a section of the newly synthesized strand of DNA and replace it with new nucleotides. 2) Direct repair -modified bases are changed back into their original structures. -Escherichia coli and some eukaryotic cells possess an enzyme called photolyase, which uses energy captured from light to break the covalent bonds that link the pyrimidines in a dimer. 3) Base excision repair -the excision of modified bases is catalyzed by a set of enzymes called DNA glycosylases, each of which recognizes and removes a specific type of modified base. -after the modified base has been removed from a nucleotide, an enzyme called AP (apurinic or apyrimidinic) endonuclease cuts the phosphodiester bond, and other enzymes remove the deoxyribose sugar 4) Nucleotide excision repair -nucleotide-excision repair removes and replaces many types of damaged DNA that distort the DNA structure. The two strands of DNA are separated, a section of the DNA containing the distortion is removed, DNA polymerase fills in the gap, and DNA ligase seals the filled-in gap.

16) What are the two major mechanisms for the repair of double-strand breaks? How do they differ?

1) Translesion DNA synthesis/ Homologous recombination 2) Nonhomologous end joining (NHEJ) Differ: Translesion DNA synthesis- the SOS repair system of E. Coli for extensive UV damage. NHEJ- double strand breaks in DNA occur from exposure to X-rays & certain types of oxygen radicals. Takes place before DNA replication occurs. Used when a sister chromatid isn't available for repair via homologous recombination

10) How does a retrotransposon move?

Always by copy & paste; reverse transcription: copy of the TE can integrate into a new genomic location. RNA is transcribed from the transposable element (DNA) and is then copied back into DNA by a special enzyme called reverse transcriptase

14) Why are transposable elements often called genomic parasites?

Because they are generally mutagenic Proteins take energy from being expressed; they both use resources & energy.

37) Explain why the corn kernel in Figure 18.34d is variegated, with some areas colored and some areas lacking pigment.

During development, transposition occurs in some cells, excising the transposable element from the pigment-encoding allele and rending it functional, so that it produces color. Because this happens in some cells and not others, the kernel has pigmented spots

41) A transposable element is found to encode a reverse transcriptase enzyme. On the basis of this information, what conclusions can you draw about the likely structure and method of transposition of this element?

Like other retrotransposons, this element probably has long terminal direct repeats and transposes through an RNA intermediate that is reverse transcribed to DNA

34) White eyes in Drosophila melanogaster result from an X-linked recessive mutation. Occasionally, white-eyed mutants give rise to offspring that possess white eyes with small red spots. The number, distribution, and size of the red spots are variable. Explain how a transposable element could be responsible for this spotting phenomenon.

Such a fly may carry an allele of the white-eye locus that contains a transposon insertion. The eye cells in these flies cannot make red pigment. During eye development, the transposon may spontaneously transpose out of the white-eye locus, restoring function to this gene so the cell and its mitotic progeny can make red pigment. Depending on how early during eye development the transposition occurs, the number and size of red spots in the eyes will be variable

8) What is the purpose of the Ames test? How are his− bacteria used in this test?

Test the mutagenic effects of chemicals; Test in which special strains of bacteria are used to evaluate the potential of chemicals to cause cancer. The Ames test detects whether a given chemical can cause a reversion mutation in his- bacteria;The Ames test uses his- strains of bacteria to test chemicals for their ability to produce his- → his+ mutations

12) Explain how Ac and Ds elements produce variegated corn kernels.

Variegation occurs because during development of the kernel, an Ac or Ds element transposes out of the pigment gene at random times in multiple cells, creating pigmented cells and sectors.