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DNA Repair, Cancer, Retrovirus, & Transposons

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1.
a.Describe in detail how a direct DNA repair mechanism works.
b.Can you think of a way in which you could inhibit this repair mechanism in bacteria that have been exposed to UV radiation?
2.
For each of the following, give a brief description:
a.DNA exonuclease
b.AP site
c.DNA ligase
d.post replication repair
3.
a.What is cancer? Include in your answer a description of oncogenes.
b.Explain how a mutated DNA repair gene could lead to a cancer.
c.If a mutation occurs in a gene in a skin cell, describe two possible outcomes for the future of that cell.
4.
a.What is a retrovirus?
b.How can a retrovirus cause the transformation of a normal cell into a cancer cell?
c.What is a transforming retrovirus and how does it cause cancer?
5.
a.What is a transposon? In you answer include two distinguishing features of a transposon.
b.What is meant by conservative and replicate transfer?
c.Briefly describe the mechanism of action of the Ds and Ac transposons as discovered in maize by McClintock.

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Short answers with web references to given questions.

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1. a. Describe in detail how a direct DNA repair mechanism works.
There are several mechanisms for DNA repair depending on the damage that needs to be repaired. During nucleotide excision repair the defective base pairs must first be recognized as being incorrectly paired by a complex of proteins. The damaged nucleotide is removed along with surrounding nucleotides by a complex of proteins including Uvr-A, -B, and -C. The region is then replaced using the correct strand as a template by DNA polymerase I. A DNA ligase links the end of the repaired region with the rest of the strand.
Web reference:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNArepair.html
http://www.web-books.com/MoBio/Free/Ch7G.htm
http://asajj.roswellpark.org/huberman/DNA_Repair/ner.html

b. Can you think of a way in which you could inhibit this repair mechanism in bacteria that have been exposed to UV radiation?
Mismatched base pair repair is the mechanism used to repair thymidine dimers created by exposure to UV radiation. This repair can be impaired by sequestering free nucleotides or energy sources that are required by the proteins involved in the repair process.

2. For each of the following, give a brief description:
a. DNA exonuclease
A DNA exonuclease can cut nucleotides from a strand of DNA at either end. It cannot cut in the middle of the strand.
Web reference:
http://www.answers.com/topic/exonuclease

b. AP site
The AP (or apurinic/apyrimidinic) site is the location of the mutated nucleotide.
Web reference:
http://www.web-books.com/MoBio/Free/Ch7G.htm
http://www.biology.neu.edu/strausslab/pdf/Review2000.pdf

c. DNA ligase
DNA ligase bind the phosphate groups of nucleotides to one another to form a strand.
Web reference: ...

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