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35 Cards in this Set

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What replication error will occur with a T-A pair?
It will mismatch to T-G and then you’ll get a Gc in the next round of replication
What replication error will occur with a G-C pair?
Mismatch to GT then to a AT in the next round of replication
What replication error will occur with an A-T pair?
Mismatch to AC then to a GC during the next round of replication
How will the replication error occur in a T-A pairing?
Thymine is usually in ketone form. But it can switch to the enol form. Enol will allow it to hydrogen bond with Guanine.
When there is a T-A mismatch to a T-G, what is recognized and what can be removed?
T is recognized because it can switch back to the keto form. However the polymerase cannot remove G. So it will cause a mutation.
What are the two ways that T and G can be paired together?
Either Guanine will switch to the enol form, or Thymine will.
What do you use to distinguise newly synthesized strand from the template in prokaryotic mismatch repair?
Methylation. The new strand is not methylated until after replication.
Describe the process of Mismatch repair?
MutH will bind to hemimethylated DNA. It nicks the dna at the unmethylated strand. Exonuclease comes in and deletes path.
What is the problem with mismatch repair in prokaryotes?
If the strand has been methylated, it can’t be regotnized from the template.
What is MutH?
Nuclease which binds to the hemimethylated DNA
What is Mut S?
A dimeric structure which slides along DNA looking for distortion (a kink in the DNA). If it recognizes, then it will clamp down on the DNA.
What is Mut L?
Stimulator for MutH
Where does the nick occur in mismatch repair of prokaryotes?
5’ or 3’ side of the mismatch. It can go in either direction.
What is homologous between prokaryotic and eukaryotic mismatch repair?
MutS and Mut L will exist. However MutL will be the one which nicks the DNA.
What is not homologous between prokaryotic and eukaryotic mismatch repair?
MutH homologue. We don’t have it. We also don’t have a hemimethylated detector. We don’t really get how it works yet.
What is a possible outcome of mismatch mutation?
Heritable colon cancer
Is damage to DNA rare?
No
What are the two main types of natural damages to DNA?
Hydrolysis and oxidation.
What occurs in depurination?
Water will interact with Guanine and remove the base. When the polymerase gets to it, it can insert whatever it wants
What happens in cytosine deamination?
Water will interact with cytosine and the NH2 group and a Hydrogen. It turns the cytosine into a uracil. This will pair with adenine and now you get a A-T bond in the next round of replication.
Descibe methylcytosine deamination?
Water comes in, NH2 and a Hydrogen comes off. You end up with Thymine. Which will then give you an A-T during the final round of replication.
Describe Adenine deamination?
Water in, NH2 and hydrogen out. You gen hypoadenine which can pair with cytosine.
Where does inevitable reactive oxygen production occur?
Cytochrome C oxidase complex 4. It occurs during the peroxide bridge step, you can leak O2/2- or OH
How far can leaked ROS travel?
No more than a few nanometers, but it can get to the nucleus.
How many times/day/generation can ROS production occur?
1000
Does oxidation occur at a high or low rate?
High
What are the sources of radicals for oxidation?
Mitochondria or ionizing radiation
Describe oxidation of Guanine
Guanine will react with a radical and turn into 8oxoguanine.
What is the problem with 8oxoguanine?
It can pair with adenine
Describe Guanine depurination?
Oxidation. Guanine will be turned into oxazolone (O) and will be able to be paired with anything. You can get any base pair in the next round.
What will occur if you are exposed to UV radiation?
Thymine will dimer off with itself. Also Cytosine can dimer off with itself. It will end up changing the shape of DNA and causing a random insertion/frameshift/deletion.
In prokaryotes how does nucleotide excision repair work?
Parts ABCD work to remove dimer damage and put back strand. UvrAB scans DNA. UvrA recognizes distortions. UvrB melts and creates a bubble and recruits UvrC. UvrC creates nicks on the 5’ and 3’ side of the lesion. UvrD is recruited by UvrB and unwinds the damaged segments and displaces the DNA and UvrC. Poly 1 and Ligase fill the gap.
Is there a way to fix UV damage?
Yes. Nucleotide excision repair!
How does eukaryotic nucleotide excision repair work?
It is homologous to prokaryotes.
What is the problem with UV damage?
It is linked to cancer