Biochem Final: Dna Damage And Repair

Front 1

What replication error will occur with a T-A pair?

Back 1

It will mismatch to T-G and then you’ll get a Gc in the next round of replication

Front 2

What replication error will occur with a G-C pair?

Back 2

Mismatch to GT then to a AT in the next round of replication

Front 3

What replication error will occur with an A-T pair?

Back 3

Mismatch to AC then to a GC during the next round of replication

Front 4

How will the replication error occur in a T-A pairing?

Back 4

Thymine is usually in ketone form. But it can switch to the enol form. Enol will allow it to hydrogen bond with Guanine.

Front 5

When there is a T-A mismatch to a T-G, what is recognized and what can be removed?

Back 5

T is recognized because it can switch back to the keto form. However the polymerase cannot remove G. So it will cause a mutation.

Front 6

What are the two ways that T and G can be paired together?

Back 6

Either Guanine will switch to the enol form, or Thymine will.

Front 7

What do you use to distinguise newly synthesized strand from the template in prokaryotic mismatch repair?

Back 7

Methylation. The new strand is not methylated until after replication.

Front 8

Describe the process of Mismatch repair?

Back 8

MutH will bind to hemimethylated DNA. It nicks the dna at the unmethylated strand. Exonuclease comes in and deletes path.

Front 9

What is the problem with mismatch repair in prokaryotes?

Back 9

If the strand has been methylated, it can’t be regotnized from the template.

Front 10

What is MutH?

Back 10

Nuclease which binds to the hemimethylated DNA

Front 11

What is Mut S?

Back 11

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.

Front 12

What is Mut L?

Back 12

Stimulator for MutH

Front 13

Where does the nick occur in mismatch repair of prokaryotes?

Back 13

5’ or 3’ side of the mismatch. It can go in either direction.

Front 14

What is homologous between prokaryotic and eukaryotic mismatch repair?

Back 14

MutS and Mut L will exist. However MutL will be the one which nicks the DNA.

Front 15

What is not homologous between prokaryotic and eukaryotic mismatch repair?

Back 15

MutH homologue. We don’t have it. We also don’t have a hemimethylated detector. We don’t really get how it works yet.

Front 16

What is a possible outcome of mismatch mutation?

Back 16

Heritable colon cancer

Front 17

Is damage to DNA rare?

Back 17

No

Front 18

What are the two main types of natural damages to DNA?

Back 18

Hydrolysis and oxidation.

Front 19

What occurs in depurination?

Back 19

Water will interact with Guanine and remove the base. When the polymerase gets to it, it can insert whatever it wants

Front 20

What happens in cytosine deamination?

Back 20

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.

Front 21

Descibe methylcytosine deamination?

Back 21

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.

Front 22

Describe Adenine deamination?

Back 22

Water in, NH2 and hydrogen out. You gen hypoadenine which can pair with cytosine.

Front 23

Where does inevitable reactive oxygen production occur?

Back 23

Cytochrome C oxidase complex 4. It occurs during the peroxide bridge step, you can leak O2/2- or OH

Front 24

How far can leaked ROS travel?

Back 24

No more than a few nanometers, but it can get to the nucleus.

Front 25

How many times/day/generation can ROS production occur?

Back 25

1000

Front 26

Does oxidation occur at a high or low rate?

Back 26

High

Front 27

What are the sources of radicals for oxidation?

Back 27

Mitochondria or ionizing radiation

Front 28

Describe oxidation of Guanine

Back 28

Guanine will react with a radical and turn into 8oxoguanine.

Front 29

What is the problem with 8oxoguanine?

Back 29

It can pair with adenine

Front 30

Describe Guanine depurination?

Back 30

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.

Front 31

What will occur if you are exposed to UV radiation?

Back 31

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.

Front 32

In prokaryotes how does nucleotide excision repair work?

Back 32

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.

Front 33

Is there a way to fix UV damage?

Back 33

Yes. Nucleotide excision repair!

Front 34

How does eukaryotic nucleotide excision repair work?

Back 34

It is homologous to prokaryotes.

Front 35

What is the problem with UV damage?

Back 35

It is linked to cancer