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Which 5 enzymes are involved in the short patch DNA repair pathway?

- DNA Glycosylase
- AP Endonuclease
- DNA Polymerase beta
- Phosphodiesterase
- DNA ligase


What does DNA glycosylase do?

Recognise the wrong base and removes it (base excision)


What does AP endonuclease do?

1. Recognises the abasic site
2. Makes cleavage on 5' side of the abasic site
3. Cuts sugar-phosphate backbone = single strand break


What does DNA polymerase beta do?

1. Adds the correct base in the abasic site opposite the unpaired base
2. Left with a phosphate flap that needs to be removed.


What does Phosphodiesterase do?

Remove the sugar-phosphate flap.


What does DNA ligase do?

Stitches the sugar-phosphate backbone back together.


Give 3 examples of DNA Glycosylase enzymes

- OGG1
- UNG2


Give an example of a scenario involving OGG1

1. Guanine is usually paired with cytosine
2. Oxidation of Guanine --> 8HG:C
3. OGG1 can remove 8HG and the base excision repair pathway can occur.


Give an example of a scenario involving MUTYH

1. If OGG1 fails to remove 8HG, it will be paired with Cytosine because it looks like guanine
2. After replication, 8HG will be paired with adenine because it looks like Thymine
4. MUTYH can do 2 things:
i) Remove Adenine --> BER
ii) Replace Adenine with C --> G:C pairing.


What happens if MUTYH doesn't do its thing?

8HG would be replicated as Thymine in the next round of replication, then paired with Adenine = point mutation


What happens if there is a mutation in MUTYH?

- Leads to MYH associated polyposis, leading to colorectal cancer.


What does UNG2 do and why is it forcedly stopped?

- UNG2 would normally detect deamination of bases and then undergo base-excision to repair the damage
- This is forcedly stopped to allow mutations to occur leading to somatic hypermutation.


Why do we need somatic hypermutation?

So there is a high variation of immunoglobulin in B cells to bind to a high variety of antigens found of bacteria and viruses.


In which part of the antibody do mutations occur?

In the variable region.


In class switch recombination, why do we want to convert IgM --> IgG?

- Because IgM is the default antibody and is the first antibody produced by the immune system.
- Converting to IgG would allow it to recognise a higher variety of antigens.


Describe the process of class switch recombination in producing IgG from IgM.

1. VDJ region gets spliced on the region near the IgM locus
2. Activation-induced deaminase and UNG2 cut out the wrong base so you have 2 breaks in the DNA strand.
3. BER happens and at the end, you stitch the DNA back together using DNA ligases.
4. VDJ region attaches on to an IgM locus, which makes IgM from IgG.


What happens if there is no UNG2 as a result of a mutation?

- It will cause hyper IgM syndrome
- Can't conduct class-switch recombination so all antibodies will be IgM.


What are the steps of single-strand break repair?

1. SSB such as missing base is detected using PARP1 and PARP 2
2. DNA end processing by XRCC1
3. DNA gap filling using DNA polymerase beta
4. DNA ligation using DNA ligase 3 and XRCC1


Describe PARP1?

- primary sensor
- abundant in chromatin
- rapidly activated when a strand break is sensed


How does PARP1 identify a SSB?

Uses NAD as an energy source to generate ADP polymers, these are put on itself or on histones, this produces a branch which is an indication for the single strand break.


What is XRCC1 and what are the binding sites on XRCC1?

It is a scaffold.
- TDP1
- Apratoxin
- AP endonuclease


What happens if there is a mutation in Apratoxin?

Ataxia-oculomotor apraxia 1


What happens if there is a mutation in PNKP?

Microcephaly with early onset seizures


What happens if there is a mutation in TDP1?

Spinocerebellar ataxia with axonal neuropathy


What happens if you don't have SSBs?

- Collapsed DNA replication
- Stalled transcription


What happens if there are too many SSBs?

Excessive PARP activation = production of ADP which is toxic = cell death/genome instability/cancer (random girl told us so not sure)