Reading Quiz #1 - DNA Repair

DNA Repair

Depurination

Releases A and G from DNA

N-glycosidic bond between the purines breaks spontaneously, the bases are released but the backbone remains. 

Consequences of Depurination

 A or G are not part of sequence anymore at the point of the depurination.

A/G are skipped over or the whole region is skipped over by DNA polymerase leading to incorrect translation, wrong protein creation

Depurination and Deamination FIX

Base Excision Repair - AP endonuclease recognizes the AP site, cuts out the damage and DNA polymerase fills in the correct base, DNA lipase seals the backbone. 

Deamination

Converts cytosine to an altered DNA base, uracil 

An amino group (NH2) is removed from the base, changing it to a different base 

Consequences of Deamination

Now Cytosine is being read as Uracil which could change which amino acids are added to the chain and ultimately which protein gets made 

Base Excision Repair Steps

1. Glycosylase recognizes and removes the incorrect base

2. The AP site is left behind. Endonuclease removes the AP site

3. Phosphodiesterase removes the backbone

4. Polymerase fills in the correct base

5. Ligase joins the new base

Does BASE EXCISION REPAIR fix small or large damage?

Small damage only - removes 1 base at a time

Does NUCLEOTIDE EXCISION REPAIR fix small or large damage?

LARGE damage - removes 24 - 32 bases

Fixes issues were DNA has a distorted shape - thymine dimers

Nucleotide Excision Repair STEPS

1. Damage recognition - scanning the DNA for thymine dimers, two thymines sticking together bending the DNA 

2. DNA unwinding - helicase unwinds the DNA around the damage creating a bubble 

3. Excision of the damage - DNA Endonucleases will cut out the damage 

4. DNA Repair Synthesis - DNA polymerase fills in the gap and ligase seals the bond 

Translesion Polymerase

Deployed by DNA polymerase only in emergencies were DNA is badly damaged to quickly to repair

Risks of Translesion Polymerase

1. High rate of base substitution and single nucleotide deletion mutations

2. Create mutations on undamaged DNA

3. NO EXONUCLEOLYTIC PROOFREADING ACTIVITY

Non-Homologous End Joining

DOES NOT NEED MATCHING DNA TEMPLATE TO GUIDE THE REPAIR 

Used to repair double strand breaks in non-dividing or G1 phase cells where no sister chromatids are available. 

Cons of Non-Homologous End Joining

• It will join the broken ends of DNA together which is FASTER but more error prone. 

• There no guarantee that two joined ends were originally next to each other 

• One broken chromosome can become covalently attached to another

• This can result in chromosomes with two centromeres or chromosomes without any at all 

STEPS OF NON-HOMOLOGOUS END JOINING

1. Break detection 

2. Bridge the ends 

3. End Processing - when the broken ends don’t match perfectly

4. Ligation - glue always by ligase 

Homologous Recombination

NEEDS A MATCHING DNA TEMPLATE

During S and G2 phases of the cell cycle, after DNA replication, the sister chromatid will be available as a template 

MORE ACCURATE THAN NHEJ BUT SLOWER

STEPS OF NON-HOMOLOGOUS END JOINING

1. Damage detection - broken ends are recognized, enzymes trim back one strand from each end creating 3’ overhangs 

2. Broken strand reconnects with the intact complementary strand 

3. DNA Polymerase extends the broken strand using the template 

4. Structure can be restored by either returning to original strands OR forming Holliday junctions which are cut later 

5. ALWAYS LIGASE AT THE END TO SEAL IT OFF 

T/F: Both NHEJ and Homologous Recombination repair double strand breaks?

True