(Dr. Heinemann) (Unit C) Topic 16 Flashcards
How is “DNA damage” defined?
Unintended changes in the sequence or structure of DNA
Main types of DNA damage
- Copying mistakes
- Depurination
- Deamination
- Pyrimidine dimers
- Other base modifications
- Strand breaks
Copying mistakes
Mistakes may still happen even with DNA polymerase proofreading
* Results in a change of sequence or a mutation
Depurination
Spontaneous hydrolyzation of N-glycosidic bond
* Results in the loss of A or G base
In depurination, is the sugar-phosphate backbone affected?
No, it remains intact
What happens as a result of depurination?
Abasic sites
* Block replication by the normal replicative DNA polymerase
Translesion DNA polymerase
Allows synthesis of DNA past abasic sites
* Either mutates that position or completely skips that position
Does translesion DNA polymerase repair damage?
No, it just allows DNA synthesis by jumping past damage and letting normal DNA polymerase do its job
Deamination
Amine group of a nitrogenous base (most commonly C) is changed to a carbonyl
* C is converted to U in this process
Is deamination:
* Spontaneous?
Yes, and it may cause a mutation
Pyrimidine dimers
Double bonds in adjacent pyrimidines (most commonly Thymines) react to form a four-membered ring structure
What are pyrimidine dimers usually caused by?
UV radiation
What allows replication past pyrimidine dimers?
Translesion DNA polymerases
* More error prone than normal replicative DNA polymerases
* Increases the risk of mutation
Other base modifications
- Ionizing radiation causes modifications to bases
- Mutagens react with DNA bases and leads to changes (ROS, polycyclic aromatic hydrocarbons etc.)
Strand breaks
Single or double stranded breaks caused by a wide variety of factors
What can cause strand breaks?
- Ionizing radiation
- Reactive oxygen species
- Mechanical stress
True or False:
Translesion polymerases can synthesize DNA past a break in the template
False, neither DNA polymerase can synthesize past breaks
What do strand breaks cause?
Chromosomal abnormalities, or result in cell death
What forms of DNA repair systems are there?
- Proofreading during DNA replication
- Mismatch repair
- Direct repair
- Base excision repair
- Nucleotide excision repair
- Non-homologous end-joining (NHEJ)
- Homologous recombination
Mismatch repair
Fix mistakes made by DNA polymerase that escaped correction by proofreading
* Success rate of 99%
In mismatch repair:
What protein detects a site of mismatch?
MutS
In mismatch repair:
In bacteria, how is it determined which strand is newly synthesized/erroneous?
Scan both strands in both directions to look for methylated base
* Unmethylated strand are newly synthesized (not methylated yet)
In mismatch repair:
Describe the process of repair
- Endonuclease nicks the backbone of newly synthesized strand across from methylated base
- Exonuclease removes the bases from the nick to the mismatch site
- Replicative DNA polymerase then fills gap created by exonuclease
Is the identification of the new strand in mismatch repair the same in prokaryotes and eukaryotes?
No
Direct repair
A few common types of damaged bases can be repaired by enzymes specific to those bases
Base Excision Repair
Fixes abasic sites, single-strand breaks, and modified bases (including deaminated bases) that are not fixed by direct repair
What are the two forms of base excision repair (BER)?
- Short patch
- Long patch
What is involved in both forms of BER?
Endonuclease cuts the backbone at the site of damage if necessary
In BER:
What does Short-Patch BER do?
Synthesis of only one new nucleotide
In BER:
What does Long-Patch BER do?
2-10 new nucleotides are synthesized
In BER:
What is the undamaged strand used for?
Used as template for new DNA synthesis in each type of BER
In BER:
What enzymes are involved in Long-Patch BER?
- Endonuclease: Cleaves ssDNA on damaged strand that has been displaced by DNA synthesis
- DNA ligase: Seals the nick that resulted from the endonuclease
Nucleotide Excision Repair (NER)
Repairs pyrimidine dimers and base modifications that distort the helical structure of DNA
How does NER work?
- Helicase unwinds dsDNA in area of damage
- Endonuclease cuts backbone of damaged strand on either side of site of damage
- DNA polymerase and DNA ligase replaces it, using undamaged strand as a template
Non-homologous end joining (NHEJ)
Fast but inaccurate
* More common method used to repair a doublestrand break
In NHEJ:
Describe the process
- Ku protein recruits both ends together
- Nuclease trims and adjusts the ends
- Polymerase extends the ends
- DNA ligase connects the two ends
Homologous recombination
REQUIRES a second copy of the chromosome
* Complementary DNA is used to synthesize new DNA to restore DNA
* Slow but accurate
In homologous recombination:
Describe the process
Recruit the DNA from the other copy of the chromosome complementary to the DNA surrounding the break
* Used as a template to synthesize new DNA to restore the strand to original condition
When is homologous recombination most convenient?
Most convenient shortly after replication when another copy of the chromosome is nearby
