TEST 3 DNA Repair and Recombination Flashcards
Three types of repair that involve excising of lesion followed by replacement?
Mismatch repair Nucleotide excision repair Base excision repair
Mismatch Repair: DNA Methylation Prokaryotes? Humans?
Occurs on adenines, if damage is detected it is excised and replaced using the undamaged strand as a template.
Humans: Occurs at CPG site where C is methylated.
What is hemimethylated?
When only the parent strand is methylated.
When do HNPCC or Lynch Syndrome result?
When there is an issue with DNA methylation used in mismatch repair.
What enzyme methylates the daughter strand?
Dam methylase
Process of mismatch repair?
- Mismatch detected
- Mut complex forms and binds
- Forms a nick at the methylation point
- Removew the DNA from the nick to the mismatch
- DNA polymerase 3 or SSB fills in the gap and ligase connects them.
What is deamination? and what enzyme removes it?
- Spontaneous reaction which converts nucleotides to different structures by removing a amine group and leaving a oxygen.
- Removed by DNA Glycosylase
What is the only nitrogenous base that can’t undergo deamination?
Thymine
What is the worse form of deamination and why?
- 5-methylcytosine:
- It deaminates to Thymine.
- Very common in cancer
What occurs in Depurination? and how?
Nitrogenous base is detached from the nucleotide, due to water binding.
note: does not occur as often in Ribonucleotides or RNA
Base-excision repair what does it do? and steps?
Fixes Deamination and depurination.
- DNA glycosylase:
- makes an abasic site
- same type of damage as depurination.
- Specific for each type of of unnatural DNA base.
- makes an abasic site
- AP endonuclease
- Removes the nucleotide
- DNA polymerase
- Fills in the long chain
- DNA Ligase fills the gap.
Epigenetic regulation through BER?
- DNA methyltransferase adds methyl groups
- TET enzymes change the methyl groups.
- BER removes the modified methyl group.
When is Nucleotide Excision Repair used and steps?
Fixes cross-linking (dimerization) of pyrimidine rings, upon exposure to ultraviolet light.
-
Excinuclease nicks at two different sites.
- This is a type of endonuclease.
- DNA helicase separates the two strands
- DNA poly fills in
- DNA ligase then seals the gap.
What causes Xeroderma Pigmentosum?
Mutation in nucleotide-excision repair
What is direct repair and how does it work?
- Directly repairs the damage via chemical reaction that reverts the damage back to the original molecule.
- The cell synthesizes a specific enzyme for just one fix, once complete it is degraded.
Type of DNA repair used to fix O6 - Methylguanine - DNA
Direct repair.
Type of DNA repair to fix Pyrimidine Dimer.
Direct DNA Repair
Why is repairing damage important during DNA replication?
- The lesion may cause a double - strand break
- This is the worst kind of DNA damage a cell can undergo.
- Prokaryotes can’t repair mid replication.
Common causes of double straded breaks?
High-energy radiation
Oxidative free radicals
Errors during replication
What are the two forms of DSB DNA repair and how are they different
- Non-homol;ogous end joining
- AKA SOS response
- Extremely error prone, always happens.
- Homologous recombination repair
-
BRCA
- abnormal enzymes cause ovarian cancer risk
-
BRCA
Crispr - Cas9 uses what form of DNA repair?
Homologous and non-homologous repair.
Type of DNA repair to repair damage due to tautomerization (wrong nucleotide on the other strand).
Mismatch repair.
Repairing damage due to depurination?
Base excision repair
Melanoma associated with UV exposure, homemade bait blocked what pathway that caused the tumor?
Nucleotide-excision repair.
What are the 3 types of Recombination?
Homologous recombination
Site-specific recombination
DNA transposition
Three functions of Homologous recombination?
How is it initiated?
What intermediates are formed?
-
Function
- DNA repair, especaily at stalled replication forks.
- Assists in segregation of chromosomes
- Enhancement of genetic diversity.
- Initiated: by double-strand breaks
- Intermediates: Holliday intermediates are formed.
Describe Unequal crossing over?
Non-homologous sites recombining with each other, causing crossing over where it should not occur.
Can cause short or long chromatids.
What is gene conversion?
- Gene Conversion
- Results in the conversion of one allele to the other allele.
- Has a GC bias.
- If a cell gets two allels of the same type instead of one of each type this can cause issues if both copies are of a bad type.
Allelic gene conversion
Conversion between two alleles of the same gene
Conversion between paralogs?
Interlocus gene conversion
Explain Site-Specific Recombination
Occurs only at specific sites
Functions in DNA integration and regulation of gene expression.
Describe DNA transposition
- Transposons use recombination to move within or between chromosomes
- Immunoglobulin gene rearrangements us a similar mechanism
What does DNA methylation do during DNA transposition?
Prevents cleavage
