Flashcards in Mechanisms of DNA Repair Deck (30):
DNA Damaging Agents
-Chemical modifications of bases
-Substances that intercalate between double-strand DNA
Form interstrand crosslinks in DNA helices
-Metabolically activated carcinogens
Spontaneous lesions- Will result in mispairing
Bromouracil vs cytosine
-Misincorporated for thymine
-Base pairs with guanine
Deamination of cytosine
Looks like uracil. Base pairs with Guanine
Deamination or depurification results in:
One mutation and one normal DNA molecule after replicaiton
Mitochondrial DNA mutations is ____ efficient than nuclear DNA repair
Less efficient. Can cause:
Cannot correct chromosomal aberrations
-Involves cutting out and resynthesizing the area of DNA surrounding the damage.
-Mechanism triggered depends on type of damage to DNA
-Undamaged DNA strand used as template
Nucleotide Excision Repair
Repairs the majority of bulky lesions in DNA due to UV-induced poto-products and addition of bulky adducts derived from cisplatin and 4-nitroquinoline oxide
Removes lesions such as pyrimidine dimers, photo-adduct products, alkylated bases
-Example of falilure: Xeroderma Pigmentosum
Base excision repair
Single nucleotide is replaced during the repair process
Abnormal bases are removed by specific DNA glycosylases
Removes abnormal bases arising from either a deamination or depurination reaction; adduct formation (e.g. methyladenosine), oxidized bases (e.g. 8-oxodG), saturated and ring-fragmented bases.
Mismatch Repair enes
Removes base mismatches, corrects insertion, deletions
-Example of mutation: hereditary nonpolyposis colon cancer
Defective nucleotide excision repair (excision endonuclease)
-Rare autosomal-recessive inherited disorder
-characterized by extreme skin sensitivity to UV light, abnormal skin pigmenation
-Some patients develop neurological symptoms
Reactive oxygen species (ROS)
Mitochondrial DNA is prone to oxidative damage, as mitochondria are the site of ROS generating respiratory chain.
Patients with Cockayne syndrome have sun sensitivity, short stature and progressive neurological degeneration, along with early senility. However, the condition is not associated with cancer. Cockayne syndrome is recessively inherited and is due to a defect in transcription-coupled NER. This is a variant of NER and operates during transcription in terminally differentiated cells such as neurons.
Steps of NER-- affected area is removed and patched
Recognition of defect by ERCC1, XPA, and XPF
A. Nuclease cleavage of phosphodiester bond and "excision" of several nucleotides adjacent to the dimer
B. "Gap" is filled by DNA polymerase in which the appropriate dNTP is added to the 3'-OH end of the clipped DNA (opposite strand will be provided to correct coding information)
C. Final joining (DNA ligase) of the 3'-OH end of the last base added to close the "gap"
Steps of NER-- thymine dimer
A.. Location of Thymine dimer
B. Cut by endonuclease
C. Bases removed by helicase
D. New bases added. Ligase seals the ends
Steps of BER-DNA Glycosylase
A. DNA Glycosylase recognizes and removes the damaged base from the DNA backbone to form an abasic site (AP)
B. AP site is recognized and cleaved by AP endonuclease which introduces a DNA strand break
C. DNA Poly B adds the appropriate dNTP to fill the nucleotide gap
D. Nick is sealed by DNA ligase
Note: BER repairs oxidative damage in mitochondria
Mitochondrial DNA is repaired by
DNA glycosylase, AP endonuclease, DNA polymerase gamma, DNA ligase
Mismatch Repair Genes (MMR)
Corrects misincorporated and deleted/inserted bases, particularly those introduced by strand slippage of DNA polymerase
When are mismatched sequences corrected?
After replicatoin-- by MMR. Scans the newly synthesized strand
Also known as hereditary nonpolyposis colon cancer
Defect in MMR protein results in susceptibility to cancer of the colon and ovaries
Tumors will display microsatellite instability: High instability of short repeated sequences
Dealkylation of guanines: Guanine alkyltransferases remove methyl/ethyl groups from alkylated guanines.
When damaged DNA escapes repair, the resultant distortion disrupts the process of replication. During DNA replication, the polymerase skips over the distortion, creating a gap on the newly synthesized strands. An exchange process takes place to remove the gap with a homologous segment from the intact strand. The resultant gap on the “donor” stand is filled by repair synthesis as replication proceeds.
Repairing Double Stranded Breaks
Homologous recombination repair (HHR)
Non-homologous end joinings (NHEJ)
Homologous recombination repair
may operate during DNA replication where it restarts broken DNA replication forks. A homologous DNA strand is used as a template to copy the missing DNA sequences. However, the requirement for a homologous template for repair is a limitation of double-strand-break repair by homologous recombination.
Non-homologous end joinings
Simply ligates the two ends together, hoping no DNA was lost during the process
-DNA-dependent Protein Kinase
involves rejoining the two ends of the break without relying on a template sequence. This process is error prone as DNA sequences may be lost prior to the repair. NHEJ is also associated with chromosomal translocations.
Immunoglobin gene rearrangements
a specialized process that utilize NHEJ to rejoin double strand breaks created by the RAG complex at specific locations in the genomes of lymphoid cells. This process results in antibody diversity in the immune system.
Proteins that prevent unwanted recombination events
-PARP/sing strand breaks
-DNA dependent protein kinase