DNA Damage & Repair Flashcards
What are the five common types of DNA damage?
Depurination (A & G)
Deamination
Oxidative damage
Pyrimidine dimers (C & T)
Double-strand breaks
What is the most common mutation in the human genome?
C → T
Cytosine is often methylated. When deaminated, methylated C becomes a T
What are the five DNA repair pathways?
Base excision repair
Nucleotide excision repair
Mismatch repair
Non-homologous end-joining
Homologous recombination
Mismatch repair, base excision repair, and nucleotide excision repair are all examples of what repair mechanism?
Excision repair
Mismatch repair is most common in what phase of the cell cycle?
S phase
What is Lynch Syndrome?
A germline mutation of mismatch repair enzymes?
Describe the mechanism of mismatch repair.
Proteins scan the DNA for structural distortions. When a distortion is identified, the proteins identify the new-synthesizing strand based on DNA nicks and selectively remove DNA between the nick and distortion. The excised area is filled by DNA polymerase and sealed by ligase.
How does base excision repair differ from nucleotide excision repair?
In base excision repair, only the damaged purine/pyrimidine base is removed and the DNA backbone remains intact. In nucleotide excision repair, the entire nucleotide and backbone are removed.
Describe the mechanism of base excision repair.
Glycosylases hydrolyze the N-glycosidic bond to remove the base from the DNA backbone. AP endonuclease cuts the backbone and removes the deoxyribose sugar. DNA polymerase then fills the gap and ligase seals nicks.
Nucleotide excision repair is often used to resolve large DNA structural distortions such as…?
Covalent attachment of hydrocarbons
Pyrimidine dimers
Describe the mechanism of nucleotide excision repair.
When distortion within the DNA is identified, helicase (TFIIH) unwinds the section of DNA. The single-strands are stabilized by single-stranded binding proteins. DNA is cleaved on both sides of the damage. DNA polymerase fills the gap and ligase seals the nicks.
What triggers Transcription Coupled Repair?
RNA polymerase II reaches a distortion on the DNA template strand during transcription and is unable to continue. This stalling triggers enzymes to repair the DNA.
Global genome repair is commonly utilized in what types of cells?
Cell that have no undergone differentiation - they don’t know what specific genes will be necessary and want to preserve all
What repair mechanisms can be used to repair double-strand breaks?
Non-homologous end joining (NHEJ)
Homology recombination (HR)
What is the dominant mechanism for double-strand break repairs? When is this mechanism used?
Non-homologous end joining
G1 phase & when sister chromatids are not present
When is homologous recombination used?
S phase, G2, when sister chromatids are present
What is the mechanism for non-homologous end joining?
The broken ends of DNA are annealed together using complementary base pairing, when possible. If compatible sequences are not present, ends of the broken DNA may be trimmed or extended prior to annealing.
What mutations may result from failure to repair DNA?
Point mutations (missense, nonsense, silent) & frameshift mutations
This type of mutation results from the addition/deletion of nucleotides that changes the reading frame.
Frameshift mutations
A nucleotide change that encodes for a different amino acid is what type of mutation?
Missense mutation
What causes a nonsense mutation?
A nucleotide change that results in a premature stop codon.
What type of mutation results from a nucleotide change that still encodes for the same wild-type amino acid?
Silent / Synonymous mutation
True/Flase. Silent/synonymous mutations always result in the same amino acid and never alter protein function.
False. While silent/synonymous mutations result in the same amino acid, they may or may not affect protein function.
What is the meaning of Locus Heterogeneity?
A genetic concept that explains different mutations in the same gene can alter disease phenotype.
What are short tandem repeats of nucleotides scattered through the genome?
Microsatellites
This concept explains that expansion of trinucleotide repeats in the DNA causes:
increased odds of inheriting; or
decreased age of disease onset; or
increased severity of disease in later generations.
Genetic anticipation
Explain the concept of DNA polymerase “slippage.”
DNA polymerase has difficultly staying in place when replicating microsatellites and is prone to errors. This may result in the addition or deletion of microsatellites.
Describe the mechanism of homologous recombination.
When a double-strand break is encountered, a nuclease digests the 5’ ends of the broken strands. One strand is exchanged and complementary base pairs with the unbroken DNA. When complete, the broken strand separates and reseals with its pair. New DNA is only on the originally broken strand.
How does non-homologous end joining differ from homologous recombination?
Non-homologous end joining is quick and error-prone. Homologous recombination is precise and results in a perfect repair.
Homologous recombination is important in what cycle division process?
Crossover between sister chromatids in meiosis
What genes are involved in formation of the joint molecule in homologous recombination and are mutated in some inherited forms of cancer?
Brca1 & Brca2
What mechanisms contribute to disease when there are large changes in repeat numbers in non-coding sequences?
Decreased trasncription
RNA gain-of-function
Fragile X syndrome is a common trinucleotide repeat disorder linked to the X chromosome that causes intellectual disability. What is the mechanism for disease?
Hypermethylation and loss of expression
What diseases are associated with RNA gain-of-function due to changes in repeat numbers?
Huntington’s Disease & Myotonic Dystrophy 1
True/False. Mitochondrial DNA is identical to all other DNA in the body.
False. Mitochondria have circular DNA that is different from other DNA in the body. In addition, DNA between mitochondria may also vary.
Mitochondrial DNA mutates at a rate 10x that of nuclear DNA. Why is this?
Exposure to reactive oxygen series & less effective repair mechanisms
From which parent does a fetus inherit mitochondrial DNA?
Maternal
What is the primary DNA repair mechanism for damage caused by UV light?
Nucleotide excision repair
UV light often causes pyrimidine dimers
What rare, autosomal disease results in defective nucleotide excision repair and the inability to repair damage from UV light?
Xeroderma Pigmentosum
