DNA Mutagenesis Flashcards
1
Q
What are the 4 major origins of DNA damage?
A
- Errors in replication
- Radiation UV, X-Rays, Gamma radiation
- Cellular metabolism (e.g. ROS)
- Chemical exposure (usually the responsible of adducts)
2
Q
Point Mutations
- What is a transition?
- What is a transversion?
- Which one is more common?
A
- Transition - AT pair replaced by GC pair or vice versa
- Transversion - AT replaced by TA or GC replaced by CG or vice versa
- Transitions are more common
3
Q
Mutations
- Silent
- Missence
- Nonsense
- Frameshift in/del
A
- Mutation occurs but does not change AA sequence (synonymous mutation)
- Mutation occurs and does change AA sequence but new AA is only slightly different from original, may not result in deleterious effects (nonsynonymous mutation)
- Mutation occurs and replaces AA with stop codon (nonsynonymous mutation)
- Single nucleotide is either inserted or deleted and the result is a major change in the downstream AA sequence, often leads to premature stop codon and protein truncation (nonsnynonymous mutation)
4
Q
Sources of error
DNA polymerase has an intrinsic error rate. What would cause these errors to be more common?
A
Cells that are dividing more often
Areas that are being transcribed more often (“hot spots”)
5
Q
What are the 2 general classes of damage?
A
Single base changes
Structural distortions
6
Q
What is an adduct?
A
Chemical modification of a base
7
Q
Single Base Changes
- What are the 2 most common sources of single base changes?
A
- Cytosine deamination (C –> U)
- Replication errors
8
Q
Structural Distortions
What are the 3 common types of DNA damage that fall in this category?
A
9
Q
A
10
Q
Consequences of DNA Damage that goes Unrepaired
A
11
Q
Nucleotide Excision Repair
- What type of DNA damage is repaired via this mechanism?
- Describe the process in general
A
Pyrimidine dimers
12
Q
Nucleotide Excision Repair Subtypes
- Global genome repair
- Transcription-coupled repair
A
- Damage can be anywhere in the genome. Xeroderma pigmentosum proteins (XP) recognize the damged size and nick the DNA on either side of the damage and remove damaged DNA. Normal DNA replication enzymes are recruited to make a new complement to replace the damaged segment that was removed.
- Damage can be anywhere in the genome but it is recognized by an RNA polymerase that is actively transcribing the part of the genome in which the damage occurred. When RNA polymerase recognizes the damage, it recruits XP proteins to remove the damaged site. DNA replication machinery would then be recruited to fill in the gap that is created by removal of damaged DNA.
13
Q
Base Excision Repair
- What type of damage is being repaired?
- Describe the process of BER and the enzymes involved.
- How does this process change if Lyase is involved after glycosylase?
- How does glycosylase recognize where to bind?
A
- Deamination, ROS, X-ray, alkylation leads to conversion of normal base (i.e. C) to abnormal base (i.e. U)
- Glycosylase recognizes that there is an abnormal base in the DNA. It binds to the DNA backbone and removes the base. AP Endonuclease recognizes there is now a missing base and binds to DNA backbone and removes the backbone, leaving a gap. DNA polymerase and DNA ligase fill the gap with the correct nucleotides and then seal the gap.
- Lyase nicks the sugar ring of the base itself
- The abnormal nucleotide will be unable to base pair with it’s complement, so it will be wobbly and move around in the DNA backbone and glycosylase recognizes this mobile base
14
Q
Mismatch Repair
- What type of DNA damage is repaired by this mechanism?
- Describe the process of mismatch repair and the enzymes involved.
- When a mutation arises that affects the ability of mismatch repair to function normally, what disease often results?
A
- Replication errors
- As DNA polymerase is moving along the DNA replicating the genome, it occassionally makes mistakes. When the DNA polymerase fails to proofread the daughter strand and correct those mistakes, this mechanism of DNA repair should kick in. The mistake (i.e. G – T pair) leads to “slippage” in the shape of the DNA, due to the fact that these bases don’t pair together so there is a small loop that develops in the strand of DNA with the error. This loop is recognized by proteins that recruit exonuclease 1 to remove nucleotides on the daughter strand both a little upstream and downstream of the slippage. After the mismatch is removed, DNA pol delta, helicase, and ligase can work together to synthesize a new segment of DNA and join it to the growing DNA strand.
- Lynch Syndrome
15
Q
Recombination
- What type of DNA damage is being repaired?
- Non-homologous end joining
- Homologous recombination
A
- Double stranded breaks in DNA from either exogenous or endogenous means
- Double stranded break occurs, DNA on either side of break degrades leading to deletion of genetic material, the ends then pair back up and re-join resulting in a loss of DNA
- Double stranded break occurs, DNA on either side of break degrades, damaged chromosome is paired up with sister chromatid and the damaged chromosome is repaired using the sister chromatid’s DNA sequence as a template.
16
Q
In Homologous recombination, what are the 2 possible outcomes?
A
- Double stranded break repair without crossing over and loss of genetic diversity
- Even though a very small amount of DNA is exchanged between 2 chromosomes, the DNA flanking the region that contains the hybrid DNA is from the same original chromosome
- Recombination occurs when the DNA flanking the hybrid DNA comes from 2 different chromosomes
- Double stranded break repair with crossing over
