Molecular Mechanisms of Mutation Flashcards
When mutations occur due to internal cellular factors, what is this called
spontaneous mutation
When mutations occur due to outer external factors, what is this called
induced mutations
Most DNA damage is caused by internal factors generated by normal metabolic processes inside the cell by…
water (hydrolysis)
oxygen (oxidation)
alkylating agents (alkylation)
What is the frequency of error in nucleotides within replication
less than 1 in a billion - it is very accurate
What is meant by mispairing due to other structures
arise through the wobble effect via flexibility in the helical structure of DNA causing base pairs to match incorrectly
OR
by protonated forms of bases
What could cause incorperated and replicated errors
tautomeric shifts or the wobble effect
What are two causes of deletions and insertions
strand slippage and unequal crossing over in meiosis
What is strand slippage
when a newly synthesized strand loops out resulting in the addition of one nucleotide on the new strand
OR
when the template strand loops out, resulting in the omission of one nucleotide on the new strand
What is unequal crossing over
exactly how it sounds
- homologous chromosomes misalign during crossing over where one crossover contains an insertion and one crossover contains a deletion
What is depurination
breakage of the covalent bond between the purine base and the 1’ carbon atom of the deoxyribose sugar
What does depurination create
an apurinic site
What is the resulting defect of depurination
no complement base can be added so a random nucleotide is incorporated (usually an A)
What is deamination
the loss of an amino group, typically from cytosine
- gives rise to uracil, which will pair with adenine during replication
- then, in the next cycle A will pair with T
*end result is a C-T transition
What is the long term result of deamination
over time, genomes become more AT rich and CG poor
What is a mutagen
an environmental agent that increases mutation rate above the spontaneous rate
What are the common classes of mutagen
base analogs
alkylating agents
deaminating chemicals
hydroxylamine
oxidative radicals
intercalating agents
radiation
What are base analogs
chemicals with structure similar to the 4 nucleotides
What is an example of a base analog
5-bromouracil (5BU) - an analog of thymine
2-aminopurine (2AP) - an analog of adenine
What are alkylating agents
mutagens that react with DNA bases and add methyl or ethyl groups
What is an example of an alkylating agent
ethylmethylsulfonate (EMS) and mustard gas
What is a deaminating chemical
addition to spontaneous deamination noted for spontaneous chemical changes
What is an example of a deaminating agent
nitrous acid
What is the function of nitrous acid
changes cytosine to thymine (C-T transition)
changes adenine to hypoxanthine which can pair to C (A-G transition)
change guanine to xanthine which can pair to T (G-A transition)
What is hydroxylamine
very specific base modifying mutagen
- adds hydroxyl group to cytosine (hydroxylaminocytosine) which increases the rare tautomer that pairs with adenine
only effects cytosine
(C-T transition)
What are oxidative radicals
reactive forms of oxygen that are produced through normal aerobic metabolism (or by chemicals/radiation)
What are intercalating agents
sandwich themselves between adjacent base pairs to distort the DNA helix
What is the end result of intercalating agent mutation
insertions or deletions - frameshifts
What are examples of an intercalating agents
ethidium bromide, acridine orange, dioxin, proflavin
What is the defect of x-ray radiation
breaks phosphodiester bonds leading to double stranded breaks
What is the defect of UV radiation
induces chemical bonds between two adjacent pyrimidine molecules on the same strand
(thymine dimers are the most frequent)
What are the 2 general features of DNA repair
mechanisms require double stranded DNA
DNA repair has built in redundancy
What is mismatch repair (MMR)
MMR identifies the new strand, and degrades the new strand between the nick and mismatched bases
- poly and ligase fill the gap using the old strand as the template
How does MMR recognize the new vs old strand in prokaryotes
the new strand is methylated, the old is not
How does MMR recognize the new vs old strand in eukaryotes
we don’t know (there is no methylation)
What happens when a mutation in MMR function arises
elevated somatic mutations - cancer
What is direct repair
reversal of mutation - restores original structure
What is base excision repair
DNA glycosylases excise the damaged base(s)
- enzymes are specific for each modified base
only the base is removed first - leaves an apurinic or apyrimidinic site
Other enzymes then remove the sugar afterward
DNA poly fills the gap and DNA ligase seals the nick
What breaks the phosphodiester bond between base and sugar in base excision repair
AP endonuclease (AP stands for apurinic/apyrimidinic)
Is base excision one step or multistep
multi step - base is removed first then sugar
What is nucleotide excision repair
- An enzyme complex recognizes the distortion in the DNA sequence and binds
- then DNA is seperated and single stranded binding proteins stabilize the single strands
- phosphodiester bonds on either side of the mutation are broken
- damaged strand removed by helicase
- gap is filled by polymerase and sealed by ligase
What is different between base excision repair and nucleotide excision repair
base excision repair - multistep (base removed first then sugar after)
nucleotide excision repair: base and sugar removed simultaneously as a unit (long strand is removed all at once)
What causes double stranded breaks
ionizing radiation
oxidative radicals
other damaging DNA agents
What is a double stranded break
both strands of the DNA helix are broken
Does a double stranded break cause mutation on its own
no, but it stalls DNA replication and could lead to chromosomal rearrangements (causing deletions, duplications, insertions, etc)
What are the two pathways to repair double stranded breaks
homology directed repair (HDR)
non homologous end joining (NHEJ)
What is homology directed repair (HDR)
- also known as homologous recombination
repairs a broken DNA strand with the genetic information contained in the sister chromatid (same system as crossing over it meiosis)
What is non homologous end joining (NHEJ)
independent of the homologous template - often occurs during the G1 phase (no sister chromatid is present here)
- proteins recognize broken ends of DNA an bind them together, leading to deletions insertions and translocations
*this is important in somatic recombination (no meiosis here)
What types of repair can fix DNA dimers
direct repair
base excision
nucleotide excision
