Lecture 6 - DNA Damage and mutation Flashcards
What is DNA damage?
DNA damage is defined as a change to the regular chemical structure of the DNA double helix.
* A break in the phosphodiester backbone of the polynucleotide chain
* Loss of a base from the deoxyribose sugar
* Alteration to the structure of a base
* Non-complementary bases in the double helix (mismatched base pairs)
DNA damage can be detected and repaired. If it is not and is subsequently replicated it leads to mutation.
**If DNA damage is replicated it causes mutation.
What is a mutatation and what are the two main types?
A mutation is a permanent heritable change in the sequence of an organism’s genome.
* Point mutations - involve alteration, insertion or deletion of one or a few bases at a time
*Chromosome mutations - rearrangement (translocation), deletion insertions. (DNA rearranged in chromosome)
What types of point mutations are there.
Point mutations
Transition - when the purine or pyrimidine bases are switched meaning AT would be replaced by GC.
Transversion - when a purine is switched with a pyrimidine and vice versa meaning that CG would be replaced with GC.
Missense - A change in the sequence causes a change in the amino acid (amino acid substitution)
Nonsense - When a change in the sequence changes a coding codon to a stop codon causing premature termination
Neutral - When a change in the sequence codes for an amino acid that is similar to the original amino acid and doesn’t change the effect of the protein
Silent - This occurs typically when there is a change at the third position on a codon. The change has no effect as the codon still codes for the same amino acid.
Frame shift - Insertion or deletion changes every subsequent codon
What are forward reverse and suppressor mutations?
Forward, Reverse and Suppressor Mutations
* Forward mutations - when the wild type ‘active’ is mutated to ‘defective’
* Reverse mutations - when the mutant ‘defective’ to wild-type ‘active’
○ A true reversion restores sequence to code for the wild type amino acid in affected protein
○ A partial reversion changes sequence at site of original mutation to some other amino acid that fully or partially restores protein function
* A suppressor mutation changes the sequence at a different location from the original mutation in a way that compensates for the original mutation
○ Intragenic - changes amino acid in same gene
○ Intergenic - changes in different gene (when proteins interact in a complex
How frequent are mutations?
Most mutations are spontaneous - arise without exposure to exogenous agents
In eukaryotes the frequency of spontaneous mutation varies across different sequence classes however there are roughly 30 new mutations in 3Gb haploid genome inherited from each parent
In prokaryotes there is 1 mutation roughly in every 1 million cell divisions
Are mutations adaptive or random?
Mutations are random not adaptive
* Adaptive - organisms ‘direct’ mutations to adapt to a particular environment (Lamarckism)
* Random - Changes that happen by chance sometimes happen to be adaptive
What can cause spontaneous mutations
Spontaneous mutations occur as a result of replication of DNA containing premutagenic damage caused by:
* DNA replication errors
○ Nucleotide or template tautomerism causing mismatches
○ Replication slippage
* Endogenous DNA damage
○ Base deamination
○ Base loss
○ Base modification as a result of exposure to metabolic products
Name the mechanisms used to ensure teh fidelity of DNA synthesis?
There are many mechanisms to ensure the fidelity of DNA synthesis
* Base pairing
* DNA polymerase
* Accessory proteins
* Mismatch repair
Mismatches arising from replication errors can become fixed as mutations following a further round of DNA replication
How can replication of tautomers lead to mutation?
Replication of rare tautomers can lead to mutation
Mismatches can be introduces as a result of base tautomerisation. Bases adopt a rare tautomeric form either in the template strand, or in the incoming nucleotide within the DNA polymerase active site. Tautomers from non-Watson-Crick base-pairs, so incorrect nucleotide incorporated, resulting in mismatch (DNA damage)
If the mismatch is not repaired, after the next round of replication a permanent sequence change (mutation) will arise.
What causes addition and deletion mutants?
Spontaneous generation of addition and deletion mutants by DNA looping-out errors during replication:
* Looping out on the template strands leads to deletion on the new strand.
Looping out on the new strand leads to base insertion on the new strand.
What causes endoginous damage?
hydrolysis - depurination
Loss of a base from a sugar (more common in purines) e.g. depurination of G - Leaves Apurinic site (AP site) with no base attached to deoxyribose (premutagenic lesion). AP sites result in random base substitution or base skipping during replication - leads to substitution/deletion. A further round of replication leads to mutation.
Endogenous damage: Alkylation (typically a methyl group)
Alkyl groups may be added to several different positions on bases by endogenous alkyl donors. Base modification may affect base pairing properties of modified base
Endogenous damage: oxidative DNA damage - leads to spontaneous mutation
Attack by reactive oxygen species. Damaged bases may be mutagenic or lead to strand breakage/replication block
This type of damage accounts for the high mutation rate in mitochondrial genomes
How do mutagens induce mutation?
Chemical mutagens
- Base analogues - 5-bromouracil induces transition mutations
- Base modifying agents -
○ Nitrous acid - deaminates (Exaggerates things that already occur)
○ Hydroxylamine hydroxylates and Methyl methane sulphonate methylates - Intercalating agents - Induce frameshift mutations
○ Intercalating agents, e.g. ethidium bromide, have flat, planar structures that insert in the minor groove of the helix, resulting in partial unwinding.
Chemical mutagens in the environment are metabolised to functional alkylating agents.
Physical mutagens
* Ionising radiation - X-rays
* Ultraviolet (UV) radiation
Guanine is particularly susceptible as it has places susceptible to oxidation, alkylation and deamination
