MBB222 - Lecture 24: DNA damage and repair

what are mutations

alterations / changes in the DNA structure that produces changes in the genetic information → if not repaired

what are some factors that can damage DNA → cause mutations

• UV light

• reactive oxygen species

• ionizing radiation

• chemical agents

what is a silent mutation

a change in the DNA code / sequence that does not alter the protein it creates

what are the two types of mutations

• point mutation

• insertions / deletions

what are point mutations

a substitution of one base pair for another

how are point mutations typically caused

caused by modification / damage of bases

what are insertions or deletions

where one / more bases are inserted or removed

how is insertions / deletions typically caused

caused by DNA intercalating agents

how does nucleotide mis-incorporation occur

• base mismatching occurs when the template base has been changed / damaged

• H bond acceptor / donor arrangement changes → favours a different base from the typical base it favours

• if damage isn’t corrected → damaged strand will cause the daughter strands to have a permanent mismatch in their DNA sequence

what are the two types of substitution

• transition

• transversion

what is transition

the replacement of one purine for another purine (or pyrimidine for another pyrimidine)

what is transversion

where a purine is substituted with a pyrimidine (vice versa)

what happens if a base modification is not quickly repaired or is not noticed

the mismatch will be introduced into the daughter strand and becomes permanent ( a mutation ) → mutations can result in a different amino acid being incorporated into a protein → can lead to the body creating a broken protein / the wrong protein / no protein at all

what are chemical mutagens

are used to modify bases → can cause point mutation

what is deamination

when a chemical mutagen is used to remove an amine group (NH2)

what is alkylation

when a chemical mutagen is used to change the H bonding ability of a base

what is an example of deaminating agents

nitrous acid → removes an amine group from aromatic primary amines

• can turn adenine → hypoxanthine

• hypoxanthine pairs with cytosine instead of thymine

• mutation occurs where: A-T → C-G

how are deaminated bases repaired

are repaired by base excision repair

what do alkylating agents do

add a methyl or ethyl group typically to purines (adenine/guanine)

what are some examples of alkylating agents

• s-adensylmethionine

• dimethylsulfate

• demethylnitrosamine

what is O6 - alkylguanine

highly mutagenic → base pairs with T instead of C

how is O6 - alkylguanine repaired

directly repaired by O6 - alkylguanine alkyltransferase → transfers the methyl group to a cysteine in it’s active site

→ enzyme is permanently alkylated ( can only be used one ) → not a true enzyme

what do intercalation agents do

presence of intercalation agents can cause insertion or deletion of one or more base pairs

what are examples of intercalating agents

• flatoaromatic molecules

• acridines

what are examples of ionizing radiation

• UV light

• X-rays

• cosmic rays

what is the common type of DNA damage associated with UV light

most common type of DNA damage is UV light around (200-400nm) → the range being part of the solar spectrum

how does UV light damage DNA

induces the condensation of 2 ethylene groups (C6/C5) in adjacent thymines on the same DNA strand → forms a cyclobutane ring → creates kinks in the double helix → could create problems during replication or pause replication

→ adjacent thymines can also dimerize - forming a bond between C4 - C6

how is UV - induced thymine dimers repaired in bacteria / plants

thymine dimers blocks replication / transcription due to the kinks in the helix

bacteria → kinks can be repaired by photolyase - specifically binds to thymine dimers and uses visible light to hydrolyze the bonds linking the adjacent thymines

what is photo reactivation

a method of direct repair

• occurs in bacteria / lower eukaryotes

since human cells do not have photolyase - what do they use for repairing thymine dimers

human cells use nucleotide excision to repair thymine dimers (or sometimes base excision repair)

what happens when thymine dimers are left untreated in human cells

can lead to melanoma (skin cancer) in humans

what is direct repair

a process where cells chemically fixed damaged DNA / RNA without removing or replacing any parts of the DNA / RNA

what is xeroderma pigmentosum (XP)

a rare inherited genetic disorder where the body can’t repair DNA damage caused by UV light

what are some examples of reactive oxygen species

• hydrogen peroxide

• hydroxyl radicals

• superoxide radicals

describe hydroxyl radicals

• is the most responsible for most oxidative damage

• highly reactive

• removes an electron from any molecule → forms a new free radical

what kind of damage does hydroxyl radicals do

• oxidation of deoxyribose / bases → damages the DNA building blocks → leads to cell death / mutations / disease (i.e. cancer)

• can break strands

how do cells counter reactive oxygen species

uses enzymes (i.e. catalase / superoxide dismutase) to convert reactive oxygen species to harmless products

what do human cells use in order to defend their cells against reactive oxygen species

uses DNA glycosylases tp repair the damages caused by reactive oxygen species through base excision repair

what is base excision repair

damaged bases are removed and replaced

what is nucleotide excision repair

damaged nucleotides are removed and replaced

what is mismatch repair

system that finds and fixes errors made when cells copy DNA

• template/daughter strands are distinguished

• short segment of daughter strand with error is removed and replaced

• many enzymes are involved in this process

what is homologous recombination

a process where similar or identical DNA sequences are swapped between two molecules

what are the general steps for base excision repair

• identify damaged base

• remove/cut base

• fill in the gap with the correct base with polymerase

• DNA strand is resealed by ligase

what are the general steps for nucleotide excision repair

• identify the damaged nucleotide

• excise damaged DNA segment

• fill the gap with polymerase

• ligase seals the strands

what are the general steps for mismatch repair

• identify mismatch on daughter strand

• excise the surrounding DNA segment

• fill gap with polymerase

• ligase to seal the strands