DNA Damage
Mutations
● a change in the DNA sequence of an organism
● mutations can result from errors in DNA replication during cell division, exposure to
mutagens or a viral infection
● can be dangerous or inconsequential
● mutations generates evolution by increasing diversity in a population
● hence, they are both harmful and beneficial
● e.g. sickle cell anemia - arises from a slight mutation
Classification of Mutations
based on cause
● spontaneous mutation
○ occur spontaneously e.g. nondisjunction during meiosis and DNA replication
● induced mutation
○ induced by a mutagen (mutation-causing agent) e.g. due to UV rays
based on level of damage
● gene/point mutation
1. change in a gene at a single nucleotide pair
2. types: base substitution, base insertion, base deletion, base inversion
● chromosomal mutation (a.k.a. gross mutation)
1. change in a gene due to alteration of chromosome structure or number
2. types:
3. chromosomal structure - deletion, inversion, translocation, duplication
4. chromosomal number - aneuploidy (hyper or hypo depending on addition or
subtraction of chromosomes), polyploidy (don’t exist in humans, observed in
plants)
based on change in nitrogenous bases
● transition: a purine replacing a purine or a pyrimidine replacing a pyrimidine
● transversion: a purine replacing a pyrimidine or vice versa
Spontaneous Mutations
due to replication error
● 1 in 10^10 nucleotide chance of error
tautomeric shift
● spontaneous rearrangement of nitrogenous bases which allow for hydrogen bonding
between mismatched base pairs
● amino: A, C; keto: G, T
● conversion can occur from amino to imino form. herein, cytosine forms a double (rather
than triple) bond and pairs with adenine
● conversion can also occur from keto to enol form, which enables thymine to form a triple
bond with guanine
slippage error
● may cause a bubble to form in the new strand
● slippage is thought to occur in sections of DNA with repeated patterns where
polymerase works faster than usual e.g. CAG
● here, the repair mechanisms may realign the template strand with the new strand to
straighten the bubble out
● the resulting double helix is expanded
spontaneous deamination
● the removal of the amine group from the bases results in different molecules
● sometimes this can occur without the presence of any agent
cytosine-G uracil-A
adenine-T hypo-xanthine-C
guanine-C xanthine-T
why is uracil not a part of DNA?
● spontaneous deamination converts C to U and the complementary G will be recognised
as a mismatch
● however, the MMR system can only work on hemi-methylated DNA, whereas such
damage can occur at any point in fully methylated DNA as well
● base excision repair (BER) also would not come in here if U was a self base
● hence, such damage could not be eliminated by any repair system
● given that U is foreign and not a part of DNA, BER comes in here to repair deamination
of cytosine in methylated DNA
Induced Mutations
● in the presence of a mutagen (external factor)
types of mutagens
● physical agent - radiation of 2 kinds:
○ non-ionising radiation e.g. UV-B
○ ionising radiation e.g. alpha, beta, gamma, X-rays
○ such agents cause pyrimidine dimerization (T-T, T-C, C-C) and DNA
fragmentation or breakage
● chemical agents
○ base analogues
○ e.g. 5-bromouracil for thymine, 2-amino purine for adenine
○ can stop replication as they don’t allow the addition of complementary bases
○ deamination by agents
○ i.e. nitrous oxide, hydroxyl amine
○ alkylating agents
○ addition of alkyl groups e.g. methyl, ethyl to bases
○ occurs most frequently with guanine
○ some common alkylating agents - ethyl methyl sulphate (EMS), methyl methyl
sulphate (MMS), N-methyl N-nitrosourea
○ oxidative agents
○ due to reactive oxygen species (ROS) e.g. O-, H2O2
○ cause transversion mutation (unlike transition mutation by the rest)
○ intercalating agents
○ e.g. ethidium bromide, acridine orange, proflavine, benzopyrene, polycyclic
hydrocarbons
○ they get inserted in spaces between dsDNA and behave like bases
○ this causes supercoiling which can result in breakage or damage to the DNA
● biological agents - viruses
○ viral genes can insert themselves in the host genome, which inactivates the gene
expression
○ e.g. in the bacterial gene lac Z which produces beta-galactosidase
Silent Mutation
● when the mutation is inconsequential when the codon generates the same amino acids
● e.g. UUC and UUU both code for phenyl alanine
● genetic code is degenerate: one amino acid can be coded for by multiple codons
● in such cases, there is a change in the DNA sequence, but the protein product is not
affected
Nonsense Mutation
● a mutation in which an amino acid coding codon is converted to a stop codon
● when a codon mutates to a stop codon and the mRNA stops forming midway
● this produces a short or truncated protein
● stop codons: UAG, UAA, UGA
Missense Mutation
● change in the nucleotide sequence leads to a change in the amino acids and, thus,
alters the protein structure
● 2 types: conservative and non-conservative
conservative
● where a polar amino acid replaces a polar amino acid or a non-polar amino acid
replaces a non-polar amino acid
non-conservative
● a polar amino acid replaces a non-polar amino acid or vice versa
● during protein folding, non-polar amino acids can only be found on the internal surfaces.
hence, if an external polar amino acid is mutated to a non-polar one, it would try to pull
inwards and may distort the protein shape.
● e.g. mutation for sickle cell anemia
Frame-Shift Mutation
● an insertion or deletion of bases that results in a shift in the reading frame of the codons
● usually occurs due to an intercalating agent
In-Del Mutation
● in stands for insertion, del stands for deletion
● in this mutation, both insertion and deletion occur and there is a change in amino acids.
the reading frame is, however, not shifted and the following the sequence remains the
same.
Intragenic Suppression
● a mutation wherein a second mutation suppresses the effect of the first mutation on the
same gene
● usually causes no net change in the original amino acid sequence
Intergenic Suppression
● a mutation wherein a second mutation suppresses the effect of the first mutation on a
different gene
● usually causes no net change in the original amino acid sequence
● AUG is the start codon and the only codon that codes for methionine
DNA Damage Sources
endogenous damage
● caused from within the body
● e.g. ROS, RNS, metabolism, inflammation, replication stress
exogenous damage
● caused from outside the body
● e.g. gamma rays, x rays, UV rays, mutagens, toxins, viruses
possible effects of DNA damage
● cell cycle arrest
● chromosomal instabillity
● carcinogenesis
● ageing
● disease
● apoptosis
