Gene mutations

What are spontaneous nucleotide base changes?

*DNA nucleotide bases can occasionally convert to alternative structures called tautomers*, with slight differences in bonding and placement of hydrogens *amino* (normal structure for adenine and cytosine) ↔ imino (rare) *keto* (normal structure for thymine and guanine) ↔ enol (rare) Tautomeric shifts can lead to base-pair mismatches and incorporation of incorrect bases during replication *This is the most common form of replication error*

What are forward and reverse mutations?

*Forward mutation*: converts a wild-type allele to a mutant allele *Reverse mutations*: convert mutant alleles to wild-type

What is mutation frequency defined as in diploids?

*The number of mutational events in a given gene over a defined period of time* (e.g. per DNA replication cycle or per cell generation)

Which human diseases are caused by mutations in genes that encode proteins involved in DNA repair mechanisms?

*Xeroderma pigmentosum* : - individuals are usually homozygous recessive for a faulty repair gene. Sufferers are photosensitive and if their skin is exposed to light develops freckles and patches of intense pigment leading to warty growths that are malignant and usually fatal. Disease symptoms are caused by mutant alleles of six different genes whose protein products are involved in DNA repair in humans.

What is a nonsense base-pair substitution mutation?

- Change codon for amino acid into STOP codon

What is a missense substitution mutation?

- Changes codon for one amino acid to codon for another amino acid - Also called nonsynonymous mutation - The effect of changin an amino acid will depend on the role of that amino acid in protein function

What is a silent base-pair substitution mutation?

- Changes one codon for an amino acid to another codon for that amino acid - NO change in amino acid (silent mutation)

What are the types of spontaneous mutation?

1) DNA replication errors 2) Spontaneous nucleotide base changes 3) DNA nucleotide lesions --> *Depurination* : removal of a purine group --> *Deamination* : removal of amino group

What are the different origins of mutation?

1) Induced mutation --> action of a mutagen --> process of inducing mutations by mutagens is called mutagenesis 2) Spontaneous mutation --> arise in absence of known mutagen --> may be caused by errors in DNA replication --> provide "background rate" of mutation --> important evidence for evolution

What is the effect of a missense mutation?

1) Less severe: conservative amino acid substitution substitutes chemically similar amino acid, less likely to alter function - often called a *neutral mutation* 2) More severe: nonconservative amino acid substitution substitutes chemically different amino acid, more likely to alter function e.g. Glycine for glutamate N.B. a mutation in the first letter of the 3 letter aa is more likely to have dire consequences

What are the different agents that lead to induced mutations?

1) Nucleotide base analogs 2) Deaminating agents 3) Alkylating agents 4) Hydroxylating agents 5) Oxidative agents 6) Intercalating agents 7) Radiation-induced DNA damage

What are the various DNA repair mechanisms found?

1) Photoreactivation repair 2) Base excision repair 3) Nucleotide excision repair

What are the types of base-pair substitution mutations?

1) Silent mutation 2) Missense mutation 3) Nonsense mutation

What is a true reversion?

A wild-type DNA sequence is restored by a second mutation within the *same codon*

What is a frameshift mutation?

Addition or deletion of one or more bases - alters all the amino acids downstream of the mutation

Examples of alkylating agents

Alkylating agents modify base structure by adding methyl or ethyl groups which can result in altered base pairing

Examples of base analogs

Base analogs are similar to nitrogenous bases of DNA, but have altered pairing properties

What is base excision repair?

Base excision repair performed by a base specific DNA glycolsylase (in this example uracil DNA glycosylase) AP endonuclease, DNA polymerase and DNA ligase.

What is photoreactivation repair?

DNA damage repaired by photoreactivation enzyme which *cleaves* the *thymine dimer bond* In E. Coli this enzyme is called photolyase

How do DNA replication errors lead to spontaneous mutations?

DNA polymerase can insert the wrong nucleotide. This is corrected by the 'proof reading' 3' to 5' exonuclease function of the DNA polymerase 99% of the time. The trinucleotide repeat disorders are *caused by DNA polymerase slipping during DNA replication and increasing the number of tri nucleotide repeats within a gene which results in longer stretches of the same amino acid within the protein* e.g. Huntington's disease (autosomal dominant) - caused by increase in length of a polyglutamine region in the Huntington protein

What are hotspots of mutation?

Genes that have elevated mutation frequencies - reason being that they have a large gene size

What is RNA splicing?

In eukaryotes, messenger RNA (mRNA) is transcribed as pre-messenger RNA (pre-mRNA) which is processed to remove intron regions. Efficient splicing of introns from pre-mRNA requires specific sequences at the intron-exon boundaries.

Examples of intercalating agents

Intercalating agents are flat, planar molecules that intercalate between base pairs distorting the DNA helix which disrupts DNA replication and causes addition or deletion of nucleotides leading to frameshift mutations. e.g. proflavin, acridine orange, ethidium bromide.

What are some splicing mutations?

Mutations that alter nucleotides required for efficient splicing at intron-exon junctions These can result in splicing errors and the production of mutant proteins due to the retention of intron sequences in the mature mRNA

What are germ-line mutations?

Mutations that occur in gametes. These mutations are inherited by offspring.

What is a second-site reversion mutation?

Occurs by mutation in a different gene and together the two mutations restore the organism to wild-type.

What is an intragenic reversion?

Occurs through mutation elsewhere in the same gene

What is Nucleotide excision repair?

Repairs lesions which distort DNA e.g thymine dimers DNA polymerase I then synthesises the new DNA strand and DNA ligase joins the single stranded nick

What does a nonsense mutation result in?

Results in premature termination of translation --> making truncated polypeptides nonfunctional

What are cryptic splice sites?

Sites that replace or compete with authentic splice sites during mRNA processing These lead to new possible forms of protein product

What are somatic mutations?

Somatic mutations are ones that occur in any cell of the body apart from germ cells (egg and sperm). These mutations can not be inherited by offspring. These can lead to cancer.

What are regulatory mutations?

Some point mutations alter the amount of protein product produced by a gene - affect regions such as: 1) promoters 2) introns 3) regions coding for 5' and 3' segments on mRNA

What affects mutation frequency?

Species with larger genomes have, on average, higher mutation frequencies

What are base-pair substitution mutations?

The replacement of one nucleotide base pair by another

What are regulatory mutations of the promoter regions?

These mutations interfere with efficient transcription initiation Some promoter mutations cause mild to moderate reductions in transcription levels, whereas others may abolish transcription, some mutations can even enhance transcription