Week 5- DNA damage and mutations part 1

What are mutations?

Heritable changes in the genetic sequence not due to genetic recombination

The ultimate source of differences among species

The cause of inherited diseases and most cancers

Random events that can occur at any position in the genome

What is most genetic variation due to?

Genetic recombination and sex

• Crossing over

• Independent assortment

How many lethal mutations does each individual carry?

1-2, but they’re recessive and not much of an issue unless you have kids with someone with the same one

Define wild-type

The normal sequence prior to mutation

Not easily defined due to genetic variation within populations

The non-diseased version of a gene

What are the types of mutations?

1. Single nucleotide variants/point mutations

2. Block substitutions: more than 1 base pair is changed

3. Insertions and deletions (indels)

4. Inversions: a stretch of DNA is flipped

5. Copy number variants

6. Rearrangements: extensive chromosomal alterations involving thousands of BPs or whole chromosomes

What are spontaneous mutations?

No known mutagens

Usually due to errors in DNA replication or the effect of endogenous compounds (ie ROS)

What are induced mutations?

Caused by mutagen

What are mutagens?

A chemical or physical agent that increases the rate of mutagenesis

Thousands

Physical mutagens can include ionising radiation and UV radiation

What are somatic mutations?

Occur in nonreproductive (non-germ) cells

Not passed onto the next generation

Can lead to disease and ageing

What are germ-line mutations?

Occur in reproductive cells

Passed onto the next generation

Responsible for genetic variation

What are unconditional mutations?

Expressed at all times

What are conditional mutations?

Expressed only under certain conditions

Give an example of a conditional mutation

Siamese cats: temperature sensitive mutation meaning tyrosinase does not break down tyrosine at high temperatures

Not breaking down tyrosine means less melanin

The parts of their body that are colder are darker (more melanin, tyrosinase working)

What are loss of function mutations?

Knockout/null mutations

Eliminate normal function- think of a car missing a tire

What are hypomorphic mutations?

Leaky mutations

Reduce normal function- think of a car with a hole in the tire

What are hypermorphic mutations?

Increase normal function

What are gain of function mutations?

Ectopic expressions

Expressed at incorrect time or in inappropriate cell types

Where can mutations occur?

• In ‘junk’ DNA: no effect on function

• In protein coding regions: effect on function

• Promoters: can increase activity of promoter or decrease

• Other DNA elements that control transcription

What are base substitution mutations?

One base pair replaced with a different base pair

Can be transition base substitutions or transversion base substitutions

What is a transition base substitution?

A pyrimidine to a pyrimidine

A purine to a purine

What is a transversion base substitution mutation?

Pyrimidine to purine

Purine to pyrimidine

What is a missense mutation?

Non-synonymous

A single nucleotide change that causes a codon to code for a different amino acid (than the wild-type) and thus causes a different amino acid to be produced in the resulting protein

What is a non conservative missense mutation?

Mutant amino acid is very different from wild type amino acid (have different properties) and thus the function of the resulting protein is affected.

I7L = isoleucine (wildtype), 7th position, to leucine (mutant)

What are conservative missense mutations?

Neutral- mutant amino acid is similar to the wild-type amino acid, protein function not affected or not affected too dramatically

What are silent mutations?

AKA synonymous. Mutation means that the codon codes for the same amino acid as the wild type

What are nonsense mutations?

Mutations that create stop codons in translation where they shouldn’t be- usually catastrophic

TGA (opal), TAA (ochre), TAG (amber)

Proteins won’t fold correctly and will degrade

What are frameshift mutations?

Can be insertion or deletion

The insertion of a new base or the deletion of an existing base- everything after the mutation will be random, the ribosome won’t stop at the intended stop codon either as everything is shifted along left or right.

Entirely up to chance where the ribosome stops as it depends when a stop codon is randomly produced in the new mutated sequence

Proteins can end up being too long or too short

Tend to be catastrophic and result in non-functioning proteins from the gene

What is a reversion mutation?

A back mutation in which the sequence has reverted back to the wild-type

What is a suppressor mutation?

A mutation that cancels out (either partially or totally) the effect of another mutation elsewhere on the genome

What is polymorphism?

AKA variant- the occurence of more than one allele in the population

What is haploinsufficiency?

When one copy of a gene is not enough to give the wild-type phenotype

If you were to have a heterozygous genotype, the mutant gene would determine the phenotype- the wild-type gene would be overpowered

What is haplosufficiency?

A single copy of the allele is enough to give the wild-type phenotype

Most diseases are recessive because of this- the wild-type gene overpowers the mutant gene

What is penetrance?

The percentage of individuals who exhibit the phenotype of the allele- in diseases, the percentage of people who suffer from the disease

What is expressivity?

The level to which the phenotype is expressed- in diseases, the severity of the disease

What type of mutation is sickle cell?

Autosomal recessive missense

What type of mutation is phenylketonuria?

A missense, autosomal recessive mutation

Wild-type is haplosufficient

What type of mutation is pelizaeus-merzbacher-like disease?

PMLD- autosomal recessive nonsense mutation

How often do DNA replication errors occur?

DNAP makes 1 mistake for every 100,000 BP added

Most mistakes immediately corrected through proof-reading

Any not corrected by proofreading corrected by postreplication mismatch repair process

10^-10 chance of mutation due to DNA replication per base per replication

What are base substitutions in DNA replication?

Tautomeric base pairs are substituted for normal base pairs

A tautomer is basically. an isomer, just more readily exchanged

Different tautomeric forms have different base pairing potentials

DNAP doesn’t correct tautomeric base pairing because the tautomeric forms of bases pair correctly

What is the tautomeric form of cytosine? What can it bond to?

Imino form of cytosine

Can bind to the amino form of adenine

=N-H instead of -N-H

What is the tautomeric form of thymine? What can it bond to?

Enol form

Hydroxyl group instead of carbonyl group

Can bind to the keto form of guanine

What is the tautomeric form of adenine? What can it bond to?

imino form of adenine

can bond to the amino form of cytosine

What is the tautomeric form of guanine? What can it bond to?

Enol form of guanine

Can bond. to the keto form of thymine

What happens when tautomeric base pairing occurs?

Tautomeric shifts

More likely to happen when a DNA strand is single-stranded, as base pairing stabilises the tautomeric forms

Repetitive bases (3+ of the same base) are rare, as they are prone to mutation

What is an insertion or deletion during DNA replication?

Created when bases in the template or nascent strand slip out of alignment during replication

Most frequently occurs during replication of repetitive DNA sequences

Trinucleotide repeats are the cause of several genetic diseases, replication can lead to trinucleotide expansion which can lead to disease

What is hydrolysis?

A form of spontaneous DNA damage, AKA oxidative deamination

Oxidising agents such as nitrous acid can increase the rate

What is produced from the oxidative deamination of cytosine?

Uracil

What is produced from the oxidative deamination of methylcystosine?

thymine

What is produced from the oxidative deamination of adenine?

hypoxanthine

What is produced from the oxidative deamination of guanine?

Xanthine

What is base loss?

Spontaneous during replication

Due to hydrolysis of the sugar-base bond (N-glycosidic bond)

Depurination and depyrimidation

Results in an abasic site- AP sites (apurinic or apyrimidinic)

If not repaired, an adenine inserted opposite the AP site during DNA replication

Which class of nucleotides is more prone to DNA damage?

Purines, as they are less stable than pyrimidines

What is oxidative damage?

Aerobic metabolism generates reactive oxygen species

(singlet oxygen, hydrogen peroxide, superoxide anion radicals, hydrogen radicals)

Cells actively scavenge reactive oxygen species, and ROS attack DNA in many ways including strand breaks and base modifications

What is methylation?

Form of spontaneous DNA damage

Methylation of adenine to form 3-methyladenine, which blocks DNA replication

Which mutations affect translation?

• Missense (nonsynonymous)

  • Change in amino acid encoded

• Nonsense (termination)

  • Create translation termination codon

• Neutral

  • Change in amino acid encoded to one with a similar function

• Silent (synonymous)

  • No change in amino acid encoded

• Frameshift

  • Shifts triplet reading of codons out of correct phase

Which mutations affect replication?

• Base substitutions

• Indels in repetitive DNA sequences

• Base loss

Which forms of DNA damage are spontaneous?

Depurination (base loss)

Deamination (hydrolysis)

Tautomerisation (base substitutions)

Methylation