Mutations

1
Mutations

• Objectives
• gtCompare and contrast somatic and germinal
  mutations.
• gtExplain the difference between a missense and a
  nonsense point mutation
• gtExplain the effect of an insertion or deletion
  and expanding triplet repeat
• gtDescribe how de novo mutations occur
• gtExplain how mutations can affect protein
  function
• gtUse a codon chart to transcribe and translate a
  DNA sequence into a polypeptide chain.

2
Mutation

• A mutation is a change in the nucleotide sequence
  that composes a gene. This is a change or
  variation from the most common or wildtype
  sequence.
• A mutant allele is an allele that differs from
  the common allele in the population (also called
  the wildtype allele).
• A mutant phenotype refers to a phenotype that
  differs from the common or wildtype phenotype.
• Mutations are not good or bad, just different
  from the majority in the population.

3
Somatic mutations

• are mutations that occur in cells of the body
  excluding the germline.
• Affects subsequent somatic cell descendants
• Limited to impact on the individual and not
  transmitted to offspring

Germline mutations

• are mutations that occur in the germline
  cells.
• Possibility of transmission to offspring

4
Point mutation

• A point mutation is a change of a single
  nucleotide to one of the other three possible
  nucleotides
• Transition
• purine replaces purine
• 
  A -gt G or G -gt A
• pyrimidine replaces pyrimidine
• 
  C -gt T or T -gt C
• Transversion
• purine replaces pyrimidine or
• pyrimidine replaces purine
• 
  A or G -gt T or C
• 
  T or C -gt A or G

5
Missense mutation

• A point mutation that exchanges one codon for
  another causing substitution of an amino acid
• Missense mutations may affect protein function
  severely, mildly or not at all.
• Hemoglobin mutation
• glutamic acid -gt valine causes sickle cell anemia

6
Single base change in hemoglobin gene causes
sickle cell anemia
7
Nonsense mutation

• A point mutation changing a codon for an
  amino acid into a stop codon (UAA, UAG or UGA).
• Premature stop codons create truncated proteins.
• Truncated proteins are often nonfunctional.
• Some truncations have dominant effects due to
  interference with normal functions.
• Most common cause of factor XI deficiency is a
  nonsense mutation change glutamic acid to a stop.
  Short protein cannot function in clotting.

8
Insertion or deletion mutations

• The genetic code is read in triplet nucleotides
  during translation.
• Addition or subtraction of nucleotides not in
  multiples of three lead to a change in the
  reading frame used for translation. Amino acids
  after that point are different, a phenomenon
  called a frameshift.
• Addition or subtraction of nucleotides in
  multiples of three leads to addition or
  subtraction of entire amino acids but not a
  change in the reading frame.

9
Insertion or deletion mutations

• Deletion is the removal of sequences.
• Two-thirds of Duchenne musular dystrophy cases
  are large deletions.
• Insertion is the addition of sequences.
• Gaucher disease is caused by a single base
  insertion creating a frameshift.
• A tandem duplication is a particular form of
  insertion in which identical sequences are found
  side by side.
• Charcot-Marie-Tooth disease is caused by a tandem
  duplication of 1.5 million bases

10
Expanding repeats

• Insertion of triplet repeats leads to extra amino
  acids.
• Some genes are particularly prone to expansion of
  repeats.
• Number of repeats correlates with earlier onset
  and more severe phenotype.
• Expansion of the triplet repeat and coincident
  increase in severity of phenotype occur with
  subsequent generations, a phenomena termed
  anticipation.

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Myotonic dystrophy a triplet repeat disease

• 5 -37 copies of CTG repeat normal
  phenotype
• 50-1000 repeats
  myotonic dystrophy
• Genes with 40 copies are unstable and can
  gain (or less commonly lose) repeat copies in
  successive generations.

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Noncoding repeats can cause phenotypes
In myotonic dystrophy the expanded repeat is not
in the exon. The expansion may affect the
exportation of the mRNA from the nucleus.
13
Triplet repeat disorders
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Example
Type of mutation
Expanding
15
Different sites in a gene can mutate and cause
distinct phenotypes

• Some beta hemoglobin mutations resulting in too
  few protein molecules cause thalessemia.
• Excess of alpha hemoglobin compared to beta
  hemoglobin leads to iron release which kills RBC
  and destroys heart, liver and endocrine glands.
• heterozygous mutation gt milder thalassemia minor
  
• homozygous mutation gt more severe thalassemia
  major

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Mutations in different parts of a gene may have
distinct impacts
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Genotype to disease phenotype

• Cystic fibrosis disease
  CFTR protein
• Duchenne muscular dystrophy
  dystrophin protein
• Familial hypercholesterolemia
  LDL receptor protein
• Hemophilia A
  Factor VIII protein
• Huntington disease
  huntingtin protein

Mutation Many different mutations, common
missing amino acid Mutation Deletion of
gene Mutation Deficient LDL receptors lead
to cholesterol buildup Mutation Absent or
deficient factor Mutation Extra nucleotides
in gene result in extra amino acids
Phenotype Lung infections, pancreatic
insufficiency Phenotype Loss of muscle
function Phenotype High blood cholesterol,
early heart disease Phenotype Slow or absent
blood clotting Phenotype Uncontrollable
movements, personality changes
18
Spontaneous mutation

• De novo or new mutations
• Not caused by exposure to known mutagen
• Errors in DNA replication
• DNA bases have slight chemical instability
• (exists in alternating forms called
  tautomers)

19
Spontaneous mutation rate

• Rate differs for different genes
• Size dependence
• Sequence dependence
• Hot spots
• On average 1 in 100,000 chance of acquiring a
  mutation in a gene each round of replication.
• Each individual has multiple new mutations. Most
  by chance are not in coding regions of genes.

20
Mutational hot spots exist

• Short repetitive sequences
• pairing of repeats may interfere with
  replication or repair enzymes
• Palindromes
• often associated with insertions or deletions
• Duplications of larger regions
• mispairing during meiosis

21
Induced mutations

• Chemicals and radiation can cause mutations.
• Chemicals causing mutations are called mutagens.
• Chemicals causing cancer are called carcinogens.
• Alkylating agents remove a base
• Acridine dyes add or remove base
• Xrays break chromosomes
• delete few
  nucleotides
• UV radiation creates thymidine dimers

22
Ames test

• is an in vitro test of the mutagenicity of a
  substance using Salmonella bacteria with mutation
  in gene for histidine.

• Bacteria are exposed to test substance.
• Growth of bacteria on media without histidine is
  recorded.
• Bacteria only grow if mutations have occurred.
• Rate of mutation is determined.
• Substance can be mixed with mammalian liver
  tissue prior to testing to mimic toxin processing
  in humans.

23
Small or large insertion or deletions
Palindromes can cause small insertion or deletions
Duplications can cause large insertion or
deletions
24
Different mutations may cause the same disorder
Mutations in the LDL receptor disrupt function
leading to increased blood cholesterol and early
heart disease.
25
Not all mutations impact protein function

• Missense mutations are those that alter the
  encoded amino acid to another amino acid.
• The alteration creates a nonsynonymous codon.

Some nonsynonymous mutations are conservative
chemically similar amino acid may not alter
function The impact of a missense mutation is
not predictable from protein sequence alone.
26
Not all mutations impact protein function

• Conditional mutations are those that only
  produce a phenotype under particular conditions
  or environments.

G6PD enzyme is used to respond to oxidants,
chemicals that strip electrons from other
molecules. High levels of oxidants occur when
eating fava beans or taking antimalarial drugs.
Conditions Individuals with mutations
in G6PD Low oxidants no
phenotype High oxidants red blood cells
burst, anemia
27
DNA Repair

• Errors in DNA replication or damage to DNA create
  mutations.
• Most errors and damage are repaired by the cell.
  
• The manner in which DNA repair occurs depends
  upon the type of damage or error.
• Different organisms vary in their ability to
  repair DNA.
• In humans, mutations in DNA replication occur in
  1 in 100 million bases.

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Mismatch repair

• Mismatch repair occurs when enzymes detect
  nucleotides that do not base pair in newly
  replicated DNA.
• The incorrect base is excised and replaced.
• The detection of mismatches is termed
  proofreading.

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Excision repair

• Damaged DNA is removed by excision of the bases
  and replacement by a DNA polymerase.

• Nucleotide excision repair
• Replaces up to 30 bases
• used in repair of UVB and some carcinogens
• Base excision repair
• Replaces 1-5 bases
• Repairs oxidative damage

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Failure of DNA repair

• When DNA repair fails, fewer mutations are
  corrected leading to an increase in the number of
  mutations in the genome.
• The protein p53 monitors repair of damaged DNA.
• If damage is too severe, the p53 protein
  promotes programmed cell death or apoptosis.
• Mutations in genes encoding DNA repair proteins
  can be inherited and lead to overall increase in
  mutations when DNA errors or damage are no longer
  fixed efficiently.

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DNA replication and repair disorders