GENE

MUTATION
AND DNA REPAIR

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 GENETIC MATERIAL
• DNA
– Primary function permanent storage of information
– Does not normally change
– Mutations do occur

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 MUTATIONS
• Mutation
– Heritable change in the genetic
material
– Permanent structural change of
DNA
• Alteration can be passed on to
daughter cells
• Mutations in reproductive cells
can be passed to offspring

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 MUTATIONS
• Mutations
– Provide allelic variation
• Ultimate source of genetic variation
• Foundation for evolutionary change
– Various phenotypic effects
• Neutral
• Harmful
• Beneficial

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 MUTATIONS
• Mutations
– Most mutations are neutral
– More likely to be harmful than beneficial to the
individual
• More likely to disrupt function
than improve function

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 MUTATIONS
• Mutations
– Many inherited diseases result from mutated genes
– Diseases such as various cancers can be caused by
environmental agents known to
cause DNA mutations
• “Mutagens”

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 MODEL ORGANISMS
• Much of our understanding of mutations is a
result of the study of model organisms
– e.g., Bacteria, yeast, Drosophila, etc.
• Amenable to analysis
• Short generation time, numerous offspring, etc.
– Often exposed to mutagenic environmental agents
• Effects of mutations are studied

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 TYPES OF MUTATIONS
• Types of mutations
– Chromosome mutations
• Changes in chromosome structure
– Genome mutations
• Changes in chromosome number
– Single-gene mutations
• Relatively small changes in DNA
structure
• Occur within a particular gene

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 TYPES OF MUTATIONS
• Mutations involve the permanent alteration of a
DNA sequence
– Alteration of base sequence
– Removal or addition of one or more nucleotides

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 MUTATIONS
• Point mutations
– Change in a single base pair within the DNA
– Two main types of point mutations
• Base substitutions
– Transition
– Transversion
• Small deletions or insertions

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 MUTATIONS
• Two types of base substitutions
– Transition
• Pyrimidine changed to another pyrimidine
– e.g., C  T
• Purine changed to another purine
– e.g., A  G
– Transversion
• Purines and pyrimidines are
interchanged
– e.g., A  C
• More rare than transitions

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 EFFECTS OF MUTATIONS
• Mutations within the coding sequence of a gene
can have various effects on the encoded
polypeptide’s amino acid sequence
– Silent mutations
– Missense mutations
• Included neutral mutations
– Nonsense mutations
– Frameshift mutations

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 EFFECTS OF MUTATIONS
• Silent mutations
– Amino acid sequence is not altered
• e.g., CCC  CCG (pro  pro)
– Genetic code is degenerate
– Alterations of the third base of a codon
often do not alter the encoded amino acid
– Phenotype is not affected

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 EFFECTS OF MUTATIONS
• Missense mutations
– Amino acid sequence is altered
• e.g., GAA GTA (glu  val)
– Phenotype may be affected

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 EFFECTS OF MUTATIONS
• Neutral mutations
– Type of missense mutation
– Amino acid sequence is altered
• e.g., CTT ATT (leu  ile)
• e.g., GAA GAC (glu  asp)
– No detectable effect on protein
function
• Missense mutations substituting
an amino acid with a similar
chemistry to the original is likely
to be neutral

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 EFFECTS OF MUTATIONS
• Nonsense mutations
– Normal codon is changed into a stop
codon
• e.g., AAA  AAG (lys  stop)
– Translation is prematurely terminated
• Truncated polypeptide is formed
– Protein function is generally affected

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EFFECTS OF MUTATIONS

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EFFECTS OF MUTATIONS

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 EFFECTS OF MUTATIONS
• Mutations occasionally produce a polypeptide
with an enhanced ability to function
– Relatively rare
– May result in an organism
with a greater likelihood
to survive and reproduce
– Natural selection may
increase the frequency of
this mutation in the
population

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 MUTATION TYPES
• Genetic terms to describe mutations
– Wild-type
• Relatively common genotype
• Generally the most common allele
– Variant
• Mutant allele altering an organism’s phenotype
– Forward mutation
• Changes wild-type allele into something else
– Reverse mutation
• “Reversion”
• Restores wild-type allele
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 MUTATION TYPES
• Genetic terms to describe mutations
– Deleterious mutation
• Decreases an organism’s chance of
survival
– Lethal mutation
• Results in the death of an organism
• Extreme example of a deleterious
mutation
– Conditional mutants
• Affect the phenotype only under a
defined set of conditions
• e.g., Temperature-sensitive (ts) mutants
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 MUTATION TYPES
• Genetic terms to describe mutations
– Suppressor mutation
• Second mutation that restores the wild-type phenotype
• Intragenic suppressor
– Secondary mutation in the same gene as
the first mutation
– Differs from a reversion
» Second mutation is at a different site
than the first
• Intergenic suppressor
– Secondary mutation in a different gene
than the first mutation

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 MUTATION TYPES
• Two general types of intergenic suppressors
– Those involving an ability to defy the genetic code
– Those involving a mutant structural gene

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 MUTATION TYPES
• Intergenic suppressor mutations involving an
ability to defy the genetic code
– e.g., tRNA mutations
• Altered anticodon region
• e.g., Recognize a stop codon
– May suppress a nonsense mutation
in a gene
– May also suppress stop codons
in normal genes

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 MUTATION TYPES
• Intergenic suppressors involving a mutant
structural gene
– Usually involve altered expression of one gene that
compensates for a loss-of-function mutation affecting
another gene
• Second gene may take over the functional role of the first
• May involve proteins participating in a common cellular
function
– Sometimes involve mutations in genetic regulatory
proteins
• e.g., Transcription factors activating other genes that can
compensate for the mutation in the first gene
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 MUTATION TYPES
• Mutations occurring outside of coding sequences
can influence gene expression
– Mutations may alter the core promoter sequence
• Up promoter mutations
– Mutant promoter becomes more like the consensus sequence
– Rate of transcription may be increased
• Down promoter mutations
– Mutant promoter becomes less like the consensus sequence
– Affinity for regulatory factors is decreased
– Rate of transcription may be decreased

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 MUTATION TYPES
• Mutations occurring outside of coding sequences
can influence gene expression
– Mutations may alter other regulatory sequences
• lacOC mutations prevent binding of
the lac repressor
– Lac operon is constituently expressed,
even in the absence of lactose
» Such expression is wasteful
» Such mutants are at a selective
disadvantage

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 MUTATION TYPES
• Mutations occurring outside of coding sequences
can influence gene expression
– Mutations may alter splice junctions
• Altered order and/or number of exons in the mRNA

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 MUTATION TYPES
• Mutations occurring outside of coding sequences
can influence gene expression
– Mutations may affect an
untranslated region of mRNA
• 5’- or 3’-UTR
• May affect mRNA stability
• May affect the ability of the
mRNA to be translated

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MUTATION TYPES

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 TRINUCLEOTIDE REPEATS
• DNA trinucleotide repeats
– Three nucleotide sequences repeated in tandem
• e.g., …CAGCAGCAGCAGCAGCAG…
• Generally transmitted normally from parent to offspring
without mutation

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 TRINUCLEOTIDE REPEATS
• Trinucleotide repeat expansion (TNRE)
– Number of repeats can readily increase from one
generation to the next
– Cause of several human genetic
diseases
• Length of a repeat has increased
above a certain critical size
• Becomes prone to frequent
expansion

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 TRINUCLEOTIDE REPEATS
• TNRE disorders
– Fragile X syndrome (FRAXA)
– FRAXE mental retardation
– Myotonic muscular dystrophy (DM)
– Spinal and bulbar muscular atrophy (SBMA)
– Huntington disease (HD)
– Spinocerebellar ataxia (SCA1)

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 TRINUCLEOTIDE REPEATS
• TNRE disorders

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 TRINUCLEOTIDE REPEATS
• TNRE disorders
– Expansion may be within a coding sequence of a gene
• Most expansions are of a CAG repeat
• Encoded proteins possess long tracts of glutamine
– CAG encodes a glutamine codon
• Presence of glutamine tracts causes aggregation of the
proteins
• Aggregation is correlated with the progression of the
disease

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 TRINUCLEOTIDE REPEATS
• TNRE disorders
– Expansion may be in a noncoding region of a gene
• Two fragile X syndromes
– Repeat produces CpG islands that become methylated
– Methylation can lead to chromosome compaction
– Can silence gene transcription
• Myotonic muscular dystrophy
– Expansions may cause abnormal changes in RNA structure

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 TRINUCLEOTIDE REPEATS
• TNRE disorders
– Severity of the disease tends to worsen in future
generations
• “Anticipation”
– Severity of the disease depends on the parent from
whom it was inherited
• e.g., In Huntingdon disease, TNRE likely to occur if
mutation gene is inherited from the father
• e.g., In myotonic muscular dystrophy, TNRE likely to occur
if mutation gene is inherited from the mother

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 TRINUCLEOTIDE REPEATS
• TNRE disorders

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 TRINUCLEOTIDE REPEATS
• TNRE disorders
– Cause of TNRE is not well understood
– Trinucleotide repeat may produce alterations in DNA
structure
• e.g., Stem-loop formation
• May lead to errors in DNA replication
– TNRE within certain genes alters gene expression
• Disease symptoms are produced

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 CHROMOSOME STRUCTURE
• Altered chromosome structure can alter gene
expression
– Inversions and translocations commonly have no
obvious phenotypic effects
– Phenotypic effects sometimes occur
• “Position effect”

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 CHROMOSOME STRUCTURE
• Altered chromosome structure can alter gene
expression and phenotype
– Breakpoint may occur within a gene
• Expression of the gene is altered
– Breakpoint may occur near a gene
• Expression is altered when moved to a new location
• May be moved next to regulatory elements influencing the
expression of the relocated gene
– i.e., Silencers or enhancers
• May reposition a gene from a euchromatic region to a
highly condensed (heterochromatic) region
– Expression may be turned off
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 CHROMOSOME STRUCTURE
• Altered chromosome structure
can alter gene expression and
phenotype
– An eye color gene relocated to a
heterochromatic region can
display altered expression
• Gene is sometimes inactivated
• Variegated phenotype results

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 SOMATIC VS. GERM-LINE
• The timing of mutations in multicellular
organisms plays an important role
– Mutations may occur in gametes or a fertilized egg
– Mutations may occur later in life
• Embryonic or adult stages
• Timing can affect
– The severity of the genetic effect
– The ability to be passed from parent to offspring

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 SOMATIC VS. GERM-LINE
• Animals possess germ-line and somatic cells
– Germ-line cells
• Cells giving rise to gametes
– Somatic cells
• All cells of the body
excluding the germ-line cells
– e.g., Muscle cells, nerve cells,
etc.

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 SOMATIC VS. GERM-LINE
• Germ-line cells
– Germ-line mutations can occur in
gametes
– Germ-line mutations can occur in a
precursor cell that produces
gametes
– All cells in the resulting offspring
will contain the mutation

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 SOMATIC VS. GERM-LINE
• Somatic cells
– Somatic mutations in embryonic
cells can result in patches of tissues
containing the mutation
• Size of the patch depends on the timing
of the mutation
• Individual is a genetic mosaic

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 CAUSES OF MUTATIONS
• Two causes of mutations
– Spontaneous mutations
• Result from abnormalities in biological
processes
• Underlying cause lies within the cell
– Induced mutations
• Caused by environmental agents
• Cause originates outside of the cell

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 CAUSES OF MUTATIONS
• Causes of spontaneous mutations
– Abnormalities in crossing over
– Aberrant segregation of chromosomes during meiosis
– Mistakes by DNA polymerase during replication
– Alteration of DNA by chemical products of normal
metabolic processes
– Integration of transposable elements
– Spontaneous changes in nucleotide structure

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 CAUSES OF MUTATIONS
• Induced mutations are caused by mutagens
– Chemical substances or physical agents originating
outside of the cell
– Enter the cell and then alter the DNA structure

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 CAUSES OF MUTATIONS
•

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 CAUSES OF MUTATIONS
• Spontaneous mutations are random events
– Not purposeful
– Mutations occur as a matter of chance
• Some individuals possess beneficial mutations
– Better adapted to their environment
– Increased chance of surviving and reproducing
• Natural selection results in differential reproductive success
– The frequency of such alleles increases in the population

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