Mutation, Transposition, and Repair

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Mutation, Transposition, and Repair
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• Gene Mutation
• 1. Mutations are Classified in Different Ways

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• - spontaneous just a mistake (typically
  in replication) assumed to be random

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• - spontaneous just a mistake (typically
  in replication) assumed to be random
• - induced caused by an external factor
  (mutagen) usually identified by increased rates
  of mutation above spontaneous levels in
  subpopulations exposed to the mutagen (radiation,
  chemicals)

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• - autosomal vs. sex-linked
• - somatic vs. germ-line (heritable)

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• - substitution (point mutation) the wrong
  base is inserted
• transition purine for purine, etc.
• transversion purine for pyrimidine, etc.

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• - substitution (point mutation) the wrong
  base is inserted
• transition purine for purine, etc.
• transversion purine for pyrimidine, etc.
• - substitutions may
• change the amino acid (new codon) missense

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• - substitution (point mutation) the wrong
  base is inserted
• transition purine for purine, etc.
• transversion purine for pyrimidine, etc.
• - substitutions may
• change the amino acid (new codon) missense
• not change the AA (redundancy) silent

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• - substitution (point mutation) the wrong
  base is inserted
• transition purine for purine, etc.
• transversion purine for pyrimidine, etc.
• - substitutions may
• change the amino acid (new codon) missense
• not change the AA (redundancy) silent
• change to stop codon nonsense

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• - substitution (point mutation) the wrong
  base is inserted
• - frameshift bases are added or deleted,
  changing all codons
• downstream.

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Substitution mutation
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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• d. By Effect on the Phenotype
• - loss-of-function (null)

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• d. By Effect on the Phenotype
• - loss-of-function (null)
• - gain-of-function (enhanced or new function)

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• d. By Effect on the Phenotype
• - loss-of-function (null)
• - gain-of-function
• - neutral (change is not in a gene, or it is
  silent)

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• d. By Effect on the Phenotype
• - loss-of-function (null)
• - gain-of-function
• - neutral (change is not in a gene, or it is
  silent)
• - biochemical (physiological), morphological,
  behavioral

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• a. By Cause
• b. By Location
• c. By Type of Change
• d. By Effect on the Phenotype
• - loss-of-function (null)
• - gain-of-function
• - neutral (change is not in a gene, or it is
  silent)
• - biochemical (physiological), morphological,
  behavioral
• - lethal and conditional

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• a. Mutation rates are low selection has
  favored organisms that can replicate their DNA
  with few errors.

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• a. Mutation rates are low selection has
  favored organisms that can replicate their DNA
  with few errors.
• b. But rates do vary by several orders of
  magnitude between different types of organisms.
  In higher eukaryotes, mutation rates (10-5
  10-6) are higher than in bacteria and viruses
  (10-8).

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift
• All bases can exist in different forms.
• In the atypical form, they bind to different
  bases.

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings

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deamination
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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings
• - depurination loss of A or G base in
  ds-DNA, and random
• replacement during replication.

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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings
• - depurination loss of A or G base in
  ds-DNA, and random
• replacement during replication.
• - oxidative damage to DNA due to normal
  metabolic production
• of oxidants, or reactive oxygen species
  (ROS) such as superoxides (O2.-), hydroxl
  radicals ( .OH), and hydrogen peroxide (H2O2)

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The most common effect is oxidation of guanine to
7,8-dihydro-8-oxoguanine. 8-oxoG is used as
an indicator of oxidative stress.
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Can bind with both Cytosine and Adenine
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In E. coli and Archeans, there are two proteins
that correct this error, either before or after
DNA replication. In eukaryotes, a related enzyme
only cleaves the 8oxoG before replication in the
G-C conformation.
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Guanine is more susceptible to oxidation as the
terminal G in a string of Gs (GGG) rather than
as a single base in sequence. In this context,
G-C rich repeats outside of genes may act as
oxidation pools, soaking up the oxidative
agents and protecting neighboring gene sequences.
(Faucher, Doublié and Jia , 2012)
http//www.mdpi.com/1422-0067/13/6/6711/htm
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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings
• - depurination loss of A or G base in
  ds-DNA, and random
• replacement during replication.
• - oxidative damage
• b. Frameshifts
• - replication slippage

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Huntingtons Chorea a trinucleotide repeat
disorder the more repeats, the more severe the
expression. CAG codes for glutamine, creating a
poly-glutamine region that eventually disrupts
protein function.
Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CAG repeats Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CAG repeats Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CAG repeats
Repeat count Classification Disease status
lt28 Normal Unaffected
2835 Intermediate Unaffected
3640 Reduced Penetrance /- Affected LATE IN LIFE
gt40 Full Penetrance Affected EARLY IN LIFE
Genetic anticipation The onset and severity of
the disorder occurs earlier and earlier in life
from one generation to the next. This occurs as
repeats are added during gametogenesis.
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Fragile-X syndrome a CGG trinucleotide repeat
disorder. Over 200 repeats in the promoter
region of the gene and the gene is methylated -
no protein is produced. The protein is important
in neural development. Absence results in mental
retardation/ intellectual disability. Most common
genetic correlate with autism (5), and 15-60 of
fragile X individuals are classified with ASD
(autism spectrum disorder). The most common
genetic cause of intellectual disability in males
(X linked).
Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CGG repeats Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CGG repeats Classification of the trinucleotide repeat, and resulting disease status, depends on the number of CGG repeats
Repeat count Classification Disease status
lt54 Normal Unaffected
50-200 premutation allele Mild or Unaffected
gt200 mutation Fragile X Syndrome
Also exhibits genetic anticipation fragile x
associated tremor/ataxia syndrome (FXATAS) and
primary ovarian insufficiency (POI)
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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings
• - depurination loss of A or G base in
  ds-DNA, and random
• replacement during replication.
• - oxidative damage
• b. Frameshifts
• - replication slippage
• - most common where there are repeat
  sequences (like tandem repeats of
  CGCGCGCGCGCGCGC).
• - because errors are common, these are
  hypermutable regions, and we differ at an
  individual level in the lengths of these
  sequences often used for DNA fingerprinting

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Variable Number Tandem Repeats (VNTR) (tandem
adjacent) - microsatellites - lt 5 base repeat
CAG CAG CAG CAG - minisatellites - gt 5 base
repeat CCCAGC CCCAGC CCCAGC
C D
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Variable Number Tandem Repeats (VNTR) -
microsatellites - lt 5 base repeat CAG CAG CAG
CAG - minisatellites - gt 5 base repeat CCCAGC
CCCAGC CCCAGC
Restriction Sites or Flanking Regions
Chop these up with a different restriction
enzyme creating restriction fragment length
polymorphisms
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• Gene Mutation
• 1. Mutations are Classified in Different Ways
• 2. The Rates of Spontaneous Mutations
• 3. How Spontaneous Mutations Occur
• a. Substitutions
• - truly random error in replication
• - tautomeric shift (same base, but different
  pairing)
• - deamination of A and C cause mispairings
• - depurination loss of A or G base in
  ds-DNA, and random
• replacement during replication.
• - oxidative damage
• b. Frameshifts
• - replication slippage
• - transposons jumping genes
• can jump into an exon and turn a
  gene off
• jump into introns and affect
  splicing pattern new gene
• carry a gene and multiply it
  through the genome

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Bacterial transposons Insertion Sequences
encode a transposase that cuts the sequence out
and inserts it elsewhere at the same restriction
site
Inverted terminal repeat
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Bacterial transposons Insertion Sequences
encode a transposase that cuts the sequence out
and inserts it elsewhere at the same restriction
site. Tn elements Have a structural gene
associated with the transposase.
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Barbara McClintock, Nobel Prize 1983
Ds dissociator it is a transposable element,
like a bacterial IS, but the transposase gene has
a loss of function mutation so it has the
cleavage sites, but cant make the transposase
itself. W a phenotypic trait like kernel
color (though the actual relationships are more
complex)
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Ac activator. Also an IS-like sequence that
produces a transposase, which recognizes and
moves Ds. Ac can move autonomously Ds cant.
The effects of Ds depend where it jumps it may
cause ds-DNA breakage (the cytological effect
McClintock associated with a change in phenotype).
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Or it can disrupt other genes turning them on
and off.
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Humans Long and Short Interspersed Elements
(LINES and SINES) 30 of the genome Other
families of transposable elements 11 Many are
not mobile their movement is repressed
Diseases - cases of hemophilia, Duchennes
muscular dystrophy, and breast cancer have been
identified that resulted from an insertion of a
transposable element into a functional gene.
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Evolutionary Effects - may cause a significant
fraction of new mutations up to 50 of
mutations in Drosophila. - Telomeres in
Drosophila are transposable elements that copy
themselves and add sections, maintaining the
length of their telomeres. Tn transposons in
bacteria transfer antibiotic genes. -
Transposons create homologous regions that
increase the liklihood of recombination - and
the unequal cross-over events that create gene
duplication and exon shuffling.
OR