Mutation and Genetic Variation

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Mutation and Genetic Variation
For every gene, there are many different alleles
- alleles are versions of the same gene that
differ in their DNA base sequence -
some alleles differ in the protein product of the
gene others do not (more on this to
follow) - your combination of alleles is
unique, and makes you you Alleles are generated
by mutations, which are changes in the DNA base
sequence
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Evolution and Alleles
Define evolution genetic change in a population
over time But what does genetic change mean,
exactly? 1. Mutation can create new alleles
that were not previously present in that
population 2. The frequency of alleles may
change Today we will consider mutation in some
detail we will then then discuss in detail the
forces that can change allele frequencies in
natural populations
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Mutation and Genetic Variation
Changes in the DNA sequence create new alleles
in every generation
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The first mutation that was characterized at the
molecular level (that is, at the DNA sequence
level) was the sickle-cell anemia allele of the
hemoglobin gene In people afflicted with the
disease, a mutation was found at amino acid 6
of the 146-amino acid hemoglobin protein
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The is an example of a point mutation 1 of
2 sources (a) random error during DNA
replication (b) error in the repair of damaged
DNA -- chemical mutagens, free radicals,
radiation
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Errors during DNA replication
DNA polymerase occasionally (but rarely) adds the
wrong nucleotide during DNA replication
Purines
If a purine (A or G) gets swapped for another
purine, the mutation is called a transition
Pyrimidines
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Errors during DNA replication
DNA polymerase occasionally (but rarely) adds the
wrong nucleotide during DNA replication
Purines
Also, if a pyrimidine (C or T) gets swapped for
another pyrimidine its a transition
Pyrimidines
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Errors during DNA replication
DNA polymerase occasionally (but rarely) adds the
wrong nucleotide during DNA replication
If one type gets swapped for the other type, its
a transversion Transversions are much
less frequent than transitions (only seen half as
often)
Purines
Pyrimidines
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Why are transition mutations more common?
inserted guanine
Transversions stick two non-complimentary
bases up against each other, causing a disruption
in the DNA helix that is more likely to get
noticed and fixed by repair enzymes
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2nd source of mutations - error in the repair
of damaged DNA (1) chemical mutagens - can
intercalate (stick into) the DNA helix,
distorting the shape and causing excision
(cutting out) of bases (2) free radicals -
uncharged oxygen atoms or OH molecules that
have single electrons - extremely oxidizing -
damage DNA bases (3) radiation - UV from
sunlight can cause thymine dimers, which need
to be excised
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Mutations may, or may not, change the amino acid
sequence
Mutations that change the corresponding mRNA
codon to another codon for the same amino acid
are called synonymous substitutions
glutamine
-C-A-A-
-C-A-G-
glutamine
-- also called silent substitutions -- common
when the change is at the 3rd position
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Mutations may, or may not, change the amino acid
sequence
glutamine glutamine
Mutations that change the corresponding mRNA
codon to a codon for a different amino acid are
called non-synonymous substitutions
-C-A-A- -C-A-A-
-C-A-G- -C-A-C-
glutamine histidine
-- these mutations alter the protein product of
the gene --
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Mutations may, or may not, change the amino acid
sequence
glutamine
- synonymous substitutions usually do not
affect the phenotype of the organism - are
neutral, meaning they have no effect on
fitness
-C-A-A-
-C-A-G-
glutamine
Neutral changes have no adaptive value to the
organism
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Mutations may, or may not, change the amino acid
sequence
non-synonymous substitutions alter the protein
product, so often affect the phenotype of the
organism
glutamine glutamine
-C-A-A- -C-A-A-
-C-A-G- -C-A-C-
glutamine histidine
-- most changes are neutral or detrimental to the
organism -- if the change is adaptive under
some circumstance, then the mutation may lead
to a higher fitness
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Loss-of-function mutations
Protein sequence
DNA sequence
normal ACA-ATG-GTA-CGA Cys-Tyr-His-Ala 1-Base A
CA-GAT-GGT-ACG Cys-Leu-Pro-Val insertion
Frameshift mutations change all subsequent amino
acids, making a dysfunctional protein
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Loss-of-function mutations
Protein sequence
DNA sequence
normal ACA-ATG-GTA-CGA Cys-Tyr-His-Ala 1-Base A
CA-GAT-GGT-ACG Cys-Leu-Pro-Val insertion 1-Base
ACA-TGG-TAC-GA Cys-Tyr-Met-Leu deletion
Frameshift mutations change all subsequent amino
acids, making a dysfunctional protein -
some viruses rely on frameshifts to make a 2nd
functional protein for genomic efficiency
(minimize amount of DNA needed)
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Loss-of-function mutations
Protein sequence
DNA sequence
normal ACA-ATG-GTA-CGA Cys-Tyr-His-Ala 1-Base A
CA-GAT-GGT-ACG Cys-Leu-Pro-Val insertion 1-Base
ACA-TGG-TAC-GA Cys-Tyr-Met-Leu deletion Mutation
ACA-ATT-GTA-CGA Cys to a stop codon
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Loss-of-function mutations
Protein sequence
DNA sequence
normal ACA-ATG-GTA-CGA Cys-Tyr-His-Ala AGG-GGG
-CTA Insertion ACA-AGG-GGG-CTA-ATG
Cys-Ser-Pro-Asp-Tyr - caused by a transposable
element, or jumping gene - transposons
inactivate the gene they disrupt, sometimes only
temporarily they may hop back out at a later
date, restoring the correct coding sequence -
many genomes are littered with transposons or
defunct former transposable sequences
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Mutation rates vary
(1) among different species (2) between the
sexes (3) among individuals (4) among genes -
generally 10-5 to 10-8 mutations per cell
division - can vary between individuals,
depending on their alleles for (a) DNA
polymerase (some less accurate than others) (b)
DNA repair enzymes (some less efficient than
others) - often the first genes to become
mutated in cancer cells are genes involved
in DNA repair
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Linkage
When alleles are close together on a chromosome
we call them linked, because crossing over is
unlikely to separate them
A B C a b c
a B C
A b c
Crossing over between A and B is very likely to
happen, so these loci are not linked
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Linkage
When alleles are close together on a chromosome
we call them linked, because crossing over is
unlikely to separate them
A B C a b c
A B C
a b c
Crossing over between A and B is very likely to
happen, so these loci are not linked Alleles
will tend to get separated by recombination
during meiosis
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Chromosome rearrangements Inversions
When 2 double-stranded breaks occur in a
chromosome, the part in between the breaks may
flip around and get re-inserted This results in
an inversion, where the gene order is reversed
between the break points relative to the normal
chromosome
DNA breaks
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Inversions 2
Inverted regions cannot line up properly with the
homologous chromosome during meiosis
A B C D E F G a b c f
e d g
(1) regions will not align during synapsis, when
homologs pair (2) crossing over would cause loss
of part of the chromosome -so- (3) alleles f, e
and d are now linked, and will be transmitted to
offspring as one big supergene
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Inversions 3
In natural populations, inversions are very
common Studies on the fruit fly Drosophila have
shown that natural selection favors certain
inversions - inversions that link alleles
for small body size together are favored
in hot, dry areas - inversions that link
alleles for large body size together are
favored in cold, wet climates
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Gene Duplication 1
Mutation can create new alleles, but how do you
get new genes? Mistakes during meiosis can
result in unequal crossing over, when a
daughter chromosome inherits duplicated regions
of a chromosome
duplicated B gene
A B C A B C
A B B C
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Gene Duplication 2
The viral enzyme reverse transcriptase can create
gene copies from mRNA transcripts, which then
get inserted back onto a chromosome
A B C A
A B C

reverse transcriptase
mRNA transcript for the A gene
DNA copy of the A gene
-
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Gene Duplication 3 polyploidy
In plants, the production of diploid gametes
during meiosis can result in tetraploid
offspring - that is, offspring with 4
copies of each chromosome Tetraploid plants
cannot produce viable offspring with normal 2N
plants, but can breed successfully with other
tetraploid individuals - new species can thus
come into existence, as a population of
plants that only interbreeds with itself
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Directed mutation controversy
First confirmation that mutation precedes
adaptation came from Luria Delbrucks 1943
experiment, called the Fluctuation Test -
tested two alternative hypotheses about how E.
coli became resistant to a virus (1) acquired
hereditary immunity hypothesis each E. coli
cell has a small chance of surviving a virus,
but survivors get acquired immunity that can
be passed to their offspring - exposure
to virus induces resistance
( adaptation) -
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Directed mutation controversy
First confirmation that mutation precedes
adaptation came from Luria Delbrucks 1943
experiment, called the Fluctuation Test -
tested two alternative hypotheses about how E.
coli became resistant to a virus (1) acquired
hereditary immunity hypothesis each E. coli
cell has a small chance of surviving a virus,
but survivors get acquired immunity that can
be passed to their offspring - prediction in
each tube, there will be a few cells that
get resistance, but only after they are
plated out with the virus
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Directed mutation controversy
(2) mutation hypothesis in some tubes, a
random mutation will happen early on get
passed to most offspring, prior to virus
exposure - will give rise to occasional
jackpot cultures that luckily got the
resistance mutation early in their family
tree - prediction there will be wildly
different s of resistant colonies from
different starting cultures, depending on
how early the mutation occurred this
was the observed result
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Directed mutation controversy
Lederberg Lederberg (1952) replica plating
experiment Put a cloth over a master plate
covered in bacteria blotted it onto many
replica plates coated with virus
Virus-resistant colonies appeared in the same
place on each replica plate - thus, those
colonies grew from resistant cells that
were already present on the master plate
- resistance was not induced by the virus....
master plate
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Directed mutation controversy
Cairns et al. (1988) argued in the journal Nature
these experiments didnt give cells a fair
chance to try to mutate to survive, because
the virus killed cells that were not already
resistant Took cells that had a frameshift
mutation in their lac gene, needed for growth
on medium where lactose is the only energy
source - normally, cells mutate from lac-
to lac at a frequency of 110-8
lactose plates 3 colonies grow (theyve
mutated to lac) no lactose no colonies grow
3108 lac- cells growing in tube of normal media
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Directed mutation controversy
Cairns et al. (1988) found that after mutants sat
on lactose-containing plates for 2-4 days,
many more colonies suddenly started to appear
- only showed up if cells were sitting on
lactose plates - were 10-100 times more
frequent than normal - no increase in rate
of mutation from ValS ValR, so there
was no across-the-board increase in mutation
rate
Day 1 Day 3 Day 5
lactose plates no lactose
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Directed mutation controversy
Cairns et al. (1988) proposed that cells were
somehow sensing that they needed to mutate
their lactose-metabolizing gene to survive..
... were able to choose which mutations will
occur by directing mutation towards the
broken lac gene - from 1988-1994, at least
5 papers argued for directed mutation
when cells were grown on a nutrient they couldnt
use This directly contradicts the fundamental
premise of Darwinian evolution by natural
selection, variation precedes adaptation -
make sure you understand why this was so
controversial!!
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Directed mutation controversy
Anderssen et al. (1998) published the following
model in Science to explain the observations
of Cairns (1) lac- frameshift mutation
still produces 1 of b-gal enzyme
encoded by wildtype lac allele (2) Cairns
expt was done with the lac- mutation on a
plasmid, which could increase the
odds of gene duplication events (3) if a
cell acquires a duplication of lac- allele, it
can grow a little more because of the
small amount of enzyme produced the
more duplications that occur, the more growth is
possible
lac-
lac- lac-
lac- lac- lac- lac-
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Directed mutation controversy
Anderssen et al. (1998) published the following
model in Science to explain the observations
of Cairns (4) this leads to invisible
micro-colonies of slow-growing cells with up
to 100 copies of the broken gene.... meaning,
100 targets for random mutation - youre 100x
more likely to get a reverse-mutation to lac
when you have 100 copies of the broken gene
lying around ! (5) once the
reverse-mutation to lac occurs, the extra broken
copies of lac- are lost and the lac cell
rapidly forms a colony Under this model, all
mutations happen by chance duplications help
the cell by producing more b-gal enzyme, which
leads to growth increases the odds of getting
a lucky lac- lac mutation
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Directed mutation controversy
Anderssen et al. (1998) confirmed experimentally
the predictions of their model, which the
directed mutation hypothesis did not predict
- residual b-gal enzyme activity was necessary in
supposedly lac- mutants, or no
late-appearing lac colonies ever appeared -
early lac cells had up to 50 copies of lac-
allele - the phenomenon required
recombination, which is not needed to fix a
frameshift mutation, but is needed for gene
duplication This story is important because it
shows that you can challenge the basic theory
of evolution through scientific experimentation
but careful experiments done for the last 150
years have, so far, all supported the premise
of Darwinian evolution by selection
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Bottom line
Natural selection is the sole evolutionary
force responsible for the adaptation of
organisms to their environment Mutation is
random with respect to the adaptive needs of
individual organisms you cannot try to mutate
to survive