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Theme 4 Module 4 Script
Slide 1:
Intro slide. Theme 4, Module 4
Slide 2: YOUR SUMMARY NOTES:
Academic Property Statement
Slide 3:
McMaster University’s Land Acknowledgement
Slide 4:
Theme 4, Module 4: DNA mutations
Slide 5:
The learning objectives of this module are to:
identify the types of mutations that can be
found in DNA molecules
examine the mechanisms in which DNA can
be repaired and finally
understand how mutations can lead to
variation in the genome.
Slide 6:
Unit 1: How common are mistakes?
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Theme 4 Module 4 Script
Slide 7:
Understanding the process of gene expression
enables us to be able to have a further appreciation YOUR SUMMARY NOTES:
as to how changes in the genetic information of a cell
can affect protein structure and function. These
changes or mutations can create devastating cellular
consequences, or a beneficial adaptation. In fact,
mutations are responsible for the large array of genes
and therefore genetic differences that can be found
among different organisms. As a result, mutations
are often considered to be the source of genetic
variation.
Mutations can be created in many ways, including
being due to environmental factors, arising due to
spontaneous mutations or even errors that occur
during the process of DNA replication. Errors in DNA
replication can lead to changes at the nucleotide level
that can be corrected, but at times are not corrected.
If not corrected, the incorrect nucleotide bases can
then be used as a template in the next round of
replication, resulting in the propagation of the
mutation. These spontaneous mutations are the
most common mutations that occur. Arising
randomly and by chance without any known cause.
Yet, how common are these mistakes?
For any given nucleotide, mutation is a very rare
event. In addition, there is variability as to the
likelihood that a new mutation will occur at a given
nucleotide base pair in a single round of replication
across different organisms. While most multicellular
animals have a relatively low probability of incurring a
new mutation at a particular nucleotide pair in a
given round of DNA replication, viruses tend to have a
much higher mutation rate, with RNA viruses having
the most probability amongst all viruses. It is
believed that this discrepancy is due to the delicate
nature of the RNA backbone of RNA viruses and
retroviruses (being more prone to damage and
breakage), in addition to the fact that there is no
proofreading capability in RNA genomes. As we
consider mutations in our genome, it is important to
distinguish between the different types of cells that
can acquire mutations in our bodies.
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Theme 4 Module 4 Script
the Lederberg’s find after stamping the colonies from
a non-selective plate onto a selective plate?
Slide 8:
Genetic information can be mutated in either somatic
or germline cells. If a mutation occurs in the somatic YOUR SUMMARY NOTES:
cell of an individual, that cell will be the progenitor of
a population of identical daughter cells following cell
division. The division of a cell with a new mutation
will lead to a patch or region of cells with that new
mutation. The earlier in the developmental cascade
in which a mutation occurs in a somatic cell, the
larger the spread of the mutated somatic cells
throughout the body of an organism. If a mutation
arises in a cell that is no longer dividing, or is post-
mitotic in the G0 cycle, then the effect of a mutation
may be largely negligible. Are somatic mutations ever
passed onto progeny? No. It is not possible. Cellular
mutations that are passed to progeny arise from
germline mutations since germ cells are the cells that
come together to produce new offspring in sexually
reproducing organisms. What this means is that
every cell in the developing embryo will carry the
mutation.
Slide 9:
Do mutations occur in response to a changing
environment? This is the basis of an experiment
conducted by Joshua and Esther Lederberg in 1952
which showed that mutations such as those of
antibiotic resistance in bacteria are random and not
directed. The experimental setup required allowing
bacteria to grow into colonies in a petri dish with non-
selective supplemented nutrients (or agar), this can
be seen as agar plate 1. The plate is referred to as
non-selective since bacterial cells are able to grow
and form colonies on it. Once bacterial colonies had
grown on the non-selective plate, the Lederbergs
“stamped” the original plate 1 onto a cloth, and then
stamped this cloth onto a new selective plate
containing the antibiotic penicillin in the agar. This
plate would only allow the growth of bacteria that are
resistant to penicillin. The process of stamping in this
manner is often referred to as replica plating and
preserves the relative arrangement of colonies on the
new plate relative to the first agar plate. What did
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Theme 4 Module 4 Script
Slide 10:
Over time, it appeared that only a few colonies that YOUR SUMMARY NOTES:
were stamped from plate 1 survived the exposure to
the penicillin on the plate 2, while most other
bacterial colonies were killed. As a result, the
Lederbergs predicted that these few colonies must
carry a mutation that makes them resistant to the
antibiotic penicillin. The question remained: Did the
colonies on the new plate evolve antibiotic resistance
as a result of exposure to penicillin or did they carry
the mutation anyway and only when exposed to
penicillin could it be detected?
Slide 11:
The process of replica plating means the original
colony that grew on the penicillin agar could be
isolated from the original non-selective agar and used
to test the hypothesis. The Lederbergs exposed the
suspected mutant colony from the original plate 1 to
penicillin. To do that, they isolated bacteria from the
original colony and cultured these cells in medium
containing penicillin. In the end, they found that they
had cultured a pure culture of antibiotic-resistant
bacteria. Remember that the colonies on plate 1
would have never been originally exposed to
penicillin. As a result, it can be concluded that the
mutation that confers penicillin-resistance existed in
the population prior to the bacteria being exposed to
penicillin in the Lederberg experiment. This is
evidence that mutations create random genetic
variation that may include the beneficial changes such
as antibiotic resistance. The new environment did
not create the beneficial mutation, but rather, the
random mutation was beneficial in the new
environment.
Slide 12:
Unit 2: DNA repair
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Theme 4 Module 4 Script
such as DNA polymerase and DNA ligase are then able
to induce DNA synthesis to close the gap and
therefore form an intact DNA strand that matches
with accurate complementarity to the template DNA
strand. This allows for mismatch repair to be
completed.
Slide 13:
Spontaneous and induced mutations occur
YOUR SUMMARY NOTES:
frequently. This would be a serious problem if the cell
had not evolved some refined mechanisms to repair
detectable mutations. Left uncorrected, mutations in
genes will lead to cell death, cancer, aging, and
disease. In addition to the mutations that can occur
during DNA replication, DNA can accrue mutations
due to mutagens or agents that can increase the
probability of mutations at specific regions along the
DNA. These mutagens can include radiation or
chemicals. However, most DNA damage can be
corrected by specialized repair enzymes of the cell.
For example, DNA ligase can repair any breaks in the
DNA backbone. Most cells contain certain DNA
ligases that are involved with DNA replication and
other DNA ligases that specialize in DNA repair of
single-stranded breaks.
Slide 14:
Mismatching of single nucleotide pairs during DNA
replication can be corrected by the proofreading
capabilities of DNA polymerase. Another
proofreading mechanism actually allows for scanning
of the DNA for potential mismatches as a second level
of quality control in DNA. A mismatched nucleotide
pair creates a kink in the DNA molecule that is
recognized by proteins that scan the DNA for damage
and errors. This allows for mismatch repair in which
an identified mismatch in the nucleotide sequence
leads to the single-stranded cleavage of the
mismatched DNA backbone by an enzyme (usually a
DNA cutting-enzyme called a nuclease) some distance
away from the mismatched nucleotide region.
Slide 15:
Once the correcting nuclease enzyme cuts the
backbone, another enzyme is able to remove
successive nucleotides from the cut DNA strand,
including the mismatched nucleotide. Other enzymes
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matched and complementary nucleotides to the
template strand.
Slide 16:
Base excision repair is a more specialized type of YOUR SUMMARY NOTES:
repair mechanism. In this mechanism, it is the
incorporation of a uracil in DNA that signals that there
is the need for DNA repair to be done. Remember
that uracil is a characteristic nucleotide that is present
in RNA molecules. If any DNA molecules accidently
incorporate a uracil into their elongating strands, the
actual presence of uracil is a signal that is detected by
a DNA uracil glycosylase enzyme which will cleave the
uracil from the sugar DNA backbone itself, leaving
behind the bare deoxyribose sugar with no attached
nitrogenous base. When excised from the backbone,
the lack of a nitrogenous base is detected by an
enzyme called AP endonuclease which cleaves the
backbone on either side of the area that lacks a base.
This will then leave an open gap that requires the
addition of a completely new nucleotide. DNA
synthesis will now be able to occur at this gap site,
which is facilitated by enzymes such as DNA
polymerase and DNA ligase, allowing for the addition
of a new and properly matched nucleotide base that
is a complementary base to the template strand.
Slide 17:
Nucleotide excision repair is another mechanism of
DNA repair which bares a lot of resemblance to the
mismatch repair mechanism. In contrast to mismatch
repair which corrects a single nucleotide pair
mismatch, nucleotide excision repair can remove and
replace more than one damaged nucleotide bases. It
is the damaged bases which signal to specific
enzymes to cleave the DNA backbone on either side
or flanking the region of damaged or mismatched
bases. Subsequent to removal, DNA synthesis is able
to completely fill the excised gap with correctly
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Theme 4 Module 4 Script
Slide 18: YOUR SUMMARY NOTES:
Unit 3: Mutations in nucleotide sequence
Slide 19:
Despite the DNA repair mechanisms that have
evolved to protect our genes, there are various types
of mutations that escape repair and can be found
within our genome. These can include small point
mutations, which involve single nucleotide pair
changes in a DNA sequence, or larger scale mutations
that involve changes in large regions of
chromosomes. Small-scale point mutations can arise
during DNA replication. We know of DNA proofing
mechanisms and the manner in which enzymes are
able to correct any nucleotide error during
replication, but it is the mutations that escape the
proofreading mechanisms of DNA replication that are
able to become a permanent change in the genome.
It is important to note that while mutations can
provide the basis for genetic variability, it is the
fidelity of DNA replication that retains point
mutations in a population of dividing cells. The most
common type of point mutation is a single nucleotide
pair substitution where one base pair is incorrectly
replaced by another pair of nucleotides. These
variations are also known as single nucleotide
polymorphisms or SNPs.
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Theme 4 Module 4 Script
While mutations in protein-coding regions of DNA can
at times lead to the production of an improved
protein or even one with new capabilities, more often
than not, mutations in protein-coding regions of DNA
lead to a useless or less active protein that has
impaired cellular function. While most substitution
mutations lead to missense mutations, a point
mutation can also change the codon for an amino
acid into a stop codon. These types of point
mutations are referred to as nonsense mutations, and
cause translation of the protein to stop prematurely.
The result is a protein that has a shorter polypeptide
sequence than the one that is encoded for in the
normal gene. As a result, a nonsense mutation can
also lead to nonfunctional proteins.
YOUR SUMMARY NOTES:
Slide 20:
As one can imagine, if a point mutation occurs in a
region that codes for an important protein, there may
be serious consequences that can be brought about
even by a single nucleotide pair point mutation.
Some changes may have no effect on the structure
and function of the encoded protein product while
others may lead to detrimental effects. Sickle-cell
anemia is one of many life-threatening disorders that
is brought about due to one single nucleotide pair
base changes in the billions of nucleotides that are
contained within our genome. The single-nucleotide
substitution that causes sickle cell anemia is a non-
synonymous or missense mutation which causes a
single amino acid substitution in the beta-globin
protein subunits of the hemoglobin molecules that
carry oxygen in our red blood cells. This single
nucleotide substitution leads to the eventual
translation of a valine amino acid instead of a
glutamate. While this may seem like a trivial change,
it actually leads to a decreased ability for the
hemoglobin molecule to bind oxygen. However, not
all point mutations lead to consequential changes in
the structure and function of a protein. At times, a
change in a nucleotide pair may transform one codon
into another that is translated into the same amino
acid. Such a mutation is an example of a synonymous
or silent mutation and is largely due to the redundant
nature of the genetic code.
Slide 21:
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Theme 4 Module 4 Script
Slide 23:
While insertions and deletions in multiples of three
can lead to single amino acid changes, a frameshift
mutation may occur whenever the number of
nucleotides inserted or deleted is not in a multiple of
three. As a result, such insertions or deletions lead to
improper grouping of nucleotides that are
downstream of the deletion or insertion site. This
leads to the improper grouping of nucleotides into
codons, or a massive missense mutation that more
often than not can end sooner or later in a nonsense,
premature termination. Frameshift mutations
therefore almost certainly lead to proteins that are
nonfunctional.
Slide 22: YOUR SUMMARY NOTES:
While single nucleotide substitutions are of the most
common point mutations, point mutations can also
consist of insertions and deletions. Insertion
mutations occur when one or more extra nucleotides
are inserted into replicating DNA, while deletion
mutations involve the skipping, or sometimes
removal of one or more nucleotides during DNA
replication. In a protein-coding region, the degree of
impact of nucleotide insertions or deletions depends
upon the size of the insertion or deletion. If for
example, three nucleotides are deleted, this can
result in a polypeptide that is missing one amino acid.
In converse, insertion of 6 nucleotides could
potentially lead to the insertion of two possible amino
acids in the resulting translated protein. The deletion
of three nucleotides in the protein coding region of a
chloride channel called the CFTR transporter is largely
the cause of the disease cystic fibrosis. Individuals
that have a three-nucleotide deletion in their genes
that code for the CFTR transporter develop thick,
sticky mucus as a result of the inability to transport
chloride ions across their cells, and as a result can
succumb to the disease due to respiratory
malfunction and bacterial infections. Due to the
nature of the mutation in the CFTR transporter, the
mutant CFTR protein is unstable and is largely
degraded prior to being able to reach the cell
membrane and become embedded to facilitate
chloride ion transport.
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Theme 4 Module 4 Script
in babies that are born. At times, regions of a
chromosome may be able to acquire small
duplications during DNA replication. While duplicated
genes tend to cause little harm to a diploid organism
due to the presence of a normal homologous
chromosome, sometimes extra gene copies that are
brought about by chromosomal mutations can confer
a specific advantage on affected individuals and can
possibly lead to a new gene being formed (with
similar function to the original gene) from this
duplication. This process is often referred to as
duplication and divergence.
Slide 24:
Unit 4: Chromosomal mutations
YOUR SUMMARY NOTES:
Slide 25:
As we have seen, point mutations are caused by
changes in one or perhaps a few nucleotides.
Chromosomal mutations are mutations that affect a
larger region of the DNA and leads to visible changes
in chromosomal structures that are distinguishable
under the microscope. There are four major types of
changes that can occur to chromosome structure that
can result in chromosomal abnormalities. These
include deletions, duplications, inversions and
reciprocal translocations. A deletion can occur when
a chromosomal fragment is lost. This can lead to the
loss of entire genes from that chromosome. If the
centromere is lost, then often times, the entire
chromosome can be lost within a few cell divisions
since it is not able to be allocated properly into
daughter cells during subsequent cell divisions. If a
deletion of a segment of a chromosome were to
occur in a diploid organism, with two homologous
chromosome pairs, a deletion in one of the
homologous chromosomes may potentially persist
depending on whether the other homolog can
compensate to provide and code for enough of the
gene product that is required for survival. If
chromosomal deletions occur within an embryo, this
will often lead to embryo death or fatal abnormalities
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translocations tend to occur in noncoding regions of
DNA in larger genomes, so these types of mutations
generally do not disrupt gene function. However, one
can imagine that there would be problem in offspring
that may inherit a gamete containing a chromosome
with a reciprocal translocation. This may occur due to
the fact that homologous chromosomes may not pair
and move together during cell division events due to
the changes brought about by the translocations. As
a result, an individual may develop from a gamete
that is missing vital genes, leading to detrimental
developmental abnormalities.
Slide 28:
Unit 5: Variation and gene evolution
YOUR SUMMARY NOTES:
Slide 26:
Another type of chromosomal mutation occurs when
the normal order of a sequence of genes in a
chromosome is reversed, producing an inversion at
that chromosomal region. An inversion occurs when
a chromosome fragment breaks off and then
reattaches to the same chromosome, but in the
reverse order. These types of mutations do not
usually lead to serious consequences since all the
genes are still present at the chromosome, however
problems can occur during the process of gamete
formation for example if breaks occur within a gene.
Yet, small inversions are quite common in large
populations and largely explains how the order of
genes in closely related species can vary, contributing
to long-term chromosomal evolution.
Slide 27:
Translocations occur when a portion of one
chromosome is able to attach to a non-homologous
chromosome. Essentially, this occurs when two non-
homologous chromosomes exchange terminal
chromosomal fragments. Like other chromosomal
mutations this can often happen when a break occurs
within the chromosome and the translocation is
carried out before the break is repaired. Reciprocal
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fetuses are nearly identical in amino acid sequence,
yet they are expressed at different levels in the fetus.
In contrast, the adult delta and beta hemoglobin
differ somewhat more in amino acid sequence and
are expressed at very different levels. However, the
interesting fact remains that the sequences of all
these gene family members are identical enough that
this provides support for a possibility that that the
existing globin genes arose through multiple
duplication and divergence events over the last 200
million years. While this is not the only way that
genes might evolve, it is an interesting example of
how errors (duplications) and mistakes (mutations)
can lead to new genes in eukaryotic cells.
Slide 30:
In this module:
We have learned that random mutations are
common in DNA
In addition, we have learned that while the cell
has various repair mechanisms that help repair
various mutations, that sometimes, mutations
can persist and are the basis for gene evolution
and adaptation
as a result, this leads to the variation that
exists when comparing across many genomes.
Slide 29: YOUR SUMMARY NOTES:
As we have seen, there are many types of mutations
that can be found in the DNA of many organisms.
While these mutations are random, many gene
families can arise from gene duplication and
mutation. An example of a type of gene family that
arose due to multiple rounds of gene duplication and
sequence divergence is the beta-globin gene family
that codes for one subunit of the oxygen carrying
molecule, hemoglobin. The beta-globin family
members consist of five different genes that are
expressed at various times throughout the
development of an embryo, fetus or adult, the
resulting genes that have evolved all have the same
function: to be able to bind to and carry oxygen in red
blood cells. It is believed that the evolution of the
beta-globin gene dates back to 200 million years ago
when there was a single duplication event from one
single copy of the beta-globin gene which led to the
evolution of what we now know as characteristic
prenatal and adult globin genes. Even within the
same gene family, there are also characteristic
differences amongst the beta-globin genes of
humans. The two gamma globin genes found in
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Theme 4 Module 4 Script