Chapter 18: Gene Mutation and DNA Repair

18.1 Effects of Mutations on Gene Structure and Function

Summary of 18.1
 A point mutation is a change in a single base pair. These can be transitions or transversion.
 Silent, missense, nonsense, and frameshift mutations may occur within the coding region of a gene
(see Table 18.1, Figure 18.1)
 Mutation may also occur within noncoding regions of a gene and affect gene expression
 Changes in chromosome structure can have a position effect that alters gene expression (see Figure
18.2, 18.2)
 With regard of timing, mutation can occur in germ-line or in somatic cell (see Figure 18.4, 18.5)

Changes in chromosome structure and number are
mutations because the genetic material has been altered
in a way that can be inherited. Changes in chromosome
structure and number affect the expression of many
genes. In comparison, a gene mutation is relatively small
change in DNA structure that affect a single gene.
Gene Mutations are Molecular Changes in the DNA
sequence of a Gene
A gene mutation occurs when the sequence of the DNA
within a gene is altered in a permanent way.
A point mutation is a change in a single base pair
within the DNA. For example, the DNA sequence shown
here has been altered by a base substitution, in which one
base is substituted for another.
5’-AACGCTAGATC-3’ 5’-AACGCGAGATC-3’
3’-TTGCGATCTAG-3’ 5’-TTGCGCTCTAG-3’
A change of pyrimidines to another, such as C to T
or purine to another, such as A to G is called transition.
This type of mutation is more common than a
transversion, in which purines and pyrimidines are
interchanged.
Besides base substitution, a short sequence of
DNA may be deleted from or added to the chromosomal
DNA.
5’-AACGCTAGATC-3’ 5’-AACGCTC-3’
3’-TTGCGATCTAG-5’ 3’-TTGCGAG-5’
5’-AACGCTAGATC-3’ 5’-AACAGTCGCTAGATC-3’
3’-TTGCGATCTAG-5’ 3’-TTGTCAGCGATCTAG-3’
Gene Mutations Can Alter the Coding Sequence
of a Gene
 Silent Mutations: Those that do not alter
amino acids sequence of the polypeptide even
though the nucleotide sequence has changed.
o occur the third base, meaning that
amino acid is not changed.
 Missense Mutations: Base substitution in
which an amino acid change does occur.
Sickle Cell Disease: Involves a mutation
in the β-goblin gene, which alters the
polypeptide sequence, so the sixth
amino acid is changed from glutamic
acid (glu) to valine (val) which alters
the structure and function of the
hemoglobin.
 Under low oxygen conditions,
the red blood cell assumes
sickle shape.
 Nonsense Mutations: Involves a change from a
normal codon to a stop codon. Thus,
terminating the translation of polypeptides
earlier than expected.
 Frameshift Mutations: Involves the addition or
deletion of several nucleotides that is not
divisible by three.
o This is a shift because codons are read
in multiple of three codons.
o The translation of the mRNA results in
a different amino acid sequence
downstream from the mutation.
Gene Mutations can Occur Outside of the Coding
Sequence and Influence Gene Expression
A mutation can occur within noncoding sequences,
thereby affecting gene expression (Table 18.2). For
example, a mutation may alter the sequence within the
core promoter of a gene.

 Up Promoter Mutations: Promoter mutations that

increase transcription
o Mutations that make a consensus
sequence are likely to be up promoter
mutations.

 Down Promoter Mutations: Causes the promoter

to become less like the consensus sequence:
o Decreasing its affinity for transcription As noted on Table 18.2, mutations can also occur in
factors. other noncoding regions of a gene and alter gene
o Decreasing the transcription rate. expression in a way that may affect phenotype.
Mutations can affect regulatory elements, for example:
For example:
𝑐
Mutations in the lac operator site called 𝑙𝑎𝑐𝑂
 Mutations that affect the untranslated
mutation, prevent:
regions of mRNA – 5’-UTR and 3’-UTR – may
 The binding of lac repressor protein
affect gene expression if they alter its ability
causing the lac operon to be constitutively
to be translated/stability.
expressed even in the absence of lactose.
 Bacteria with 𝑙𝑎𝑐𝑂𝑐 are at a disadvantage
 Mutations in eukaryotic genes can alter splice
compared with the wild-type E. Coli strain
junctions and affect the order of number of
because they waste their energy
exons contained within mRNA
expressing the lac operon when it’s not
needed.
Gene Mutations are Also Given Names that Changes in Chromosome Structure can Affect the
Describe how they affect the wild-type Genotype Expression of a Gene
and Phenotype.
Generic Terms used to describe the effect of mutation
to a wild-type genotype or phenotype:

Wild Type: A relatively prevalent genotype or

phenotype in a natural population.

Mutant Alleles: A mutation that change a wild-type

genotype by altering the DNA sequences of a gene.

Reversion: A reverse mutation, that changes a mutant

allele back to a wild-type allele.

Terms for mutants that are often characterized by their

differential ability to survive:

Neutral Mutations: Do not alter protein functions, so it

does not affect survival or reproductive success.

Deleterious Mutations: Decreases the chances of

survival and reproduction.

Lethal Mutation: Result in death of the cell or organism.

Beneficial Mutation: Enhances the survival or

reproductive success of an organism.

In some cases, an allele may be either

deleterious or beneficial depending on the
genotype and/or environmental conditions. An
example is the sickle call allele:
 In a homozygous state: it decreases the
chances of survival
 In heterozygous and wild-type allele:
increases chances of survival due to
malarial resistance.

A change in chromosome structure can also be

Conditional Mutants: Affect the phenotype only under a
defined condition.
An example is a temperature-sensitive (ts)
mutant.
For example, an E coli strain:
 carrying a ts mutation may be able to
grow from 33℃ to 38 ℃ but not
between 40℃ and 42℃.
 A wild-type strain can grow at either
temperature range.
associated with an alteration in the expression of single
gene.
In some cases, a chromosomal rearrangement may
affect a gene because a chromosomal breakpoint: a
region where two chromosome pieces break and rejoin
with other chromosome pieces.
o A breakpoint with the middle of a gene is very
likely to inhibit gene function because it
separates the gene into two pieces.
In other cases, a gene may be left intact, but its expression
may be altered when it is moved to a new location, this is
known as a position effect.
How do position effects alter gene expression?
1. A gene may be moved next to regulatory sequence
for a different gene, such as a silence or enhancer,
that influences the expression of the relocated gene
(Figure 18.2a)
2. A chromosome rearrangement may reposition a
gene from a less condensed, or euchromatic
chromosome, where it is active, to a very highly
condensed, or heterochromatic chromosome
(Figure 18.2b)
o When moved to a heterochromatic region
its expression is turned off
This second types of position effect produces a
variegated phenotype in which the expression of a
gene is variable.
 For genes that affect pigmentation, this
produces a mottled appearance rather than
an even color (Figure 18.3)
 This occurs because the degree of
heterochromatin formation varies across
different regions of the eye.
Mutations can occur is Germ Line or Somatic Cells
The term germ line refers to cells that give rise to the
gametes such as egg and sperm.
F
Germ-Line Mutations
A germ-line mutation can occur directly in a sperm
or egg cell, or it can occur in precursor cell that
produces the gametes.
If a mutant gamete participates in
fertilization, all cells of the resulting
offspring will contain the mutation (Figure
18.4a)
 Likewise, when an individual with a
germ-line mutation produces
gametes, the mutation may be passed
along to future generations.
o Happens in all cell
Somatic Mutations
The somatic cells comprise all cells of the body
excluding the germ-line cells (Muscle, nerve and skin
cells)
Figure 18.4b illustrates the consequences of
mutations that took place during the embryonic
stage.
In this example, a somatic mutation has occurred
within a single embryonic cell.
As the embryo grows, this single cell is the
precursor for many cells of the adult
organism. Therefore, in the adult, a portion
of the body contains the mutation.
 The size of the affected region
depends on the timing of mutation
(the earlier the mutation – the larger
the affected region)
 An example is a path of white hair
18.3 Spontaneous Mutations

 Spontaneous mutations result from natural biological and chemical processes, whereas induced mutation are
caused by environmental agents (See Table 18.4)
 Three common ways that mutations can arise spontaneously is by depurination, demination, and tautomeric shift
(see Figures 18.7-18.9)
 Reactive oxygen species (ROS) can cause spontaneous mutations by oxidizing bases in DNA (see Figure 18.10)
 In individuals with a trinucleotide repeat expansion (TNRE) a trinucleotide repeat increases above a certain
critical size end becomes prone to frequent expansion. This type of mutation, called dynamic mutation, is
responsible for certain types of human disease. The repeats can expand due to hairpin formation during DNA
replication (see Table 18.5, Figure 18.11)

Geneticist categorize the cause of mutation in one or two
ways.
1. Spontaneous Mutations: Changes in DNNA
structure that result from natural biological or
chemical processes.
2. Induced Mutations: Caused by environmental
agents
Spontaneous Mutations can Arise by
Depurination, Deamination, and Tautomeric
Shifts
Depurination: the removal of a purine (adenine or
guanine) from the DNA.
o The covalent bond between deoxyribose
and purine is unstable and undergoes a
spontaneous reaction with water that
release the base form sugar, creating an
apurinic site.

Deamination: Involves the removal of an amino

group from the cytosine base, producing uracil.
(Figure 18.8a)

Figure 18.8b show the deamination of 5-

methylcytosine.
o The methylation of cytosine form 5-
methlycytosine.
o If 5-methylcytosine is deaminated, the
resulting base is thymine (normal
constituent of DNA)
o This is a problem for DNA repair because
DNA repair proteins cannot distinguish
which is the incorrect base – thymine that
was originally base-paired with the
methylated cytosine. (Produces Hot Spot
for Mutations)

Tautomeric Shift: A temporary change in base

structure.

In this case, the tautomer’s are bases, which exist

in keto and eno or amino and imino forms.

These can interconvert by a chemical reaction

that involves the migration of a hydrogen atom
and a switch of a single bond and adjacent double
bond.
The common, stable form of guanine and thymine is the
keto form: the common form of adenine and Cytosine is
the amino acid form (Figure 18.9a)
At a low rate, G and T can interconvert to an enol form,
and A and C can change to an imino form.
These can cause a mutation because these rare forms of
the bases do not conform to the AT/GC rule of base
pairing.
Instead, if one of the bases is in the enol or imino from,
hydrogen bounding will promote TG and CA base pairs, as
shown in Figure 18.9b
How does a tautomeric shift cause a mutation? It
must occur immediately prior to DNA replication.
As show in Figure 18.9c, a thymine base is the
template stand has undergone a tautomeric shift
prior to the replication of the complementary
daughter strand.
As shown, a thymine base in the template strand has
undergone a TS prior to the replication, the daughter
stand incorporates a guanine opposite this thymine,
creating a base mismatch.
If repairs fail, the next round of DNA replication will
produce a double helix with a CG base pair, whereas
the correct base pair should be TA.
Oxidative Stress May lead to DNA Damage and
Mutation
Reactive Oxygen Species (ROS), such as hydrogen peroxide,
superoxide, and hydroxyl radical, are products of oxygen
metabolism in all aerobic organism.
Oxidative Stress: refers to an imbalance between the
production of ROS and an organism ability to break them
down.
o If ROS over accumulates, one particularly harmful
consequence is oxidative DNA damage, which refers
to changes in DNA structure that are caused by ROS.
The most thoroughly studied guanine oxidation is 7,8-
dihydro-8-oxoguanine (8-oxoG)
 Measure the amount of 8-oxoG in a sample of
DNA to determine the extent of oxidative
stress.
Why are oxidized bases harmful? In the case of 8-oxoG, it
base pairs with adenine during DNA replication, causing
mutation in which a GC base pair become a TA base pair
(Transversion Mutation)
Caused by environmental agents such as:
o UV light
o X-rays
o Cigarrate Chemicals
DNA Sequences Know as Trinucleotides Repeats are
Hotspot for Mutations
Several human genetic diseases are caused by an unusual
mutation known as trinucleotide repeat expansion (TNRE) – a
repeat sequence of three nucleotide that can readily increase
in number from one generation to the next
o A person with TNRE disorder, the length of a
trinucleotide repeat has increased above a certain
critical size.
The expansion is within the coding sequence of the
gene. Such an expansion is CAG repeat because
CAG encodes glutamine. These repeats cause the
encode protein to contain long tracts of glutamine.
 Causes proteins to aggregate (correlates
with the progression of the disease)
Some TNRE disorders have the unusual feature of a
progressively worsening severity in future
generation – a phenomenon called dynamic
mutation.
 The trinucleotide repeat of CAG has
expanded from n=11 tandem copies to
n=18.
How does TNRE occur? The key aspect of TNRE is
that the triplet repeat can from a stem-loop (Figure
18.11a)
The formation of stem-loop during DNA replication
can lead to an increase in length of DNA region if it
occurs in the newly made daughter strand (Figure
18.11b)
1. DNA replication proceeds just past the
TNRE.
2. When the hairpin forms, DNA polymerase
temporarily slips off the template strand
3. DNA polymerase backs up and hops back
on the template strand and resumes DNA
replication from the end of the stem-loop.
4. Stem-loops are short-lived. Can leave gaps
in the opposite strand
5. This gap is later filled by DNA poly. And
ligase
 Base Modification

Chemical mutagens act by covalently modifying the

structure of bases,

Example:

Nitrous acid (HNO2) replace s amino group with keto

group (-NH2 to =O), a process called deamination.
o Changes cytosine to uracil and adenine to
hypoxanthine (Figure 18.12)

Com
18.4 Induced Mutations

Spontaneous mutation can occur in many ways. They result

form natural biological processes. In this section we will
study induced mutation that are caused by environmental
agents.

- Enter the cell and lead to changes in DNA structure

- Mutagens agents know to alter the structure of DNA
which lead to mutation Other chemical mutagens also disrupt the
appropriate pairing between nucleotides by
alkylating bases with DNA.
Mutagens Alter DNA Structure in Different Ways
During Alkylation:
First, mutagenic agents are often involved in the
development of cancer o Methyl or Ethyl group are covalently attached
to the bases.
Second, new mutation may be deleterious - Nitrogen mustard
- Ethyl methanesulfonate (EMS)
- Mutagens may have harmful effect on future
offspring
Base Analogs
Compound such as 5-bromouracil(5BU) and 2-
aminopurine are base analogs that become incorporated
into daughter strand during DNA replication.
- 5BU can be incorporated into DNA instead
of thymine
- 5BU base-pairs with adenine
- Under relative high rates, 5BU undergoes
tautomeric shift (pairs with guanine) Figure
18.13a
When tautomeric shift occurs during DNA replication,
5BU causes a mutation in which a TA base pair is
changed to 5BU-G base pair (Figure 18.13b)
This is a transition, because the adenine has been
changed to a guanine, both of which are purines
 5BU promotes a change of an AT base pair into a
GC base pair.
Ionizing Radiation
 X-rays
 Gamma rays
These can penetrate deeply into biological material,
where it produces chemically reactive molecules know as
free radicals.
o Results in base deletion, oxidized bases
Nonionizing
 UV light
Contains less energy, penetrates only the surface of an
organism, such as the skin.
UV light is knowing to cause DNA mutation such as:
 Formation of crosslinked thymine dimers
(interfere with transcript and ND replication)
18.5 DNA Repair
Damaged Bases can be directly repaired
In a few cases, the covalent modification of nucleotide by
mutagen can be reversed by specific cellular enzymes.
UV light cause the formation of thyme dimers.
 Bacteria, fungi, most plants and some animal
produce an enzyme called photolyase that
recognize thymine dimer and splits them, which
return DNA to original condition
The repair mechanism itself requires light and is known as Figure 18.17 illustrates the steps involved in DNA
photoreactivation (restores the structure of DNA) repair via N-glycosylase.

 Photolyase is critical for DNA repair enzyme for 1. N-glycosylase recognizes a uracil within the
many plant species (plants are exposed to sunlight) DNA and cleave the bond between the sugar
and bases
 Release uracil base and leave behind an
A protein, alkyltransferase (transfers methyl or ethyl from apyrimidinic site
the base to a cysteine side chain) removes methyl or ethyl
groups from guanine bases that have been mutagenized by
alkylating agent such as nitrogen mustard and EMS. (Figure
18.16b)

2. AP endonuclease makes a cut on the 5’ site

3. Following this cut one of two* things can
happen
1) In Humans, the DNA is repaired in
two possible ways.
- DNA polymerase β has the
enzymatic ability to remove a site
that is missing a base, and then insert
nucleotide with the correct base in its
place
- DNA polymerase δ or ϵ can
synthesis a short segment of DNA,
which generate a flap which is
removed by the endonuclease.

Base Excision repair, removes a Damaged Base

A second type of repair system, called base excision repair
(BER) is responsible for removing non-helix distorting
changes that affect the structure of individual bases.

BER involves the function of an enzyme know as DNA N-

glycosylases (recognizes particular type of abnormal
structures)

Can eliminate abnormal bases such as:

 Uracil
 3-methyladenine
 7-ethylguanine
4. The final step is carried out by DNA ligase
 Thymine dimer
which close a gap in the DNA
Nucleotide excision repair systems remove segments Mismatch repair systems recognize and correct a
of damaged DNA. base pair mismatch
An important process of DNA repair is the nucleotide Another type of abnormality is a base pair mismatch
excision repair (NER) system which repair bulky, helix- (AT/GC rule of base pairing)
distorting lesion.
DNA polymerase has a 3’ to 5’ proofreading ability that
NER can repair: detects mismatches and removes them. If this fails, cells
have additional DNA repair systems such as mismatch
 Chemically modified bases
 Missing bases repair system that the detect base mismatches and fixes
 Crosslinks them.

How does it determine which base to remove?

In E. Coli, the NER system require four key proteins, If it’s due to an error in DNA replication, if the newly
designates UvrA,-D which recognize and remove a short made daughter stand contains the incorrect base,
segment of a damaged DNA strand whereas the parental strand is normal. It repairs the
Uvr = Ultraviolet light repair newly made strand rather than the parental.

Prior to DNA replication, the parental DNA has already

been methylated. Therefore, newly replicated DNA is
hemimethylated – only parental DNA strand is
methylated.

Hemimethylation provide a way for DNA repair system

to distinguish between the parental DNA stand and the
daughter strand.

Mismatch repair uses three proteins the MutS, MutL,

and MutH to detect the mismatch and remove
mismatches bases. (Figure 18.20)

In eukaryotes, NER system operate similar as bacteria

Several human diseases are inherited defects in

genes involved in NER.
 Xeroderma pigmentosum(XP)
 Cockanye syndrome (CS).
A common characteristic of both is an
increased sensitivity to sunlight because
of an inability to repair UV-induced
lesion
The net result is that the mismatch has been corrected by
removing the incorrect region in the daughter stand and
then resynthesizing the correct sequence using the
parental DNA as a template.

Double-stand breaks be repaired by homologous

recombination repair and by nonhomologous end
joining
A type of DNA damage that can occur within living cells, is
the breakage of chromosome – DNA double-stand break
(DSB) which is the most dangerous.

DSNs can be cause by ionizing radiation (X-rays or gamma

rays), chemical mutagen and certain drug used for
chemotherapy.

DSB can result in chromosomal rearrangement such as an

inversion and translocation.

How are DSBs repaired? There are two mechanism:

1. Homologues recombination repair (HRR):
occurs when homologous DNA stand, usually from
a sister chromatid (disadvantage: only available
during S and G2) are used to repair DSB.
 During nonhomologous end joining, the two
broken end of DNA are simply pieced back
together (Figure 18.22). Requires the
participation of several protein that play key
roles in process.

2. Nonhomologous end joining (NHEJ): One

advantage of NHEJ is that it doesn’t involve the
participation of a sister chromatid, so it can occur at
any stage of the cell cycle.
 Disadvantage is the NHEJ results in a small
deletion in the region that has been repaired.