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CHAPTER 16
GENE MUTION
AND DNA REPAIR
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INTRODUCTION

The term mutation refers to a heritable change in
the genetic material

Mutations provide allelic variations



On the positive side, mutations are the foundation for
evolutionary change
On the negative side, mutations are the cause of many
diseases
Since mutations can be quite harmful, organisms
have developed ways to repair damaged DNA
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16-2
16.1 CONSEQUENCES OF
MUTATIONS

Mutations can be divided into three main types

1. Chromosome mutations


2. Genome mutations



Changes in chromosome number
3. Single-gene mutations


Changes in chromosome structure
Relatively small changes in DNA structure that occur within a
particular gene
Types 1 and 2 were discussed in chapter 8
Type 3 will be discussed in this chapter
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16-3
Gene Mutations Change the
DNA Sequence

A point mutation is a change in a single base pair

It involves a base substitution
5’ AACGCTAGATC 3’
3’ TTGCGATCTAG 5’



5’ AACGCGAGATC 3’
3’ TTGCGCTCTAG 5’
A transition is a change of a pyrimidine (C, T) to
another pyrimidine or a purine (A, G) to another purine
A transversion is a change of a pyrimidine to a purine or
vice versa
Transitions are more common than transversions
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16-4
Gene Mutations Change the
DNA Sequence

Mutations may also involve the addition or deletion
of short sequences of DNA
5’ AACGCTAGATC 3’
3’ TTGCGATCTAG 5’
5’ AACGCGC 3’
3’ TTGCGCG 5’
Deletion of four base pairs
5’ AACGCTAGATC 3’
3’ TTGCGATCTAG 5’
5’ AACAGTCGCTAGATC 3’
3’ TTGTCAGCGATCTAG 5’
Addition of four base pairs
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16-5
Gene Mutations Can Alter the
Coding Sequence Within a Gene

Mutations in the coding sequence of a structural
gene can have various effects on the polypeptide

Silent mutations are those base substitutions that do not
alter the amino acid sequence of the polypeptide


Due to the degeneracy of the genetic code
Missense mutations are those base substitutions in which
an amino acid change does occur


Example: Sickle-cell anemia (Refer to Figure 16.1)
If the substituted amino acids have similar chemistry, the mutation
is said to be neutral
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16-6
Gene Mutations Can Alter the
Coding Sequence Within a Gene

Mutations in the coding sequence of a structural
gene can have various effects on the polypeptide

Nonsense mutations are those base substitutions that
change a normal codon to a termination codon

Frameshift mutations involve the addition or deletion of
nucleotides in multiples of one or two


This shifts the reading frame so that a completely different amino
acid sequence occurs downstream from the mutation
Table 16.1 describes all of the above mutations
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16-7
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16-8
Gene Mutations and Their Effects
on Genotype and Phenotype

In a natural population, the wild-type is the most
common genotype

A forward mutation changes the wild-type genotype
into some new variation



If it is beneficial, it may move evolution forward
Otherwise, it will be probably eliminated from a population
A reverse mutation has the opposite effect

It is also termed a reversion
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16-9

Mutations can also be described based on their
effects on the wild-type phenotype


When a mutation alters an organism’s phenotypic
characteristics, it is said to be a variant
Variants are often characterized by their differential
ability to survive

Deleterious mutations decrease the chances of survival



The most extreme are lethal mutations
Beneficial mutations enhance the survival or reproductive
success of an organism
Some mutations are called conditional mutants

They affect the phenotype only under a defined set of
conditions
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16-10

A second mutation will sometimes affect the
phenotypic expression of another

These second-site mutations are called suppressor
mutations or simply suppressors

Suppressor mutations are classified into two types

Intragenic suppressors


The second mutant site is within the same gene as the first
mutation
Intergenic suppressors

The second mutant site is in a different gene from the first
mutation
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16-11
Gene Mutations in Noncoding
Sequences

These mutations can still affect gene expression

A mutation, may alter the sequence within a promoter

Up promoter mutations make the promoter more like the
consensus sequence


They may increase the rate of transcription
Down promoter mutations make the promoter less like the
consensus sequence

They may decrease the rate of transcription

A mutation can also alter splice junctions in eukaryotes

Refer to Table 16.2 for other examples
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16-12
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16-13
Changes in Chromosome Structure
Can Affect Gene Expression


A chromosomal rearrangement may affect a gene
because the break occurred in the gene itself
A gene may be left intact, but its expression may be
altered because of its new location


This is termed a position effect
There are two common reasons for position effects:

1. Movement to a position next to regulatory sequences


Refer to Figure 16.2a
2. Movement to a position in a heterochromatic region

Refer to Figure 16.2b AND 16.3
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16-19
Regulatory sequences
are often bidirectional
Figure 16.2
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16-20
Mutations Can Occur in
Germ-Line or Somatic Cells

Geneticists classify the animal cells into two types

Germ-line cells


Somatic cells


All other cells
Germ-line mutations are those that occur directly in a
sperm or egg cell, or in one of their precursor cells


Cells that give rise to gametes such as eggs and sperm
Refer to Figure 16.4a
Somatic mutations are those that occur directly in a body
cell, or in one of its precursor cells

Refer to Figure 16.4b AND 16.5
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16-21
The size of the patch
will depend on the
timing of the mutation
The earlier the mutation,
the larger the patch
An individual who has
somatic regions that are
genotypically different
from each other is called
a genetic mosaic
Therefore, the
mutation can be
passed on to future
generations
Figure 16.4
Therefore, the mutation cannot be
passed on to future generations
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16.2 OCCURRENCE AND
CAUSES OF MUTATION

Mutations can occur spontaneously or be induced

Spontaneous mutations

Result from abnormalities in cellular/biological processes


Induced mutations


Caused by environmental agents
Agents that are known to alter DNA structure are termed
mutagens


Errors in DNA replication, for example
These can be chemical or physical agents
Refer to Table 16.4
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16-23
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16-24
Spontaneous Mutations Are
Random Events

Are mutations spontaneous occurrences or causally
related to environmental conditions?

This is a question that biologists have asked themselves
for a long time 

Jean Baptiste Lamarck


Proposed that physiological events (e.g. use and disuse) determine
whether traits are passed along to offspring
Charles Darwin

Proposed that genetic variation occurs by chance

Natural selection results in better-adapted organisms
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16-25
Contain many mutations
at exactly the same site
within the gene
Figure 6.20
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16-32
Mutation Rates and Frequencies

The mutation frequency for a gene is the number of
mutant genes divided by the total number of genes
in a population

If 1 million bacteria were plated and 10 were mutant
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 The mutation frequency would be 1 in 100,000 or 10

The mutation frequency depends not only on the
mutation rate, but also on the


Timing of the mutation
Likelihood that the mutation will be passed on to future
generations
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16-33
Causes of
Spontaneous Mutations

Spontaneous mutations can arise by three types of
chemical changes

1. Depurination

2. Deamination

3. Tautomeric shift
The most common
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16-34
Causes of
Spontaneous Mutations

Depurination involves the removal of a purine
(guanine or adenine) from the DNA

The covalent bond between deoxyribose and a purine
base is somewhat unstable

It occasionally undergoes a spontaneous reaction with water that
releases the base from the sugar

This is termed an apurinic site

Fortunately, apurinic sites can be repaired

However, if the repair system fails, a mutation may result during
subsequent rounds of DNA replication
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16-35
Three out of four (A, T and G)
are the incorrect nucleotide
There’s a 75% chance
of a mutation
Figure 16.8
Spontaneous depurination
16-36

Deamination involves the removal of an amino group
from the cytosine base

The other bases are not readily deaminated
Figure 16.9

DNA repair enzymes can recognize uracil as an
inappropriate base in DNA and remove it

However, if the repair system fails, a C-G to A-T mutation will result
during subsequent rounds of DNA replication
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16-37

Deamination of 5-methyl cytosine can also occur
Figure 16.9


Thymine is a normal constituent of DNA
This poses a problem for repair enzymes


They cannot determine which of the two bases on the two DNA
strands is the incorrect base
For this reason, methylated cytosine bases tend to create
hot spots for mutation
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16-38

A tautomeric shift involves a temporary change in
base structure (Figure 16.10a)

The common, stable form of thymine and guanine is the
keto form


The common, stable form of adenine and cytosine is the
amino form


At a low rate, A and C can interconvert to an imino form
These rare forms promote AC and GT base pairs


At a low rate, T and G can interconvert to an enol form
Refer to Figure 16.10b
For a tautomeric shift to cause a mutation it must
occur immediately prior to DNA replication

Refer to Figure 16.10c
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16-39
Common
Figure 16.10
Rare
16-40
Figure 16.10
16-41
Temporary
tautomeric shift
Figure 16.10
Shifted back to
its normal fom
16-42
Types of Mutagens


An enormous array of agent can act as mutagens
to permanently alter the structure of DNA
The public is concerned about mutagens for two
main reasons:



1. Mutagens are often involved in the development of
human cancers
2. Mutagens can cause gene mutations that may have
harmful effects in future generations
Mutagenic agents are usually classified as
chemical or physical mutagens

Refer to Table 16.5
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16-52
Mutagens Alter DNA Structure
in Different Ways

Chemical mutagens come into three main types

1. Base modifiers

2. Base analogues

3. Intercalating agents
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16-54

Base modifiers covalently modify the structure of a
nucleotide


For example, nitrous acid, replaces amino groups with
keto groups (–NH2 to =O)
This can change cytosine to uracil and adenine to
hypoxanthine

These modified bases do not pair with the appropriate nucleotides
in the daughter strand during DNA replication

Refer to Figure 16.13

Some chemical mutagens disrupt the appropriate pairing
between nucleotides by alkylating bases within the DNA

Examples: Nitrogen mustards and ethyl methanesulfonate (EMS)
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16-55
These mispairings
create mutations in the
newly replicated strand
Figure 16.13 Mispairing of modified bases
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16-56

Intercalating agents contain flat planar structures
that intercalate themselves into the double helix

This distorts the helical structure

When DNA containing these mutagens is replicated, the
daughter strands may contain single-nucleotide additions
and/or deletions

Examples:


Acridine dyes
Proflavin
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16-57

Base analogues become incorporated into daughter
strands during DNA replication

For example, 5-bromouracil is a thymine analogue

It can be incorporated into DNA instead of thymine
Normal pairing
This tautomeric shift
occurs at a relatively
high rate
Mispairing
Figure 16.14
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16-58
In this way, 5-bromouracil can promote a change
of an AT base pair into a GC base pair
Figure 16.14
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16-59

Physical mutagens come into two main types



1. Ionizing radiation
2. Nonionizing radiation
Ionizing radiation





Includes X rays and gamma rays
Has short wavelength and high energy
Can penetrate deeply into biological molecules
Creates chemically reactive molecules termed free radicals
Can cause




Base deletions
Single nicks in DNA strands
Cross-linking
Chromosomal breaks
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16-60

Nonionizing radiation





Includes UV light
Has less energy
Cannot penetrate deeply
into biological molecules
Causes the formation of
cross-linked thymine
dimers
Thymine dimers may
cause mutations when that
DNA strand is replicated
Figure 16.15
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16-61
Testing Methods Can Determine If
an Agent Is a Mutagen

Many different kinds of tests have been used to
evaluate mutagenicity

One commonly used test is the Ames test


Developed by Bruce Ames
The test uses a strain of Salmonella typhimurium that cannot
synthesize the amino acid histidine



It has a point mutation in a gene involved in histidine biosynthesis
A second mutation (i.e., a reversion) may occur restoring the
ability to synthesize histidine
The Ames test monitors the rate at which this second mutation
occurs
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16-62
Provides a
mixture of
enzymes that
may activate a
mutagen
The control plate
indicates that
there is a low
level of
spontaneous
mutation
Figure 16.16 The Ames test for mutagenicity
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