Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display CHAPTER 16 GENE MUTION AND DNA REPAIR.

Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

CHAPTER 16

GENE MUTION

AND DNA REPAIR

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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Mutations can be divided into three main types 1. Chromosome mutations

Changes in chromosome structure 2. Genome mutations

Changes in chromosome number 3. Single-gene mutations

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


16.1 CONSEQUENCES OF MUTATIONS

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A point mutation is a change in a single base pair It involves a base substitution

Gene Mutations Change the DNA Sequence

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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


Mutations may also involve the addition or deletion of short sequences of DNA

Gene Mutations Change the DNA Sequence

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5’ AACGCGC 3’3’ TTGCGCG 5’


5’ AACAGTCGCTAGATC 3’3’ TTGTCAGCGATCTAG 5’

Deletion of four base pairs

Addition of four base pairs


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

Gene Mutations Can Alter the Coding Sequence Within a Gene

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Mutations in the coding sequence of a structural gene can have various effects on the polypeptide

Gene Mutations Can Alter the Coding Sequence Within a Gene

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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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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

Gene Mutations and Their Effects on Genotype and Phenotype

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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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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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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

Gene Mutations in Noncoding Sequences

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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

Changes in Chromosome Structure Can Affect Gene Expression

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Regulatory sequences are often

bidirectional


Geneticists classify the animal cells into two types Germ-line cells

Cells that give rise to gametes such as eggs and sperm 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 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

Mutations Can Occur in Germ-Line or Somatic Cells

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Figure 16.416-22

Therefore, the mutation can be

passed on to future generations

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 cannot be passed on to future generations

Mutations can occur spontaneously or be induced

Spontaneous mutations Result from abnormalities in cellular/biological processes

Errors in DNA replication, for example

Induced mutations Caused by environmental agents Agents that are known to alter DNA structure are termed

mutagens These can be chemical or physical agents

Refer to Table 16.4


16.2 OCCURRENCE AND CAUSES OF MUTATION

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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

Spontaneous Mutations Are Random Events

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Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display 16-32Figure 6.20

Contain many mutations at exactly the same site within

the gene


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

The mutation frequency would be 1 in 100,000 or 10-5

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

Mutation Rates and Frequencies

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Spontaneous mutations can arise by three types of chemical changes

1. Depurination

2. Deamination

3. Tautomeric shift

Causes of Spontaneous Mutations

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The most common


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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Causes of Spontaneous Mutations

16-36Spontaneous depurinationFigure 16.8

Three out of four (A, T and G) are the incorrect nucleotideThere’s a 75% chance

of a mutation


Deamination involves the removal of an amino group from the cytosine base The other bases are not readily deaminated

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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


Deamination of 5-methyl cytosine can also occur

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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

Figure 16.9


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 At a low rate, T and G can interconvert to an enol 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 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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16-40Figure 16.10

RareCommon

16-41Figure 16.10

16-42Figure 16.10

Temporary tautomeric shift

Shifted back to its normal fom


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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Types of Mutagens


Chemical mutagens come into three main types

1. Base modifiers

2. Base analogues

3. Intercalating agents

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Mutagens Alter DNA Structure in Different Ways


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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Mispairing of modified basesFigure 16.13

These mispairings create mutations in the newly replicated strand


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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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

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Figure 16.14

Normal pairing This tautomeric shift occurs at a relatively

high rate

Mispairing


Figure 16.14

In this way, 5-bromouracil can promote a change of an AT base pair into a GC base pair


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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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


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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Testing Methods Can Determine If an Agent Is a Mutagen

16-63The Ames test for mutagenicityFigure 16.16

Provides a mixture of

enzymes that may activate a

mutagen

The control plate indicates that there is a low

level of spontaneous

mutation

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Documents

site mutations

polypeptide gene mutations

deleterious mutations

singlegene mutations

nonsense mutations

consequences of mutations

reversion gene mutations

neutral gene mutations