1. CHAPTER 16 GENE MUTION AND DNA REPAIR
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2. 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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3. 16.1 CONSEQUENCES OF MUTATIONS
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
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4. 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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5. 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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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
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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7. 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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8. 16-8
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9. 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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10. Some mutations are called conditional mutants
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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11. Suppressor mutations are classified into two types
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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12. 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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13. 16-13
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14. 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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15. Regulatory sequences are often bidirectional
Figure 16.2
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16. Mutations Can Occur in Germ-Line or Somatic Cells
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
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17. 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
Therefore, the mutation cannot be passed on to future generations
Figure 16.4
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18. 16.2 OCCURRENCE AND CAUSES OF MUTATION
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
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19. 16-24
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20. 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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21. Contain many mutations at exactly the same site within the gene
Figure 6.20
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22. 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
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
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23. 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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24. 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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25. 16-36 Figure 16.8 Spontaneous depurination
Three out of four (A, T and G) are the incorrect nucleotide
There’s a 75% chance of a mutation
Spontaneous depurination
Figure 16.8
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26. 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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27. 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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28. These rare forms promote AC and GT base pairs
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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29. Common
Rare
Figure 16.10
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30. Figure 16.10
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31. Shifted back to its normal fom Temporary tautomeric shift
Figure 16.10
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32. 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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33. 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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34. 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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35. These mispairings create mutations in the newly replicated strand
Mispairing of modified bases
Figure 16.13
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36. 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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37. This tautomeric shift occurs at a relatively high rate
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
Mispairing
This tautomeric shift occurs at a relatively high rate
Figure 16.14
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38. 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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39. 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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40. 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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41. 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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42. Provides a mixture of enzymes that may activate a mutagen
The control plate indicates that there is a low level of spontaneous mutation
The Ames test for mutagenicity
Figure 16.16
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