Gene Mutations and DNA Repair Benjamin A. Pierce GENETICS A Conceptual Approach FIFTH EDITION CHAPTER 18 Gene Mutations and DNA Repair © 2014 W. H. Freeman and Company 1

People with a mutation in the tinman gene, named after Tin Man, in The Wizard of Oz, often have congenital heart defects. [Mary Evans Picture Library/Alamy.]

18.1 Mutations Are Inherited Alterations in the DNA Sequence The Importance of Mutations Categories of Mutations Types of Genetic Mutations Phenotypic Effects of Mutations Suppressor Mutations

The Importance of Mutations Mutations: sustainer of life and cause of great suffering Source of all genetic variation, which further provides the raw material for evolution Source of many diseases and disorders Useful for probing fundamental biological processes

Categories of Mutations Somatic mutations Germ-line mutations Gene vs. chromosomal mutations

Figure 18.1 The two basic classes of mutations are somatic mutations and germ-line mutations.

Types of Gene Mutations (based on their molecular nature) Base substitutions Transition Transversion Insertions and deletions Frameshift mutations In-frame insertions and deletions Expanding nucleotide repeats Increase in the number of a copies of a set of nucleotides

Figure 18.2 Three basic types of gene mutations are base substitutions, insertions, and deletions.

Figure 18.3 A transition is the substitution of a purine for a purine or of a pyrimidine for a pyrimidine; a transversion is the substitution of a pyrimidine for a purine or of a purine for a pyrimidine.

Figure 18.4 The fragile-X chromosome is associated with a characteristic constriction (fragile site) on the long arm. [Visuals Unlimited.]

Figure 18.5 A model of how the number of copies of a nucleotide repeat may increase in replication.

Concept Check 1 Which of the following changes is a transition base substitution? Adenine is replaced by thymine. Cytosine is replaced by adenine. Guanine is replaced by adenine. Three nucleotide pairs are inserted into DNA.

Concept Check 1 Which of the following changes is a transition base substitution? Adenine is replaced by thymine. Cytosine is replaced by adenine. Guanine is replaced by adenine. Three nucleotide pairs are inserted into DNA.

Phenotypic Effects of Mutations Forward mutation: wild type  mutant type Reverse mutation: mutant type  wild type Missense mutation: amino aciddifferent amino acid Nonsense mutation: sense codon nonsense codon Silent mutation: codonsynonymous codon Neutral mutation: no change in function

Figure 18.6 Base substitutions can cause (a) missense, (b) nonsense, and (c) silent mutations.

Phenotypic Effects of Mutations Loss-of-function mutations Gain-of-function mutations Conditional mutation Lethal mutation

Suppressor Mutations Suppressor mutation: a mutation that hides or suppresses the effect of another mutation Intragenic Intergenic

Figure 18.7 Relation of forward, reverse, and suppressor mutations.

Figure 18.8 An intragenic suppressor mutation occurs in the gene containing the mutation being suppressed.

Figure 18.9 An intergenic suppressor mutation occurs in a gene other than the one bearing the original mutation. (a) The wild-type sequence produces a full-length, functional protein. (b) A base substitution at a site in the same gene produces a premature stop codon, resulting in a shortened, nonfunctional protein. (c) A base substitution at a site in another gene, which in this case encodes tRNA, alters the anticodon of tRNATyr; tRNATyr can pair with the stop codon produced by the original mutation, allowing tyrosine to be incorporated into the protein and translation to continue.

Mutation Rates Factors affecting mutation rates Variation in mutation rates Adaptive mutations

Factors Affecting Mutation Rates Frequency with which a change takes place in DNA The probability that when a change takes place, that change will be repaired The probability that a mutation will be detected

Adaptive Mutation Genetic variation critical for evolutionary change that brings about adaptation to new environments Stressful conditions, where adaptation might be necessary to survive, induces increased mutation in bacteria

18.2 Mutations Are Potentially Caused by a Number of Different Factors Spontaneous replication errors Spontaneous chemical changes Chemically induced mutations Radiation

Spontaneous Replication Errors Tautomeric shifts Mispairing due to other structures Incorporation errors and replication errors Causes of deletion and insertions Strand slippage Unequal crossing over

Figure 18.10 Nonstandard base pairings can occur as a result of the flexibility in DNA structure.

Figure 18.11 Wobble base pairing leads to a replicated error.

Figure 18.12 Insertions and deletions may result from strand slippage.

Figure 18.13 Unequal crossing over produces insertions and deletions.

Spontaneous Chemical Changes Depurination: loss of purine Deamination: loss of an amino group

Figure 18.14 Depurination (the loss of a purine base from a nucleotide) produces an apurinic site.

Figure 18.15 Deamination alters DNA bases.

Chemically Induced Mutations Mutagen Base analogs

Figure 18.16 5-bromouracil (a base analog) resembles thymine, except that it has a bromine atom in place of a methyl group on the 5-carbon atom. Because of the similarity in their structures, 5-bromouracil may be incorporated into DNA in place of thymine. Like thymine, 5-bromouracil normally pairs with adenine but, when ionized, it may pair with guanine through wobble.

Figure 18.17 5-bromouracil can lead to a replicated error.

Chemically Induced Mutations Alkylating agents: donate alkyl group Ethylmethylsulfonate EMS Mustard gas Deamination: nitrous acid Hydroxylamine: add hydroxyl group

Figure 18.18 Chemicals may alter DNA bases.

Chemically Induced Mutations Oxidative reaction: superoxide radicals Hydrogen peroxide Intercalating agents: proflavin, acridine orange, and ethidium bromide

Figure 18.19 Oxidative radicals convert guanine into 8-oxy-7, 8-dihydrodeoxyguanine.

Figure 18. 20 Intercalating agents Figure 18.20 Intercalating agents. Proflavin and acridine orange (a) insert themselves between adjacent bases in DNA, distorting the three-dimensional structure of the helix (b).

Concept Check 2 Base analogs are mutagenic because of which characteristic? They produce changes in DNA polymerase that cause it to malfunction. They distort the structure of DNA. They are similar in structure to the normal bases. They chemically modify the normal bases.

Concept Check 2 Base analogs are mutagenic because of which characteristic? They produce changes in DNA polymerase that cause it to malfunction. They distort the structure of DNA. They are similar in structure to the normal bases. They chemically modify the normal bases.

Radiation Radiation greatly increases mutation rates in all organisms Pyrimidine dimer: two thymine bases block replication. SOS system in bacteria: SOS system allows bacteria cells to bypass the replication block with a mutation-prone pathway.

Figure 18. 21 Pyrimidine dimers result from ultraviolet light Figure 18.21 Pyrimidine dimers result from ultraviolet light. (a) Formation of thymine dimer. (b) Distorted DNA.

18.3 Mutations Are the Focus of Intense Study by Geneticists Detecting Mutations with the Ames Test Radiation Exposure in Humans

Figure 18.22 The Ames test is used to identify chemical mutagens.

Figure 18.23 Hiroshima was destroyed by an atomic bomb on August 6, 1945.

18.4 Transposable Elements Cause Mutations Transposable elements: sequences that can move about the genome Transposition: movement of the transposons Features: Flanking direct repeats Terminal inverted repeats

Figure 18.24 Flanking direct repeats are generated when a transposable element inserts into DNA.

Figure 18. 25 Many transposable elements have common characteristics Figure 18.25 Many transposable elements have common characteristics. (a) Most transposable elements generate flanking direct repeats on each side of the point of insertion into target DNA. Many transposable elements also possess terminal inverted repeats. (b) These representations of direct and indirect repeats are used in illustrations throughout this chapter.

18.4 Transposable Elements Cause Mutations Transposons cause mutations by: Inserting into another gene Promoting DNA rearrangements Examples: Approximately half of spontaneous mutations in Drosophila Human genetic diseases The color of grapes

Figure 18.26 Red and white grape color in grapes resulted from insertion and deletion of a retrotransposon.

Figure 18.27 Many chromosomal rearrangements are generated by transposition.

Transposable Elements in Bacteria DNA transposons constitute two major groups: Insertion sequences Composite transposons

Figure 18.27 Many chromosomal rearrangements are generated by transposition.

Figure 18.28 Insertion sequences are simple transposable elements found in bacteria.

Figure 18.29 Tn10 is a composite transposon in bacteria.

Figure 18.30 Mu is a transposing bacteriophage.

Transposable Elements in Eukaryotes Two primary groups: Similar to transposable elements in bacteria short inverted repeats P elements in Drosophila Ac and Ds elements Retrotransposons Ty elements in yeast Copia elements in Drosophila Alu sequences in humans

Figure 18.32 Variegated (multicolored) kernels in corn are caused by mobile genes.

Figure 18.33 Ac and Ds are transposable elements in maize.

Figure 18.34 Transposition results in variegated maize kernels.

Figure 18.35 Hybrid dysgenesis in Drosophila is caused by the transposition of P elements.

18.5 A Number of Pathways Repair Changes in DNA Mismatch Repair Direct Repair Base-Excision Repair Nucleotide-Excision Repair

Figure 18.36 Many incorrectly inserted nucleotides that escape proofreading are corrected by mismatch repair.

Figure 18.37 Direct repair changes nucleotides back into their original structures.

Concept Check 3 Mismatch repair in bacteria distinguishes between old and new strands of DNA on the basis of __________. differences in base composition of the two strands modification of histone proteins base analogs on the new strand methyl groups on the old strand

Concept Check 3 Mismatch repair in bacteria distinguishes between old and new strands of DNA on the basis of __________. differences in base composition of the two strands modification of histone proteins base analogs on the new strand methyl groups on the old strand

Figure 18.38 Base-excision repair excises modified bases and then replaces one or more nucleotides.

Figure 18.39 Nucleotide-excision repair removes bulky DNA lesions that distort the double helix.

18.5 A Number of Pathways Repair Changes in DNA Repair of Double-Strand Breaks Translesion DNA Polymerases Genetics Diseases and Faulty DNA Repair