BIO 222 Chap 18: Mutations in DNA

Mutations in DNA

• Mutations are alterations in the DNA sequence of an organism that are inherited
• Mutations are essential for creating genetic variation and are the raw material for evolution, while also contributing to diseases and disorders
• Mutations are valuable for understanding fundamental biological processes

Categories of Mutations

• Somatic mutations occur in nonreproductive cells and are passed to new cells through mitosis, creating a clone of cells with the mutation, but are not passed to offspring
• Germ-line mutations occur in cells that give rise to gametes and can be passed to approximately half of the next generation through meiosis and sexual reproduction
• Gene mutations affect single genes, while chromosomal mutations affect the structure or number of chromosomes

Types of Gene Mutations

• Base substitutions occur when one base is replaced by another
• Transitions are base substitutions where a purine replaces a purine or a pyrimidine replaces a pyrimidine
• Transversions are base substitutions where a purine replaces a pyrimidine or vice versa
• Insertions occur when one or more nucleotide pairs are added to the DNA
• Deletions occur when one or more nucleotide pairs are removed from the DNA
• Frameshift mutations result from indels that alter the reading frame of the gene, leading to a completely different amino acid sequence downstream of the mutation
• In-frame insertions and deletions consist of a multiple of three nucleotides which do not alter the reading frame
• Expanding nucleotide repeats involve an increase in the number of copies of a set of nucleotides, which can lead to genetic diseases

Human Genetic Diseases Caused by Expanding Nucleotide Repeats

• Fragile-X syndrome is caused by CGG repeats, with a normal range of 6-54 copies and a disease range of 50-1500 copies
• Huntington disease is caused by CAG repeats, with a normal range of 9-37 copies and a disease range of 37-121 copies
• Myotonic dystrophy is caused by CTG repeats, with a normal range of 5-37 copies and a disease range of 44-3000 copies

How Nucleotide Repeats Increase

• DNA strands separate
• During replication, a hairpin forms on the newly synthesized strand causing part of the template strand to be replicated twice
• The result includes an increase copies of the nucleotide repeat

Phenotypic Effects of Mutations

• A forward mutation changes a wild-type allele to a mutant allele
• A reverse mutation changes a mutant allele back to a wild-type allele
• A missense mutation results in a different amino acid in the protein
• A nonsense mutation results in a premature stop codon, leading to a shortened protein
• A silent mutation changes a codon but does not alter the amino acid sequence due to the degeneracy of the genetic code
• A neutral mutation alters the amino acid sequence of a protein, but does not change its function
• A loss-of-function mutation results in a complete or partial loss of protein function
• A gain-of-function mutation causes the appearance of a new trait or function, or causes a trait to appear in the wrong tissue or at the wrong time
• A conditional mutation only affects the phenotype under certain conditions
• A lethal mutation causes premature death

Suppressor Mutations

• A suppressor mutation hides or suppresses the effect of another mutation
• An intragenic suppressor mutation occurs within the same gene as the original mutation
• An intergenic suppressor mutation occurs in a different gene from the original mutation

Mutation Rate Factors

• Mutation rates are affected by the frequency with which a change takes place in DNA, the probability that a change will be repaired, and the probability that a mutation will be detected

Examples of Mutation Rates in Different Organisms

• Bacteriophage T2 has a lysis inhibition mutation rate of 1 × 10-8 per replication
• Escherichia coli has a lactose fermentation mutation rate of 2 × 10-7 per cell division
• Neurospora crassa has an inositol requirement mutation rate of 8 × 10-8 per asexual spore
• Drosophila has an eye color mutation rate of 4 × 10-5 per gamete
• Humans exhibit a Huntington disease mutation rate of 1 × 10-6 per gamete

Adaptive Mutation

• Adaptive mutation is a genetic variation that brings about adaptation to new environments
• Stressful conditions induce increased mutation in bacteria

Causes of Mutations

• Spontaneous replication errors
• Spontaneous chemical changes
• Chemically induced mutations
• Radiation

Spontaneous Replication Errors

• Tautomeric shifts: Purine and pyrimidine bases exist in different forms called tautomers which cause errors in base pairing
• Incorporation errors and replication errors
• Strand slippage during replication
• Unequal crossing over

Spontaneous Chemical Changes

• Depurination: loss of a purine
• Deamination: loss of an amino group

Chemically Induced Mutations

• Mutagens: chemicals which increase rate of genetic mutation
• Base analogs: chemicals with structures similar to those of any 4 standard nitrogenous bases
• Alkylating agents: donate alkyl groups
• Deamination: nitrous acid
• Hydroxylamine: add hydroxyl group
• Oxidative reaction: superoxide radicals
• Intercalating agents: proflavin, acridine orange, and ethidium bromide

Radiation

• Radiation increases mutation rates
• Pyrimidine dimers: two thymine bases block replication
• SOS system in bacteria allows cells to bypass the replication block with a mutation-prone pathway

How to Detect Mutations

• Use the Ames test

Transposable Elements

• Transposable elements are sequences that can move about the genome
• Transposition is the movement of transposable elements
• Features include flanking direct repeats and terminal inverted repeats

How Flanking Direct Repeats are Generated

• Staggered cuts are made in the target DNA
• A transposable element inserts itself into the DNA
• Gaps are filled in by DNA polymerase
• Replication of the single-stranded DNA creates the flanking direct repeats

Common characteristics for transposable elements

• Terminal inverted repeat
• Flanking direct repeat

Transposition Process

• DNA transposition
• Replicative transposition: a new copy of the transposable element inserts in a new location, and the old copy stays behind
• Nonreplicative transposition: the old copy excises from the old site and moves to a new site
• RNA intermediate transposition
• Control of transposition where organisms limited by methylating the DNA in regions where transposons are common
• 45% of the human genome consists of sequences related to transposable elements, mostly retrotransposons

Mutagenic Effects

• Transposons cause mutations by inserting into genes and promoting DNA rearrangements
• Examples include half of spontaneous mutations in Drosophila, human genetic diseases, and the color of grapes

Transposable Elements in Bacteria

• DNA transposons consisting of two major groups
• Insertion sequences carry only the genetic information needed for transposition
• Composite transposons flanked by two copies of an insertion sequence that may itself transpose
• Noncomposite transposons that lack insertion sequences

Insertion Sequence Elements

• Includes Transposase gene
• 23-bp terminal inverted repeat
• 9-bp flanking direct repeat

Bacterial Transposon Elements

• Tn10 can contain the IS10L tetR gene and IS10R
• Flanking direct repeat
• Tn10 (9300 bp)

Transposable Elements in Eukaryotes

• Two primary groups
• Similar to transposable elements in bacteria
• Short inverted repeats including including elements P elements in Drosophila and Ac and Ds elements
• Retrotransposons including Ty elements in yeast Copia elements in Drosophila Alu sequences in humans

The discovery of transposable elements

• Barbara McClintock was the first to discover transposable elements
• She discovered that Variegated kernels (multicolored) are caused by mobile genes
• Ac and Ds are transposable elements in maize

DNA Repair

• Mismatch Repair
• Direct Repair
• Base-Excision Repair
• Nucleotide-Excision Repair

Mismatch Repair

• Mismatched bases and small insertions or deletions resulting from replication errors are corrected
• In bacteria, methyl groups on the old strand distinguish it from the new strand
• Enzymes cut out a section of the newly synthesized strand and replace it

Direct Repair

• Altered nucleotides are restored to their original structures
• Enzymes recognize and remove specific modified bases
• The entire nucleotide is then removed and replaced

Base-Excision Repair

• An AP endonuclease cleaves the phosphodiester bond on the 5' side of the AP site
• DNA polymerase adds new nucleotides to the exposed 3' -OH group

Nucleotide-Excision Repair

• Many types of DNA repair, including damage induced by ultraviolet light
• DNA helicase separates the two strands
• Single strand breaking protein stabilizes the single strand
• Damaged DNA releases and the space is filled with nucleotides using DNA polymerase

Translesion DNA polymerases

• Allow replication to proceed past bulky distortions in the DNA
• Often introduce errors as they bypass the distorted region

Genetic Diseases and Faulty DNA Repair

• Genetic defects are frequently the underlying cause of several genetic defects
• Many of those diseases are characterized as a predisposition to Cancer