Ch 16: Gene Mutation and DNA Repair

Consequences of Mutation

Mutations are molecular changes on DNA sequence A point mutation is a change in a single base pair within the DNA (425). A base substitution is a point mutation in which one base is substituted for another base (425) A change from one pyrimidine to another or one purine to another is called a transition. When purines and pyrimidines are interchanged, it's called a transversion. Mutations can alter coding sequences Silent mutations are those that do not alter amino acid sequence of the polypeptide, even though the nucleotide sequence has changed (425). Occur in 3rd base so that specific amino acid is not changed. Missense mutations are base substitutions in which an amino acid change does occur (425). Nonsense mutations involve a change from a normal codon to a stop codon (425). Frameshift mutations involve the addition or deletion of a number of nucleotides that is not divisible by 3, which shifts reading frame (425). Mutations are more likely to produce polypeptides that have reduced rather than enhanced function (425). Missense mutations are less likely to alter function b/c only 1 amino acid is changed.  Missense mutations has no detectable effect on protein function, it is called a neutral mutation.  Occasionally, mutations will produce an enhanced polypeptide, but it's relatively rare (427).

The Names of Gene Mutations

Names describe how they affect wild-type A wild type is a relatively prevalent genotype (427). When mutation is rare in a population, it's generally referred to as a mutant allele (427), A reversion will change a mutant allele back to a wild-type. A deleterious mutation will decrease the chances of survival and reproduction (427). A beneficial mutation will enhance the survival or reproductive success of an organism (427). Sometimes an allele may be either deletarious or beneficial depending on genotype and/or environment (427).  Conditional mutants affect the genotype only under a defined set of conditions (427). Sometimes, a second mutation will affect the phenotypic expression of a first mutation. These are called suppressor mutations (427). Differs from a reversion b/c it occurs at a DNA site distinct from first mutation. Intragenic suppressors occur within the same gene as the first mutation. Often involves a change in protein structure that compensates for an abnormality.  Intergenic suppressors occur in a different gene from the first mutation. Usually involve a change in the expression of 1 gene that compensates for a loss of function mutation affecting another gene.  The structure of another protein may be altered so it can take over role of the first, defective protein.  Alternatively, these suppressors may involve proteins that participate in a common cellular pathway.  In some cases these may involve proteins where each subunit is encoded by a different gene (multimetric proteins) There's some that involves mutations in genetic regulatuory proteins. First mutation causes a protein to be defective, so a suppressor mutation occurs in a gene that encodes a transcription factor, which activates another gene that can compensate.  Less commonly, these may involve mutations in nonstrructural genes that enable the cell to defy genetic code.

Trinucleotide Repeats

TNREs are hotspots for mutation Trinucleotide repeat expansion refers to the phenomenon in which a repeated sequence of 3 nucleotides readily increase in number from 1 generation to the next (429). In normal people, certain genes and chromosomal locations contain trinucleotide sequences that are repeated in tandem. These are transferred from one generation to the next, usually without mutation (429). In people with TNRE disorders, the length of a trinucleotide repeat has increased above a certain critical size and becomes prone to frequent expansion. In some cases these occur in coding sequences (429). In the cases of 2 fragile X syndromes, the repeat produces CpG islands become methylated, which leads to chromatin compaction and silencing of gene transcription. Typically, the expansion is a CAG repeat (429). This encodes for glutamine, which causes the proteins to aggregate and the disease to progress further Their severity tends to worsen in further generations, called anticipation (429). Does not occur with all disorders; depends on if the disease is inherited from the mother or the father (430). Suggests that TNRE can happen more frequently in oogenesis or spermatogenesis, depending on particular gene involved. Not well understood at DNA level (430).

Changes in Chromosome Structure

Affects the expression of a gene In some cases, a chromosomal rearrangement may affect a gene b/c a chromosomal breakpoint occurs within a gene (430). A breakpoint is the region where 2 chromosome pieces break and rejoin with other chromosome pieces. In some cases a gene may be left intact, but its expression is altered when its moved to a new location . When this happens, the change in gene location is said to have a position effect (430). There are 2 common explanations for how position effects alter genes (430): A gene may be moved next to regulatory sequences, such as silences or enhances, that influence expression. A chromosomal rearrangement may reposition a gene from a less condensed region to a very highly condensed region, causing it to be turned off. Mutations in germ-line or somatic cells A germ line mutation can occur directly in a sperm or egg cell, or it can occur in a precursor cell that produces a gamete (431). A somatic mutation that occurs within a single embryonic cell can cause a portion of an individuals body to contain the mutation (431-432). Size depends on the timing of mutation. The earlier the mutation, the larger the region. An individual that has genotypically different somatic regions is called a genetic mosaic.

Occurance and Causes of Mutation

Spontaneous mutations are changes in DNA structure that result from abnormalities in biological processes (432). Induced mutations are caused by environmental agents (432). Agents known to alter the structure of DNA are called mutagens (433). Spontaneous mutations are random According to physiological adaptation hypothesis, the rate of mutation in bacteria should be a relatively constant value and depend on exposure to the bacteriophage (433). In contrast, the random mutation hypothesis depends on the timing of the mutation (433). The fluctuation test is consistent with a random mutation hypothesis, in which the timing of a mutation during the growth of a culture greatly affects the number of mutant cells. The random mutation hypothesis is now known as the random mutation theory. According to this theory, mutations are a random process that can occur in any gene and do not involve exposure of an organism to a particular condition that selects for different types of mutations (434). The random mutation view has changed a little. Some genes mutate at a much higher rate than other genes, likely due to size. (434) Relative locations of genes within a chromosome may cause some genes to be more susceptible. Some single genes have hot spots (434). Mutation rates & frequencies  as quantitive assessments The term mutation rate is the likelihood that a gene will be altered by a new mutation (434). Number of new mutations in a given gene per cell generation. Mutation rate is not a constant number. Certain environment agents can increase rate of induced mutations to a much higher value than spontaneous mutation rate (434). Mutation rates vary substantially from species to species and even within different strains of the same species (434) One explanation for variation is the many different causes of mutation (434). Mutation frequency for a gene is the number of mutant genes divided by the total number of genes within a population (435). Depends on mutation rate, timing of mutation, and likelihood that a mutation will be passed to future generations.

Mutagens Altering DNA Strucutre

Mutagens alter DNA structure in different ways The public is concerned for 2 important reasons (440):  Mutagenic agents are often involved in development of cancer. Mutations can be harmful for future offspring. In some cases, non-mutagenic agents can be altered to a mutagenically active form (440). Certain foods contain antioxidents (440). Some mutagens act by covalently modifying the structure of bases (440) Nitrous oxide replaces amino groups with keto groups, a processes called deamination. This can change cytosine to uracil and adenine to hypoxanthine. When altered DNA replicates, modified bases do not pair w/appropriate bases in newly made strand. Uracil pairs with adenine, hypoxanthine pairs with cytosine. Other chemical mutagens can disrupt appropriate pairing between nucleotides by alkylating bases within DNA (441). Methyl or ethyl groups are covalently attached to the bases. Examples include nitrogen mustard and ethyl methanesulfonate.  Some mutagens exert their effects by directly interfering w/the DNA replication process (441). Acridine dyes, such as proflavin, contain flat structures that intercalate between adjacent base pairs, thereby distorting helical structure. When DNA containing these mutagens is replicated, single-nucleotide additions and/or deletions can be incorporated into newly made daughter strands. Compounds like 5-bromouracil (5BU) and 2-aminopurine are base analogues that become incorporated into daughter strands during DNA replication (441), 5BU is a thymine analogue that can replace thymine in DNA. Thus, it will base-pair with guanine, causing a mutation in which a TA base pair is changed to a 5BU-G base pair. DNA molecules are sensitive to physical agents like radiation (441). Short wavelength radiation and high energy, known as ionizing radiation, can alter DNA structure. Ionizing radiation penetrates into biological tissues and creates chemically active molecules known as free radicals. These can cause base deletions, single nicks in DNA strands, cross-linking, and even chromosomal breaks. Non-ionizing radiation contains less energy, so it penetrates only the surface (441). UV light causes the formation of cross-linked thymine dimers, which interfere w/transcription and DNA replication.

DNA Repair

Damaged bases can be directly repaired An enzyme called photolyase that can repair thymine dimers by splitting the dimers, which returns the DNA to its original condition (443). Directly restores structure of DNA. Alkyltransferase is a protein can remove methyl or ethyl groups from guanine bases that have been mutagenized by alkylating agents (443). Transfers the methyl/ethyl group from base to a cystine side chain. Base excision repair Base excision repair involves the function of DNA N-glycosylases, which can recognize an abnormal base and cleave the bond between it and the sugar in the DNA backbone, creating an apurinic or apyrimidinic site (443). AP endonuclease recognizes the abnormal nucleotide left over and makes a cut on the 5' side so DNA polymerase removes the abnormal region and replaces it with normal nucleotides. Nucleotide excision repair systems Nucleotide excision repair system can repair many different types of DNA damage (443). Several nucleotides in the damaged strand are removed from the DNA, and intact strand is used as a template for resynthesis of a normal complementary strand (443-444).