What is a Mutation?

MUTATION

As we learned earlier, the sequence of deoxyribonucleotide bases in the genes (def) that make up a organism's DNA determines the order of amino acids in the proteins and polypeptides made by that organism. This order of DNA bases constitutes an organism's genotype (def). A particular organism may possess alternate forms of some genes. Such alternate forms of genesare referred to as alleles (def). The physical characteristics an organism possesses, based on its genotype and the interaction with its environment, make up its phenotype .

Mutation (def) is an error during DNA replication that results in a change in the sequence of deoxyribonucleotide bases (def) in the DNA. Spontaneous mutation (def) occurs naturally (a normal mistake rate) about one in every million to one in every billion divisions and is probably due to low level natural mutagens normally present in the environment. Induced mutation (def) is caused by mutagens, substances that cause a much higher rate of mutation.

A. Spontaneous Mutation (def)

1. Mechanisms of mutation

a. Substitution of a nucleotide (point mutations (def)): substitution of one deoxyribonucleotide for another during DNA replication (see Fig. 17). This is the most common mechanism of mutation. Substitution of one nucleotide for another is a result of tautomeric shift, a rare process by which the hydrogen atoms of a deoxyribonucleotide base move in a way that changes the properties of its hydrogen bonding. For example, a shift in the hydrogen atom of adenine enables it to form hydrogen bonds with cytosine rather than thymine. Likewise, a shift in the hydrogen atom in thymine allows it to bind with guanine rather than adenine.

b. Deletion or addition of a nucleotide (frameshift mutations (def)): deletion or addition of a deoxyribonucleotide during DNA replication (see Fig. 18 andFig. 19).

2. Results of mutation

One of four things can happen as a result of these mechanisms of mutation and the resulting change in the deoxyribonucleotide base sequence mentioned above:

a. A missense mutation (def) occurs. This is usually seen with a single substitution mutation and results in one wrong codon (def) and one wrong amino acid (see Fig. 20).

b. A nonsense mutation occurs (def). If the change in the deoxyribonucleotide base sequence results in transcription (def) of a stop or nonsense codon(def), the protein would be terminated at that point in the message (see Fig. 21).

c. A sense mutation (def) occurs. This is sometimes seen with a single substitution mutation when the change in the DNA base sequence results in a new codon still coding for the same amino acid (see Fig. 22). (With the exception of methionine, all amino acids are coded for by more than one codon.)

d. A frameshift mutation occurs (def). This is seen when a number of DNA nucleotides not divisible by three is added or deleted. Remember, the genetic code is a triplet code where three consecutive nucleotides code for a specific amino acid. This causes a reading frame shift and all of the codons and all of the amino acids after that mutation are usually wrong (see Fig. 23); frequently one of the wrong codons turns out to be a stop or nonsense codon and the protein is terminated at that point.

B. Induced Mutation (def) is caused by mutagens, substances that cause a much higher rate of mutation.

Chemical mutagens generally work in one of three ways.

·         Some chemical mutagens, such as nitrous acid and nitrosoguanidine, work by causing chemical modifications of purine and pyrimidine bases that alter their hydrogen-bonding properties. For example, nitrous acid converts cytosine to uracil which then forms hydrogen bonds with adenine rather than guanine.

·         Other chemical mutagens function as base analogs. They are compounds that chemically resemble a nucleotide base closely enough that during DNA replication, they can be incorporated into the DNA in place of the natural base. Examples include 2-amino purine, a compound that resembles adenine, and 5-bromouracil, a compound that resembles thymine. The base analogs, however, do not have the hydrogen-bonding properties of the natural base.

·         Still other chemical mutagens function as intercalating agents. Intercalating agents are planar three-ringed molecules that are about the same size as a nucleotide base pair. During DNA replication, these compounds can insert or intercalate between adjacent base pairs thus pushing the nucleotides far enough apart that an extra nucleotide is often added to the growing chain during DNA replication. An example is ethidium bromide.

Certain types of radiation can also function as mutagens.

·         Ultraviolet Radiation. The ultraviolet portion of the light spectrum includes all radiations with wavelengths from 100 nm to 400 nm. It has low wave length and low energy. The microbicidal activity of ultraviolet (UV) light depends on the length of exposure: the longer the exposure the greater the cidal activity. It also depends on the wavelength of UV used. The most cidal wavelengths of UV light lie in the 260 nm - 270 nm range where it is absorbed by nucleic acid.

In terms of its mode of action, UV light is absorbed by DNA and causes adjacent thymine bases on the same DNA strand to covalently bond together, forming what are calledthymine-thymine dimers (see Fig. 24). As the DNA replicates, nucleotides do not complementary base pair with the thymine dimers and this terminates the replication of that DNA strand. In the case of bacteria, however, most of the damage from UV radiation actually comes from the cell trying to repair the damage to the DNA by a process called SOS repair. In very heavily damaged DNA containing large numbers of thymine dimers, a process called SOS repair is activated as kind of a last ditch effort to repair the DNA. In this process, a gene product of the SOS system binds to DNA polymerase allowing it to synthesize new DNA across the damaged DNA. However, this altered DNA polymerase loses its proofreading ability resulting in the synthesis of DNA that itself now contains many misincorporated bases. (Most of the chemical mutagens mentioned above also activate SOS repair.)

·         Ionizing Radiation. Ionizing radiation, such as X-rays and gamma rays, has much more energy and penetrating power than ultraviolet radiation. It ionizes water and other molecules to form radicals (molecular fragments with unpaired electrons) that can break DNA strands and alter purine and pyrimidine bases.

A point mutation is the simplest kind of genetic mutation. See the dramatic effects that can arise from such a small substitution in the genome.

Simple Substitution

A genetic mutation is any change in the DNA code (genome) of a cell. Of all the ways the genome can be changed, the simplest type of mutation is the point mutation. In a point mutation, a single base is substituted for another, changing the meaning of a single codon, leaving the rest of the gene unchanged. Geneticists recognize four types of point mutations, based on the effect on the genome.

Synonymous Mutations (Silent Mutations)

With 61 codons for 20 amino acids, many of the codons are "synonyms," coding for the same amino acid. Each amino acid can be indicated by up to six different codons (in the case of leucine); only two (methionine and tryptophan) have only one codon. In most cases, the synonyms differ by only one base, so it is possible for a point mutation to result in a codon for the same amino acid.

For example, the DNA codons CAA, CAG, CAT, and CAC all code for the amino acid valine. If a strand of DNA undergoes a point mutation in the codon CAA that changes it to CAG, it would still code for valine. This type of substitution is called a synonymous or sense mutation; it is also known as a silent mutation because there is no change in the amino acid sequence. (Find out how "silent" mutations can still have an effect on the gene and its resulting protein.)

Missense Mutations

A missense mutation is a point mutation that causes a codon to code for a different amino acid. The most notorious missense mutation is the one that causes sickle cell anemia. In this disease, one of the codons in an important hemoglobin gene has changed from CTC to CAC, resulting in the amino acid valine instead of glutamic acid. Chemically, these two amino acids are very dissimilar, so this simple change has a significant effect on the structure of hemoglobin protein, causing the disease symptoms.

A missense mutation might be less significant if the change is between two similar amino acids. For example, a change from CTC (glutamic acid) to CTG (aspartic acid) may not have a dramatic effect on the resulting protein because these two amino acids are similar (both are acidic).

Nonsense Mutations and Stop-Codon Mutations

Three codons in the genetic code tell the cell to stop adding amino acids to a protein because the end of the gene has been reached. In a nonsense mutation, a codon that stands for an amino acid mutates to one of these three stop codons. (The term "nonsense mutation" is used because the stop codon has "no sense" for an amino acid—as opposed to a "missense mutation," in which the resulting codon has the "wrong sense" for an amino acid.) Nonsense mutations cause the protein to be cut off early and therefore incomplete, which usually renders it non-functional. Cystic fibrosis is a disease caused by a nonsense mutation.

A stop-codon mutation is the opposite of a nonsense mutation: it changes a stop codon into a codon for an amino acid, causing the protein to become too large. The added section may consist of part of another protein from the genome—or it may be complete "gibberish," if the addition comes from a non-coding region ofDNA. This lesser-known type of mutation, like a nonsense mutation, generally renders its protein non-functional, and may even result in a harmful protein. A rare disease called familial British dementia is caused by a stop-codon mutation that causes mutated amyloid protein to "clog" the brain (see Nature vol. 399 (1999), pp. 776-781).