What are mutation and mutagenesis?

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A mutation is a heritable change in the nucleotide sequence of DNA. Depending on the location and function of the altered DNA sequence, the effect of a mutation can range from undetectable to causing major deformities and even death. Mutation is a natural process by which new genetic diversity is generated. However, environmental mutagens can increase mutation rates and have a serious effect on health.
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A mutation is any change in the genetic material that can be inherited by the next generation of cells or progeny. A mutation can occur at any time in the life of any cell in the body. If a mutation occurs in a reproductive cell, the change can be passed to an offspring through the egg or sperm. The new mutation could then affect the phenotype of the offspring and be passed on to later generations. However, if the mutation occurs in cells of the skin, muscle, blood, or other somatic (body) tissue, the new mutation will be passed on to other body cells only when that cell divides. This can produce a mosaic group of cells carrying the new genetic change. Most of these are undetectable and have no effect on the carrier. An important exception is a somatic mutation that causes the affected cell to lose control of the cell cycle and divide uncontrollably, resulting in cancer. Many environmental chemicals and agents that cause mutations (such as x-rays and ultraviolet radiation) are therefore capable of causing cancer.

Mutation can also have an important, beneficial role in natural populations of all organisms. The ability of a species to adapt to changes in its environment, combat new diseases, or respond to new competitors is dependent on genetic diversity in the population’s gene pool. Without sufficient resources of variability, a species faced with a serious new stress can become extinct. The reduced population sizes in rare and endangered species can result in reduced genetic diversity and a loss of the capacity to respond to selection pressures. Zoo breeding programs often take data on genetic diversity into account when planning the captive breeding of endangered species. The creation of new agricultural crops or of animal breeds with economically desirable traits also depends on mutations that alter development in a useful way. Therefore, mutation can have both damaging and beneficial effects.

The Role of Mutations in Cell Activity and Development

The genetic information in a cell is encoded in the sequence of subunits, or nucleotides, that make up a molecule of DNA. A mutation is a change in the nucleotide sequence of DNA, and it can range from changing just a single nucleotide in the DNA molecule to altering long pieces of DNA. To appreciate how such changes can affect an organism, it is important to understand how information is encoded in DNA and how it is translated to produce a specific protein. There are four different nucleotides in the DNA molecule: adenine (A), guanine (G), thymine (T), and cytosine (C). The DNA molecule is composed of two complementary strands linked together by hydrogen bonding, a process called base-pairing. Guanine (G) and adenine (A) are purine bases, which pair up with pyrimidine bases thymine (T) and cytosine (C). For example, an adenine on one strand should always pair with a thymine on the other strand (A-T), and a guanine on one strand should always pair with a cytosine on the other strand (G-C). When the expression of a gene is activated, one of the two strands of DNA is used as a template for the synthesis of a single-stranded molecule called messenger RNA (mRNA). The completed mRNA molecule is then transported out of the nucleus, where it binds with ribosomes (small structures in the cytoplasm of the cell), and a protein is made using the mRNA’s nucleotide sequence as its coded message. The nucleotides of the mRNA are read on the ribosome in triplets, with every three adjacent nucleotides (called a codon) corresponding to one of the twenty amino acids found in protein.

Thus the sequence of nucleotides eventually determines the order of amino acids that are linked together to form a specific protein. The amino acid sequence in turn determines how the protein will function, either as a structural part of a cell or as an enzyme that will catalyze a specific biochemical reaction. A gene is often at least one thousand base-pairs or longer, so there are many points at which a genetic change can occur. If a mutation takes place in an important part of the gene, even the change of a single amino acid can cause a major change in protein function. For example, sickle-cell disease is a good illustration of this. In sickle-cell disease, a single base substitution mutation in a gene causes the sixth codon in the mRNA to change from GAG to GUG. When this modified mRNA is used to create a protein, the amino acid valine is substituted for the normal glutamic acid in the sixth position in a string of 146 amino acids. This small change causes the protein to form crystals and thus deform cells when the amount of available oxygen is low. Since this protein is part of the oxygen-carrying hemoglobin molecule in red blood cells, this single DNA nucleotide change has potentially severe consequences for an affected individual.

Types of Mutation

Mutations are often categorized by the type of change that has occurred to the DNA, as well as the effect that the mutation has on the function of the encoded protein. For example, a point mutation is defined as a single change to the nucleotide sequence of DNA. The simplest kind of point mutation is a base substitution, whereby one base pair is replaced by another (for example, the replacement of an A-T base pair at one point in the DNA molecule by a C-G base pair). A more specific way of describing a base substitution mutation depends on the nature of the bases involved. For example, a transition mutation occurs when a purine replaces a purine, or a pyrimidine replaces another pyrimidine. A transversion mutation occurs when a purine replaces a pyrimidine, or vice versa. These mutations can change the sequence of the codon triplet used to build the protein, where consequently the wrong amino acid is added to the protein at that point. This type of base substitution mutation that encodes a different amino acid is called a missense mutation. Similarly, if a single base substitution mutation changes a codon triplet to what is called a stop codon (these sequences normally occur only at the end of a gene to signal where the message ends), the protein stops production and the result is an incomplete or truncated protein. This type of base substitution mutation that encodes a stop codon is called a nonsense mutation. These point mutations often affect the function of the protein, at least in minor ways. However, some base substitutions do not change the nature of the amino acid. Since several different combinations of triplets can code for the same amino acid, not all base changes will result in an amino acid substitution, and these mutations are therefore called silent mutations.

Another category of mutations called frameshifts can have significant effects on protein structure. A frameshift mutation occurs when one or more nucleotides are added to, or lost from, the DNA strand when it is duplicated during cell division. Since translation of the mRNA is done by the ribosomes adding one amino acid to the growing protein for every three adjacent nucleotides, adding or deleting one nucleotide will effectively shift that reading frame so that all following triplet codons are different. By analogy, one can consider the following sentence of three-letter words: THE BIG DOG CAN RUN FAR. If a base (for example, a letter X, in this analogy) is added at the end of the second triplet, the “sentence” will still read three letters at a time during translation and the meaning will be completely altered. THE BIX GDO GCA NRU NFA R. In a cell, a nonfunctional protein is produced unless the frameshift is near the terminal end of the gene.

Some types of mutations, known as chromosome mutations, alter the structural integrity of DNA on a larger scale, affecting not only a single point in a gene but also one or more genes within a chromosome. There are four major kinds of mutations involving changes to genes at the chromosomal level. A deletion or deficiency is produced when two breaks occur in the chromosome but are repaired by leaving out the middle section. For example, if the sections of a chromosome are labeled with the letters ABCDEFGHIJKLMN and chromosome breaks occur at F-G and at K-L, the broken chromosome can be erroneously repaired by enzymes that link the ABCDEF fragment to the LMN fragment. The genes in the unattached middle segment, GHIJK, will be lost from the chromosome. Losing these gene copies can affect many different developmental processes and even cause the death of the organism. Chromosomal breaks and other processes can also cause some genes to be duplicated. A duplication is the converse of a deletion, and occurs when a gene sequence or chromosomal segment is repeated (for example, ABCDEFGHDEFGHIJKLMN). Gene duplication can result in the over-expression of genes, an event detrimental in such a case where an oncogene (a gene that promotes the growth of cancer when mutated or over-expressed) is duplicated. A third kind of chromosomal mutation, called an inversion, changes the orientation of the gene(s) when the segment between two chromosomal breaks is reattached backward (for example, ABCDJIHGFEKLMN). Chromosome segments can also be moved from one kind of chromosome to another in a structural change called a translocation. Some examples of heritable Down syndrome are caused by this type of chromosomal rearrangement, where part of chromosome 21 is translocated to another chromosome.

The loss or addition of an entire chromosome, a condition known as aneuploidy (characterized by having an abnormal number of chromosomes), is a significant source of genetic disorders in humans. Whole chromosomes can be lost or gained by errors during cell division. In animals, almost all examples of chromosome loss are so developmentally severe that the individual cannot survive to birth. On the other hand, since extra chromosomes provide an extra copy of each of their genes, the amount of each protein they code for is unusually high, and this, too, can create biochemical abnormalities for the organism. In humans, an interesting exception is changes in chromosome number that involve the sex-determining chromosomes, especially the X chromosome (the Y is relatively silent in development). Since normal males have one X and females have two, the cells in females inactivate one of the X chromosomes to balance gene dosage. This dosage compensation mechanism can, therefore, also come into operation when one of the X chromosomes is lost or an extra one is inherited because of an error in cell division. The resulting conditions, such as Turner syndrome and Klinefelter syndrome, are much less severe than the developmental problems associated with other changes in chromosome number.

Mutation Rate

There are several different sources of genetic change. For example, errors can occur when the DNA molecule is being duplicated during cell division. In simple organisms such as bacteria, about one thousand nucleotides are added to the duplicating DNA molecule each second. The speed is not as great in plants and animals, but errors still occur when mispairing between A and T or between C and G nucleotides occurs. Additionally, some mutations are generated spontaneously, caused by changes or damage to DNA that occurs in the process of normal cell biochemistry. These kinds of alterations to the structure or composition of DNA (such as strand breaks or depurination) can be classified as DNA damage, or genetic damage. Other sources of damage can be traced to environmental factors that can increase mutation rates. Fortunately, almost all of this initial genetic damage is repaired by enzymes that recognize and correct errors in nucleotide pairing or DNA strand breaks. It is the unrepaired genetic damage that leads to new mutations.

Spontaneous mutation rates vary to some extent from one gene to another and from one organism to another, but one major source of variation in mutation rates comes from external agents called mutagens that act on the DNA to increase damage or inhibit repair. One of the most widely used techniques for measuring theactivity of a chemical mutagen was developed in the 1970s by Bruce Ames. The Ames test uses bacteria that have a mutation that makes them unable to produce the amino acid histidine. These bacteria cannot survive in culture unless they are given histidine in the medium. To test whether a chemical increases the mutation rate, it is mixed with a sample of these bacteria, and they are placed on a medium without histidine. Any colonies that survive represent bacteria in which a new mutation has occurred to reverse the original defect (a back-mutation). Since many chemicals that cause mutations also cause cancer, this quick and inexpensive test is now used worldwide to screen potential carcinogenic, or cancer-causing, agents. Mutation rates in mice are measured by use of the specific-locus test. In this test, wild-type male mice are mated with females that are homozygous for up to seven visible, recessive mutations that cause changes in coat color, eye color, and shape of the ear. If no mutations occur in any of the seven genes in the germ cells of the male, the male offspring will all be wild type in appearance. However, a new mutation in any of the seven genes will yield a progeny with a mutant phenotype (for example, a new coat color). The same cross can also be used to identify new mutations in females. Since mice are mammals, they are a close model system to humans. Thus, results from mutation studies in mice have helped identify agents that are likely to be mutagenic in humans.

Types of Mutagens

Mutagens can cause a change in the genetic material. One primary way that mutations are generated in cells occurs when the nucleotide bases (A, T, C, or G) are modified or damaged in a way that makes their original identity unrecognizable during DNA replication. There are several different types of mutagens characterized by their mutagenic effects on cells. One type of mutagen involves compounds that mimic nucleotide bases, called base analogs. These compounds share similar properties with nucleotide bases that allow them to substitute for nucleotide bases in DNA. However, base analogs tend to base-pair during DNA replication incorrectly, resulting in the generation of a mutation in the new strand of DNA. A well-known example of a base analog is 5-bromo-uracil, an analog of thymine (T) that base-pairs with guanine (G) instead of the correct nucleotide adenine (A). 5-bromo-uracil therefore ultimately causes a transition mutation, where a T-A base-pair is replaced with C-G.

Other types of mutagens can modify nucleotide bases by altering their chemical makeup. For example, nitrous acid produced by the metabolism of nitrites in the diet causes the deamination (removal of the amino group) of cytosine, guanine, or adenine. This modification changes the identity of the original nucleotide base so that its base-pairing properties are altered during DNA replication, promoting the incorporation of the wrong nucleotide base in the newly synthesized strand of DNA.

Chemicals that are capable of intercalating DNA are also mutagens. Intercalating agents, such as ethidium bromide or acridines, are planar ringed compounds that interact with DNA and insert themselves into open spaces, causing the DNA to expand. During DNA replication, the expanded base is read as two instead of one, thus resulting in the addition of an extra base into the new DNA strand, causing a frameshift mutation.

Other mutagens with severe consequences are those that alter the size and structure of nucleotide bases. Chemical agents such as benzo[a]pyrene, a compound found in products of combustion and cigarette smoke, can be metabolically activated in cells to produce reactive compounds that attach to DNA and form bulky adducts on nucleotide bases. Damaged nucleotide bases formed by these mutagens are capable of blocking or halting DNA replication when cells are undergoing division. Blocked replication, in turn, can stimulate cells to use several different pathways for continuing the replication of DNA past the damage, a process known as DNA damage tolerance. However, some types of DNA damage tolerance work at the expense of generating new mutations.

Mutagens can be used in genetic studies with model organisms to induce germinal mutations that can be inherited by offspring. Offspring organisms that exhibit interesting phenotypes can then be further studied to identify which gene mutation caused the phenotype, an experimental approach called forward genetics. Mutagens are and will continue to be useful for studying the process of mutagenesis.

The Use of Mutations to Study Development

Mutations offer geneticists a powerful tool to analyze development. By understanding the way development is changed by a mutation, one can determine the role the normal gene plays. Although most people tend to think of mutations as causing some easily visible change in the appearance of a plant or animal (such as wrinkled pea seeds or white mouse fur), some mutations are actually lethal when present in two copies (homozygous). These lethal mutations affect some critical aspect of cell structure or other fundamental aspect of development or function. Genes turn on and off at specific times during development, and by studying the abnormalities that begin to show when a lethal mutation carrier dies, a geneticist can piece together a picture of the timing and role of important gene functions.

Another useful insight comes from mutations with effects that vary. A major source of genetic variation comes from polymorphisms, which comprise mutations that were selected for over multiple generations to become common in more than 1 percent of a population. Traits affected by polymorphisms are often reflected in the observable variation between individuals of a population, such as coat colors of animals or blood types of humans. Some mutations affect a single gene, yet exhibit multiple phenotypes, a characteristic termed as pleiotrophy. Pleiotrophy occurs when a gene has more than one function, and a mutation in that gene can therefore disrupt multiple biological processes. Other unique mutations can have phenotypic effects that depend on the conditions, such as temperature, in which the individual develops. An interesting example of such temperature sensitivity is the fur color of Siamese cats. A mutation causes the biochemical pathway for pigmentation to be active at cool temperatures, but inactive at warmer body temperatures. For this reason, a Siamese cat will be pigmented only in the cooler parts such as the tips of the ears and tail.

It would be a mistake, however, to think that all mutations have large phenotypic effects. Many complex traits are produced by many genes working together and are affected by environmental variables. These are called quantitative traits because they are measured on some kind of scale, such as size, number, or intensity. The mutations that affect quantitative traits are not different, except perhaps in the magnitude of their individual effects, from other kinds of gene mutation. Mutations in quantitative traits are a major source of heritable variation on which natural and artificial selection can act to change a phenotype.

Impact and Applications

It will probably never be possible to eliminate all mutation events because many mutations are caused by small errors in normal DNA duplication when cells divide. Learning how mutations affect cell division and cell function can help one to understand processes such as cancer and birth defects that can often be traced to genetic change. Some explanations of processes such as aging have focused on mutation in somatic cells. Mutation is also the source of genetic variation in natural populations, and the long-term survival of a species depends on its ability to draw on this variation to adapt to new environmental conditions.

Two aspects of mutagenesis will continue to grow in importance. First, environmental and human-made mutagens will continue to be a source of concern as technological advances occur. Many scientists are working to monitor and correct potential mutagenic hazards. Second, geneticists have developed invaluable molecular tools for utilizing genetic engineering to produce preplanned mutations. For example, site-directed mutagenesis is a technique used to introduce specific mutations into DNA using short strands of single-stranded DNA (called primers) carrying a specific mutation of interest. The primers carrying the mutation are machine-made and are used in a reaction containing DNA polymerase to “prime” and synthesize the mutated version of the gene, carried on a vector. The resulting mutated DNA can be propagated and used to transform the cells of an organism that can use the mutated gene as a template for generating protein. This tool offers several advantages for studying the effects of specific mutations. Directed mutagenesis of DNA may also offer a way to correct preexisting genetic defects or alter phenotypes in planned ways. Mutation is, therefore, a double-edged sword, both a source of problems and a source of promise.

Key terms alleles : different forms of a gene characterized by sequence variation at the same genetic locus of a chromosome gene pool : the collective set of alleles carried by members of a species or population of organisms; multiple alleles in the gene pool provide the variation that allows adaptation to new conditions genome : the complete hereditary information of an organism encoded in DNA genotype : the set of alleles an organism possesses in its genome germinal mutation : a mutation in a reproductive cell (gamete), which can be passed from a parent to its offspring mutagen : a chemical, physical, or biological agent that causes an increased rate of mutation mutagenesis : the process of producing a change in the nucleotide sequence of DNA mutant : an individual carrying a mutation; this term typically refers to a genetic change that causes a phenotype different from wild type mutation rate : the probability of a mutation occurring in the genetic material over a given time period, such as a cell division cycle or a generation phenotype : the observable effects of a gene; phenotypes include physical appearance, biochemical activity, cell function, or any other measurable factor somatic mutation : a mutation that occurs in a body cell and may produce a group of mutant cells but is not transmitted to the next generation wild type : the most common genetic makeup of an organism; a mutation alters the genotype of a wild type organism to produce a mutant phenotype Bibliography

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