Genetic Mutation

An allele is an alternative form of a gene. Most, if not all genes have alternative forms causing the resulting protein to function slightly differently. But are there alleles that cause proteins to function dramatically differently or not function at all? A mutation is a change in the DNA or RNA sequence, and many mutations result in new alleles. Some of these changes can be beneficial. In fact, evolution could not take place without the genetic variation that results from mutations. But some mutations are harmful. There are also chromosomal mutations, large changes with dramatic effects.

Causes of Mutation

Is it possible for mutations to occur spontaneously, or does there have to be a cause of the mutation? Well, the answer is that both are possible. A spontaneous mutation can just happen, possibly due to a mistake during DNA replication or transcription. Mutations may also occur during mitosis and meiosis. A mutation caused by an environmental factor, or mutagen, is known as an induced mutation. Typical mutagens include chemicals, like those inhaled while smoking, and radiation, such as X-rays, ultraviolet light, and nuclear radiation. Table 1 lists some spontaneous mutations that are common.

Types of Mutations

In multicellular organisms, mutations can be subdivided into germline mutations, which can be passed on to descendants, and somatic mutations, which cannot be transmitted to the next generation. Germline mutations change the DNA sequence within a sperm or egg cell, and therefore can be inherited. This inherited mutation may result in a class of diseases known as a genetic disease. The mutation may lead to a nonfunctional protein, and the embryo may not develop properly or survive. Somatic mutations may affect the proper functioning of the cell with the mutation. During DNA replication, the mutation will be copied. The two daughter cells formed after cell division will both carry the mutation. This may lead to the development of many cells that do not function optimally, resulting a less than optimal phenotype. Various types of mutations can all have severe effects on the individual. These include point mutations, framehift mutations and chromosomal alterations.

Keep in mind, some mutations may be beneficial or have no effect. Mutations that have no effect will not affect the expression of the gene or the sequence of amino acids in an encoded protein.

Chromosomal Alterations

Chromosomal alterations are large changes in the chromosome structure. They occur when a section of a chromosome breaks and rejoins incorrectly, or does not rejoin at all. Sometimes the segment may join backwards or reattach to another chromosome altogether. These mutations are very serious and usually lethal to the zygote or embryo. If the embryo does survive, the resulting organism is usually sterile and thus, unable to pass along the mutation.

The five types of chromosomal alterations are deletions, duplications, insertions, inversions, and translocations (Figure 1).

1. Deletions: removal of a large chromosomal region, leading to loss of the genes within that region.
2. Duplications (or amplifications): lead to multiple copies of a chromosomal region, increasing the number of the genes located within that region. Some genes may be duplicated in their entirety.
3. Insertions: the addition of material from one chromosome to a nonhomologous chromosome.
4. Inversions: reversing the orientation of a chromosomal segment.
5. Translocations: interchange of genetic material between nonhomologous chromosomes.

Figure 1: Chromosomal alterations. Deletion: the blue segment has been removed; Duplication: the blue segment has been duplicated; Inversions: the blue segment has been reversed; Insertion: the yellow segment has been removed from chromosome 4 and placed into chromosome 20; Translocation: a green segment from chromosome 4 has been exchanged with a red segment from chromosome 20.

Point Mutations

As the name implies, point mutations occur at a single site within the DNA. Lets look at the example below:

THE BIG FAT CAT ATE THE RED RAT.

A change at any one position could result in a sequence that does not make sense. Such as:

THE BIG FAT SAT ATE THE RED RAT.

As shown above, point mutations exchange one nucleotide for another and are known as base substitution mutations. These mutations are often caused either by chemicals or by a mistake during DNA replication. A transition exchanges a purine for a purine (A \(\rightarrow\) G) or a pyrimidine for a pyrimidine, (C \(\rightarrow\) T), and is the most common point mutation. Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T \(\rightarrow\) A/G). Point mutations that occur within the protein coding region of a gene are classified by the effect on the resulting protein:

1. Silent mutations: which code for the same amino acid.
2. Missense mutations: which code for a different amino acid.
3. Nonsense mutations: which code for a premature stop codon.

These mutations may result in a protein with the same function, with altered function, or with no function. Silent mutations, as they code for the same amino acid, will have no altered effect on the protein. Missense mutations may have a minor effect or a dramatic effect on the protein. Nonsense mutations usually have the most dramatic effet. Depending on the position of the premature stop codon, nonsense mutations may result in an unstable mRNA that cannot be translated, or in a much ”smaller” protein without any activity.

Deletions and Insertions

As pointed out earlier, a deletion or insertion in the DNA can alter the reading frame. Deletions remove one or more nucleotides from the DNA, whereas insertions add one or more nucleotides into the DNA. These mutations in the coding region of a gene may also alter splicing of the mRNA (splice site mutation). Mutations which alter the reading frame are known as frameshift mutations. Splice site mutations and frameshift mutations both can dramatically change the mRNA, altering the final protein product.

Effect-on-Function Mutations

For a cell or organism to maintain homeostasis, the proteins work in a highly defined and regulated manner. It may take just one protein not working correctly to interrupt homeostasis. A protein having more or less activity than normal, or a different activity or function, may be enough to interrupt homeostasis. Mutations that may result in altered function of the gene product or protein are loss-of-function and gain-of-function mutations, as well as dominant negative mutations.

Loss-of-function mutations result in a gene product or protein having less or no function. Gain-of-function mutations result in the gene product or protein having a new and abnormal function. Dominant negative mutations have an altered gene product that acts in a dominant manner to the wild-type gene product.

Significance of Mutation

Imagine the coding sequence (broken up into codons) TAC CCC GGG. This is a fairly generic coding sequence. It transcribes into the following mRNA: AUG GGG CCC, which would translate into start-glycine-proline. As glycine is encoded by four codons (GGG, GGA, GGC, GGU), any change in the third position of that codon will have no effect. The same is true for the codon for proline. But what about changes in the other nucleotides in the sequence? They could have potentially dramatic effects. The effects depend on the outcome of the mutation. Obviously any change to the start codon will interrupt the start of translation. Turning the simple glycine into the nonpolar (and relatively large) tryptophan (UGG codon) could have dramatic effects on the function of the protein.

Once again, a mutation is the change in the DNA or RNA sequence. In multicellular organisms, mutations can be subdivided into germline mutations and somatic mutations. Germline mutations occur in the DNA of sex cells, or gametes, and are therefore potentially very serious. These mutations can be passed to the next generation. Somatic mutations, which occur in somatic, or body, cells, cannot be passed to the next generation (offspring). Mutations can be harmful, beneficial, or have no effect. If a mutation does not change the amino acid sequence in a protein, the mutation will have no effect. In fact, the overwhelming majority of mutations have no significant effect, since DNA repair mechanisms are able to mend most of the changes before they become permanent. Furthermore, many organisms have mechanisms for eliminating otherwise permanently mutated somatic cells.

A gene pool is the complete set of unique alleles in a species or population. Mutations create variation in the gene pool. Populations with a large gene pool are said to be genetically diverse and very robust. They are able to survive intense times of natural selection against certain phenotypes. During these times of selection, individuals with less favorable phenotypes resulting from deleterious alleles (due to mutations) may be selected against and removed from the population. Concurrently, the more favorable mutations that cause beneficial or advantageous phenotypes tend to accumulate in that population, resulting, over time, in evolution.

Harmful Mutations

Mutations can result in errors in protein sequence, creating partially or completely nonfunctional proteins. These can obviously result in harm to the cell and organism. To function correctly and maintain homeostasis, each cell depends on thousands of proteins to all work together to perform the functions of the cell. When a mutation alters a protein that plays a critical role in the cell, the tissue, organ, or organ system may not function properly, resulting in a medical condition. A condition caused by mutations in one or more genes is called a genetic disorder. However, only a small percentage of mutations cause genetic disorders; most have no impact on health. If a mutation does not change the protein sequence or structure, resulting in the same function, it will have no effect on the cell. Often, these mutations are repaired by the DNA repair system of the cell. Each cell has a number of pathways through which enzymes recognize and repair mistakes in DNA (Figure 2). Because DNA can be damaged or mutated in many ways, the process of DNA repair is an important way in which the cell protects itself to maintain proper function.

Figure 2: DNA repair. Shown is a model of DNA ligase repairing chromosomal damage. DNA ligase is an enzyme that joins broken nucleotides together by catalyzing the formation of a bond between the phosphate group and deoxyribose sugar of adjacent nucleotides in the DNA backbone.

A mutation present in a germ cell can be passed to the next generation. If the zygote contains the mutation, every cell in the resulting organism will have that mutation. If the mutation results in a disease phenotype, the mutation causes what is called a hereditary disease. On the other hand, a mutation that is present in a somatic cell of an organism will be present (by DNA replication and mitosis) in all descendants of that cell. If the mutation is present in a gene that is not used in that cell type, the mutation may have no effect. On the other hand, the mutation may lead to a serious medical condition such as cancer.

Beneficial Mutations

A very small percentage of all mutations actually have a positive effect. These mutations lead to new versions of proteins that help an organism and its future generations better adapt to changes in their environment. The genetic diversity that results from mutations is essential for evolution to occur. Without genetic diversity, each individual of a species would be the same, and no one particular individual would have an advantage over another. Adaptation and evolution would not be possible. Beneficial mutations lead to the survival of the individual best fit to the current environment, which results in evolution.

Mutations and Cancer

In the cell cycle, cancer was described as developing due to unregulated cell division. That is, cancer is a disease characterized by a population of cells that grow and divide without respect to normal limits. These cancerous cells invade and destroy adjacent tissues, and they may spread throughout the body.

Nearly all cancers are caused by mutations in the DNA of the abnormal cells. These mutations may be due to the effects of carcinogens, cancer causing agents such as tobacco smoke, radiation, chemicals, or infectious agents. These carcinogens may act as an environmental “trigger,” stimulating the onset of cancer in certain individuals and not others. Do all people who smoke get cancer? No. Complex interactions between carcinogens and an individual’s genome may explain why only some people develop cancer after exposure to an environmental trigger and others do not. Do all cancers need an environmental trigger to develop? No. Cancer causing mutations may also result from errors incorporated into the DNA during replication, or they may be inherited. Inherited mutations are present in all cells of the organism.

Oncogenes and Tumor Suppressor Genes

Mutations found in the DNA of cancer cells typically affect two general classes of genes: oncogenes and tumor suppressor genes. In “normal,” non-cancerous cells, the products of proto-oncogenes promote cell growth and mitosis prior to cell division; thus, proto-oncogenes encode proteins needed for normal cellular functions. Mutations in proto-oncogenes can modify their expression and the function of the gene product, increasing the amount of activity of the product protein. When this happens, they become oncogenes; thus, the cells have a higher chance of dividing excessively and uncontrollably. Cancer-promoting oncogenes are often activated in cancer cells, giving those cells abnormal properties. The products of these genes result in uncontrolled cell growth and division, protection against programmed cell death, loss of respect for normal tissue boundaries, and the ability to become established in diverse tissue environments. Proto-oncogenes cannot be removed from the genome, as they are critical for growth, repair and homeostasis. It is only when they become mutated that the signals for growth become excessive.

In “normal” cells, the products of tumor suppressor genes temporarily discourage cell growth and division to allow cells to finish routine functions, especially DNA repair. Tumor suppressors are generally transcription factors, activated by cellular stress or DNA damage. The function of such genes is to stop the cell cycle in order to carry out DNA repair, preventing mutations from being passed on to daughter cells. However, if the tumor suppressor genes are inactivated, DNA repair cannot occur. Tumor suppressor genes can be inactivated by a mutation that either affects the gene directly or that affects the pathway that activates the gene. The consequence of the lack of DNA repair is that DNA damage accumulates, is not repaired, and inevitably leads to cancer.

Several Mutations to Cause Cancer

Typically, a series of several mutations in these genes that activate oncogenes and inactivate tumor suppressor genes is required to transform a normal cell into a cancer cell (Figure 3). Cells have developed a number of control mechanisms to overcome mutations in proto-oncogenes. Therefore, a cell needs multiple mutations to transform into a cancerous cell. A mutation in one proto-oncogene would not cause cancer, as the effects of the mutation would be masked by the normal control of mitosis and the actions of tumor suppressor genes. Similarly, a mutation in one tumor suppressor gene would not cause cancer either, due to the presence of many ”backup” genes that duplicate its functions. It is only when enough proto-oncogenes have mutated into oncogenes and enough tumor suppressor genes have been deactivated that the cancerous transformation can begin. Signals for cell growth overwhelm the signals for growth regulation, and the cell quickly spirals out of control. Often, because many of these genes regulate the processes that prevent most damage to the genes themselves, DNA damage accumulates as one ages.

Figure 3: Cancers are caused by a series of mutations. Each mutation alters the behavior of the cell. In this example, the first mutation inactivates a tumor suppressor gene, the second mutation inactivates a DNA repair gene, the third mutation creates an oncogene, and a fourth mutation inactivates several more tumor suppressor genes, resulting in cancer. It should be noted that it does not necessarily require four or more mutations to lead to cancer.

Usually, oncogenes are dominant alleles, as they contain gain-of-function mutations. Meanwhile, mutated tumor suppressors are generally recessive alleles, as they contain loss-offunction mutations. A proto-oncogene needs only a mutation in one copy of the gene to generate an oncogene; a tumor suppressor gene needs a mutation in both copies of the gene to render both products defective. There are instances when, however, one mutated allele of a tumor suppressor gene can render the other copy non-functional. These instances result in what is known as a dominant negative effect.