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20.1: Types of Mutations - Biology


Mutations (changes in a gene sequence) can result in mutant alleles that no longer produce the same level or type of active product as the wild-type allele. Any mutant allele can be classified into one of five types: (1) amorph, (2) hypomorph, (3) hypermorph, (4) neomorph, and (5) antimorph.

  • Amorph alleles are complete loss-of-function. They make no active product – zero function. The absence of function can be due to a lack of transcription (gene regulation mutation) or due to the production of a malfunctioning (protein coding mutation) product. These are also sometimes referred to as a Null allele.
  • Hypomorph alleles are only a partial loss-of-function. They make an incompletely functioning product. This could occur via reduced transcription or via the production of a product that lacks complete activity. These alleles are sometimes referred to as Leaky mutations, because they provide some function, but not complete function.

Both amorphs and hypomorphs tend to be recessive to wild type because the wild type allele is usually able to supply sufficient product to produce a wild type phenotype (called haplo-sufficient - see Chapter 6). If the mutant allele is not haplo-sufficient, then it will be dominant to the wild type.

While the first two classes involve a loss-of-function, the next two involve a gain-of-function – quantity or quality. Gain-of-function alleles are almost always dominant to the wild type allele.

  • Hypermorph alleles produce more of the same, active product. This can occur via increased transcription or by changing the product to make it more efficient/effective at its function.
  • Neomorph alleles produce an active product with a new, different function, something that the wild type allele doesn’t do. It can be either new expression (new tissue or time) or a mutation in the product to create a new function (additional substrate or new binding site), not present in the wild type product.

Antimorph alleles are relatively rare, and have an activity that is dominant and opposite to the wild-type function. These alleles usually have no normal function of their own and they interfere with the function from the wild type allele. Thus, when an antimorph allele is heterozygous with wild type, the wild type allele function is reduced. While at the molecular level there are many ways this can happen, the simplest model to explain antimorph effect is that the product acts as a dimer (or any multimer) and one mutant subunit poisons the whole complex. Antimorphs are also known as dominant negative mutations.

Identifying Muller’s Morphs - All mutations can be sorted into one of the five morphs base on how they behave when heterozygous with other alleles – deletion alleles (zero function), wild type alleles (normal function), and duplication alleles (double normal function).


Point Mutation

A point mutation is a type of mutation in DNA or RNA, the cell’s genetic material, in which one single nucleotide base is added, deleted or changed. DNA and RNA are made up of many nucleotides. There are five different molecules that can make up nitrogenous bases on nucleotides: cytosine, guanine, adenine, thymine (in DNA) and uracil (in RNA), abbreviated C, G, A, T, and U. The specific sequence of nucleotides encodes all the information for carrying out all cell processes. In general, a mutation is when a gene is altered through a change in DNA structure this may refer even to entire sections of chromosomes. A point mutation is specifically when only one nucleotide base is changed in some way, although multiple point mutations can occur in one strand of DNA or RNA.


Contents

Early approaches to mutagenesis relied on methods which produced entirely random mutations. In such methods, cells or organisms are exposed to mutagens such as UV radiation or mutagenic chemicals, and mutants with desired characteristics are then selected. Hermann Muller discovered in 1927 that X-rays can cause genetic mutations in fruit flies, [6] and went on to use the mutants he created for his studies in genetics. [7] For Escherichia coli, mutants may be selected first by exposure to UV radiation, then plated onto an agar medium. The colonies formed are then replica-plated, one in a rich medium, another in a minimal medium, and mutants that have specific nutritional requirements can then be identified by their inability to grow in the minimal medium. Similar procedures may be repeated with other types of cells and with different media for selection.

A number of methods for generating random mutations in specific proteins were later developed to screen for mutants with interesting or improved properties. These methods may involve the use of doped nucleotides in oligonucleotide synthesis, or conducting a PCR reaction in conditions that enhance misincorporation of nucleotides (error-prone PCR), for example by reducing the fidelity of replication or using nucleotide analogues. [8] A variation of this method for integrating non-biased mutations in a gene is sequence saturation mutagenesis. [9] PCR products which contain mutation(s) are then cloned into an expression vector and the mutant proteins produced can then be characterised.

In animal studies, alkylating agents such as N-ethyl-N-nitrosourea (ENU) have been used to generate mutant mice. [10] [11] Ethyl methanesulfonate (EMS) is also often used to generate animal, plant, and virus mutants. [12] [13] [14]

In a European Union law (as 2001/18 directive), this kind of mutagenesis may be used to produce GMOs but the products are exempted from regulation: no labeling, no evaluation. [15]

Prior to the development site-directed mutagenesis techniques, all mutations made were random, and scientists had to use selection for the desired phenotype to find the desired mutation. Random mutagenesis techniques has an advantage in terms of how many mutations can be produced however, while random mutagenesis can produce a change in single nucleotides, it does not offer much control as to which nucleotide is being changed. [5] Many researchers therefore seek to introduce selected changes to DNA in a precise, site-specific manner. Early attempts uses analogs of nucleotides and other chemicals were first used to generate localized point mutations. [16] Such chemicals include aminopurine, which induces an AT to GC transition, [17] while nitrosoguanidine, [18] bisulfite, [19] and N 4 -hydroxycytidine may induce a GC to AT transition. [20] [21] These techniques allow specific mutations to be engineered into a protein however, they are not flexible with respect to the kinds of mutants generated, nor are they as specific as later methods of site-directed mutagenesis and therefore have some degree of randomness. Other technologies such as cleavage of DNA at specific sites on the chromosome, addition of new nucleotides, and exchanging of base pairs it is now possible to decide where mutations can go. [11] [8]

Current techniques for site-specific mutation originates from the primer extension technique developed in 1978. Such techniques commonly involve using pre-fabricated mutagenic oligonucleotides in a primer extension reaction with DNA polymerase. This methods allows for point mutation or deletion or insertion of small stretches of DNA at specific sites. Advances in methodology have made such mutagenesis now a relatively simple and efficient process. [3]

Newer and more efficient methods of site directed mutagenesis are being constantly developed. For example, a technique called "Seamless ligation cloning extract" (or SLiCE for short) allows for the cloning of certain sequences of DNA within the genome, and more than one DNA fragment can be inserted into the genome at once. [2]

Site directed mutagenesis allows the effect of specific mutation to be investigated. There are numerous uses for example, it has been used to determine how susceptible certain species were to chemicals that are often used In labs. The experiment used site directed mutagenesis to mimic the expected mutations of the specific chemical. The mutation resulted in a change in specific amino acids and the affects of this mutation were analyzed. [3]

The site-directed approach may be done systematically in such techniques as alanine scanning mutagenesis, whereby residues are systematically mutated to alanine in order to identify residues important to the structure or function of a protein. [22] Another comprehensive approach is site saturation mutagenesis where one codon or a set of codons may be substituted with all possible amino acids at the specific positions. [23] [24]

Combinatorial mutagenesis is a site-directed protein engineering technique whereby multiple mutants of a protein can be simultaneously engineered based on analysis of the effects of additive individual mutations. [25] It provides a useful method to assess the combinatorial effect of a large number of mutations on protein function. [26] Large numbers of mutants may be screened for a particular characteristic by combinatorial analysis. [25] In this technique, multiple positions or short sequences along a DNA strand may be exhaustively modified to obtain a comprehensive library of mutant proteins. [25] The rate of incidence of beneficial variants can be improved by different methods for constructing mutagenesis libraries. One approach to this technique is to extract and replace a portion of the DNA sequence with a library of sequences containing all possible combinations at the desired mutation site. The content of the inserted segment can include sequences of structural significance, immunogenic property, or enzymatic function. A segment may also be inserted randomly into the gene in order to assess structural or functional significance of a particular part of a protein. [25]

The insertion of one or more base pairs, resulting in DNA mutations, is also known as insertional mutagenesis. [27] Engineered mutations such as these can provide important information in cancer research, such as mechanistic insights into the development of the disease. Retroviruses and transposons are the chief instrumental tools in insertional mutagenesis. Retroviruses, such as the mouse mammory tumor virus and murine leukemia virus, can be used to identify genes involved in carcinogenesis and understand the biological pathways of specific cancers. [28] Transposons, chromosomal segments that can undergo transposition, can be designed and applied to insertional mutagenesis as an instrument for cancer gene discovery. [28] These chromosomal segments allow insertional mutagenesis to be applied to virtually any tissue of choice while also allowing for more comprehensive, unbiased depth in DNA sequencing. [28]

Researchers have found four mechanisms of insertional mutagenesis that can be used on humans. the first mechanism is called enhancer insertion. Enhancers boost transcription of a particular gene by interacting with a promoter of that gene. This particular mechanism was first used to help severely immunocompromised patients I need of bone marrow. Gammaretroviruses carrying enhancers were then inserted into patients. The second mechanism is referred to as promoter insertion. Promoters provide our cells with the specific sequences needed to begin translation. Promoter insertion has helped researchers learn more about the HIV virus. The third mechanism is gene inactivation. An example of gene inactivation is using insertional mutagenesis to insert a retrovirus that disrupts the genome of the T cell in leukemia patients and giving them a specific antigen called CAR allowing the T cells to target cancer cells. The final mechanisms is referred to as mRNA 3' end substitution. Our genes occasionally undergo point mutations causing beta-thalassemia that interrupts red blood cell function. To fix this problem the correct gene sequence for the red blood cells are introduced and a substitution is made. [5]

Homologous recombination can be used to produce specific mutation in an organism. Vector containing DNA sequence similar to the gene to be modified is introduced to the cell, and by a process of recombination replaces the target gene in the chromosome. This method can be used to introduce a mutation or knock out a gene, for example as used in the production of knockout mice. [29]

Since 2013, the development of CRISPR-Cas9 technology has allowed for the efficient introduction of different types of mutations into the genome of a wide variety of organisms. The method does not require a transposon insertion site, leaves no marker, and its efficiency and simplicity has made it the preferred method for genome editing. [30] [31]

As the cost of DNA oligonucleotide synthesis falls, artificial synthesis of a complete gene is now a viable method for introducing mutations into a gene. This method allows for extensive mutation at multiple sites, including the complete redesign of the codon usage of a gene to optimise it for a particular organism. [32]


Deletion

If a mistake is made during meiosis that causes part of a chromosome to break off and become lost, this is called a deletion. If the deletion occurs within a gene that is vital for the survival of an individual, it could cause serious problems and even death for a zygote made from that gamete with the deletion. Other times, the part of the chromosome that is lost does not cause fatality for the offspring. This type of deletion changes the available traits in the gene pool. Sometimes the adaptations are advantageous and will become positively selected for during natural selection. Other times, these deletions actually make the offspring weaker and they will die off before they can reproduce and pass the new gene set down to the next generation.


10 Unusual Genetic Mutations in Humans

No two people are alike, due to the subtly different ways our genomes are expressed. But sometimes these biological differences lead to genetic mutations that are extremely rare, and sometimes debilitating. Historically, many people suffering from these mutations were labeled monsters or freaks — but today, we know they are simply part of the broad spectrum of genetic variations in our species. Here are 10 of the most unusual genetic mutations we've identified in humans.

1. Progeria

This genetic disorder is as rare as it is severe. The classic form of the disease, called Hutchinson-Gilford Progeria, causes accelerated aging.

Most children who have progeria essentially die of age-related diseases around the age of 13 , but some can live into their 20s. Death is typically caused by a heart attack or stroke. It affects as few as one per eight million live births .

The disease is caused by a mutation in the LMNA gene, a protein that provides support to the cell nucleus. Other symptoms of progeria include rigid (sclerotic) skin, full body baldness (alopecia), bone abnormalities, growth impairment, and a characteristic “sculptured” nasal tip.

Progeria is of great interest to gerontologists who hope connect genetic factors to the aging process. Image: HBO.

2. Uner Tan Syndrome

Uner Tan syndrome is a somewhat controversial condition, whose most obvious property is that people who suffer from it walk on all fours. UTS is a syndrome that was proposed by the Turkish evolutionary biologist Üner Tan after studying five members of the Ulaş family in rural Turkey. These individuals walk with a quadrupedal locomotion, use primitive speech, and have a congenital brain impairment (including “disturbed conscious experience”). The family was featured in a 2006 BBC2 documentary called, " The Family That Walks On All Fours ." Tan describes it like this:

The genetic nature of this syndrome suggests a backward stage in human evolution, which is most probably caused by a genetic mutation, rendering, in turn, the transition from quadrupedality to bipedality. This would then be consistent with theories of punctuated evolution.

The new syndrome, says Tan, “may be used as a live model for human evolution.” Some experts think this is bunk, and that genetics may have very little to do with it.

3. Hypertrichosis

Hypertrichosi s is also called “werewolf syndrome” or Ambras syndrome, and it affects as few as one in a billion people and in fact, only 50 cases have been documented since the Middle Ages.

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People with hypertrichosis have excessive hair on the shoulders, face, and ears. Studies have implicated it to a rearrangement of chromosome 8. It happens due to a disruption of the “crosstalk” between the epidermis and the dermis as hair follicles form in the 3-month fetus at the eyebrows and down to the toes. Normally, signals from the dermis send the messages to form follicles. As a follicle forms, it sends signals to prevent the area around it from also becoming a follicle, which results in the equal spacing of our five million or so follicles. Most of our body parts ignore the messages to form follicles, which explains why most of us are relatively hairless.

4. Epidermodysplasia Verruciformis

Epidermodysplasia verruciformis is an extremely rare disorder that makes people prone to widespread human papillomavirus (HPV) infection. This infection causes scaly macules and papules ( cutaneous squamous cell carcinomas ) to grow on the hands, feet, and even face. These skin “eruptions” appear as wart-like lesions — and even wood-like and horn-like growths — with reddish-brown pigmented plaques. Typically, the skin tumors start to emerge in people between the age of 20 and 40, and the growths tend to appear on areas exposed to the sun. Also called Lewandowsky-Lutz dysplasia, there is no known cure, though treatments to scale back the growths are possible.

The disorder was brought to the public’s attention in November 2007 when a video of a 34-year-old Indonesian man named Dede Koswara appeared on the internet . In 2008, he underwent surgery to have 13 pounds (6 kg) of the warts removed . After the lesions and horns were extracted from his hands, head, torso, and feet, his hands were grafted with new skin. In all, about 95% of the warts were removed.


D. Definitions & NSF-Grantee Relationships

1. Definitions

a. An AUTHORIZED ORGANIZATIONAL REPRESENTATIVE (AOR)/AUTHORIZED REPRESENTATIVE means the administrative official who, on behalf of the proposing organization is empowered to make certifications and representations and can commit the organization to the conduct of a project that NSF is being asked to support as well as adhere to various NSF policies and grant requirements.

b. A GRANT AGREEMENT 3 means a legal instrument of financial assistance between NSF and a grantee that, consistent with 31 USC 6302, 6304:

(1) Is used to enter into a relationship the principal purpose of which is to transfer anything of value from NSF to the grantee to carry out a public purpose authorized by a law of the United States (see 31 USC 6101(3)) and not to acquire property or services for NSF's direct benefit or use

(2) Is distinguished from a cooperative agreement in that it does not provide for substantial involvement between NSF and the grantee in carrying out the activity contemplated by the NSF award.

NSF awards the following two types of grants:

(a) A STANDARD GRANT means a type of grant in which NSF agrees to provide a specific level of support for a specified period of time with no statement of NSF intent to provide additional future support without submission of another proposal.

(b) A CONTINUING GRANT means a type of grant in which NSF agrees to provide a specific level of support for an initial specified period of time, usually a year, with a statement of intent to provide additional support of the project for additional periods, provided funds are available and the results achieved warrant further support.

c. A COST REIMBURSEMENT AWARD means a type of grant under which NSF agrees to reimburse the grantee for work performed and/or costs incurred by the grantee up to the total amount specified in the grant. Such costs must be allowable in accordance with the applicable cost principles. Accountability is based primarily on technical progress, financial accounting and fiscal reporting. Except under certain programs and under special circumstances, NSF grants and cooperative agreements are normally cost reimbursement type awards.

d. A FIXED AMOUNT AWARD means a type of award in which NSF provides a specific level of support without regard to actual costs incurred under the award. This type of NSF award reduces some of the administrative burden and recordkeeping requirements for both the grantee and NSF. Accountability is based primarily on performance and results.

e. A COOPERATIVE AGREEMENT means a legal instrument of financial assistance between NSF and an awardee that, consistent with 31 USC 6302-6305:

(1) Is used to enter into a relationship the principal purpose of which is to transfer anything of value from NSF to the grantee to carry out a public purpose authorized by a law of the United States (see 31 USC 6101(3)) and not to acquire property or services for NSF's direct benefit or use

(2) Is distinguished from a grant in that it provides for substantial involvement between NSF and the grantee in carrying out the activity contemplated by the NSF award.

In the case of NSF, assistance awards involve the support or stimulation of scientific and engineering research, science and engineering education or other related activities. NSF is authorized to use grants or cooperative agreements for this purpose. Grants, however, are the primary mechanism of NSF support.

f. A GRANTEE means the organization or other entity that receives a grant and assumes legal and financial responsibility and accountability both for the awarded funds and for the performance of the grant-supported activity. NSF grants are normally made to organizations rather than to individual Principal Investigator/Project Director(s). Categories of eligible proposers may be found in Chapter I.F.

g. PRINCIPAL INVESTIGATOR/PROJECT DIRECTOR (PI/PD) - see PAPPG Exhibit II-3, Definitions of Categories of Personnel.

2. NSF-Grantee Relationships

a. Grants will be used by NSF when the accomplishment of the project objectives requires minimal NSF involvement during performance of the activities. Grants establish a relationship between NSF and the grantee in which:

(1) NSF agrees to provide up to a specified amount of financial support for the project to be performed under the conditions and requirements of the grant. NSF will monitor grant progress and assure compliance with applicable standards.

(2) The grantee agrees to perform the project as proposed, to the prudent management of the funds provided and to carry out the supported activities in accordance with the provisions of the grant. (See Chapter VI.B, for the documents that comprise an NSF grant.)

b. Cooperative agreements will be used by NSF when the accomplishment of the project objectives requires substantial ongoing Foundation involvement during the project performance period. Substantial agency involvement may be necessary when an activity is technically and/or managerially complex and would require extensive or close coordination between NSF and the awardee. This, however, does not affect NSF's right to unilaterally suspend or terminate support for cause or consider termination in accordance with Chapter XII, if it is in the best interest of NSF or the Government. The doctrine of substantial involvement is set forth in the Federal Grant and Cooperative Agreement Act of 1977 (31 USC 6301-6308).

NSF utilizes two types of cooperative agreements:

    Standalone Cooperative Agreement (CA), which consists of a cooperative agreement for a single, unified award where there is no need to provide separate, discrete funding and oversight for the projects or programs under that award.

Examples of projects suitable for cooperative agreements include: management of research centers, large curriculum projects, multi-user facilities, projects which involve complex subcontracting, construction or operations of major in-house university facilities and major instrumentation development, and projects in which NSF participates with other stakeholder agencies or organizations that have influence over project direction and/or development.

Under a cooperative agreement, the awardee has primary responsibility for the conduct of the project. To the extent that NSF does not reserve responsibility for coordinating or integrating the project activities with other related activities or does not assume a degree of shared responsibility for certain aspects of the project, all such responsibilities remain with the awardee. While NSF will monitor the cooperative agreement in accordance with the terms and conditions of the award, the Foundation will not assume overall control of a project or unilaterally change or direct the project activities.

The cooperative agreement will specify the extent to which NSF will advise, review, approve or otherwise be involved with project activities, as well as NSF's right to require more clearly defined deliverables. NSF may provide advice, guidance or assistance of a technical, management, or coordinating nature and may require that the awardee obtain NSF prior approval of specific decisions, milestones, or project activities. Substantial involvement is incorporated in key areas of accountability in both financial and programmatic award terms examples include prior agency approval requirements, type and frequency of project plans, special reporting requirements, and project and awardee reviews that NSF will conduct during the term of the award.

Cooperative agreements for construction are generally funded through a separate appropriation from Congress for Major Research Equipment and Facilities Construction (MREFC). NSF maintains the MREFC appropriations in a separate budget account, for major construction projects that successfully undergo a rigorous selection process. MREFC funds cannot be co-mingled with funds for activities other than construction therefore, NSF issues a separate award for operations and other activities related to commissioning and management of the facility or major instrument. The awardee is required to maintain an accounting system capable of segregating MREFC and operating costs, and to ensure that such costs are applied accordingly.

Many major facility awards, including those for NSF-supported Federally Funded Research and Development Centers (FFRDCs), consist of a cooperative agreement as an umbrella award, establishing the overall basic provisions of the award, and separate cooperative support agreements. The cooperative support agreements contain specific terms and conditions for construction activities, management and operations, research activities that are co-sponsored by other agencies, and any other focused activities that NSF needs to monitor separately from the overall objectives of the cooperative agreement.


Base-Pair Insertions and Deletions

Mutations can also occur in which nucleotide base pairs are inserted into or deleted from the original gene sequence. This type of gene mutation is dangerous because it alters the template from which amino acids are read. Insertions and deletions can cause frame-shift mutations when base pairs that are not a multiple of three are added to or deleted from the sequence. Since the nucleotide sequences are read in groupings of three, this will cause a shift in the reading frame. For example, if the original, transcribed DNA sequence is CGA CCA ACG GCG. and two base pairs (GA) are inserted between the second and third groupings, the reading frame will be shifted.

  • Original Sequence: CGA-CCA-ACG-GCG.
  • Amino Acids Produced: Arginine/Proline/Threonine/Alanine.
  • Inserted Base Pairs (GA): CGA-CCA-GAA-CGG-CG.
  • Amino Acids Produced: Arginine/Proline/Glutamic Acid/Arginine.

The insertion shifts the reading frame by two and changes the amino acids that are produced after the insertion. The insertion can code for a stop codon too soon or too late in the translation process. The resulting proteins will be either too short or too long. These proteins are for the most part defunct.


A close-up of DNA

All living organisms, from the tiniest bacteria to plants and human beings are built up from microscopic cells (in the case of bacteria, the entire organism is a single cell). At the very core of these cells is DNA or deoxyribonucleic acid the molecular blueprint for nearly every aspect of existence.

If one begins to zoom in on the structure of DNA, the first level of magnification consists of two intertwined chains in the shape of a double helix. Each chain is made of a sequence of nucleotides. In turn, each nucleotide is a complex of three entities: a sugar called deoxyribose, phosphate groups and a nitrogen-containing base (that is, a compound that is ready to accept a hydrogen ion). DNA nucleotides can have the following bases: adenine (A), guanine (G), cytosine (C) and thymine (T). Nucleotides are often referred to by the base they contain.

The sugars and phosphates of the various nucleotides sit at the chain part of the double helix, while the nucleotide bases reach across the gaps to latch onto bases on the other side. All in all, DNA really looks like a double helical ladder with bases as rungs, a common analogy. The bases latch on to one another in a very specific way: adenine (A) to thymine (T) and cytosine to (C) to guanine (G). This is known as complementary base pairing.

When one refers to a DNA sequence, it indicates the sequence of nucleotides on one of its strands. Because nucleotides bind to one another in a predictable manner, knowing the sequence of one strand makes it easy to fill in the sequence of the other.


IV. Mutagens

A. Chemical mutagens

It is possible to distinguish chemical mutagens by their modes of action some of these cause mutations by mechanisms similar to those which arise spontaneously while others are more like radiation (to be considered next) in their effects.

1. Base analogs

  • bromouracil (BU)--artificially created compound extensively used in research. Resembles thymine (has Br atom instead of methyl group) and will be incorporated into DNA and pair with A like thymine. It has a higher likelihood for tautomerization to the enol form (BU*)
  • aminopurine --adenine analog which can pair with T or (less well) with C causes A:T to G:C or G:C to A:T transitions. Base analogs cause transitions, as do spontaneous tautomerization events.

2. Chemicals which alter structure and pairing properties of bases

  • nitrous acid--formed by digestion of nitrites (preservatives) in foods. It causes C to U, meC to T, and A to hypoxanthine deaminations. [See above for the consequences of the first two events hypoxanthine in DNA pairs with C and causes transitions. Deamination by nitrous acid, like spontaneous deamination, causes transitions.
  • nitrosoguanidine, methyl methanesulfonate, ethyl methanesulfonate--chemical mutagens that react with bases and add methyl or ethyl groups. Depending on the affected atom, the alkylated base may then degrade to yield a baseless site, which is mutagenic and recombinogenic, or mispair to result in mutations upon DNA replication.

3. Intercalating agents

All are flat, multiple ring molecules which interact with bases of DNA and insert between them. This insertion causes a "stretching" of the DNA duplex and the DNA polymerase is "fooled" into inserting an extra base opposite an intercalated molecule. The result is that intercalating agents cause frameshifts.

4. Agents altering DNA structure

  • --large molecules which bind to bases in DNA and cause them to be noncoding--we refer to these as "bulky" lesions (eg. NAAAF)
  • --agents causing intra- and inter-strand crosslinks (eg. psoralens--found in some vegetables and used in treatments of some skin conditions)
  • --chemicals causing DNA strand breaks (eg. peroxides)

B. Radiation

1. EM spectrum

The longest waves (AM radio) have the least energy while successively shorter waves and increasing energy are seen with FM radio, TV, microwaves, infrared, visible, ultraviolet (UV), X and gamma radiation. The portion which is biologically significant is UV and higher energy radiation.

2. Ionizing radiation

UV radiation is not ionizing but can react with DNA and other biological molecules and is also important as a mutagen.

The units now used for ionizing radiation of all types are rems (roentgen equivalent man): 1 rem of any ionizing radiation produces similar biological effects. The unit used previously was the rad (radiation absorbed dose). However, the effects of different types of radiation differ for one rad unit: one rad of alpha particles has a much greater damaging effect than one rad of gamma rays alpha particles have a greater RBE (relative biological effectiveness) than gamma rays. The relationship between these units is that:

In addition to the energy type and total dose of radiation the dose rate should be considered: the same number of rems given in a brief, intense exposure (high dose rate) causes burns and skin damage versus a long-term weak exposure (low dose rate) which would only increase risk of mutation and cancer.

3. Sources of radiation

In addition, humans have created artificial sources of radiation which contribute to our radiation exposure. Among these are medical testing (diagnostic X-rays and other procedures), nuclear testing and power plants, and various other products (TV's, smoke detectors, airport X-rays).

Taken together, our overall total average exposure from all sources is about 350 mrem/year the major contributor of which is from radon exposure. See the graph on page 281 of your text for the breakdown.

4. Biological effects of radiation

sublethal dose (100-250 rems): nausea and vomiting early 1-2 wk. latent period followed by malaise, anorexia, diarrhea, hair loss, recovery (latency due to time it takes hematopoetic or other damage to show up)

lethal dose (350-450 rems): nausea and vomiting early 1 wk. latent period followed by above with more severe symptoms including internal bleeding a 50% chance of death [LD50 : dose at which half of exposed individuals will die ca. 400 rems for humans]. Death is due to blood cell or gastrointestinal failure.

supralethal dose (>650 rems): nausea and vomiting early, followed by shock, abdominal pain, diarrhea, fever and death within hours or days. Death is due to heart or CNS damage.

For the affected tissues and organs, the number of destroyed cells and the likelihood of their replacement determines the survival chances. The long term effects include increased cancer risk and increased risk of mutations in one's offspring.

5. Genetic effects of radiation

  • -breaks in one or both strands (can lead to rearrangements, deletions, chromosome loss, death if unrepaired this is from stimulation of recombination)
  • -damage to/loss of bases (mutations)
  • -crosslinking of DNA to itself or proteins

6. UV (ultraviolet)

UV is normally classified in terms of its wavelength: UV-C (180-290 nm)--"germicidal"--most energetic and lethal, it is not found in sunlight because it is absorbed by the ozone layer UV-B (290-320 nm)--major lethal/mutagenic fraction of sunlight UV-A (320 nm--visible)--"near UV"--also has deleterious effects (primarily because it creates oxygen radicals) but it produces very few pyrimidine dimers. Tanning beds will have UV-A and UV-B. To see a graphic representation of the wavelengths of UV and ozone absorption, click here.

The major lethal lesions are pyrimidine dimers in DNA (produced by UV-B and UV-C)--these are the result of a covalent attachment between adjacent pyrimidines in one strand. This is shown here for a thymine-thymine dimer and here for a thymine-cytosine dimer. These dimers, like bulky lesions from chemicals, block transcription and DNA replication and are lethal if unrepaired. They can stimulate mutation and chromosome rearrangement as well.


What is a gene variant and how do variants occur?

A gene variant is a permanent change in the DNA sequence that makes up a gene. This type of genetic change used to be known as a gene mutation, but because changes in DNA do not always cause disease, it is thought that gene variant is a more accurate term. Variants can affect one or more DNA building blocks (nucleotides) in a gene.

Gene variants can be inherited from a parent or occur during a person’s lifetime:

  • Inherited (or hereditary) variants are passed from parent to child and are present throughout a person’s life in virtually every cell in the body. These variants are also called germline variants because they are present in the parent’s egg or sperm cells, which are also called germ cells. When an egg and a sperm cell unite, the resulting fertilized egg cell contains DNA from both parents. Any variants that are present in that DNA will be present in the cells of the child that grows from the fertilized egg.
  • Non-inherited variants occur at some time during a person’s life and are present only in certain cells, not in every cell in the body. Because non-inherited variants typically occur in somatic cells (cells other than sperm and egg cells), they are often referred to as somatic variants. These variants cannot be passed to the next generation. Non-inherited variants can be caused by environmental factors such as ultraviolet radiation from the sun or can occur if an error is made as DNA copies itself during cell division.

Some genetic changes are described as new (de novo) variants these variants are recognized in a child but not in either parent. In some cases, the variant occurs in a parent’s egg or sperm cell but is not present in any of their other cells. In other cases, the variant occurs in the fertilized egg shortly after the egg and sperm cells unite. (It is often impossible to tell exactly when a de novo variant happened.) As the fertilized egg divides, each resulting cell in the growing embryo will have the variant. De novo variants are one explanation for genetic disorders in which an affected child has a variant in every cell in the body, but the parents do not, and there is no family history of the disorder.

Variants acquired during development can lead to a situation called mosaicism, in which a set of cells in the body has a different genetic makeup than others. In mosaicism, the genetic change is not present in a parent’s egg or sperm cells, or in the fertilized egg, but happens later, anytime from embryonic development through adulthood. As cells grow and divide, cells that arise from the cell with the altered gene will have the variant, while other cells will not. When a proportion of somatic cells have a gene variant and others do not, it is called somatic mosaicism. Depending on the variant and how many cells are affected, somatic mosaicism may or may not cause health problems. When a proportion of egg or sperm cells have a variant and others do not, it is called germline mosaicism. In this situation, an unaffected parent can pass a genetic condition to their child.

Most variants do not lead to development of disease, and those that do are uncommon in the general population. Some variants occur often enough in the population to be considered common genetic variation. Several such variants are responsible for differences between people such as eye color, hair color, and blood type. Although many of these common variations in the DNA have no negative effects on a person’s health, some may influence the risk of developing certain disorders.