DNAMutation

Lecture 4

Lecture overview• One look around a room tells you that each person

has slight differences in their physical make up — and therefore in their DNA. These subtle variations in DNA are called polymorphisms (literally "many forms"). Many of these gene polymorphisms account for slight differences between people such as hair and eye color. But some gene variations may result in disease or an increased risk for disease. Although all polymorphisms are the result of a mutation in the gene, geneticists only refer to a change as a mutation when it is not part of the normal variations between people.

Aims

• To understand mutation, mutagen, mutants.• Classification of mutations.• Types of mutagens.• Mutagen & carcinogen.

Mutation

In biology, a mutation is a randomly derived change to the nucleotide sequence of the genetic material of an organism.

• Mutations can be caused by copying errors in the genetic material during cell division( DNA replication), or by exposure to mutagens (chemical, physical or viruses).

• In multi-cellular organisms with dedicated reproductive cells, mutations can be subdivided into germ line mutations, which can be passed on to descendants, and somatic mutations, which are not usually transmitted to descendants.

*By effect on structure1- Small-scale mutations:- such as those affecting a

small gene in one or a few nucleotides, including: A- Point mutations: Exchange a single nucleotide for

another, there are different types of point mutation:-

*Transitions: Exchanges a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T).(Most common)

*Transversions: Exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). (Less common)

Classification of mutation

*Insertions add one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements (e.g. AT repeats).

*Deletions remove one or more nucleotides from the DNA.

B-Frame-shift mutationIn a frame shift mutation, one or more bases are inserted or deleted. This type of mutation disrupt the reading frame thus make the DNA meaningless and often results in a shortened protein. Frame shift mutation can classified to:-

• DeletionOriginal The fat cat ate the wee rat.Deletion The fat ate the wee rat.• Insertion Original The fat cat ate the wee rat.Insertion The fat cat xlw ate the wee rat.• Inversion

In an inversion mutation, an entire section of DNA is reversed.

Original The fat cat ate the wee rat.Inversion The fat tar eew eht eta tac.

2- Large-scale mutations in chromosomal structure, including:

A- Deletion of large chromosomal regions, leading to loss of the genes within those regions.

B- Translocation: interchange of genetic parts from non-homologous chromosomes.

C-Inversion: reversing the orientation of a chromosomal segment.

D- Amplifications (or gene duplications) leading to multiple copies of all chromosomal regions, increasing the dosage of the genes located within them.

Deletion Duplication Inversion

• Loss-of-function mutations are the result of gene product having less or no function.

• Gain-of-function mutations change the gene product such that it gains a new and abnormal function.

• Lethal mutations are mutations that lead to the death of the organisms which carry the mutations.

*By effect on function

In applied genetics it is usual to speak of mutations as either harmful or beneficial.

• A harmful mutation is a mutation that decreases the fitness of the organism.

• A beneficial mutation is a mutation that increases fitness of the organism, or which promotes traits that are desirable.

*By effect on fitness

Conditional mutation is a mutation that has wild-type (or less severe) phenotype under certain "permissive" environmental conditions and a mutant phenotype under certain "restrictive" conditions. For example, a temperature-sensitive mutation can cause cell death at high temperature (restrictive condition), but might have no deleterious consequences at a lower temperature (permissive condition).

*Special classes

Causes of mutationMutations may occur spontaneously (spontaneous mutations) or induced (induced mutations) caused by Mutagens.

*Spontaneous mutations can arise as a result of:

1- DNA replication errors and polymerase accuracy. A- Base alterations

Taotomeresim – A base is changed by the repositioning of a hydrogen atom, altering the hydrogen bonding pattern of that base resulting in incorrect base pairing during replication.

Deamination - Hydrolysis changes a normal base to an atypical base containing a keto group in place of the original amine group. Examples include C → U and A → HX (hypoxanthine), and 5MeC (5-methylcytosine) → T.

B- Base damageDepurination – Loss of a purine base (A or G) to

form an apurinic site (AP site). Alkylation can occur through reaction of compounds such as S-adenosyl methionine with DNA. Alkylated bases may be subject to spontaneous breakdown or mispairing.

** Alkylation, the addition of alkyl (methyl, ethyl, occasionally propyl) groups to the bases or backbone of DNA.

2- Spontaneous genetic rearrengment mutationsDeletion, duplication, ……..etc

• Induced mutations on the molecular level can be caused by either Chemical or Physical mutagens.

1- Chemical mutagens The first report of mutagenic action of a

chemical was in 1942 by Charlotte Auerbach, who showed that nitrogen mustard (component of poisonous mustard gas used in World Wars I and II) could cause mutations in cells.

A- Base analogsThese chemicals structurally resemble purines

and pyrimidines and may be incorporated into DNA in place of the normal bases during DNA replication: examples are

*bromouracil (BU), resembles thymine (has Br atom instead of methyl group) and will be incorporated into DNA and pair with A like thymine.

*aminopurine --adenine analog which can pair with T or with C; causes A:T to G:C or G:C to A:T transitions.

B- Chemicals which alter the structure and pairing properties of bases (base modifiers). Example … *nitrous acid-- formed by digestion of nitrites (preservatives) in foods. It causes C to U, meC to T, and A to hypoxanthine deaminations. *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, or mispair to result in mutations upon DNA replication.

C- Intercalating agentsacridine orange, proflavin, ethidium bromide (used in labs as dyes and mutagens), 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.

D- Agents altering DNA structureIncludes a variety of different kinds of agents. These may be:

• Large molecules which bind to bases in DNA and cause them to be noncoding "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)

Physical mutagens (Radiation)

Natural sources of radiation produce so-called background radiation. These include cosmic rays from the sun and outer space, radioactive elements in soil and terrestrial products (wood, stone) and in the atmosphere (radon). One's exposure due to background radiation varies with geographic location.

Sources of radiation

Artificial sources: 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 various other products (TV's, smoke detectors, airport X-rays).

Types of radiation• Ionizing radiation

- Alpha, Beta, Neutron,  X-ray and Gamma

•  Non-ionizing radiation (electromagnetic radiation)

- Visible light, Infrared, Microwave, Radio waves, Very low frequency (VLF), Extremely low frequency (ELF), Thermal radiation (heat) and Black body radiation.

Non Ionizing radiation

• 1. EM spectrum

Visible light and other forms of radiation are all types of electromagnetic radiation (consists of electric and magnetic waves). The length of EM waves (wavelength) varies widely and is inversely proportional to the energy they contain: this is the basis of the so-called EM spectrum.

• UV (ultraviolet)UV radiation is less energetic,

and therefore non-ionizing, but its wavelengths are preferentially absorbed by bases of DNA and by aromatic amino acids of proteins, so it has important biological and genetic effects.

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 (because it creates oxygen radicals) but it produces very few pyrimidine dimers.

• 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. 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.

• . Ionizing radiationX- and gamma-rays are energetic

enough that they produce reactive ions (charged atoms or molecules) when they react with biological molecules; thus they are referred to as ionizing radiation.

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.

• Biological effects of radiationIonizing radiation produces a range of

damage to cells and organisms primarily due to the production of free radicals of water (the hydroxyl or OH radical). Free radicals possess unpaired electrons and are chemically very reactive and will interact with DNA, proteins, lipids in cell membranes, etc. Thus X-rays can cause DNA and protein damage which may result in organelle failure, block cell division, or cause cell death. The rapidly dividing cell types (blood cell-forming areas of bone marrow, gastrointestinal tract lining) are the most affected by ionizing radiation and the severity of the effects depends upon the dose received.

• Genetic effects of radiationIonizing radiation produces a range of

effects on DNA both through free radical effects and direct action:

• 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).• cross linking of DNA to itself or proteins

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