Mutation Biochemistry and Molecular Biology

Mutation

Introduction

Mutation. Mutations are happening in our cells all the time, but almost none of these affect our health. This is very different than what we often see in science fiction in movies. In real life, a mutation is never so beneficial that it turns a person into a superhero or does something bizarre like cause them to grow wings. There are many reasons that mutations usually don't have major consequences. One reason is that our cells have very sophisticated machinery for repairing mutations very quickly. So there's not enough time for them to cause problems. Another is that most mutations occur in somatic cells like muscle cells or skin cells and can only affect the cell where the mutation occurred and cells that grow from that cell.

Definition

Mutation is the change in our DNA base pair sequence due to various environmental factors such as UV light, or mistakes during DNA replication. The DNA sequence is specific to each organism. It can sometimes undergo changes in its base-pairs sequence. It is termed as a mutation. A mutation may lead to changes in proteins translated by the DNA.

Classification of mutation

A. The Type of Cell Involved

1. Somatic mutations

Mutations that are in the somatic tissues of the body. Mutations are not transmitted to progeny. The extent of the phenotypic effect depends upon whether the mutation is dominant o recessive (dominant mutations generally have a greater effect). The extent of the phenotypic effect depends upon whether it occurs early or late in development (early arising mutations have a greater effect).

2. Germinal mutations

Mutations that are in the germ tissues of the body. Mutations may be transmitted to pregnancy Dominant mutations are seen in first generation after the mutation occurs. If a female gamete containing an X-linked mutation is fertilized, the males will show the mutant phenotype.

B. Mode of Origin

(1) Spontaneous mutations

The spontaneous mutations occur suddenly in the nature and their origin is unknown. They are also called “background mutation” and have been reported in many organisms such as, Oenothera, maize, bread molds, microorganisms (bacteria and viruses), Drosophila, mice, man, etc.

(2) Induced mutations

Besides naturally occurring spontaneous mutations, the mutations can be induced artificially in the living organisms by exposing them to abnormal environment such as radiation, certain physical conditions (i.e., temperature) and chemicals.

C. Direction of Mutation

1. Forward mutations

In an organism when mutations create a change from wild type to abnormal phenotype, then that type of mutations are known as forward mutations. Most mutations are forward type.

2. Reverse or back mutations

The forward mutations are often corrected by error correcting mechanism, so that an abnormal phenotype changes into wild type phenotype.

D. Size and Quality

1. Point mutation

When heritable alterations occur in a very small segment of DNA molecule, i.e., a single nucleotide or nucleotide pair, then this type of mutations are called “point mutations”. The point mutations may occur due to following types of sub nucleotide change in the DNA and RNA.

– Deletion mutations. The point mutation which is caused due to loss or deletion of some portion (single nucleotide pair) in a triplet codon of a cistron or gene is called deletion mutation.

– Insertion or addition mutation. The point mutations which occur due to addition of one or more extra nucleotides to a gene or cistron are called insertion mutations. The mutations which arise from the insertion or deletion of individual nucleotides and cause the rest of the message downstream of the mutation to be read out of phase, are called frameshift mutations.

– Substitution mutation. A point mutation in which a nucleotide of a triplet is replaced by another nucleotide, is called substitution mutation.

2. Multiple mutations or gross mutations.

When changes involving more than one nucleotide pair, or entire gene, then such mutations are called gross mutations. The gross mutations occur due to rearrangements of genes within the genome. It may be:

The rearrangement of genes may occur within a gene. Two mutations within the same functional gene can produce different effects depending on gene whether they occur in the cis or trans position.
The rearrangement of gene may occur in number of genes per chromosome. If the numbers of gene replicas are non-equivalent on the homologous chromosomes, they may cause different types of phenotypic effects over the organisms.
Due to movement of a gene locus new type of phenotypes may be created, especially when the gene is relocated near heterochromatin. The movement of gene loci may take place due to following method:

Translocation. Movement of a gene may take place to a non-homologous chromosome, and this is known as translocation.
Inversion. The movement of a gene within the same chromosome is called inversion.

E. Phenotypic Effects

1. Morphological mutations, are mutations that affect the outwardly visible properties of an organism (i.e. curly ears in cats)

2. Lethal mutations, are mutations that affect the viability of the organism (i.e. Manx cat).

3. Conditional mutations, are mutations in which the mutant allele causes the mutant phenotype only in certain environments (called the restrictive condition). In the permissive condition, the phenotype is no longer mutant.

Example. Siamese cat – mutant allele causes albino phenotype at the restrictive temperature of most of the cat body but not at the permissive temperature in the extremities where the body temperatures is lower.

4. Biochemical mutations, are mutations that may not be visible or affect a specific morphological characteristic but may have a general affect on the ability to grow or proliferate. For example, the bacterium Escherichia coli does not require the amino acid tryptophan for growth because they can synthesize tryptophan

F. Magnitude of Phenotypic Effect

1. Dominant mutations

The mutations which have dominant phenotypic expression are called dominant mutations. For example, in man the mutation disease aniridia (absence of iris of eyes) occurs due to a dominant mutant gene.

2. Recessive mutations

Most types of mutations are recessive in nature and so they are not expressed phenotypically immediately. The phenotypic effects of mutations of a recessive gene is seen only after one or more generations, when the mutant gene is able to recombine with another similar recessive gene.

3. Isoalleles

Some mutations alter the phenotype of an organism so slightly that they can be detected only by special techniques. Mutant genes that give slightly modified phenotypes are called isoalleles. They produce identical phenotypes in homozygous or heterozygous combinations.

H. Type of Chromosome Involved

1. Autosomal mutations: This type of mutation occurs in autosomal chromosomes.

2. Sex chromosomal mutations: This type of mutation occurs in sex chromosomes.

Mechanism of mutation

(A) TAUTOMERIC SHIFTS

•Watson and Crick pointed out that the specific base pairing and structures of the bases in DNA are not static, Hydrogen atoms and Amino nitrogen shifts their position known as TAUTOMERIC SHIFTS.

•Tautomeric shifts are rare and alters pairing potential.

•The bases would be expected to exist in their less stable tautomeric forms for only short periods of time. If a base existed in the rare form at the moment that it was being replicated or being incorporated into a nascent DNA chain, a mutation would result.

(B) ERRORS IN THE DNA REPLICATIONS

• DNA polymerase I enzymes are very accurate about the addition of the correct bases and there complementary base pairing with the template strand.

• Polymerase enzymes do make mistakes at a rate of about 1 per every 100,000 nucleotides.

• To fix the mistakes immediately during replication DNA polymerase I do proofreading (3’ to 5’), by recognizing and replacing the incorrectly inserted nucleotide so that replication can continue.

• Proofreading fixes about 99% of these types of errors.

• After replication, Mismatch repair reduces the final error rate.

• Error rates: Before proof reading: 1 in 1 lakh bases

After proof reading: 1 in 10 lakh bases

After Mismatch Repair: 1 in 10 crore bases.

• Incorrectly paired nucleotides cause deformities in the secondary structure of the final DNA molecule.

• During mismatch repair, enzymes recognize and fix these deformities by removing the incorrectly paired nucleotide and replacing it with the correct nucleotide.

Naturally occurring damage to the DNA, generate mutations known as spontaneous lesions. Common spontaneous lesions are,

Depurination
Deamination
Oxidatively damaged bases

DEPURINATION

Loss of a purine (A/G) after the breakage of the glycosidic bond between base and the deoxyribose.
Apurinic sites are removed by the DNA repair mechanism but if a base inserted across from apurinic site, results to mutation.
Lesions are known as APURINIC SITES, these sites cannot specify a base complementarity.
Transversion occurs.

DEAMINATION:

Loss of amino group in A / C / G converts the amino groups to keto groups and changes the hydrogen-bonding potential of the modified bases.
Deamination of guanine produces xanthine, it base pairs with cytosine.
Deamination of guanine is not mutagenic.
Deamination of adenine results in A:T → G:C transitions.
Deamination of cytosine produces G:C → A:T transitions.

OXYDATIVELY DAMAGED BASES

Active oxygen species produced by normal aerobic metabolism Superoxide radicals (O2), Hydrogen peroxide (H2O2), Hydroxyl radicals (-OH)
Cause oxidative damage to DNA, also to precursors of DNA (such as GTP), resulting in mutation. Eg. The 8-oxo-7-hydrodeoxyguanosine (8-oxo dG, or GO) mispairs with A, resulting in a high level of G T transversions.

(D) BASE ANALOGS

Chemical compounds mimic the nitrogenous bases, possess the pairing properties like that of the normal nitrogenous bases.
Base analogs incorporate incorrect nucleotides during replication and causes mutation.
Base analogs exist only in single strand, but substitutes the nucleotides in all replicating DNA copies descended from the original strand. well as pairings that• Base analogue will result in altered base structures as affects DNA replication and transcription of genes.
E.g. 5-Bromouracil (5 BU)& 2 Aminopurine (2AP). 2-amino-purine (2-AP) is analog of adenine can pair with thymine and produce A·T G·C transitions Protonated 2-AP is incorporated by mis-pairing with cytosine, leads to G·C A·T transitions 2-AP : Thymine & 2-AP: Cytosine
5-BU is a thymine analog, the bromine at this position changes the charge distribution and increases the frequency of tautomeric shifts.
5-BU pairs with Adenine in keto form. After a tautomeric shift to its enol form, 5-bromouracil pairs with Guanine.

(E) SPECIFIC MISPAIRING:

Some mutagens are not incorporated into the DNA but alter a base to form a specific mis-pair.
Alkylating agents such as ethylmethanesulfonate (EMS), nitrosoguanidine (NG), operate by this pathway.
EMS and NG add alkyl groups (an ethyl group in EMS and a methyl group in NG) to many positions on all four bases.
Addition of oxygen at position 6 of guanine to create an O-6-alkylguanine. This addition leads to direct mis-pairing with thymine, and would result in G·C A·T transitions.
Alkylating agents can also modify the bases in dNTPs (where N is any base), which are precursors in DNA synthesis.

(F) INTERCALATING AGENTS

The intercalating agents form another important class of DNA modifiers includes proflavine, acridine orange and Class of chemicals termed as ICR compounds.
These agents are planar molecules that mimic base pairs and are able to slip themselves in (intercalate) between the stacked nitrogen bases at the core of the DNA double helix .
In this intercalated position, such an agent can cause an insertion or deletion of a single nucleotide pair

(G) BASE DAMAGE

•Large number of bases damage affects the specific base pairing and blocks the replication and causes mutation.

•Reasons:

Ultraviolet rays
Ionization radiation
Aflatoxin

ULTRAVIOLET RAYS

•UV light damages the bases by generating different type of alterations in DNA called as photoproducts .

•Photoproducts causes mutation by uniting two different lesions adjacent to pyrimidine residues in the same strand. These lesions are the cyclobutane pyrimidine, photodimer and the 6-4 photoproduct

IONIZING RADIATION

•Forms ionized and excited molecules that can damage DNA directly.

•Ionizing radiations ionizes the water of the cell, produce reactive oxygen species ( • OH, O2−, and H2O2) which damages the DNA by forming different adducts and degradation products.

•Thymidine glycol and 8-oxo dG, both can result in mutations.

•Radiations breaks the N-glycosydic bond and form apurinic or apyrimidinic sites, and it can cause strand breaks this is the most lethal effects of ionizing radiation.

AFLATOXIN

• Aflatoxin B1 is a powerful carcinogen that attaches to guanine at the N-7 position, and breaks the bond between the base and the sugar, liberate the base and generates an apurinic site.

• Aflatoxin B1 is a member of a class of chemical carcinogens known as bulky addition products and they bind covalently to DNA

Reference