Mutation
Mutations : Latin mutare means to change. Mutation is any heritable change in the genetic material (usually DNA sequence or RNA sequence) and they are a main cause of diversity among organisms. Mutations can happen at any time, in any cell , at many different levels, and they can have widely differing consequences. Although various types of molecular changes exist, the word "mutation" typically refers to a change that affects the nucleic acids. In cellular organisms, these nucleic acids are the building blocks of DNA, and in viruses they are the building blocks of either DNA or RNA The effect of a mutation is determined by the type of cell containing the mutant allele, by the stage in the life cycle or development of the organism that the mutation affects, and, in diploid organisms, by the dominance or recessiveness of the mutant allele.
Mutation were initially characterized as altered phenotypes or phenotypic expression. Mutations can be classified in a variety of ways. In multicellular organisms, one distinction is based on the type of cell in which the mutation first occurs: those that arise in cells and ultimately form gametes are germ-line mutations, all others are somatic mutations. In somatic mutation reproductive cells are not affected, such a mutant allele will not be transmitted to the progeny and may not be detected or be recoverable for genetic analysis. If mutations occur in non-germline cells, then these changes can be categorized as somatic mutations. The word somatic mutations only affect the present organism's body. From an evolutionary perspective, somatic mutations are uninteresting, unless they occur systematically and change some fundamental property of an individual--such as the capacity for survival. For example, cancer is a potent somatic mutation that will affect a single organism's survival. As a different focus, evolutionary theory is mostly interested in DNA changes in the cells that produce the next generation. In higher plants, somatic mutations can often be propagated by vegetative means (without seed production), such as grafting or the rooting of stem cuttings. Mutations that are most useful for genetic analysis and the effects of whose can be turned on or off at will are called conditional mutations. These mutations produce changes in phenotype in one set of environmental conditions (called the restrictive conditions) but not in another (called the permissive conditions). For example, A temperature sensitive mutation, is a conditional mutation whose expression depends on temperature. Usually, restrictive temperature is high, and the organism exhibits a mutant phenotype above this critical temperature. The permissive temperature is lower, and under permissive conditions the phenotype is wild type or nearly wild type.
Temperature-sensitive mutations are frequently used to block particular steps in biochemical pathways in order to test the role of the pathways in various cellular processes, such as DNA replication. Mutations can also be classified by other criteria, such as the kinds of alterations in the DNA, the kinds of phenotypic effects produced, and whether the mutational events are spontaneous in origin or were induced by exposure to a known mutagen (a mutation-causing agent). Spontaneous usually means that the event that caused a mutation is unknown, and spontaneous mutations are those that take place in the absence of any known mutagenic agent.
Types of Mutation
1. Point mutation
Mutations that alter a single nucleotide are called point mutation. Point mutation occurs from the base pair substitution in the DNA base pair. It is called base pair substitution mutation. Base pair changes can be result from the mistake in replication and repair. Mistake in base pairing may occurs due to the different form of bases i.e. tautomerism (imino and enol form); which causes them to miss pair in spite of high fidelity of replication and proof reading.
Point mutation may be:
1. Substitutions 2. Frame shift mutations
1. Substitutions
Substitutions mutation may be due to:
i. Transitions
During mutation, if purine (A, G) is replace by other purine and the pyrimidine (C, T) is replaced by other pyrimidine, such type of mutation is called transition point mutation. Generally this type of mutation occurs when the base of template nucleotide takes a rare tautomeric form. These tautomeric shifts ( keto to imino or enol form) changes the hydrogen bonding characteristics of the bases.
– Purine changes to an alternate purine (A=G)
– pyrimidine changes to an alternate pyrimidine (C=T)
ii. Transversions
In transversion mutations, a purine is substituted for a pyrimidine, or a pyrimidine for a purine. These mutations are rarer due to the steric problems of pairing purines with purines and pyrimidines with pyrimidines. This type of mutation is rare due to steric hinderance problem of pairing of purine with purines and pyrimidines with pyrimidines. e.Purine changes to pyrimidine (A/G→C/T)
pyrimidine changes to Purine (C/T→A/G)
2. Silent mutations
If the base substitution in the DNA template specify the same amino acid and amino acid sequence is not altered, such type of mutation is called silent. This type of mutation is due to degeneracy nature of code. Silent mutation does not affect the phenotypic expression and could not be detected until the developments of nucleic acid sequencing techniques. For eg, UCA codes for serine and change in the third base (UCU) still codes for serine.
3. Mis-sense mutations
Alterations of the base sequence that result in the incorporation of a different amino acid from the one present in the normal protein; than such type of mutation is called mis-sense mutation. The effect may be complete loss of activity, partial loss or no change in activity at all. (acceptable, partially acceptable or unacceptable with regard to the function of protein molecule). e.g., Sickle cell anemia.
6th amino acid – glutamate (GAG) of normal hemoglobin A change to valine (GUG)- hemoglobin S of sickle cell anemia.
4. Nonsense mutations
Sometimes, the codon with the altered base may become a termination ( or nonsense codon).
If mutation that replaces a codon for an amino acid (sense codon) with one of the three stop codon (translation termination codon) (UAA, UAG or UGA) which results in premature termination of the protein during synthesis, such mutation is called nonsense mutation.
5. Neutral mutation: Mis-sense mutation in which the new amino acid is chemically similar to the one it is replacing. The resulting polypeptide will not be much different from the original polypeptide, in terms of how well it functions.
6. Frameshift mutations
If a base pair or few base pair are deleted or added to the DNA nucleotide base, that causes the shifting of coden reading frame encoding polypeptide, such mutation is called frame shift mutation. Addition or deletion of base pair that is not a multiple of 3 will causes frame shift.
These mutations generally occur where there is a short stretch of the same nucleotide. In such a location, the pairing of template and new strand can be displaced by the distance of the repeated sequence leading to additions or deletions of bases in the new.
7. Lethal mutations
The gene that encode polypeptide which are essential for growth no matter what condition the bacteria found; are called essential genes (lethal genes). eg genes encoding RNA polymerase, helicase. Lethal mutations, when expressed, result in the death of the microorganism. Since the microorganism must be able to grow in order to be isolated and studied, lethal mutations are recovered only if they are recessive in diploid organisms or conditional (see the following) in haploid organisms.
▪ Mutation that eventually results in the death of an organism carrying the mutation are
▪ Mutation in DNA,RNA and protein synthesis mechanism.
▪ P53 etc
8. Suppression Mutation
If The second mutation in DNA that restores the function lost by the primary mutation, such type of mutation is called suppression mutation; where first mutation has been suppressed mutation and second mutation is called suppressor mutation. In another word, nucleotide sequence change at site A is restore by producing nucleotide sequence change in site B is called suppression mutation.
Suppression Mutation mutation are of 2 types
– Intragenic suppressor (within the same gene )
– Intergenic suppressor (occurs in a different gene )
I. Intragenic suppression
Intra – within
Mutation in a gene is suppressed by another mutation in the same gene is called intragenic suppression mutation, where a phenotype caused by a primary mutation is ameliorated by a second mutation. The suppressing mutation might be a true revertant, restoring the original DNA sequence; or it might affect a different codon, causing an amino acid change at another position that now restores the function of that protein closer to wild-type activity.
II. Intergenic suppressor
If the deleterious effects of a mutation in a gene are overcome by a mutation in another gene, the process is called extragenic or intergenic ( inter- between) suppression. The suppressing mutation may restore the activity of mutated gene product or provide another gene to take the place of original gene.
– Non sense suppression.
9. Induced mutations/Mutagens
Virtually any agent that directly damages DNA, alters its chemistry, or interferes with repair mechanisms, will induce mutations. Induced mutation is bring about by the physical, chemical or biological agents. These agents may induced mutation or increase the rate of mutation. Such agents is called the mutagens and process is called mutagenesis. Mutagens can be conveniently classified according to their nature and mechanism of action.
Broadly mutagens are classified as :
I. Chemicals
II. Radiation /physical
III. Biological
I. Chemical mutagens/Chemical agents
a. Base analogs
Base analogs are structurally similar to normal nitrogenous bases and can be incorporated into the growing polynucleotide chain during replication. Once in place, these compounds typically exhibit base pairing properties different from the bases they replace and can eventually cause a stable mutation. (These molecules mimic the nucleotide which result in faulty pairing). When these base analogs are incorporate at a site in DNA in place of original nucleotides, most of time replication may occurs normally.
Some base analogs
• 5 bromo-uracil (analogue of thymine)
• 2-aminopurine (analouge of adenine)
• 5 bromodeoxyuridine
• 2,6 diaminopurine
5 bromo-uracil (analogue of thymine) - A widely used base analog is 5-bromouracil (5-BU), an analog of thymine. It undergoes a tautomeric shift from the normal keto form to an enol, much more frequently than does a normal base. The enol forms hydrogen bonds like cytosine and directs the incorporation of guanine rather than adenine. The mechanism of action of other base analogs is similar to that of 5-bromouracil.
b. Alkylating agent
An alkylating agent that adds methyl groups to nucleotides i.e. to the DNA (methyl or ethyl). Alkylation increase possibility of ionization with the introduction of pairing errors. Alkylation mostly occurs in purine (N7-guanine, N3-adenine) and alkylated base may be lost to depurination.
-many chemicals including some poison gases (mustard gas), DMS (dimethyl sulfate), EMS, etc
-often react with keto groups and lock base in its enol-like form/tautomer.
React with bases, sugars and phosphates of DNA
• Add alkyl groups
• Most problems associated with modified bases
c. Intercalating agents
Intercalating agents distort DNA to induce single nucleotide pair insertions and deletions. These mutagens are planar, multiple ring molecules which insert themselves (intercalate) between the stacked bases of the helix. 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. Intercalating agents include acridines such as proflavin and acridine orange.
e. Radiation/Physical agents
All energy on Earth is a series of electromagnetic components of varying wavelength.
Ultraviolet light and forms of ionizing radiation can damage DNA i.e.
