Mutations

Mutation !  Mutation occurs when a DNA gene is damaged or changed in such a

way as to alter the genetic message carried by that gene

!  Mutation: when phenotypic changes are due to changes in the genotype

!  Mutation : a process that produces a gene or chromosome that differs from the wild type

!  Wild type (wt) : a microorganism that exhibits a natural, nonmutated characteristic, Wild type standard for what “normal” is for an organism. Please remember that what is considered wild type today may have been a mutant in the evolutionary past.

The term “mutation” is derived from Latin word meaning “to

change”.

Mutations are important because they increase genetic variation.

Organisms selected as reference strains are called wild type

!  Mutations can occur in two different directions:

!  A forward mutation is a mutation which changes a wild type allele into a new allele (for example, a mutation in one of the genes coding for color producing enzymes may change a wild type [normal color] allele into an albino allele)

!  A true reversion (reverse mutation) is a mutation which changes a mutant allele back into a wild type allele (for example, in the previous example, a reversion would be another mutation at exactly the same location of the first mutation, which simply reverses the change made the first time, changing the albino allele back into a wild type [normal] allele). As you might expect, true reversions are much less common than forward mutations because the "target area" is much smaller. A typical gene is hundreds of bases long; a forward mutation can be achieved by altering any one of many of those bases. But a reversion must hit exactly the previously altered base, and must alter it in such a way as to change it back to what was originally in that position

!  A suppressor mutation seems like a reversion, but is actually a second change in the same gene, at a different site in the gene, which compensates for the forward mutation in the behavior of the gene product. The gene actually now has two differences when compared to the original wild type, but the protein made following its instructions works just like the original, wild type protein.

converts phenotype to wt but not necessarily DNA sequence to wt

mutation from wt to mutant form

mutation from mutant form to wt

! Some mutations harmful: decreased activity, loss of activity

! Some mutations beneficial: new or enhanced activity (this drives evolution)

Gametic –mutations must occur to the DNA in the sex

cells, testis of males, ovaries of females, inherited can be passed down to a person�s

children

Somatic – mutation originally occur

in normal body cells, not inherited cannot be passed

on to your children

Mechanisms of Mutations

!  Spontaneous mutation: random change in the DNA arising from errors in replication

!  Induced mutation: are defined as those that arise after purposeful treatment with mutagens

Mechanisms of Mutations

1.  Spontaneous mutation: random change in the DNA arising from errors in replication

!  Spontaneous mutations are those that arise in the absence of known mutagen treatment.

!  Spontaneous mutation occurs naturally about one in every million to one in every billion divisions(replicated genes). Mutation rates of individual genes in bacteria range from 10-3 to 10-5 per bacterium per division. Most spontaneous mutations occur during DNA replication.

!  Changes in the sequence of template DNA (mutations) can deeply affect the type of protein end product produced. For a particular bacterial strain under defined growth conditions, the mutation rate for any specific gene is constant and is expressed as the probability of mutation per cell division.

Also called background mutations

many spontaneous errors are repaired.

Mutation caused by mismatch wobble base pairing.

Normal pairing typically occurs in the next round of replication; frequency of mutants in F2 is 1/4.

GT pairs are targets for correction by proofreading and other repair systems.

Wobble-pairing T-G, C-A, A-G, T-C

Different types DNA replication errors

Addition and deletion by DNA looping-out. Different types DNA replication errors

DNA loops out on template strand, DNA polymerase skips bases, and deletion occurs.

DNA loops out on new strand, DNA polymerase adds untemplated bases

Mechanisms of Mutations

2.  Induced mutation: are defined as those that arise after purposeful treatment with mutagens, environmental agents that are known to increase the rate of mutations.

!  Induced Mutations, that can be artificially induced in the living organisms by exposing them to abnormal environment such as chemicals and physical mutagens

Mutagen = agent in environment that brings about DNA mutation. Usually chemically or physically interact with DNA to cause change.

Once mistake is fixed into the DNA the change is permanent.

Chemical Mutagens:

!  change the sequence of bases in a DNA gene in a number of ways;

A.  Mimic the correct nucleotide bases in a DNA molecule, but fail to base pair correctly during DNA replication.

B.  Remove parts of the nucleotide, again causing incorrect base pairing during DNA replication.

C.  Add hydrocarbon groups to various nucleotides, also causing incorrect base pairing during DNA replication.

A.  Nitrous acid: converts A so it pairs with C instead of T

B. Nucleoside (sugar + N-base) analogs: takes place of normal nucleosides unable to base pair (Hydrogen bond) correctly

Nucleoside analogs: have chemical structure similar to a base but do not

base pair correctly

C. Intercalating agents: push nucleotides apart so extra is added

Ethidium bromide Acridine dyes

!  Toxins (smoke, soot, mold) create frameshift mutations

Benzopyrene (cigarette smoke)

Physical Mutagens:

!  Radiation High energy radiation from a radioactive material or from X-rays, Gamma Rays,

!  is absorbed by the atoms in water molecules surrounding the DNA. This energy is transferred to the electrons which then fly away from the atom. Left behind is a free radical, which is a highly dangerous and highly reactive molecule that attacks the DNA molecule and alters it in many ways.

!  Radiation can also cause double strand breaks (Sugar –Phosphate backbone) in the DNA molecule, which the cell's repair mechanisms cannot put right.

!  Sunlight contains ultraviolet radiation UV light (the component that causes a suntan) which, when absorbed by the DNA causes a cross link to form between certain adjacent bases. In most normal cases the cells can repair this damage, but unrepaired dimers of this type cause the replicating system to skip over the mistake leaving a gap, which is supposed to be filled in later.

!  Unprotected exposure to UV radiation by the human skin can cause serious damage and may lead to skin cancer and extensive skin tumors.

!  UV light: links T to C, does not allow T-A or C-G, Links neighboring T to T to form Thymine dimmers. Length of exposure determines how severe the damage.

UV: causes crosslinking of T bases (Thymine dimer) which can prevent

unwinding for replication or transcription

Types of Mutations Types - according to phenotype Morphological - mutations that affect the outwardly visible characteristic of an organism Biochemical - 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.

!  Most microorganisms are prototrophs which means that they can grow on a simple growth medium including an energy source and inorganic salts. Biochemical mutations include those that affect proteins or enzymes required to grow on various nutrients or to synthesize various components. Thus, these mutations cause the microorganisms to become auxotrophs (they must be supplied with additional nutrients if they are to grow). For example, the bacterium Escherichia coli does NOT require the amino acid tryptophan for growth because it can synthesize tryptophan. However, there are E. coli mutants that have mutations in the trp genes. These mutants are auxotrophic for tryptophan, and tryptophan must be added to the medium for growth.

Conditional only see mutant phenotype under certain conditions (i.e. temperature sensitive mutation)

Loss of function vs. gain of function a) Loss of function mutations are those that destroy the function of the gene product. b) Gain of function mutations are those that produce a new function for the gene product.

Lethal mutation results in death of the organism when expressed. Sometimes some mutations affect vital functions and the bacterial cell become nonviable. Hence those mutations that can kill the cell are called lethal mutation.

Types – according to genotype

!  Point mutations Substitution of a nucleotide: Base substitution, involves the changing of single base in the DNA sequence. This mistake is copied during replication to produce a permanent change

a) Mutation at the DNA level (1) Transition purine purine Convert a purine-pyrimidine to the other purine-pyrimidine.

•  4 types of transitions; A ↔ G and T ↔ C •  Most transitions results in synonymous substitution.

(2) Transversions purine pyrimidine or pyrimidine purine Convert a purine-pyrimidine to a pyrimidine-purine.

•  8 types of transversions; A ↔ T, G ↔ C, A ↔ C, and G ↔ T •  Transversion more likely to result in nonsynonymous substitution.

Purines A , G

Pyrimidines T , C

b) mutation at DNA level and classified according to effect at protein level

(1) Silent – mutant codon encodes same amino acid (2) Neutral – mutant codon encodes functionally equivalent amino acid (sometimes also called silent) (3) Missense – mutant codon encodes chemically different amino acid (4) Nonsense – mutant codon results in the generation of a stop codon

Nonsense

Missense

Silent

Various Point Mutations

!  Silent mutation: Sometimes a single substitution mutation change in the DNA base sequence results in a new codon still coding for the same amino acid. Since there is no change in the product, such mutations are called silent.

!  Missense mutation: Missense mutations are DNA mutations which lead to changes in the amino acid sequence (one wrong codon and one wrong amino acid) of the protein product. This could be caused by a single point mutation or a series of mutations.

!  Nonsense mutation: A mutation that leads to the formation of a stop codon is called a nonsense mutation. Since these codon cause the termination of protein synthesis, a nonsense mutation leads to incomplete protein products

!  Frameshift mutation: Frameshift mutations involve the addition or deletion of base pairs causing a shift in the “reading frame” of the gene. This causes a reading frame shift and all of the codons and all of the amino acids after that mutation are usually wrong. Since the addition of amino acids to the protein chain is determined by the three base codons, when the overall sequence of the gene is altered, the amino acid sequence may be altered as well.

Insertion or deletion of one or more nucleotide pairs – change in the reading frame for the synthesis of a protein due to insertion or deletion of base pairs in any amount except multiples of three

1. Insertion mutations – mutations from the insertion of base pairs cause frameshift 2. Deletion mutations – mutations from the deletion of base pairs also cause frameshifts