DNA MUTATION
INTRODUCTION
• Mutation is the process by which the sequence of base pairs in a DNA
molecule is altered. A mutation may result in a change to either a DNA base
pair or a chromosome.
• A cell with a mutation is a mutant cell. If a mutation happens to occur in a
somatic cell (in multicellular organisms), it is a somatic mutation—the
mutant characteristic affects only the individual in which the mutation occurs
and is not passed on to the succeeding generation. In contrast, a mutation in
the germ line of sexually reproducing organisms—a germ-line mutation—
may be transmitted by the gametes to the next generation, producing an
individual with the mutation in both its somatic and its germ-line cells.
TYPES OF MUTATION
1. Point mutations
Point mutations fall into two general categories:
A. A base-pair substitution mutation is a change from one base pair to another in DNA, and
there are two general types.
• A transition mutation is a mutation from one purine–pyrimidine base pair to the other
purine–pyrimidine base pair, such as A–T to G–C. Specifically, this means that the purine on one
strand of the DNA (A in the example) is changed to the other purine, while the pyrimidine on the
complementary strand (T, the base paired to the A) is changed to the other pyrimidine.
• A transversion mutation is a mutation from a purine–pyrimidine base pair to a pyrimidine–purine
base pair, such as G–C to C–G. Specifically, this means that the purine on one strand of the DNA is
changed to a pyrimidine while the pyrimidine on the complementary strand is changed to the purine
that base pairs with the altered pyrimidine (G in this example).
B. A missense mutation is a gene mutation in which a base-pair change causes a change
in an mRNA codon so that a different amino acid is inserted into the polypeptide. A
phenotypic change may or may not result, depending on the amino acid change involved.
2. A nonsense mutation is a gene mutation
in which a base-pair change alters an mRNA
codon for an amino acid to a stop (non sense)
codon (UAG, UAA, or UGA). A nonsense
mutation causes premature termination of
polypeptide chain synthesis, so shorter-than
normal polypeptide fragments (often non
functional) are released from the ribosomes.
3. A neutral mutation is a base-pair change in a gene that changes a codon in the mRNA such that
the resulting amino acid substitution produces no detectable change in the function of the protein
translated from that message.
A neutral mutation is a subset of missense mutations in which the new codon codes for a different
amino acid that is chemically equivalent to the original or the amino acid is not functionally important
and therefore does not affect the protein’s function. Consequently, the phenotype does not change. In
the example below an AT-to-GC transition mutation changes the codon from AAA (lysine) to AGA
(arginine). Because arginine and lysine have similar properties —both are basic amino acids—the
protein’s function may not alter significantly.
4. A silent mutation —also known as a synonymous mutation—is a mutation that changes a
base pair in a gene, but the altered codon in the mRNA specifies the same amino acid in the
protein. In this case, the protein obviously has a wild-type function. For example, in the example
below, a silent mutation results from an AT-to-GC transition mutation that changes the codon
from AAA to AAG, both of which specify lysine.
5. Frameshift mutation: If one or more base pairs are added to or deleted from a proteincoding gene, the reading frame of an mRNA can change downstream of the mutation. An addition
or deletion of one base pair, for example, shifts the mRNA’s downstream reading frame by one
base so that incorrect amino acids are added to the polypeptide chain after the mutation site.
This usually results in a non functional protein. Frameshift mutations may generate new stop
codons, resulting in a shortened polypeptide; they may result in longer-than-normal proteins
because the normal stop codon is now in a different reading frame; or they may result in a
significant alteration of the amino acid sequence of a polypeptide. In the example below, an
insertion of a G–C base pair scrambles the message after the codon specifying glutamine.
CLASSIFICATION OF MUTATIONS
Mutations can be classified according to different criteria.
• cause (spontaneous vs. induced)
• effect on DNA (point vs. chromosomal, substitution vs. insertion/deletion,
transition vs. transversion)
• effect on an encoded protein (nonsense, missense, neutral, silent, and
frameshift.
SPONTANEOUS AND INDUCED
MUTATIONS
• Spontaneous mutations are naturally occurring mutations.
• Induced mutations occur when an organism is exposed either deliberately or accidentally to
a physical or chemical agent, known as a mutagen, that interacts with DNA to cause a
mutation. Induced mutations typically occur at a much higher frequency than do
spontaneous mutations.
SPONTANEOUS MUTATIONS.
• All types of point mutations occur spontaneously.
• Spontaneous mutations can occur during DNA replication, as well as during other stages of
cell growth and division.
• In humans, the spontaneous mutation rate for individual genes varies between 104 and 4x106
per gene per generation. Most spontaneous errors are corrected by cellular repair systems,
only some errors remain uncorrected as permanent changes.
CAUSES OF SPONTANEOUS MUTATION
DNA Replication Errors
• Base-pair substitution mutations—point mutations
involving a change from one base pair to another—can
occur if mismatched base pairs form during DNA
replication. non–Watson-Crick base pairing can result if a
base is in a rare tautomeric state, the enol form. Here, the
rare form of G forms a mismatched base pair with T in the
template strand of the DNA. If this mismatch is not
repaired, a GC-to-AT transition mutation is produced after
replication
Spontaneous Chemical Changes.
• Depurination and deamination of particular bases are two common chemical events that
produce spontaneous mutations. These events create damaged sites in the DNA.
• Depurination is the loss of a purine from the DNA when the bond hydrolyzes between the
base and the deoxyribose sugar, resulting in an apurinic site. Depurination occurs because the
covalent bond between the sugar and purine is much less stable than the bond between the
sugar and pyrimidine and is very prone to breakage.
• A mammalian cell typically loses thousands of purines in an average cell generation period. If
such damages are not repaired, there is no base to specify a complementary base during DNA
replication, and the DNA polymerase may stall or dissociate from the DNA.
• Deamination is the removal of an amino group from a base. For example, the deamination
of cytosine produces uracil, which is not a normal base in DNA, although it is a normal base
in RNA.
• A repair system replaces most of the uracils in DNA, thereby minimizing the mutational
consequences of cytosine deamination. However, if the uracil is not replaced, an adenine will
be incorporated into the new DNA strand opposite it during replication, eventually
resulting in a CG-to-TA transition mutation
INDUCED MUTATIONS
• Mutations can be induced by exposing organisms to physical mutagens, such as radiation, or to
chemical mutagens.
• Deliberately induced mutations have played, and continue to play, an important role in the
study of mutations. Since the rate of spontaneous mutation is so low, geneticists use mutagens
to increase the frequency of mutation so that a significant number of organisms have
mutations in the gene being studied.
Radiation
• UV light causes mutations by increasing the chemical energy of certain molecules, such as
pyrimidines, in DNA. One effect of UV radiation on DNA is the formation of abnormal
chemical bonds between adjacent pyrimidine molecules in the same strand of the double
helix.
• This bonding is induced mostly between adjacent thymines, forming what are called thymine
dimers usually designated T^T. (C^C, C^T, and T^C pyrimidine dimers are also produced by
UV radiation but in much lower amounts.) This unusual pairing produces a bulge in the DNA
strand and disrupts the normal pairing of T bases with corresponding A bases on the
opposite strand. Replication cannot proceed past the bulge, so the cell will die if enough
pyrimidine dimers remain unrepaired
CHEMICAL MUTAGENS.
• Chemical mutagens include both naturally occurring chemicals and synthetic substances. These
mutagens can be grouped into different classes based on their mechanism of action.
• Base analogs are bases that are similar to those normally found in DNA. Like normal bases, base
analogs exist in normal and rare tautomeric states. In each of the two states, the base analog pairs with
a different normal base in DNA.
• One base analog mutagen is 5-bromouracil (5BU), which has a bromine residue instead of the methyl
group of thymine. In its normal state, 5BU resembles thymine and pairs with adenine in DNA. In its rare
state, it pairs with guanine. 5BU induces mutations by switching between its two chemical states once
the base analog has been incorporated into the DNA.
• If 5BU is incorporated in its normal state, it pairs with
adenine. If it then changes into its rare state during
replication, it pairs with guanine instead. In the next
round of replication, the 5BU–G base pair is resolved
into a C–G base pair instead of the T–A base pair. By
this process, a TA-to-CG transition mutation is
produced. 5BU can also induce a CG-to-TA transition
mutation if it is first incorporated into DNA in its rare
state and then switches to the normal state during
replication.
• Base-modifying agents are chemicals that act as mutagens by modifying the chemical structure and
properties of bases. a deaminating agent, a hydroxylating agent, and an alkylating agent.
• Nitrous acid, is a deaminating agent that removes amino groups (-NH2) from the bases guanine, cytosine,
and adenine. Treatment of guanine with nitrous acid produces xanthine, but because this purine base has the
same pairing properties as guanine, no mutation results. Treatment of cytosine with nitrous acid produces
uracil, which pairs with adenine to produce a CG-to-TA transition mutation during replication.
• Likewise, nitrous acid modifies adenine to produce hypoxanthine, a base that pairs with cytosine rather than
thymine, which results in an AT-to-GC transition mutation.
Intercalating agents
• Examples are acridine, and ethidium bromide (commonly used to stain
DNA in gel electrophoresis experiments)—insert (intercalate)
themselves between adjacent bases in one or both strands of the DNA
double helix, causing the helix to relax. If the intercalating agent inserts
itself between adjacent base pairs of the DNA strand that is the template
for new DNA synthesis, an extra base (chosen at random; G in the figure)
is inserted into the new DNA strand opposite the intercalating agent.
• After one more round of replication, during which the intercalating agent
is lost, the overall result is a base-pair addition mutation. (C–G is added)
If the intercalating agent inserts itself into the new DNA strand in place
of a base, then when that DNA double helix replicates after the
intercalating agent is lost, the result is a base-pair deletion mutation. (T–A
is lost). If a base-pair addition or base-pair deletion point mutation occurs
in a protein-coding gene, the result is a frameshift mutation.
• Environmental Mutagens
• Every day, we are heavily exposed to a wide variety of chemicals in our environment. The chemicals
may be natural ones, such as those synthesized by plants and animals that we eat as food, or manmade ones, such as drugs, cosmetics, food additives, pesticides, and industrial compounds.
• Our exposure to chemicals occurs primarily through eating food, absorption through the skin, and
inhalation. Many of these chemicals are mutagenic. For a mutagenic chemical to cause DNA changes,
it must enter cells and penetrate to the nucleus, which many chemicals cannot do.
• Some chemicals are converted from non-mutagenic to mutagenic by our metabolism. That is, when
these chemicals are directly tested for mutagenic activity on, say, a bacterial species, no mutations
result. But, after they are processed in the body, they become mutagens. For example, benzopyrene,
a polycyclic aromatic hydrocarbon found in cigarette smoke, coal tar, automobile exhaust fumes, and
charbroiled food, is non-mutagenic. But its metabolite, benzopyrene diol epoxide, which is both a
mutagen and a carcinogen, can induce cancer.
Repair of DNA Damage
• There are two general categories of repair systems, based on the way they function.
• Direct reversal repair systems correct damaged areas by reversing the damage
• Excision repair systems cut out a damaged area and then repair the gap by new DNA synthesis.
1. Direct Reversal Repair of DNA Damage
a. Mismatch Repair by DNA Polymerase Proofreading
When an incorrect nucleotide is inserted, the polymerase often detects the mismatched base
pair and corrects the area by “backspacing” to remove the wrong nucleotide and then resuming
synthesis in the forward direction.
b. Repair of UV-Induced Pyrimidine Dimers. Through photoreactivation, or light repair, UV
light-induced thymine (or other pyrimidine) dimers are reverted directly to the original form by
exposure to near-UV light in the wavelength range from 320 to 370 nm. Photoreactivation
occurs when an enzyme called photolyase is activated by a photon of light and splits the dimers
apart.
2. Excision Repair of DNA Damage
Many mutations affect only one of the two strands. In such cases, the DNA damage can be excised and
the normal strand used as a template for producing a corrected strand. Depending on the damage,
excision may involve a single base or nucleotide, or two or more nucleotides. Each excision repair system
involves a mechanism to recognize the specific DNA damage it repairs.
a, Base Excision Repair. Damaged single bases or nucleotides are most commonly repaired by
removing the base involved and then inserting the correct base. A repair glycosylase enzyme removes the
damaged base from the DNA by cleaving the bond between the base and the deoxyribose sugar. Other
enzymes then cleave the sugar–phosphate backbone before and after the now baseless sugar, releasing
the sugar and leaving a gap in the DNA chain. The gap is filled with the correct nucleotide by a repair
DNA polymerase and DNA ligase, with the opposite DNA strand used as the template. Mutations
caused by depurination or deamination are examples of damage that may be repaired by base excision
repair
• Nucleotide Excision Repair. This was discovered in isolated
mutants of E. coli that, after UV irradiation, showed a higher
than normal rate of induced mutation in the dark. These UVsensitive mutants were called uvrA mutants (uvr for “UV
repair”). The uvrA mutants can repair thymine dimers only
with the input of light, meaning they have a normal
photoreactivation repair system. However, uvr (wild-type) E.
coli can repair thymine dimers in the dark. Because the normal
photoreactive repair system cannot operate in the dark, the
investigators hypothesized that there must be another lightindependent repair system. They called this system the dark
repair or excision repair system, now typically referred to as
the nucleotide excision repair (NER) system. The NER system
in E. coli also corrects other serious damage-induced
distortions of the DNA helix.