Although distinctly different from each other, DNA damage and mutation are related because DNA damage often causes errors of DNA synthesis during replication or repair; these errors are a major source of mutation. Given these properties of DNA damage and mutation, it can be seen that DNA damage is a special problem in non-dividing or slowly-dividing cells, where unrepaired damage will tend to accumulate over time.
On the other hand, in rapidly-dividing cells, unrepaired DNA damage that does not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell's survival.
Thus, in a population of cells composing a tissue with replicating cells, mutant cells will tend to be lost. However, infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer.
Thus, DNA damage in frequently dividing cells, because it gives rise to mutations, is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging. Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information.
Without access to a template, cells use an error-prone recovery mechanism known as translesion synthesis as a last resort. Damage to DNA alters the spatial configuration of the helix, and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place.
Direct reversal[ edit ] Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of the four bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone. The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases.
Another type of damage, methylation of guanine bases, is directly reversed by the protein methyl guanine methyl transferase MGMT , the bacterial equivalent of which is called ogt. This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic. However DNA polymerase inserts incorrect nucleotide at frequency of Most of the difference between the two values is accounted for by the 3' to 5' exonuclease proofreading activity of the DNA polymerase in both bacteria and eukaryotes.
When an incorrect nucleotide is inserted, the polymerase detects the mismatched base pairs and corrects the area by back spacing to remove the wrong nucleotide and then resuming synthesis in the forward directions. Mutator mutants have much higher than normal mutation frequency for all genes. These mutants have mutations in genes for proteins whose normal functions are required for accurate DNA replication.
For example mut D mutator gene of E. The mut D mutants are defective in 3' to 5' proofreading activity, so that many incorrectly inserted nucleotide are left unrepaired . Repair of UV induced pyrimidine dimers. Through photo reactivation or light repair, UV light induced thymine other pyrimidines dimmers are reverted directly to the original form by exposure to near-UV light in the wavelength range from to nm.
Photo reactivation occurs when an enzyme called photolyase is activated by a photon of light and splits the dimmers apart.
Photolyase has been found in bacteria and in simple eukaryotes but not in humans . Repaired of alkylation damage Alkylating agents transfer alkyl groups usually methyl or ethyl groups onto the bases. The mutagen MMS methylates the oxygen of carbon 6 in guanine. This enzyme remove methyl group from guanine thereby changing the base back ti its original form. Similar specific system exist to repair alkylated thymine. Mutations of the genes encoding this repair enzymes results in a much higher rate of spontaneous mutation .
Methyl Directed Mismatch Repair Dispite prrofreading of DNA polymerase, a number of mismatched base pair remain uncorrected after replication has been completed.
In the next round of replication this errors will become fixed as mutations if they are not repaired. This system recognizes mismatched base pairs, excises the incorrect bases, and then carry out repair synthesis .
Single-strand damage[ edit ] Structure of the base-excision repair enzyme uracil-DNA glycosylase excising a hydrolytically-produced uracil residue from DNA. The uracil residue is shown in yellow. When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand.
In base excision repair, repair glycosylases  enzyme removes the damaged base from the DNA by cleaving the bond between base and deoxyribose sugars.
These enzymes remove a single nitrogenous base to create an apurinic or apyrimidinic site AP site. The gap is then sealed by enzyme DNA ligase . Nucleotide excision repair NER repairs damaged DNA which commonly consists of bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light.
Damaged regions are removed in 12—24 nucleotide-long strands in a three-step process which consists of recognition of damage, excision of damaged DNA both upstream and downstream of damage by endonucleases , and resynthesis of removed DNA region.
These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. This is followed by removal of damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase. It was noted in some studies that double-strand breaks and a "cross-linkage joining both strands at the same point is irreparable because neither strand can then serve as a template for repair.
The cell will die in the next mitosis or in some rare instances, mutate. If these overhangs are compatible, repair is usually accurate. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms insertions or translocations.
NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid available in G2 after DNA replication or a homologous chromosome as a template.
DSBs caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion cause collapse of the replication fork and are typically repaired by recombination. MMEJ starts with short-range end resection by MRE11 nuclease on either side of a double-strand break to reveal microhomology regions.
There is pairing of microhomology regions followed by recruitment of flap structure-specific endonuclease 1 FEN1 to remove overhanging flaps. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until they find complementary partner strands. In the final step there is crossover by means of RecA -dependent homologous recombination.
Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them. DNA polymerase IV or V, from the Y Polymerase family , often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides.
The polymerase switching is thought to be mediated by, among other factors, the post-translational modification of the replication processivity factor PCNA. If left uncorrected, these adducts, after misreplication past the damaged sites, can give rise to mutations. In nature, the mutations that arise may be beneficial or deleterious—this is the driving force of evolution. An organism may acquire new traits through genetic mutation, but mutation may also result in impaired function of the genes, and in severe cases, cause the death of the organism.
Mutation is also a major source for acquisition of resistance to antibiotics in bacteria and possibly to antifungal agents in yeasts. Initially, the ability of radiation and chemical mutagens to cause mutation was exploited to generate random mutations, but later techniques were developed to introduce specific mutations.
Humans on average naturally pass 60 new mutations to their children but fathers pass more mutations depending on their age, transmitting an average of two new mutations with every additional year of their age to the child. In contrast, a mutation is a change in the nucleic acid sequence that can be replicated; hence, a mutation can be inherited from one generation to the next.
Damage can occur from chemical addition adduct , or structural disruption to a base of DNA creating an abnormal nucleotide or nucleotide fragment , or a break in one or both DNA strands. The incorrect insertion in the new strand will occur opposite the damaged site in the template strand, and this incorrect insertion can become a mutation i.
Furthermore, double-strand breaks in DNA may be repaired by an inaccurate repair process, non-homologous end joining , which produces mutations. Mutations can ordinarily be avoided if accurate DNA repair systems recognize DNA damage and repair it prior to completion of the next round of replication. Mechanisms[ edit ] Mutagenesis may occur endogenously, for example, through spontaneous hydrolysis, or through normal cellular processes that can generate reactive oxygen species and DNA adducts, or through error in replication and repair.
The mechanism by which mutation arises varies according to the causative agent, the mutagen , involved. Most mutagens act either directly, or indirectly via mutagenic metabolites, on the DNA producing lesions. Some, however, may affect the replication or chromosomal partition mechanism, and other cellular processes. Mutagenesis may also be self-induced by unicellular organisms when environmental conditions are very restrictive, for instance, in presence of toxic substances like antibiotics or, in yeasts, in presence of an antifungal agent or in absence of a nutrient    Many chemical mutagens require biological activation to become mutagenic.
An important group of enzymes involved in the generation of mutagenic metabolites is cytochrome P Mutagens that are not mutagenic by themselves but require biological activation are called promutagens. Many mutations arise as a result of problems caused by DNA lesions during replication, resulting in errors in replication. This induces the SOS response , an emergency repair process that is also error-prone, thereby generating mutations. In mammalian cells, stalling of replication at damaged sites induces a number of rescue mechanisms that help bypass DNA lesions, but which also may result in errors.
The Y family of DNA polymerases specializes in DNA lesion bypass in a process termed translesion synthesis TLS whereby these lesion-bypass polymerases replace the stalled high-fidelity replicative DNA polymerase, transit the lesion and extend the DNA until the lesion has been passed so that normal replication can resume. These processes may be error-prone or error-free.
Spontaneous hydrolysis[ edit ] DNA is not entirely stable in aqueous solution. Under physiological conditions the glycosidic bond may be hydrolyzed spontaneously and 10, purine sites in DNA are estimated to be depurinated each day in a cell. Adenine is preferentially incorporated by DNA polymerases in an apurinic site.
Cytidine may also become deaminated to uridine at one five-hundredth of the rate of depurination and can result in G to A transition. Eukaryotic cells also contain 5-methylcytosine , thought to be involved in the control of gene transcription, which can become deaminated into thymine.
Modification of bases[ edit ] Bases may be modified endogenously by normal cellular molecules. For example, DNA may be methylated by S-adenosylmethionine , and glycosylated by reducing sugars.
Many compounds, such as PAHs, aromatic amines , aflatoxin and pyrrolizidine alkaloids , may form reactive oxygen species catalyzed by cytochrome P These metabolites form adducts with the DNA, which can cause errors in replication, and the bulky aromatic adducts may form stable intercalation between bases and block replication. The adducts may also induce conformational changes in the DNA. Some adducts may also result in the depurination of the DNA;  it is, however, uncertain how significant such depurination as caused by the adducts is in generating mutation.
Some alkylating agents such as N- Nitrosamines may require the catalytic reaction of cytochrome-P for the formation of a reactive alkyl cation.
For example, cells isolated from a human astrocytoma , a type of brain tumor, were found to have a chromosomal deletion removing sequences between the Fused in Glioblastoma FIG gene and the receptor tyrosine kinase ROS , producing a fusion protein FIG-ROS. When DNA polymerase encounters an abasic site, DNA replication is usually blocked, which may itself lead to a single-stranded or double-stranded break in the DNA helix. Early methods of mutagenesis produced entirely random mutations; however, later methods of mutagenesis may produce site-specific mutation. This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. If only a single nucleotide is affected, they are called point mutations.
Based on the occurrence of mutation on each chromosome, we may classify mutations into three types. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired.
This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. A synonymous substitution replaces a codon with another codon that codes for the same amino acid, so that the produced amino acid sequence is not modified. Aldehydes containing O-HN2 groups can serve to stabilize the abasic site by reacting with the aldehyde group. Allen Orr.
Such genome wide transcriptional response is very complex and tightly regulated, thus allowing coordinated global response to damage. By effect on function[ edit ] Loss-of-function mutations, also called inactivating mutations, result in the gene product having less or no function being partially or wholly inactivated. In multicellular organisms with dedicated reproductive cells , mutations can be subdivided into germline mutations , which can be passed on to descendants through their reproductive cells, and somatic mutations also called acquired mutations ,  which involve cells outside the dedicated reproductive group and which are not usually transmitted to descendants.
Mitochondrial DNA mtDNA is located inside mitochondria organelles , exists in multiple copies, and is also tightly associated with a number of proteins to form a complex known as the nucleoid. The uracil residue is shown in yellow. Deletions remove one or more nucleotides from the DNA. Some natural occurring chemicals may also promote crosslinking, such as psoralens after activation by UV radiation, and nitrous acid.
A new germline mutation not inherited from either parent is called a de novo mutation. DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. Methyl Directed Mismatch Repair Dispite prrofreading of DNA polymerase, a number of mismatched base pair remain uncorrected after replication has been completed. Biological activity[ edit ] AP sites in living cells can cause various and severe consequences, including cell death. Through photo reactivation or light repair, UV light induced thymine other pyrimidines dimmers are reverted directly to the original form by exposure to near-UV light in the wavelength range from to nm. These reactions can further promote phosphoester bond cleavage.
Irradiated environments contain radicals, which can contribute to AP sites in multiple ways. Mutations can ordinarily be avoided if accurate DNA repair systems recognize DNA damage and repair it prior to completion of the next round of replication. Several of Muller's morphs correspond to gain of function, including hypermorph and neomorph.