Genetic Analysis: Chapter 12 (Gene Mutation, DNA Repair, and Homologous Recombination)

Two types of base pair substitutions that can occur.

1. Transition Mutation - in which one purine replaces the other (A replaces G, or vice versa) or one pyrimidine replaces the other (C replaces T or vice versa). 2. Transversion Mutations - in which a purine is replaced by a pyrimidine, or vice versa.

Three types of Reverse mutation or reversion

1. True reversion - the wild type DNA sequence is restored to encode its original message by a second mutation at the same site or within the same codon 2. Intragenic reversion - a reversion that occurs through mutation elsewhere in the same gene 3. Second-site reversion - a reversion produced by mutation in a different gene; also known as: suppressor mutations because the second mutation, by restoring wild type appearance, and be said to suppress the mutant phenotype generated by the first mutation

Steps of NHEJ (4 steps)

1. ds breaks are recognized by a protein complex that attaches to each of the broken ends of the DNA duplex. 2. The complex then trims back the free ends of each broken strand. 3. Reaction leaves blunt ends on each side of the break. 4. The blunt ends are ligated by ligase lV. Completion of NHEJ produces an intact DNA duplex and allows replication across the repaired region in the upcoming replication cycle, although reaction removes nucleotides that cannot be replaced.

Gene conversion

A process of directed DNA sequence change that occurs by base pair mismatch repair within heteroduplex DNA.

Alkylating agents

Add bulky side groups such as methyl (CH3) and ethyl (CH3-Ch3) groups to nucleotide bases. These added groups are called bulky adducts. -Ethyl methanesulfonate is a powerful alkylating agent that adds an ethyl group to thymine or to guanine -Bulky adducts - interfere with normal DNA base pairing and may distort the DNA double helix.

Nonhomologous end joining (NHEJ)

Allows cells to reacquire the capability to full replicate their genome, although the process inevitably leads to mutation.

Spontaneous mutations

Arise in cells without being induced by exposure of DNA to a physical, chemical, or biological agent capable of creating DNA damage. These mutations arise primarily through errors in DNA replication and through spontaneous changes in the chemical structure of nucleotide bases.

Average mutation rates

As low as 1x10^-9 to as high as 1x10^-4

The p53 pathway

Controls cellular response to mutation by deciding either: 1. To pause the cell cycle at the G1-to-S transition to allow time for mutation repair. 2. To direct the cell to undergo programmed cell death

Hotspots of mutation

Individual genes or regions of genomes where mutations occur much often than average

Mutation rate

Measured as the number of times mutation alters a particular gene per replication cycle or per generation.

Regulatory Mutations

Occur in noncoding regions of genes, such as promoters, intron, and regions coding 5'-UTR and 3'-UTR segments of mRNA. None of these regions directly encodes amino acids, but mutations in these regions can lead to the production of abnormal mRNAs that, in turn, produce mutant proteins. There are four types.

Induces mutations

Produced be interaction between DNA and a physical, chemical, or biological agent that generates damage resulting in mutation.

Trinucleotide Repeat Disorders

Strand slippage mutations that cause a variety of hereditary diseases in humans and other organisms. -The wild-type alleles of the genes in question normally have a variable number of DNA Trinucleotide repeats -Expansion of the number of Trinucleotide repeats caused by strand slippage blocks the production of wild-type protein.

Mutagens

The agents generating mutation-inducing DNA damage.

Homologous recombination

The exchange of genetic material between homologous molecules of DNA. *All organisms undertake homologous recombination

Mutation Rate in sexually reproducing diploids

The number of mutational events in a given gene per generation

Point mutations

These kinds of localized mutations occur at a specific or identifiable location in a gene

SOS repair

This is a last ditch effort to repair dying cell. SOS repair is accomplished by activating specialized DNA polymerases in a process known as translesion DNA synthesis.

UV-Induced DNA damage and mutation (Photoproducts)

UV irradiation alters DNA nucleotides by inciting the formation of addition bonds that form aberrant structures called photoproducts (cause DNA replication to stall)

The formation of heteroduplex DNA for alleles A1 and A2 that differ by substitution on one base pair

a) A segment of allele A1 contains a C-G base pair, whereas allele A2 contains an A-T base pair at the same location. Segregation produces a 2:2 ascus. b) Crossover between homologous chromosomes generates heteroduplex DNA containing G-A and C-T base pair mismatches between the otherwise complementary strands.

Synthesis-dependent strand annealing (SDSA)

ds breaks that can be repaired after replication by exploiting the intact sister chromatid to repair the damaged chromatid in an error free repair process.

Mutation Rate in bacteria and other haploid organisms

measured as the number of times mutation alters a particular gene per replication

Opposite sense resolution

-A resolution in which one Holliday junction is resolved by a NS cut and the other by an EW cut is much more common. -The resulting chromosomes are recombinant, and lead to production of recombinant progeny.

Same sense resolution

-Involves either two north south (NS) resolution cuts or two east west (EW) resolution cuts. (rarely occurs) -Flanking markers do not recombine though heteroduplex regions remain.

Direct repair of UV-induced photoproducts (2 types)

-UV radiation is the most common mutagen for most organisms. -Organisms have a variety of ways to identify and repair UV-induced DNA damage (Thymine dimers) 1. Photoreactive repair - (does not exist in humans) 2. UV repair

Gene conversion process (3 steps)

1. Directed Change is base pair mismatch repair that switches the nucleotide sequence of one allele to that of another allele that is already present because the organism is heterozygous in the portion of the genome where heteroduplex DNA forms. 2. It is most readily detected in fungi that form an ascus, a sack of haploid spores that are the products of meiosis. 3. Gene conversion is detected by the production of aberrant ratios of spores in the eight celled ascus, 5:3 OR 6:2 rather than the expected 4:4.

Direct Repair of DNA Damage (4 types)

1. Mismatch Repair 2. Nucleotide Base Excision Repair 3. Nucleotide Excision Repair 4. Direct Repair of UV-Induced Photoproducts

Pyrimidine dimer (2 types)

1. Thymine dimer: has two covalent bonds joining the 5 and 6 carbons of adjacent thymine's in the same DNA strand. 2. 6-4 photoproduct: also joins adjacent thymine's by formation of a bond between the 6 carbon of one thymine and the 4 carbon on the other thymine. -Either of these dimeric complexes can also involve the other pyrimidine, cytosine. -The formation of these dimers distorts DNA by pulling the dimerized nucleotide bases closer together and disrupting hydrogen bond formation with their complementary nucleotides on the opposite strand.

Gene mutations

A change in DNA sequence - substituting, adding, or deleting one or more DNA base pairs

Nucleotide base analogs

A chemical compound that has a structure similar to one of the DNA nucleotide bases -They can work it way into DNA and pair with nucleotide base in the DNA duplex-DNA polymerases cannot distinguish these analogs from normal nucleotide bases due to their similarity in molecular size and shape. -For example; 5-bromodeoxyuridine acts as a analog of thymine.

Hydroxylating agents

Adds a hydroxyl (OH) group to a recipient compound -Hydroxylamine adds a hydroxyl group to cytosine, creating hydroxylaminocytosine, which often pairs with guanine but frequently mispairs with adenine, creating C-G to T-A transition mutations.

Holliday Junction Resolution

Connections between homologs must be resolved before metaphase: Bacteria use RuvAB and RuvC Eukaryotes use Rad51c-XRCC3 Archaea use proteins with closer homology to eukaryotes. Two resolution patterns occur: 1. Same sense resolution (rarely occurs) 2. Opposite sense resolution (more common)

Reverse mutation or reversion

Converts a mutation to a wild type or near wild type state, there are several types

Forward mutation "mutation"

Converts a wild type allele to a mutant allele

Homologous recombination in bacteria and archaea

Homologous recombination occurs during events such as conjugation and as a consequence of the repair of ds breaks.

Frame shift Mutations

Mutant polypeptide contains an altered amino acid sequence from the point of mutation to the end of the polypeptide. Results in the complete loss of protein function and thus produces null alleles. Insertion or deletion of one or more base pairs in the coding sequence of a gene leads to addition or deletion of mRNA nucleotides, altering the reading frame of the codon sequence, beginning at the point of mutation.

Deaminating agent

Nitrous acid (HNO2) removes an amino group from any nucleotide, and in most cases, deamination produces no mutagenic effect. -Deamination of 5-methylctosine leads to a G-C to A-T base pair substitution -Deamination of adenine produces hypoxanthine, which can mispairs with cytosine and lead to an A-T to G-C base pair substitution mutation

Type of Photoproduct

Pyrimidine dimers-are produced by the formation of one or two additional covalent bonds between adjacent pyrimidine dinucleotides in the strand of DNA

DNA damage repair disorders

Resulting from mutations in genes that participate in DNA damage repair or in the signaling or initiating of damage repair, cause an organism to be highly sensitive to chemical mutagens

Translesion DNA Synthesis

Short lived process that allows DNA replication by alternative polymerases (Pol V) across lesion that block the action of DNA Pol lll, the main DNA-replicating polymerase in E. coli.

The Bacterial RecBCD Pathway

The RecBCD pathway is the system of homologous recombination in bacteria. 1. It relies on DNA ds breaks to initiate the process which attracts the RecA protein ( a homolog of the eukaryotic and archaeal protein Rad51). 2. The multiprotein complex-RecBCD then attaches to the region of a bacterial chromosome with bound RecA, promoting single strand invasion and D loops formation (similar to that seen in SDSA) 3. RecBCD activity is followed by binding of RuvAB and RuvC and the Ruv complex completes the homologous recombination between the bacterial DNA.

Homologous recombination in eukaryotes

Whereas a limited amount of homologous recombination takes place during mitosis, recombination between homologous chromosomes is essential in prophase 1 of meiosis. Homologous recombination during meiosis in initiated by controlled ds DNA breaks.

Mismatch Repair

-Base pair mismatches, such as those generated by tautomeric shifts of nucleotide bases, can be detected by mismatch repair. -Repair enzymes must be able to distinguish between the original DNA strand, with the correct nucleotide, and the new DNA strand with the mismatched nucleotide, which is accomplished by the sensitivity of mismatch repair enzymes to methylation of specific nucleotides in the original DNA strand. -In E. coli, methylation is particularly common on adenine of 5'-GATC-3' sequences.

DNA Damage Signaling Systems

-Biochemical mechanisms to recognize DNA damage and initiate a damage repair response consist of tightly regulated genetic processes involving numerous genes and proteins. -In humans and other animals, a multiprotein complex acts as a genomic sentry to identify damage -This damage response process is active throughout the cell cycle and is especially important in regulating the G1-to-S transition.

Gene conversion begins with Heteroduplex DNA

-Biologists studying conversion realized that the aberrant allele ratios sometimes observed could only occur if heteroduplex DNA formed during crossing over. -Heteroduplex DNA can include nucleotide mismatches -Different ratios can result from a heteroduplex, depending on how the mismatches are repaired.

DNA intercalating agents

-DNA intercalating agents can squeeze their way between DNA base pairs. -They can find their way between base pairs and distort in the DNA duplex; they can attach to nucleotide bases to form bulky adducts that contribute to DNA distortion. -These distortions lead to DNA strand nicking that is not efficiently repaired, resulting in frameshift mutations due to gain or loss of one or more nucleotides.

Spontaneous Nucleotide Base Changes

-DNA nucleotide bases are organic chemical structures that can occasionally convert to alternative structures called tautomers (the same composition and general arrangement but a slight difference in bonding and placement of a hydrogen -It changes the three-dimensional structure of the nucleotide base: more stable common form to rare, less stable. -Tautomeric shifts - affecting nitrogenous bases can lead to base-pair mismatich between a rare tautomer on one DNA strand and a common form on the complementary strand. -This is the most common form of DNA replication error.

Consequences of the formation of photoproducts

-DNA repair systems of most organisms can identify and correct most pyrimidine dimers. -Those that are not repaired cause disruption of replication because when DNA polymerase encounters thymines in a dimer on the template strand, it attempts to add complementary adenines to the nascent DNA strand. But he first adenine fails to form the necessary hydrogen bonds, because the placement of its complementary partner is distorted. It attempts to add the second adenine and resume synthesis in the thymine dimer region-but with the same negative result. -Continued repetition of these unsuccessful attempts to replicate across the thymine dimer causes replication to stall at this point.

DNA Replication Errors

-DNA replication has a very high fidelity due to the proofreading ability of DNA polymerases and the operation of DNA base-pair mismatch repair systems. -Genomic regions containing short repetitive sequences whose number can be either increased or decreased by replication errors. -Replication errors in such regions are another source of hotspots of mutation.

Radiation Induced DNA Damage

-Electromagnetic energy is conveyed in waves, or rays, and categorized by its wavelength -One category of electromagnetic energy is visible light: wavelengths 750nm to 380nm -All forms of radiant energy with wavelength less than 380nm can cause DNA damage and are mutagenic, including ultraviolet radiation, X-rays, gamma rays, and cosmic energy.

Translesion synthesis in eukaryotes

-In eukaryotes, bypass polymerases are always present in cells and the regulatory mechanism guiding the choice of polymerase decides which polymerase binds to PCNA, the eukaryotic sliding clamp. -When replication stalls at a DNA lesion, Rad 6 protein that is always present at the replication form adds a ubiquitin (Ub) group to PCNA, which causes an alteration of conformation, giving the bypass polymerase a strong affinity for ubiquitinated PCNA. (bypass polymerase Rad 6 recruits PCNA instead of Pol V like in eukaryotes) -Bypass polymerase displaces normal DNA polymerase and carries out translesion synthesis of DNA in a error prone manner as well.

Other types of radiation

-Irradiation that has higher energy than that of UV waves includes X-rays and radioactive materials -These can cause DNA damage in multiple ways, the most serious being the induction of DNA single strand or double strand breaks. -These breaks potentially block DNA replication and thus pose a significant threat to the integrity and survival of affected cells.

DNA Repeat Mutations

-Mutations altering the number of DNA repeats occur via strand slippage. -The DNA polymerase of the replisome temporarily dissociates from the template strand as it moves across a region of repeating DNA sequence -During dissociation, a portion of newly replicated DNA forms a temporary hairpin structure. -Reasssociation of DNA polymerase and resumption of replication leads to re-replication of a portion of the repeat region, increasing the length of the repeat region in the daughter strand.

Oxidizing agents (Oxidative reactions)

-Oxidation is a chemical process of electron transfer by addition of an oxygen atom or removal of an atom of hydrogen. -Oxidizing agents such as bleach and hydrogen peroxide, cause oxidative reactions that can lead to mutations -For example; oxidized guanine can mispairs with adenine, leading to a transversion mutation (G-C to T-A)

The Holliday Model (2 important features)

-Proposed by Robin Holliday in 1964 1. The meiotic recombination is now known to be initiated by double stranded DNA breaks. 2. The double stranded breaks initiating meiotic recombination are generated in a programmed manner by the activity of a specialized enzyme.

The Double Stranded Break Model of Meiotic Recombination

-Proposed by Szostak that the creation of ds breaks controlled by the activity of a specific protein was the foundation of meiotic recombination. 1. Meiotic recombination is initiated by the protein Spo11. 2. Spo11 is a dimeric protein that generates asymmetric ds cuts in one chromatid, then the proteins Mrx and Exo1 associate with Spo11. 3. Spo11 degrades; Mrx and associated proteins (homologs of RecBCD) resect the single strands. 4. The proteins Rad51 and Dmc1 (RecA homologs) help form a strand exchange assemblage, facilitating strand invasion and formation of a D loop. 5. The heteroduplex is ds DNA formed from DNA of different homologs and it may contain nucleotide mismatches. 6. The invading strand is extended with DNA synthesis guided by the intact template strands assisted by RecBCD homologs. 7. A second heteroduplex region has formed. The 3' end of the invading strand next connects with the 5' end of a strand segment that was initially part of the invading strand, to form a second Holliday junction. 8. The nonsister chromatids of the recombining chromosomes are interconnected by double Holliday junctions (DHJs).

Photoreactive repair (phr)

-Pyrimidine dimers can be directly repaired by Photoreactive repair in bacteria, single celled eukaryotes, plants and some animals (not in humans) -The enzyme photolyase uses visible light energy to break the bonds formed during pyrimidine dimerization -In E. Coli, photolyase is encoded by the Photoreactive (phr) repair gene, mutations of which result in a substantial increase in UV-induced mutations in bacteria.

Overcoming the problems caused by photoproducts

-Replication blockage by pyrimidine dimers induces reinitiation of DNA synthesis at an adjacent RNA primer site. Then reinitiation of replication potentially leaves gaps spanning dozens to hundreds of nucleotides in newly synthesized DNA strands. -The gaps are subsequently filled by translesion DNA synthesis which is carried out by specialized bypass DNA polymerases that can replicate across gaps. -These DNA polymerases lack proofreading activity so they are more prone to replication error.

The Ames Test Procedure

-Strains of Salmonella typhimurium that are his- are used. -They carry various types of mutations (frameshift or base pair substitution) affecting their ability to synthesize histidine. -The bacteria are exposed to the chemical to be tested, plus an extract of purified liver enzymes, and plated on medium lacking histidine. -A positive result, indicating that the test compound is mutagenic, is shown by a significant increase in the reversion rate in bacterial cells that have one kind of mutation over cells that have the other kind of mutation and over the spontaneous reversions rate.

Ames test

-The Ames test exposes bacteria to experimental compounds in the presence of a mixture of purified enzymes produced by the mammalian liver. -The Ames test mimics the biological defense processes that take place in the liver of animals exposed to chemical compounds and the purpose of the test is to detect whether the original compound or any of its normal breakdown products are mutagens.

Tautomeric Shifts can lead to base-pair substitution mutations

-The rare tautomer of thymine mispairs with guanine during DNA replication -A tautomeric shift of thymine switches it back to its common, more stable form, leaving a base pair mismatch of T-G. If this mismatch is not repaired, DNA replication produces one chromatid with a wild type T-A base pair and the sister chromatid with a C-G base pair substitution mutation. -This is a transition mutation: G replaces A and C replaces T.

Base Pair Substitution Mutation definition and the three types.

-The replacement of one nucleotide base pair by another. 1. Silent Mutation - a base pair substitution mutation producing an mRNA codon specifying the same amino acid as the wild-type mRNA. 2. Missense Mutation - a base pair substitution that results in an amino acid change to the protein. 3. Nonsense Mutation - a base pair substitution that creates a stop codon in place of a codon specifying an amino acid.

UV repair

-UV repair is a form of nucleotide excision repair, widely distributed among organisms from bacteria to humans to directly repair UV-induced damage to DNA -Certain proteins recognize DNA damage and other proteins remove a short region of the strand containing the photoproduct. -In E. coli, UV repair is carried out by protein products of four UV repair genes called uvr-A, uvr-B, uvr-C, and uvr-D.

Translesion synthesis; The SOS system in E. coli

-When Pol lll stalls at damaged DNA, RecA protein coats the template strand ahead of the lesion (already bound by SSB protein); this forms a DNA-RecA-SSB complex. -The active RecA also activates transcription of several genes, including pol V. -Pol V displaces Pol lll, synthesizes a short portion of the daughter strand across the DNA lesion, and is then replaced by Pol lll, which resumes its normal replication activity.

Nucleotide base excision repair

-a multistep process that identifies and removes modified bases and then replaces the entire nucleotide -DNA glycosylases recognize and remove a modified base to generate and apurinated (AP) site. -AP endonuclease then removes the remainder of the nucleotide; DNA polymerase and DNA ligase fill the nucleotide gap and seal the sugar-phosphate backbone.

Nucleotide excision repair

-repair system that recognizes and removes bulky adducts that distort DNA. -Bulky modifications such as O^6-ethylguanine and 4-ethylthymine by alkylating agents and distortions created by damage done by UV light are targeted by this repair mechanism -Enzymes recognize and bind to the damaged region, followed by removal of a short segment of nucleotides from the damaged strand. The missing nucleotides are replaced by the activity of DNA polymerase followed by that of DNA ligase.

2 key protein players in DNA Damage Signaling Systems

1. BRCA 1 - is the protein product of the first gene implicated in familial breast and ovarian cancer susceptibility 2. ATM - Plays a pivotal role in sensing DNA damage acquired through chemical or radiation exposure by serving as a signal transduction molecule to activate transcription of the p53 gene, which activates the "p53 repair pathway"

Four types of mutations

1. Base Pair Substitution Mutations (3 types) 2. Frame shift Mutations 3. Regulatory Mutations (4 types) 4. Forward Mutation and Reversion

The pattern of mismatch repair also determines the aberrant ratios in the eight celled ascus by gene conversion (3 options)

1. Both mismatch repairs favor a single allele (A1 in this case) and produces an ascus containing an aberrant 6:2 ratio. 2. Just one rather than both base pair mismatches are repaired before the DNA replication cycle and produces and ascus containing an aberrant 5:3 ratio. 3. No mismatch repair takes place. The spores are arrayed in a 3:1:1:3 pattern, a distribution called an aberrant 4:4 ratio.

Mismatch repair and gene conversion patterns in a four celled ascus (3 options)

1. Both mismatches repair by converting the sequence to that of A2 and creates 3:1 ascus 2. Both mismatches repair by converting the sequence to that of A1 and creates a different 3:1 ascus 3. The pattern of mismatch repair produces an ascus with an aberrant 2:2 ration in which A1 and A2 are in alternating order instead of the like alleles being side by side as expected normally.

Bypass polymerase vs. Pol lll

1. Bypass polymerases are able to replicate across DNA lesions that stall pol lll. 2. Bypass polymerases do not have 3'-to-5' exonuclease capacity and are unable to remove newly added nucleotides that fail to hydrogen bond with the template strand nucleotide. 3. Bypass polymerases are prone to making replication errors because they lack proofreading capabilities. 4. Bypass polymerases synthesize only short segments of DNA and they fall off the template strand after synthesizing a small number of nucleotides.

Chapter 12 take home message

1. Gene mutations are rare and random 2. Mutations change DNA sequence, alter polypeptide composition and function causing phenotypic variation. 3. Spontaneous nucleotide changes can lead to mutation. 4. Chemical mutagens and radiation can damage DNA and produce mutations. 5. DNA repair systems can directly repair DNA damage or can remove and replace damaged segments 6. Specialized enzymes can bypass a blockage of DNA replication caused by unpaired damage 7. Controlled DNA ds breaks initiate homologous recombination and also recombination between homologous chromosomes in meiosis. 8. Gene conversion is a directed DNA sequence change associated with homologous recombination.

Double-Strand Break Repair (2 mechanisms)

1. Nonhomologous end joining - An error prone repair process which repair double stranded (ds) breaks occurring BEFORE DNA replication. 2. Synthesis-dependent strand annealing - An error-free process which repairs ds breaks AFTER the completion of DNA replication.

Chemical mutagens mode of action on DNA (6)

1. Nucleotide base analogs 2. Deaminating agents 3. Alkylating agents 4. Hydroxylating agents 5. Oxidizing agents 6. DNA intercalating agents

Regulatory Mutations - 4 Types

1. Promoter mutations - alter consensus sequence nucleotides and interfere with efficient transcription initiation. 2. Splicing mutations - is a genetic mutation that inserts, deletes or changes a number of nucleotides in the specific site at which splicing takes place during the processing of precursor messenger RNA into mature messenger RNA. Inaccurate removal of intron sequences from pre-mRNA 3. Cryptic Splice Sites - certain base pair substitution mutations produce new splice sites that replace or compete with authentic sites during pre-mRNA processing. These newly formed splice sites are known as cryptic splice sites. 4. Polyadenylation mutations - processing of the 3' end of eukaryotic mRNAs is initiated by the presence of a 5' AAUAAA 3' polyadenylation signal sequence, and mutation of this sequence can block proper 3' processing of mRNA.

SDSA process (4 steps)

1. SDSA begins with the trimming of one of the broken strands, followed by attachment of the protein Rad51. 2. Rad51 binds to the strands and facilitates the invasion of the intact sister chromatid by the resected end of the strand from the sister chromatid. 3. The strand invasion process displaces on strand of the duplex and creates a displacement (D) loop. 4. Replication within the loop synthesizes new DNA strands from intact template strands. The sister chromatids are reformed by dissociation and annealing of the nascent strand to the other side of the break, resulting in the replacement of the excised DNA with a duplex identical to the sister chromatid.

3 models that explain the molecular mechanism of homologous recombination

1. The Holliday Model 2. The Bacterial RecBCD Pathway 3. The Double Stranded Break Model of Meiotic Recombination

Two categories of DNA repair processes

1. Those that directly repair DNA damage and restore it to its wild-type state. 2. Those that allow the organism to circumvent problems such as blocked DNA replication, which can occur when damage is not repaired but which leave the DNA damage in place.

What the 4 types of Direct Repair of DNA damage have in common...

DNA polymerase 1 uses the complementary strand to synthesize a replacement for the missing segment; DNA ligase seals the sugar-phosphate backbone.

DNA Nucleotide Lesions Type 2

Deamination: the loss of an amino (NH2) group form a nucleotide base. -Deamination of cytosine is the deamination event most often associated with mutation. -When cytosine is deaminated, an oxygen atom usually takes its place, converting the cytosine into uracil -DNA mismatch repair removes the uracil from the DNA and replaces it with cytosine, restoring the wild-type sequence. Deamination of methylated cytosine: when methylated cytosine is deaminated, a thymine base is produced, which mismatches with guanine. -The mismatch repair system will either restore the wild type G-C pair or will replace it with a mutant A-T base pair. -If mismatch repair does not occur prior to replication, replication will produce two sister chromatids, one with the mutant A-T pair and one with the wild type G-C pair.

DNA Nucleotide Lesions Type 1

Depurination: the loss of one of the purines, adenine or guanine, from a nucleotide by breakage of the covalent bond at the primary carbon of deoxyribose that links the sugar to the nucleotide base. -This forms a DNA lesion known as an apurinic (AP) site. -Adenine is most commonly used to fill apurinic sites during DNA replication. -The cause a G-C to T-A mutation in this case.