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How do point mutations arise from mistakes in DNA replication?

How do point mutations arise from mistakes in DNA replication?



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Hi! I'm trying to make sense of this illustration (from the textbook Biological Science by Scott Freeman).

The general question is: How do point mutations arise from mistakes in DNA replication?

If you don't mind, however, I'd like to explain how I interpret the illustration so you can see the confusion. As the original molecule of DNA is replicated (in gray), a mistake occurs in the synthesis of the bottom strand in the new molecule (the noncomplimentary bases G and T have been paired together). Now, it seems like a second replication is required for the mutation to arise: the defective molecule is replicated resulting in two new molecules, one free of mistakes (because it takes as its template the top strand) and one "wrong" where the mutation is present.

But my doubt is, wouldn't the middle molecule already constitute a mutation? If a mRNA were to transcribe that sequence, the codon is already different from the original molecule. Must a DNA molecule be replicated two times for a mutation to arise (where the first time a mistake is made and a second where such mistake is, let's say, "consolidated")?

Thank you very much in advance.


Source of your misunderstanding

Your misunderstanding is very comprehensible as the figure is misleading.

The figure only shows a single event of replication. What you see as a second replication resulting into two double stranded molecules is NOT an event of replication. It actually represents the two possible outcomes from a 'mismatch repair mechanism'. The termDNA replicationwritten on the figure should be replaced byPossible outcomes of DNA repair. The molecule that contains theG-Tmismatch is therefore just a temporary state that will very quickly be changed to either theT-Astate (bottom right of your figure) or to theG-Cstate (upper right of your figure). More information below.

DNA repair

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

The type of DNA repair that is of interest on the figure is called "DNA mismatch repair"

DNA mismatch repair

DNA mismatch repair is a system for recognizing and repairing erroneous insertion, deletion, and mis-incorporation of bases that can arise during DNA replication and recombination, as well as repairing some forms of DNA damage.

There are specific enzymes to repair a mismatch such as theG-Tmismatch represented on your figure. These enzymes can either repairG-TintoG-Cor intoA-T. If the repair isA-T(lower outcome in the figure) then a mutation would have occurred. If the repair isG-C(upper outcome in the figure) then we are back to the original sequence and no mutation would have occurred.

Note that the probability of the two possible outcomes is different from 0.5 as these enzymes have ways to try to figure out which was the original strand and which was the newly replicated strand. You can learn much more about the mechanism of DNA mismatch repair on the wikipedia > DNA mismatch repair.


Point mutation

A point mutation or substitution is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. [1] Point mutations have a variety of effects on the downstream protein product—consequences that are moderately predictable based upon the specifics of the mutation. These consequences can range from no effect (e.g. synonymous mutations) to deleterious effects (e.g. frameshift mutations), with regard to protein production, composition, and function.


Gene mutations can arise during DNA replication. Explain why different types of gene mutation may have different effects on the encoded polypeptide.

Gene mutations arise due to errors in DNA replication and include insertion, deletion, substitution, inversion, duplication and translocation of bases. Each triplet of bases encodes one amino acid. Therefore, base mutation can change the amino acid sequence of the polypeptide encoded by the gene. However, the effect on the polypeptide depends on the type of mutation. For example, due to the degenerate nature of the genetic code, a substitution of one base may result in a triplet that encodes the same amino acid as was encoded by the original base sequence, in which case there will be no effects on the encoded polypeptide. However, some mutations could drastically affect the encoded amino acid. For example, a substitution may result in a triplet that encodes a premature stop codon. This would result in a truncated amino acid sequence - which is the primary structure of a polypeptide - which would in turn affect the secondary and tertiary structures of the polypeptide and could impair or abolish its function.

Another type of mutation that could significantly affect the encoded polypeptide is an indel - an insertion or deletion - as these can cause a frameshift. In a frameshift, the sequence of bases that encodes the amino acid chain is shifted to another reading frame. For example, a region of the gene may be read in the following triplets: GCG CAA GAT. If the first G is deleted, the whole base sequence shifts so the triplets are now read as CGC AAG AT… and so on. Indels can therefore severely alter the amino acid sequence and hence the secondary and tertiary polypeptide structures, which again may significantly reduce or abolish the function of the polypeptide.


IU research on mutation 'hotspots' in DNA could lead to new insights on cancer risks

BLOOMINGTON, Ind. -- New research from Indiana University has identified "hotspots" in DNA where the risk for genetic mutations is significantly elevated.

images/dams/zousrw4zew_w768.jpg" />View print quality image Patricia Foster. Photo by Indiana University Communications

These mutations arise because "typos" can occur as DNA replicates during cellular division. A recent analysis, which found that random mistakes in DNA play a large role in many cancer types, underscores the need to understand more about what triggers these errors.

The IU-led research, conducted in E. coli, appears in two papers in the "Highlights" section of the August issue of the journal Genetics. The "hotspots" identified are specific to E. coli and related bacteria, but the work could provide a roadmap to identifying similar trouble spots in human DNA.

"This research gets us closer to understanding how the cell's replication machinery interacts with DNA," said Patricia Foster, a professor emerita in the IU Bloomington College of Arts and Sciences' Department of Biology. "If you can understand exactly why an error occurs at a particular point on the DNA in bacteria, it gets you closer to understanding the general principles."

Foster is the first author on one of the two papers. The other paper’s first author is Brittany Niccum, a Ph.D. student in Foster’s lab at the time of the study.

The risk for cancer from DNA replication errors is highest in certain tissues -- like the prostate and bones -- where a higher rate of cellular renewal means there are more opportunities for mistakes to occur as the DNA is copied.

"There are parts of the genome that contain 'cancer drivers,' where changes in the DNA can allow tumor cells to proliferate," Foster said. "If you could know what sections of the DNA had a higher risk for mutation, you might be able to focus your analysis on these 'hotspots' to predict what will happen next."

images/dams/xtr1sqcrqk_w768.jpg" />View print quality image E. coli bacteria were used to study the sequences in DNA where the risk for mutation is significantly elevated. Photo courtesy of the National Institute of Allergy and Infectious Diseases

In E. coli, the researchers found that the chances of DNA replication errors were up to 18 times more likely in DNA sequences where the same chemical "letter" in the sequence repeats multiple times in a row. They also found that errors were up to 12 times more likely in DNA sequences with a specific pattern of three letters.

These patterns of letters in the DNA sequence had been previously identified as common locations for replication errors. But Foster said the sheer volume of data in the new studies -- with analysis across the bacteria's entire genome of 30,000 mutations accumulated during 250,000 generations -- provide the "statistical weight" required to pinpoint the error rates with an unprecedented level of accuracy.

The studies also underline the importance of two systems in DNA replication: a "proofreader" enzyme and a molecular pathway called mismatch repair. Both serve as a defense against mistakes from the enzyme -- called DNA polymerase -- that copies the genome at a staggering rate of 1,000 letters per second.

This proofreader function resets the copying process after detecting a mistake. The IU researchers found that "switching off" this function caused 4,000 times more errors. Switching off mismatch repair, a backup system for the proofreader, caused 200 times more errors.

"When we switch off these backup systems, we start to see 'pure' errors -- the places where the polymerase is more likely to make a mistake without intervention from other processes, " Foster said. "Until now, I don't think anyone could truly see the seriousness of these error hotspots in DNA."


How do point mutations arise from mistakes in DNA replication? - Biology

A Mutagen is an environmental agent that causes a mutation. The process of inducing a mutation is called mutagenesis. There are many known mutagens, including:

There is much evidence which has been collected over time to show the effects of radiation on genetic material. Before the technology was available to study DNA there was a correlation made between those who worked with radiation over prolonged periods of time and negative mutations. But even this was not identified until the 1990's. Leukaemia and other cancers are common amongst those who have had prolonged exposure.

The radiation can break up strands of DNA or even whole chromosomes if the energy level of the radiation is high enough. Ultraviolet radiation from the sun can cause the deletion of bases in the DNA strand as well as cause the Thymine bases to link together and therefore not allow replication to occur properly.

Changes made to somatic cells can not be passed on to future generations. However mutations made in the gametic cells may produce alleles that can be inherited. This can have drastic results for a populations genetic variability and therefore repercussions on evolution.


Scientists Identify Fleeting Quantum Jitters that Drive Mutation Rate in DNA

Scientists in the U.S. have described how the DNA double helix contains an intrinsic timer that determines how often mutations might occur spontaneously. The team led by Ohio State University’s Zucai Suo, Ph.D., and Duke University’s Hashim M. Al-Hashimi, Ph.D., used a technique known as nuclear magnetic resonance (NMR) relaxation dispersion to recognize how the bases in a double-stranded helix of DNA undergo fleeting changes in their shape—lasting just a thousandth of a second—which allow polymerase enzymes to insert the wrong base during DNA replication. The researchers claim that these rare mismatches could underlie genetic changes that drive evolution as well as the development of diseases such as cancer.

“Increasing or decreasing the rates of spontaneous mutations could significantly alter the ability of an organism to evolve or alter its susceptibility to disease,” said Prof. Al-Hashimi, James B. Duke Professor of Biochemistry and Chemistry at the Duke University School of Medicine. “An interesting question is: What determines the mutation rate in a living organism. From there, we can begin to understand the specific conditions or environmental stressors that can elevate errors.” The researchers report their findings in Nature, in a paper entitled “Dynamic Basis for dG•dT Misincorporation via Tautomerization and Ionization.”


When cells divide, their DNA must be replicated. DNA polymerase enzymes have the job of inserting the right bases into the right positions in a new strand as it is constructred, by matching the new base pair up with its opposite number—cytosine (C) with guanine (G) and adenine (A) with thymine (T). However, this matching process isn’t infallible, and a mistake is made in roughly one in every 10,000 bases. If the error isn’t corrected, it remains fixed in place as a mutation in the new DNA.

James D. Watson and Francis H.C. Crick postulated that DNA bases can exist as alternative states, or rearrangements—known as tautomeric and anionic forms—back in 1953 when they first described the structure of the DNA double helix, the researchers write. However, scientists have also since confirmed that DNA replication is tightly controlled so that mismatches are a rarity. “In their paper describing the structure of the DNA double helix, Watson and Crick proposed that if nucleotide bases adopted their energetically unfavourable tautomeric forms, mismatches could pair up in a Watson–Crick (WC)-like geometry and potentially give rise to spontaneous mutations,” the researchers write. “Decades later, it is well established that the replicative and translational machineries have a tight control over the WC geometry to discriminate against mismatches.”

Evidence also suggests that while uncommon, tautomeric and anionic WC-like mismatches can “evade such fidelity checkpoints” and give rise to replication errors, the authors point out. To investigate this further, in 2015 the Duke team used the NMR relaxation dispersion technique to witness these shape-shifting tautomeric and anionic shape shifts in bases, which they anticipated might play “unique roles in DNA damage induction and repair, nucleic acid recognition, chemical modifications of nucleic acids, and catalysis.”

For their latest study, the researchers used an enhanced version of the technology to capture these blink-of-an-eye conformational changes in G and T and demonstrate that these “quantum jitters” happened at about the same rate as a polymerase incorporates a G-T mismatch.

The Duke University and Ohio State University researchers also fed their data into a kinetic model to track movements that led to altered states and mismatches. These results showed that tautomeric forms were more common under normal conditions, whereas anionic forms dominated in the presence of mutagens and environmental stress. The findings also indicated that the frequency at which bases shape-shifted was dependent upon on the DNA sequence. One G- and C-rich region can be associated with more incidences of shape-shifting, and so the inclusion of more mutations, than a region rich in As and Ts. “The sequence-dependent tautomerization or ionization step was inserted into a minimal kinetic mechanism for correct incorporation during replication after the initial binding of the nucleotide, leading to accurate predictions of the probability of dG•dT misincorporation across different polymerases and pH conditions and for a chemically modified nucleotide, and providing mechanisms for sequence-dependent misincorporation,” the authors state. “Our data indicate that the formation of WC-like anionic and tautomeric mismatches help to determine the frequency of dG•dT misincorporation and its dependence on pH, chemical modifications and possibly sequence.”

“In the past, we knew DNA polymerases make mistakes during DNA replication but did not know how they do it,” comments Zucai Suo, Ph.D., Ohio State professor of chemistry and biochemistry. “Now, our study provides a mechanistic sense for how the mistakes arise.” Prof. Al-Hashimi adds that, “The textbook depiction of the iconic double helix shows a static double-stranded structure, but it turns out that on rare occasions it can morph into other shapes that exist for exceptionally small periods of time. Though some might question the importance of such states, there are a growing number of studies showing they can be major drivers of biology and disease. Given the difficulty in observing these phenomena, it makes you wonder how many more states are out there dictating the outcomes of biology that we don't even know about.”

The results provide “convincing validation for the chemical origins of mutations proposed by Watson and Crick in 1953,” adds Myron Goodman, Ph.D., a professor of molecular biology and chemistry at the University of Southern California, who was not involved in the study. “It is significant scientifically, and even though it took about 65 years to prove, it also demonstrates the folly of ever betting against Watson and Crick.”

The researchers also plan to continue investigating how alternative states might be responsible for errors in other processes. “The approach presented here can be applied to examine the roles of other tautomeric and anionic mismatches in replication, transcription, translation and DNA repair,” they conclude.


Human Pol ε-dependent replication errors and the influence of mismatch repair on their correction

Mutations in human DNA polymerase (Pol) ε, one of three eukaryotic Pols required for DNA replication, have recently been found associated with an ultramutator phenotype in tumors from somatic colorectal and endometrial cancers and in a familial colorectal cancer. Possibly, Pol ε mutations reduce the accuracy of DNA synthesis, thereby increasing the mutational burden and contributing to tumor development. To test this possibility in vivo, we characterized an active site mutant allele of human Pol ε that exhibits a strong mutator phenotype in vitro when the proofreading exonuclease activity of the enzyme is inactive. This mutant has a strong bias toward mispairs opposite template pyrimidine bases, particularly T • dTTP mispairs. Expression of mutant Pol ε in human cells lacking functional mismatch repair caused an increase in mutation rate primarily due to T • dTTP mispairs. Functional mismatch repair eliminated the increased mutagenesis. The results indicate that the mutant Pol ε causes replication errors in vivo, and is at least partially dominant over the endogenous, wild type Pol ε. Since tumors from familial and somatic colorectal patients arise with Pol ε mutations in a single allele, are microsatellite stable and have a large increase in base pair substitutions, our data are consistent with a Pol ε mutation requiring additional factors to promote tumor development.

Keywords: DNA polymerase DNA replication Mismatch repair Mutagenesis.


Method of DNA repair linked to higher likelihood of genetic mutation

Researchers from Indiana University-Purdue University Indianapolis and Umea° University in Sweden report in a study published in the February 15, 2011, issue of PLoS Biology that a method by which cells repair breaks in their DNA, known as Break-induced Replication (BIR), is up to 2,800 times more likely to cause genetic mutation than normal cell repair.

Accurate transmission of genetic information requires the precise replication of DNA. Errors in DNA replication are common and nature has developed several cellular mechanisms for repairing these mistakes. Mutations, which can be deleterious (development of cancerous cells), or beneficial (evolutionary adaption), arise from uncorrected errors. When one or many cells repair themselves using the efficient BIR method, accuracy is lost.

"When BIR occurs, instead of using a "band aid" to repair a chromosomal break, the broken piece invades another chromosome and initiates replication which happens at the wrong place and at the wrong time and probably with participation of wrong proteins," said Anna Malkova, Ph.D., associate professor of biology at the School of Science at IUPUI, who led the study.

The researchers used yeast to investigate the level of mutagenesis associated with BIR and found that the method's proclivity to cause mutation was not affected by where on the DNA the repair was made.

Why is BIR so inaccurate as compared to normal replication?

"We didn't find a smoking gun," said Malkova, also an adjunct associate professor of medical and molecular genetics at the Indiana University School of Medicine. "We think there are at least four changes to replication machinery that must occur to create a perfect storm or synergy which make BIR repair so mutagenic."

For example, during BIR, the researchers found a dramatic increase in concentration of nucleotides -- the building blocks used to form DNA.

"Our findings strongly suggest that mutagenesis caused by BIR doesn't happen slowly, it occurs in surges -- sudden bursts which may lead to cancer," said Malkova, who is a geneticist. "We plan to continue investigating BIR in the hope of finding clues as to why this mechanism of cell repair is so likely to cause mutations. The ultimate goal, of course, is to prevent those mutations that cause cancer."


Question: 1. How Often Do Mutations Occur During DNA Replication? How Does The Cell Repair These Mutations? How Do Mutagens And Carcinogens Affect These Processes And Lead To The Development Of Cancer? 2. BRCA1 And BRCA2 Are Genes That Are Normally Involved In What Cellular Function? How Do Mutations In These Genes Predispose An Individual To Develop Cancer? .

5. What kind of mutation has occurred in the DNA of people with cystic fibrosis? How does the mutation affect the function of lung cells? Why would individuals that are heterozygous for CF have an advantage over normal individuals?

6. How are mutations inherited? How does the process meiosis differ from mitosis? What mechanisms during meiosis ensure that the genetic material passed on to offspring will be diverse?

7. What is the difference between dominant and recessive alleles? If the mutation that causes a disease is recessive how will it be inherited? Conversely if the mutation is dominant how will it be inherited?


History

The cellular reproduction process of meiosis was discovered by Oscar Hertwig in 1876. Mitosis was discovered several years later in 1882 by Walther Flemming.

Hertwig studied sea urchins, and noticed that each egg contained one nucleus prior to fertilization and two nuclei after. This discovery proved that one spermatozoon could fertilize an egg, and therefore proved the process of meiosis. Hermann Fol continued Hertwig's research by testing the effects of injecting several spermatozoa into an egg, and found that the process did not work with more than one spermatozoon. ⎱]

Flemming began his research of cell division starting in 1868. The study of cells was an increasingly popular topic in this time period. By 1873, Schneider had already begun to describe the steps of cell division. Flemming furthered this description in 1874 and 1875 as he explained the steps in more detail. He also argued with Schneider's findings that the nucleus separated into rod-like structures by suggesting that the nucleus actually separated into threads that in turn separated. Flemming concluded that cells replicate through cell division, to be more specific mitosis. ⎲]

Matthew Meselson and Franklin Stahl are credited with the discovery of DNA replication. Watson and Crick acknowledged that the structure of DNA did indicate that there is some form of replicating process. However, there was not a lot of research done on this aspect of DNA until after Watson and Crick. People considered all possible methods of determining the replication process of DNA, but none were successful until Meselson and Stahl. Meselson and Stahl introduced a heavy isotope into some DNA and traced its distribution. Through this experiment, Meselson and Stahl were able to prove that DNA reproduces semi-conservatively. ⎳]