When we think about threats to our wellbeing and survival, some of the first things humans think about is war, famine, climate change, nuclear war, poverty, crime or any number of other terrible realities of modern life. However, on the cellular scale, there is one clear and present danger that stands above everything else—damaged or mutated DNA.
For a cell, there is nothing worse than mutated DNA because this can result in the creation of incorrect proteins, some of which can lead to serious diseases, including cancer! Damage to DNA can also come from external sources, so the cell must be able to defend against that threat as well. There are various “checkpoints” that DNA must pass before it is allowed to be passed on. While many mutations aren’t dangerous—and some are even beneficial!—cells are still hyper-vigilant about the integrity of their DNA and go to great lengths to prevent such errors. This article will explore some of the methods and means by which cells defend their most precious possession—genetic material!
Before we get into the potential errors that can occur in genetic material, we must have a basic understanding of the replication process itself. During DNA replication in the nucleus of a cell, the genetic material is copied, so that this material can be accurately passed on to daughter cells. Essentially, a double-sided DNA molecule is copied to produce a second identical DNA molecule.
This process occurs in three main steps: splitting the DNA molecule in half, priming the separate halves for replication, and assembling the new DNA molecules. As you know, DNA has a double helix shape, and this will uncoil, which essentially unzips the DNA molecule. Various enzymes will move along the individual halves, preparing the nucleotides for replication.
DNA polymerase is a critical enzyme that will then assemble the new side of the DNA molecule, matching up appropriate nitrogenous base pairs with free nucleotides from the nucleus. Due to the concept of complementary base pairing, adenine and tyrosine (A & T) base pairs will be matched together, and cytosine and guanine (C & G) nucleotides will also be paired along the strand. The polymerase completely encloses the unzipped strand as it assembles and attaches the new partner strand, resulting in a new double-stranded DNA molecule. In humans, this process happens very quickly—around 50 nucleotide pairings per second!
Not only is DNA polymerase the enzyme that assembles the nucleotides during DNA replication, but it is also responsible for checking its own work. For example, if the polymerase detects that a base has been incorrectly placed (e.g., pairing a cytosine to an adenine, rather than a guanine), it can immediately remove the error before continuing on down the strand. This rapid response to errors is called DNA proofreading, and is the first step that cells have in terms of defending against replication errors, mutations, and the various consequences of such mistakes.
DNA Mismatch Repair
Unfortunately, as any writer knows, proofreading is rarely perfect, so mistakes still appear in the DNA and need to be fixed after replication is complete. This is when DNA mismatch repair takes over; this is a slightly more involved process than proofreading, as the DNA strand has now been completed and sealed.
To begin with, a team of proteins and enzymes get to work on the area of the strand where the mistake occurred. A protein complex binds to the mis-paired base and enzymes cut out a small section of nucleotides on either side of the error. In a freshly replicated strand of DNA, the “new side” will lack methyl groups, which enables the protein complexes and enzymes to know which side of the strand to repair.
A DNA polymerase (from the proofreading step) will then re-attach to the DNA strand and “fix” the mistake by placing the correct nitrogenous base pairs on the strand. This is slightly more time-intensive than basic proofreading, but it’s all relative, and this editing process can be completed in a fraction of a second!
General DNA Repair
The two methods above are specifically related to errors and fixes surrounding the replication process. While many genetic coding errors occur during the replication process, that isn’t the only source of mutations or damage in our DNA! Our genetic material can also be damaged as a result of radiation, chemicals and other external sources. Thus, there also need to be repair processes for DNA when the damage occurs during the normal life of a cell.
The simplest version of this repair is simply damage reversal, which is typically required in response to chemical exposure. When certain chemicals enter the cell, those molecules or groups may bind to the nucleotide bases of the DNA, thus altering how they pair during replication. This mis-pairing could lead to mutations, but our cells have mechanisms to remove such additional, unwanted molecules and ensure that the bases behave normally during replication.
Base excision repair is a quick and simple replacement process, in which a single mis-paired base (one that changed through chemical interaction, or by slipping through both proofreading and mismatch repair processes) must be removed and replaced. An enzyme will detect this incorrect nucleotide base, bind to the strand, and remove the incorrect base. A polymerase will come to fill in the gap with the right base, and an enzyme called ligase will seal up the DNA backbone.
Nucleotide excision repair is a bit more complicated, as these “errors” in the DNA strand often involve more than one base pair, or a short chunk of the genetic code. As mentioned above, when certain chemical groups bind to our DNA, they can change the behavior and replication accuracy of the strand. Damage from radiation can cause sections of DNA to interact with itself, thus leading to mutations. These damaged sections of DNA will be addressed by DNA helicase, which cracks open the strand and wrinkles the strand around the damaged section of DNA. That entire section will be removed, a DNA polymerase will organize and place the correct and undamaged base pairs, and ligase will once again seal the gap where the repair work was done.
Finally, if the entire DNA strand breaks, or both sides of the strand have become damaged and require replacement, double-stranded break repair comes into play. There are two varieties of this repair, one that simply sticks the broken halves back together, with the addition of some extra nucleotides. These act like “glue”, and will likely cause some mutations, but it is a better solution than allowing hundreds of genes and large sections of chromosomes to be forever separated and lost. The more delicate double-stranded method involves recombination from the non-damaged homologue of the chromosome. The two homologues come together in the cell and the damaged section is directly copied and reconstituted from the undamaged partner. This form of repair does not usually result in additional mutations.
There is another, more drastic approach to correcting errors that can happen in a cell. When a mutation is considered too difficult to repair, or if it is immediately deleterious to the health of the cell, proteins can be produced that instruct the cell to commit suicide. This form of self-destruction is called apoptosis. This is considered the last resort of a cell that is desperate not to pass on a mutation to future cells through replication and cell division.
More specifically, there is a protein called p53 that is generated in the case of serious genetic mutation and it encourages the cell to end its own life and cease and replication processes, which greatly lowers the risk of the mutation being passed on; the cost of one cell is far less than the damage that a fast-growing cancerous tumor can wreak on an organism. These proteins will also slow down cell division, giving the cell more time to correct any mistakes or undergo the steps of apoptosis.
The Bad News
Despite having so many mechanisms to protect itself against DNA damage, some of these protective mechanisms are also vulnerable to mutation. Remember, everything that happens in a cell is programmed through the DNA. In other words, if there is a mutation in the section of DNA that controls the production of DNA polymerase, or the p53 protein, or the behavior of glycolase, some of these defensive measures may not be as effective. This can lead to multiple mutations in the same cell, which can begin to compound on one another. This is when cancerous growth can begin. Rarely does a single mutation lead to cancerous cell growth; it requires multiple mutations affecting both the replication process and the defensive measures to combat such errors.
A Final Word
Life in the nucleus is a constant battle that requires perpetual attention to detail. With thousands of base pairs being copied in billions of different cells every minute of our lives, mistakes are bound to happen. We are fortunate that the incredible detailed directions for life (DNA) also designed certain preventative measures to keep our cells safe from mistakes and mutations. While these systems aren’t always perfect, they serve a critical role in our long-term survival and health!