DNA Repair - Online Tutor, Practice Problems & Exam Prep

DNA repair mechanisms are crucial for maintaining genomic integrity. Key pathways include base excision repair, which removes damaged nucleotides using DNA glycosylases, and nucleotide excision repair, which fixes distortions in the double helix. Mismatch repair corrects errors post-replication by recognizing methylation patterns. Translesion synthesis serves as a last resort for stalled DNA polymerases, albeit with a high error rate. Double-strand breaks can be repaired via non-homologous end joining or homologous recombination, the latter utilizing sister chromatids for accurate repair.

DNA Proofreading

Hi. In this video, we're going to be talking about DNA repair. So, DNA damage occurs often, and it's repaired in a lot of different ways. So, one of the or a couple of the ones that we've talked about previously, the first is DNA proofreading, and DNA proofreading is just the process of repairing a nucleotide that's been added in error, and so it repairs a mispaired base. And so this is one that we've already talked about and is a major part in repairing that damaged DNA. There are other ways that are maybe less specific. We're going to talk about individual pathways, but I did want to throw this other pathway in, and this is just that there are a lot of different enzymes that can reverse the damage of DNA. So, for instance, there's an enzyme, CPD photolyase, and this is an enzyme that repairs dimers caused from UV light. So, UV light, it hits our skin anytime we go outside. It's going to cause dimers, and there are these enzymes in there that go and repair this. Then there's enzymes forced to every type of specific DNA. And these kind of exist, I mean, of course, they're pathways, but they exist outside of the major pathways that we're going to talk about later. So, these are kind of the first two, just like summarizing different ways that DNA damage can be repaired. So here's an example of proofreading. We have DNA polymerase. This is being copied. There's some type of error that happens here, where C is paired with T, not supposed to be proofreading, goes back, excises that C, and makes the correct TA pairing as it extends forward. So that is one major way that DNA damage is repaired. Let's turn the page and talk about more specific pathways.

Repair Pathways

Okay. So now let's talk about some individual pathways that repair different types of specific damage. The first one is called the base excision repair or BER pathway. This pathway removes and replaces damaged nucleotides. Here is how it happens: There's an enzyme called DNA glycosylases that comes in and identifies a damaged DNA base, cutting it away from the sugar backbone. Following this, another enzyme, deoxyriophosphodiesterase, which, I know, is a mouthful, steps in. This enzyme cuts out the section of DNA that's neighboring around the base. Then, DNA polymerase comes in, fills the gap with the correct nucleotides, and finally, DNA ligase comes in to seal the gap. So here we have a damaged base in blue. Glycosylase comes in and cuts it out, more things are cut out, and DNA polymerase synthesizes that section while DNA ligase repairs and ensures everything is sealed. BER is responsible for fixing a damaged base.

We also have Nucleotide Excision Repair (NER). This repair mechanism fixes damage that distorts the double helix. We've discussed different ways the double helix can be distorted, and if it is distorted, it creates a hump that various proteins and enzymes, like polymerases, can't overcome. It has to be fixed to return the double helix to its normal structure. NER is responsible for fixing such distortions. There are two types of NER: global and transcription-coupled. The global type fixes damage anywhere in the genome, and the transcription-coupled type addresses areas near actively transcribed regions of DNA. They essentially operate in the same way, although they may involve different proteins. So, when some kind of damage occurs, proteins recognize it and recruit more proteins to the area. Eventually, around a 30 nucleotide segment is removed, DNA polymerase fills the gap, and DNA ligase seals it. Thus, the distortions are corrected. However, defects in NER can cause serious diseases, including xeroderma pigmentosum, often referred to as light allergies, though they are not truly allergies but instead a sensitivity to light. UV light, for example, causes various dimers, and without a functional NER, these dimers persist, leading to cancers and skin lesions because the body cannot repair the damage caused by light.

Finally, we have mismatch repair. This system repairs DNA damage occurring as insertions or deletions, usually immediately following replication. Here's how it works: A mismatched base, arising from an insertion or deletion, is recognized by the proteins specific for mismatch repair. The challenge, however, is identifying which base is incorrect. For example, in the sequence "TTTCGCAAGC," let's say there is an insertion that creates a mismatch. Proteins must determine whether it is the "A" or the "C" that is mismatched, and they do this based on the methylation status of the DNA. Histone proteins in DNA are methylated, but only on the old strand; the new strand, just replicated, lacks methylation. Therefore, the proteins use the unmethylated strand to determine that it contains the mutation, whereas the methylated strand is used as a template for repair. DNA polymerase then fills in the gap using the methylated strand, and DNA ligase seals it. Here, the mismatch and the methylation statuses are depicted, with proteins coming in to repair the mismatch.

These are our three major types of DNA repair. With that, let's now turn the page.

Translesion Synthesis

Okay. So now let's talk about an unusual type of DNA repair called Translesion Synthesis. Translesion Synthesis is a really poor DNA repair pathway, and it's usually only used as a last resort. So, there's nothing else the cell can do, but it wants to prevent death, so it's going to use this pathway. What it does is typically repair types of DNA damage that cause the DNA polymerase to stall while it's replicating. And so, if it can't continue replicating, then the DNA is severely damaged, it can't replicate, it can't divide, and that usually triggers the cell to kill itself. Now the cell doesn't want to kill itself, so if there's any way that it can keep this DNA polymerase going and keep replicating, it wants to use it, and so it uses the Translesion Synthesis Pathway.

What happens is if there's some kind of distortion or mutation that causes the DNA polymerase to stall, then it sends in these extra polymerases called translusional or bypass polymerases, and they are recruited to the area. Translesion polymerases actually have the ability to overcome various helical distortions that cause the other polymerase to stall. They can move, but we lose some efficiency with that because they have no proofreading, so they can't fix anything that's wrong, they have a very high error rate, and they only do a few nucleotides at a time before they fall off.

Generally what happens is the replicating polymerase stalls because there's some kind of DNA damage here in red. The translesion polymerase will come in and it will overcome this DNA damage, but then it falls off because it's not very good at what it does, and therefore the replicating polymerase is added back on and it keeps going. Generally, that's how it works. And so it's good enough to overcome this distortion, but what it doesn't do is it doesn't fix the damage. Right? That DNA damage is still there, and now it's being passed on to another cellular generation, and it has a higher error rate and can cause mutations in addition to the one that's already existing that isn't repaired because there's no proofreading. Like I said, it's really poor, but it keeps the cell from death. And that is what's important for the cell at this point because it doesn't want to die but needs to replicate itself. And so, Translesion Synthesis is what allows the cell to prevent itself from dying in the instance of mutations. So with that, let's now move on.

Double Strand Breaks

Okay. So now let's talk about double-stranded breaks, which are a very serious type of DNA error and DNA mutation. Double-strand breaks occur when both strands are broken, and they can be repaired in two ways. The first is called non-homologous end joining. You may see it abbreviated as NHEJ. Essentially, it just takes the areas that are broken and sticks them back together. Proteins come in, they recognize, they say, "Oh, DNA damage has happened." Proteins come in, trim off the area, and DNA ligase just connects them back together. This type of repair occurs outside of the S phase. Now remember, the S phase is the point of mitosis where the DNA is replicated. Right? And, if the DNA is not actively being replicated, there's nothing else it can do other than just sort of stick it together. So non-homologous end joining occurs then, but obviously, that's not ideal, because whatever caused the break and whatever is missing due to the break is not repaired. You can end up with some serious gene distortions due to double-strand breaks.

The second form is homologous recombination, which we've gone over before in a different way in terms of recombining genes and crossing over during meiosis. But it can also be used to repair double-stranded breaks. Now, this occurs directly after replication because you have to have those extra copies to do it. What you do is you use sister chromatids that have now been replicated as a template to repair the broken strand. It's similar to crossing over, so the strand that's broken sort of invades the sister chromatid strand where the DNA is, and a DNA polymerase uses that as the template to repair it. But this is different from crossing over. Right? Because in crossing over, the non-sister chromatids are used, whereas in homologous recombination for DNA repair, the sister chromatids are used. And that's an important difference to understand. Homologous recombination for repair uses sister chromatids, whereas crossing over uses non-sister chromatids. This is also known as synthesis-dependent strand annealing. You'll see that potentially it's the same process. In non-homologous end joining, there's been a break, and they're just sort of glued back together, just sort of stuck back together through DNA ligase, and that can be very damaging because whatever was here before is now lost for good. Homologous recombination uses the breaks that occurred here. Right? There are the breaks. But these strands invade the sister chromatids and use that as a template to replicate and repair, so that you replace what has been lost. But again, this happens during replication because you have those extra sister chromatids to be able to do this with.

So with that, let's now move on.

Which of the following repair pathways repairs damage that causes distortions in the double helix?

• A. Base Excision Repair
• B. Nucleotide Excision Repair
• C. Mismatch Repair
• D. Homologous Recombination

Which of the following repair pathways uses a methylated strand of DNA to correct DNA damage?

• A. Base Excision Repair
• B. Nucleotide Excision Repair
• C. Mismatch Repair
• D. Homologous Recombination

True or False:Translesion DNA synthesis is the first mechanism the cell uses to repair DNA damage?

• A. True
• B. False

Which of the following pathways is an error-free way to repair double-stranded breaks?

• A. Homologous recombination
• B. Non-homologous end joining
• C. Translesion synthesis
• D. Mismatch repair

Here’s what students ask on this topic:

What is the role of DNA proofreading in DNA repair?

DNA proofreading is a crucial mechanism in DNA repair that corrects errors during DNA replication. DNA polymerase, the enzyme responsible for synthesizing new DNA strands, has a proofreading function. When an incorrect nucleotide is incorporated, the polymerase detects the mismatch, excises the incorrect base, and replaces it with the correct one. This process ensures high fidelity in DNA replication, reducing the occurrence of mutations. Proofreading is essential for maintaining genomic stability and preventing diseases caused by genetic mutations.

How does base excision repair (BER) work?

Base excision repair (BER) is a DNA repair pathway that corrects damaged nucleotides. The process begins with DNA glycosylases recognizing and removing the damaged base, creating an abasic site. Next, an enzyme called AP endonuclease cuts the DNA backbone at this site. DNA polymerase then fills in the gap with the correct nucleotide, and DNA ligase seals the strand. BER is crucial for fixing small, non-helix-distorting base lesions, maintaining genomic integrity.

What is the difference between nucleotide excision repair (NER) and base excision repair (BER)?

Nucleotide excision repair (NER) and base excision repair (BER) are both DNA repair mechanisms but differ in their targets and processes. NER fixes bulky, helix-distorting lesions, such as thymine dimers caused by UV light. It involves removing a short single-stranded DNA segment containing the lesion, followed by DNA polymerase filling the gap and DNA ligase sealing it. In contrast, BER targets small, non-helix-distorting base lesions. It involves removing the damaged base by DNA glycosylases, followed by AP endonuclease cutting the DNA backbone, DNA polymerase filling the gap, and DNA ligase sealing the strand.

What is translesion synthesis, and why is it considered a last resort?

Translesion synthesis is a DNA repair mechanism used as a last resort when DNA polymerase stalls at a lesion during replication. Specialized translesion polymerases bypass the lesion, allowing replication to continue. However, these polymerases lack proofreading ability, leading to a high error rate and potential mutations. Despite its low fidelity, translesion synthesis prevents cell death by enabling replication to proceed, making it a critical, albeit error-prone, pathway for survival under severe DNA damage conditions.

How are double-strand breaks in DNA repaired?

Double-strand breaks (DSBs) in DNA are repaired through two main pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly ligates the broken DNA ends without a template, which can lead to mutations. It is active throughout the cell cycle but is error-prone. HR, on the other hand, uses a sister chromatid as a template for accurate repair, ensuring high fidelity. HR occurs during the S and G2 phases of the cell cycle when sister chromatids are available. Both pathways are crucial for maintaining genomic stability.