DNA Repair and Recombination - Online Tutor, Practice Problems & Exam Prep

DNA damage can occur through various mechanisms, including depurination, deamination, thymine dimers from UV exposure, and double-strand breaks. Repair processes include mismatch repair, nucleotide excision repair for bulky lesions, and double-strand break repair via non-homologous end joining or homologous recombination. Homologous recombination utilizes a homologous chromosome as a template to accurately repair breaks, forming structures known as Holliday junctions. This process is crucial for maintaining genomic integrity and preventing diseases like xeroderma pigmentosum, which results from defective DNA repair mechanisms.

DNA Damage

Hi. In this video, we're going to be talking about DNA repair and recombination. So first, let's give an overview of the different types. Let me actually write it with a pen. Types of DNA damage. So the first type is called depurination. This is when purine bases, so the A and G nucleotides, are spontaneously lost, kind of like missing teeth. Here we have an example of this. We have our A nucleotide here, and it's lost. This is an example of depurination.

Then we have deamination. Deamination is when a base is chemically converted into a different base. A good example of this is cytosine being changed into a uracil. Here we have a DNA double helix, we have our cytosine here, and some chemical modification happens, turning it into a uracil called deamination. It doesn't have to be cytosine to uracil. It can be a lot of different combinations that I didn't list here, but it's just a chemical conversion of one base into a different one.

Then we have the thymine dimer, and this is actually caused by UV light. So anytime you go outside, you're exposed to the sun's UV rays, thymine dimers form. What thymine dimers are is 2 adjacent thymine dimerized. Here we have UV light usually from the sun, and then they cause, like, a dimerization of these thymine, which you can see here in yellow. And it will distort the double helix causing lots of problems. This happens anytime you go outside. Luckily, our body can handle these and repair them very quickly, but they do happen all the time.

And finally, you have double strand break, and that's when both strands of DNA are damaged in some way. So before, these were connected, a break right here, and that caused them to separate. Obviously, if DNA is damaged and not repaired in some way by the body, it can cause serious disease. One example of this is xeroderma pigmentosa. You may be familiar with this. There have been movies and things about people with a "light allergy." Well, it's not really an allergy at all. It's just the inability to repair DNA damage caused from UV lights, so things like those thymine dimers. If you can't repair them, then anytime you're exposed to the sun, you get a bunch of DNA damage, and it can really cause significant issues to your skin, and you get lots of rashes and burns, and it's a pretty horrible disease, so you have to stay out of the light. There are many other different types of diseases that result from unrepaired DNA damage. So those are the 4 types of DNA damage.

Now, let's turn the page.

Repair Mechanisms

Okay. So now, let's talk about the different ways that DNA is repaired. Every type of mutation in the cell is going to be repaired in a different way. Let's go through some of the 4 main ways. The first one is mismatch repair. Mismatch repair fixes mismatched or lost bases, and it usually does this directly after DNA replication. How this is recognized is there's a double helix of DNA. Right? And let's say that somewhere in it, there's a mismatch nucleotide. Well, this mismatch nucleotide will actually result in some kind of distortion in the double helix. And the enzyme can come in, recognize that distortion and fix the nucleotide. Mismatch repair can remove nucleotides that have been damaged from chemicals, so we call this deamination, remember? The enzyme responsible for this is DNA glycosylase. What happens here is if you have correctly matched nucleotides and there's one that's incorrectly matched, DNA glycosylase will come in, it'll recognize this nucleotide, it will excise it, and then replace it with the correct nucleotide. So when it's been replaced with the correct nucleotide, that's great. Usually, base excision repair will only cut out and replace the one nucleotide. It can handle a small segment of nucleotides, but typically, it does the one.

Then we have nucleotide excision repair, which fixes bulky lesions like thymine dimers. We refer to this one most like a cut and paste method because if you have a bunch of nucleotides that are correctly matched and then you get one that isn't, what happens is the enzyme comes in and will actually cut out a large segment. It cuts that segment out, and then it comes back in, and will replace all the correct nucleotides. And then DNA ligase has to come back in and seal where it cut in the beginning. You have a cut enzyme that comes in and cuts out a big segment of nucleotides involving the wrong one, and then you have DNA ligase that comes back in and seals it back up once it has been replaced.

Finally, you have double-strand break repair, and this occurs when both strands of the DNA double helix are damaged. There are 2 ways; the first is non-homologous end joining. You have 2 strands of DNA, there's a break right here. They get cut out, so it looks more like this. What happens in non-homologous end joining is that these ends are just joined back together. Then we have homologous recombination, which I'm going to talk a lot more about in a few other videos. Homologous recombination is when the cell uses undamaged DNA as a template to repair the break. Instead of just joining it back together, which you can imagine can be pretty damaging to the cell if it is missing a big segment or something, it can actually use other DNA sequences to repair. I'm going to talk about homologous recombination very soon.

So with that, let's now turn the page.

Homologous Recombination

Hello, everyone. In this lesson, we are going to be learning about how cells are able to fix double-stranded breaks in their DNA. The way that they're able to fix double-stranded breaks in their DNA is they're going to use this process called homologous recombination. You've probably heard of homologous recombination before; that's probably a familiar term. And that is because when we usually learn about homologous recombination, we're learning about meiosis and the creation of gametes. Because homologous recombination is going to be a major step in meiosis, and it is going to create genetically unique gametes. And that is because homologous recombination is going to allow homologous chromosomes to exchange information. But I also wanted you guys to know that homologous recombination has another very, very important job, and that is going to be able to fix these very detrimental breaks that happen in DNA. So homologous recombination can also fix double-stranded breaks in the DNA. Double-stranded breaks are incredibly detrimental for the cell and the DNA itself. The DNA will start to degrade and become damaged. If the cell can't fix that break, then the cell will probably go into apoptosis. So cells don't want to go into apoptosis if they don't have to, so they do have mechanisms to attempt to fix these double-stranded breaks. And, we're going to go over how homologous recombination does that in these 8 steps. Okay? So, let's first start off with the very first step. Obviously, we're going to have a break in the DNA. And I'm going to go through these steps with these figures. So these are going to be homologous chromosomes. Okay? So these are homologous chromosomes. And that's why we are going to call it homologous recombination. Because to be able to fix this break that we see here in the DNA, we're going to have to recruit that chromosome's homologous chromosome. So we have the red chromosome and the blue chromosome, and they are homologues to one another. So we can see that the cell has recognized that a double-stranded break has occurred right here. So what is going to happen? That homologous chromosome is going to be recruited, and the process of homologous recombination is going to begin. The next thing that I want you guys to know that is going to happen is you're going to have these endonucleases, which are like cutting proteins. These endonucleases are going to remove some of the damaged DNA. So, let's say this is an endonuclease here, and then we have an endonuclease here. And what's going to happen is these endonucleases are going to cut the DNA. They're actually going to degrade the DNA. So, endonucleases degrade the damaged DNA in the 5' to 3' direction. And they're going to do this because we do need single-stranded areas of these chromosomes for this particular process to work. And as you guys can see, even though there is a break, they're still double-stranded. But we want it to be single-stranded for this to work properly, away some of the damaged DNA. And, you guys can see the results of that down here. So you guys can see that this whole section of single-stranded DNA were supposed to be in those yellow spots are now gone, and that is because those endonucleases or cutting proteins have removed it. So then the next thing that is going to happen is to stabilize this now single-stranded DNA. The RecA proteins are going to bind to the single-stranded broken DNA and to the single-stranded non-broken DNA. And basically, this is just here for stability, to ensure that the, DNA itself doesn't begin to degrade because it's very broken right now and slightly single-stranded, and DNA does not like to be that way, so the RecA protein is there for stability and making sure that it does not degrade. Okay? So now, let's go on to the next step. What's going to happen is single broken strand and single undamaged strands interact with their complementary regions. And this is generally going to be called strand invasion. So strand invasion is going to happen. And this is going to be strand invasion into the homologous chromosome that didn't have a break in it, or into the blue strand. Okay? So you're going to have strand invasion. It is now beginning to interact with its complementary region in the homologous chromosome. And this is able to happen because these red and blue chromosomes should have pretty much the exact same or very, very close to the same DNA sequence because they are homologous chromosomes. So that single-stranded piece of the red chromosome should find its complementary match inside of the blue chromosome, and it's going to bind with the blue chromosome, and that's going to be the process of strand invasion. You guys can kind of see it does invade the blue chromosome space. It kind of sticks itself inside of the blue chromosome, and it's going to create this loop structure. So now that invasion has begun, you're going to see the DNA repair actually begin. And this is where the blue chromosome, the undamaged chromosome, is being used as a template strand for the damaged chromosome to rebuild that section of the red chromosome that is missing. Okay, guys? And I want you guys to know that these structures that you see here, these x-like structures, these are very important. These are called Holiday Junctions. They're named after the individual who actually discovered them and worked with them, so that's why they're named Holiday. His last name was Holiday. And they're going to be where these two segments of DNA cross one another. So, in the first strand invasion, there's a single holiday junction, but this particular structure here is called a double Holiday Junction. Because there are 2 of them. And this is a very characteristic, a very unique characteristic of homologous recombination. You're going to see this bubble of DNA, and then you're going to see a double holiday structure. So now that the strand has invaded and the holiday junctions have formed, we're now going to see DNA polymerase come in and begin to build these new segments of DNA. So, you guys can see here that the DNA is building in this direction, and there are going to be new DNA bases being built on this red strand that makes it complementary to the blue strand. And once the red strand has been filled with its complementary bases, it is going to be done with DNA repair. The same thing's going on up here. The DNA strand is being built, and all of these new nucleotides are being added to the red strand that are complementary to the blue strand, which is the template strand. I hope that makes sense. I know that this can be kind of hard to wrap your brain around, but that's what's happening. The blue strand is being used as a template to build the extension of the broken red strand to fill in the gaps so that the red strand is no longer missing an important DNA sequence. Okay? So that is going to be what happens. And then, once all of those DNA segments have been put together correctly, we're going to see that those segments are going to be ligated together. They're going to be glued together. And then they're going to, either cut those holiday junctions or untwist those holiday junctions. But, just so you guys know, branch migration is going to occur whenever the damaged section of DNA is being elongated. Holiday is going to move in the direction that it is building. And that's so it can add more and more to the damaged DNA, so the holiday junction will be sliding as that new DNA is being built. That is called branch migration. I just thought you guys should know what branch migration is in case you guys see it in one of your tests. So once the DNA repair has been completed, those holiday junctions need to be unformed. They need to go away because we can't have our two homologous chromosomes intertwined with one another. That's just not the way it's going to work. So you can either cut the holiday junctions or you can untwist the holiday junctions. So, just so you guys know, whenever the holiday junctions are not cut, they're simply unraveled, that is called Disillusion. This is where the holiday junctions unwind. And, generally, you're going to have no crossover. Crossover is going to be when the homologous chromosomes actually exchange genetic material that doesn't have anything to do with the damaged area. It's like exchanging extra genetic material. And whenever dissolution happens, those holiday junctions are simply going to unwind from each other, and then there's going to be no crossing over occurring. The only thing that is given to the homologous DNA is going to be it's going to fill in the damaged area. No extra DNA. Okay? Now, whenever those holiday junctions are cut in particular ways, you can have the process of resolution. Resolution is going to be where the holiday junctions are cleaved. And what I mean by that is, let me scroll up so you guys can see a Holiday Junction. What I mean by that is an enzyme is going to come along and it's going to cut the holiday junction. So all of the DNA above the cut is going to go into the red chromosome, and all of the DNA below the cut is going to go into the blue chromosome. So commonly with resolution cutting, you're going to have extra genetic material being exchanged, and you're generally going to have crossing over occur. But whenever you're just simply unwinding the holiday junction in disillusion, you're not going to have crossover. But if you cut it, you generally are going to have crossover. Okay? So, let me write that down for you guys. This generally leads to crossover. Not all the time if the cut is perfect, but a lot of the time it's going to lead to crossover. So once those holiday junctions have the two strands that are cleaved, now the, sorry. Now the DNA helices, those two homologous chromosomes are no longer interacting. They are their own independent chromosomes. And like I said, this cleavage can result in crossing over causing DNA exchange outside of the breakpoint or the damaged area. And sometimes, this means that you can have some problems where noncomplementary regions between the two helices are joined. And generally, this is going to be fixed by base excision repair. So, yes, homologous recombination does fix these major double-stranded breaks, but it's not perfect. And sometimes you'll have, noncomplementary regions in one of the homologous chromosomes due to homologous recombination, and you're going to have base excision repair come in and fix it. Okay? Now, these are going to be two examples of where those chromosomes that we talked about up there did not cross over or they did cross over. So, you guys can see that right here, the only thing that is given to the red one was the area that was damaged. The only thing that was exchanged was enough DNA to fix the damaged area. However, over here, you guys can see that there's a whole blue strand down here, and then some red, and some more red. And it's obvious there was a lot exchanged that was more than just the damaged area, and that is going to be crossover. Resolution generally leads to crossover and disillusion generally leads to non-crossover. I hope that was helpful, guys. I know homologous recombination can be a little bit tricky and a little bit difficult to understand, but I just want you guys to know that homologous recombination is where homologous chromosomes interact with one another to repair a double-stranded DNA break. Okay, everyone. Let's go on to our next topic.

Which of the following is not a type of DNA damage repair?

• A. Mismatch repair
• B. Base Excision repair
• C. Lost nucleotide repair
• D. Double Strand Break repair

Which of the following types of DNA damage occurs when a base is chemically converted into another base?

• A. Depurination
• B. Deaminatino
• C. Thymine Dimer

Which type of DNA repair is responsible for fixing bulky lesions through a 'cut and paste' method?

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

Homologous recombination occurs directly after DNA replication?

• A. True
• B. False

Here’s what students ask on this topic:

What are the main types of DNA damage?

The main types of DNA damage include depurination, deamination, thymine dimers, and double-strand breaks. Depurination involves the loss of purine bases (adenine and guanine), while deamination is the chemical conversion of one base into another, such as cytosine to uracil. Thymine dimers are caused by UV light, leading to the dimerization of adjacent thymine bases, which distorts the DNA helix. Double-strand breaks occur when both strands of the DNA helix are severed, posing a significant threat to genomic integrity if not repaired.

How does mismatch repair work in DNA repair mechanisms?

Mismatch repair corrects errors that occur during DNA replication, such as mismatched bases. The process involves recognizing distortions in the DNA helix caused by mismatched nucleotides. Enzymes like DNA glycosylase excise the incorrect nucleotide, and DNA polymerase fills in the correct base. Finally, DNA ligase seals the repaired segment. This mechanism ensures the fidelity of DNA replication and prevents mutations from being passed on to daughter cells.

What is the role of homologous recombination in DNA repair?

Homologous recombination is crucial for repairing double-strand breaks in DNA. It uses a homologous chromosome as a template to accurately repair the break. The process involves several steps, including endonuclease activity to create single-stranded DNA, strand invasion, and the formation of Holliday junctions. DNA polymerase then synthesizes new DNA using the homologous chromosome as a template. This method ensures high-fidelity repair, maintaining genomic stability and preventing cell death or diseases.

What are thymine dimers and how are they repaired?

Thymine dimers are lesions formed when two adjacent thymine bases covalently bond due to UV light exposure, distorting the DNA helix. They are primarily repaired by nucleotide excision repair (NER). In NER, an enzyme complex recognizes the distortion, excises a segment of the DNA containing the dimer, and then DNA polymerase fills in the gap with the correct nucleotides. Finally, DNA ligase seals the repaired segment, restoring the DNA's integrity.

What is xeroderma pigmentosum and how is it related to DNA repair?

Xeroderma pigmentosum (XP) is a genetic disorder characterized by extreme sensitivity to UV light, leading to a high risk of skin cancers. It results from defects in the nucleotide excision repair (NER) pathway, which is responsible for repairing UV-induced DNA damage like thymine dimers. Individuals with XP cannot effectively repair this damage, leading to the accumulation of mutations and severe skin abnormalities. Avoiding UV exposure and using protective measures are crucial for managing the condition.