DNA Repair Mechanisms - Online Tutor, Practice Problems & Exam Prep

DNA repair mechanisms are crucial for maintaining genetic integrity. DNA Polymerase proofreading corrects mismatches during replication by backtracking and excising incorrect nucleotides. When proofreading fails, mismatch repair identifies and resynthesizes erroneous regions using methylation to distinguish old from new strands. Base excision repair targets damaged nitrogenous bases, while nucleotide excision repair removes thymine dimers caused by UV light. Photoreactivation utilizes photolyase to directly repair thymine dimers. The SOS repair system acts as a last resort for extensive DNA damage, albeit with a risk of mutations. Understanding these processes is vital for comprehending cellular resilience and genetic stability.

DNA Polymerase Proofreading

In this video, we're going to begin talking about DNA repair by specifically focusing on DNA Polymerase Proofreading. DNA Polymerase is an enzyme that is important for replicating or building DNA. It has the ability to identify and correct mismatches in the DNA. When we talk about mismatches, we need to recall the Watson and Crick base pairing rules, where As in the DNA always base pair with Ts and Gs in the DNA always base pair with Cs. However, a mismatch would be if, for example, a T were to base pair with a C instead, which is not the correct match, and so we call this a mismatch.

DNA polymerase has the ability to identify and correct any mismatches that can occur naturally when it is synthesizing DNA. It is able to correct these mismatches by the process called DNA proofreading. DNA proofreading proofreads the DNA for errors and makes corrections, just like you can proofread your English essay before you turn it into your English professor to check for errors. DNA proofreading allows the DNA polymerase to check the DNA for errors.

The way DNA proofreading works is that it is able to correct errors by backtracking in a backwards 3' to 5' direction, and it's able to excise or remove the incorrect nucleotide. We refer to this backtracking as a 3' to 5' exonuclease activity, which refers to the cleavage of a nucleotide from the end of the DNA to help remove the incorrect nucleotide. Once the incorrect nucleotide has been removed, the DNA Polymerase can go ahead and add the correct nucleotide, and replication can then continue as normal.

If we take a look at our image below, we can get a better understanding of DNA polymerase proofreading. The pink structure you see represents the DNA Polymerase. The DNA Polymerase builds the brand new strands in a 5' to 3' direction. Occasionally, DNA Polymerase can make mistakes as it is matching these base pairs. If it makes a mistake, as seen here in this image, where it accidentally base pairs a T with a C (since Ts are supposed to be base paired with As, and Cs are supposed to be base paired with Gs, not with Ts), this is a mistake. However, DNA polymerase proofreading allows it to correct these mismatches. The incorrect nucleotide, a T, is going to be removed through the DNA polymerase's 3' to 5' exonuclease activity. Once the incorrect nucleotide has been removed, the DNA polymerase can go ahead and incorporate the correct nucleotide, a G, creating a correct match and allowing DNA replication to continue.

While DNA polymerase proofreading is very effective, occasionally it is not perfect and will not be able to correct these mismatches. The cell still needs to require other types of repair mechanisms in case the proofreading happens to miss a mistake that passes through. This concludes our brief lesson on DNA Polymerase Proofreading, and we'll be able to get some practice applying these concepts and learn about other DNA repair mechanisms as we move forward in our course. I'll see you all in our next video.

DNA polymerase proofreading works by removing a mismatched base in the _______ direction, then replaces it with the correct base synthesized in the ________ direction.

• A. 5' to 3' ; 5' to 3'.
• B. 3' to 5' ; 5' to 3'.
• C. 3' to 5' ; 3' to 5'.
• D. 5' to 3' ; 3' to 5'.

Mismatch Repair

In this video, we're going to continue to talk about DNA repair by focusing specifically on mismatch repair. And so when proofreading by DNA polymerase fails to correct a mutation, which can occasionally happen, the cell will then resort to mismatch repair. Now mismatch repair is a DNA repair mechanism, as its name implies, is going to fix mismatched nucleotides. And it does this by removing and then re-synthesizing regions of DNA. Now recall from our previous lesson videos that the DNA template strand can actually be distinguished from the newly built DNA strand via methylation, the addition of a CH₃ functional group. And so recall that the old DNA template strand is going to be methylated, whereas the newly built DNA strand is not yet methylated. And so, the methylation helps enzymes distinguish between the old template strand and the newly built DNA strand.

Now mismatch repair occurs in a series of 4 steps that we have numbered down below in our image. And so, this image is focusing on mismatch repair. And in the very first step of mismatch repair, what you'll notice is we have the template strand is on the bottom here, and notice the old template strand is methylated, so it has these CH₃ groups. And then the newly built DNA strand is at the top, and it is not yet methylated. And what you'll notice is that the incorrect nucleotide is going to be mismatched during DNA replication. And so, notice here in the DNA we have a mismatched nucleotide highlighted here in yellow. And so, this mismatch that you see right here, recall that Gs are supposed to be base-paired with Cs, not with As, and so this is a mismatched nucleotide.

So then in step number 2, a specific enzyme is going to cut the new DNA strand near the mismatch site. And again, the enzyme can distinguish between the new and the old DNA strand because, again, the old DNA strand, the template is methylated, but the new DNA strand is not yet methylated. And so it's going to cut the new DNA strand as you see here at a site near the mismatch. And then in step number 3, this enzyme is going to remove a short stretch of the new DNA strand, and this is going to include the mismatched nucleotide. And so notice here that the short stretch, a short region has been removed and that includes the mismatched nucleotide.

And then what happens is the DNA polymerase enzyme is able to come back into play and synthesize a new DNA fragment. And the new DNA fragment we've color-coded here in a reddish color just so that you can visually identify it. And so, the new DNA fragment is going to contain the correct nucleotide, and so it would have repaired that mismatch. And then a DNA ligase enzyme is going to come and seal the new fragment to create a single molecule. And so what you have here is the new DNA fragment has repaired that mismatch and now there is a C here when previously there was a mismatch, and there was an A, and so this is basically the fundamental steps of mismatch repair.

And so that concludes our brief lesson on mismatch repair and once again we'll be able to get some practice applying these concepts and learn about other DNA repair mechanisms as we move forward in our course. So I'll see you all in our next video.

Why is methylation important for the mismatch repair mechanism of DNA?

• A. They mark the new strand of DNA.
• B. They mark where proteins need to bind and remove the damaged DNA.
• C. They mark the template strand of DNA.
• D. They are removed to repair the mutation.
• E. They mark where degradation of the new strand must take place.

What kind of DNA damage is repaired using the mismatch repair mechanism?

• A. Point mutations made during DNA replication.
• B. Point mutations caused by chemical mutagens.
• C. Point mutations caused by irradiation.
• D. Double-strand breaks in DNA made during replication.

Base Excision Repair

In this video, we're going to talk about base excision repair. Base excision repair is a DNA repair mechanism that replaces and repairs damaged nitrogenous bases that may have been damaged through some kind of chemical modification to the nitrogenous base. Base excision repair uses enzymes called glycosylases. These glycosylases can identify the damaged bases and then remove them. Base excision repair occurs in a series of three steps that we have numbered down below in our image. Notice the image below is focusing on base excision repair, which utilizes enzymes known as DNA Glycosylases, represented in this image as a green circle that you see highlighted right here.

The DNA glycosylase enzyme identifies the DNA distortion caused by the damaged nitrogenous base. After it identifies the distortion, you can see that the DNA backbone here is distorted, it will then remove the damaged nitrogenous base. Here you can see that the damaged nitrogenous base is the guanine that's chemically modified. It is being removed, as you see here, by the DNA glycosylase enzyme. Then, another enzyme will come in and cut the sugar phosphate backbone at the site where the damaged nucleobase used to be. Here you can see the enzyme comes in and cuts the sugar phosphate backbone. What happens next is that the DNA polymerase enzyme comes back into play, and its 3' to 5' exonuclease activity removes and then replaces the damaged region of DNA, and DNA ligase will seal it together. Here, the new DNA has been removed and replaced, and now the correct nitrogenous base has been implemented.

This concludes our brief lesson on base excision repair. We'll be able to get some practice applying these concepts and learn about other DNA repair mechanisms as we move forward. So, I'll see you all in our next video.

What is the function of DNA glycosylase during base excision repair?

• A. Addition of the correct nucleotide.
• B. Cleavage of the phosphodiester bond.
• C. Addition of the correct nucleobase.
• D. Removal of the incorrect nucleotide.
• E. Removal of the incorrect nucleobase.

Nucleotide Excision Repair

In this video, we're going to continue to talk about DNA repair mechanisms by focusing specifically on mechanisms that repair Thymine Dimers, including Nucleotide Excision Repair. Recall from our previous lesson videos that Thymine Dimers occur when covalent bonds form between adjacent Thymine Nucleotides or Thymine bases in the DNA. These Thymine Dimers can cause issues because they can prevent replication and prevent transcription as it occurs normally. These Thymine Dimers must be repaired, and they can be repaired in one of two ways. They can be repaired via nucleotide excision repair, or they can be repaired via photoreactivation. Now, in this video, we're going to focus on nucleotide excision repair, and then later in a different video, we'll talk about photoreactivation. Both are going to repair Thymine Dimers.

Nucleotide excision repair is going to once again repair Thymine Dimers. It does this by removing a region of DNA that overlaps the dimer. Nucleotide excision repair occurs in a series of three steps that we have numbered down below in our image. This image is focused on nucleotide excision repair, which again is going to repair Thymine Dimers. What you'll notice here, in this image, we're showing you the formation of a Thymine Dimer. Thymine Dimer will form when the DNA is exposed to UV light, ultraviolet light. For example, here we're showing you the sun, and the sun has radiation including UV ultraviolet light, and that can cause Thymine Dimers to form. Notice that we have two adjacent Thymine bases, and they are covalently bound. Again, this can cause issues, and these thymine dimers need to be repaired.

Nucleotide excision repair involves an enzyme identifying the thymine dimer, then cutting out a fragment of the DNA that overlaps the dimer. Here you can see that the cut is happening here and over here, and it is removing this region of DNA that contains the thymine dimer. The DNA polymerase enzyme is going to synthesize a new DNA fragment, and the DNA ligase will seal it into place. You can see here that the new DNA fragment is color-coded in red, and you'll see that the new DNA fragment replaces the old fragment that contained the thymine dimer. Now we have the DNA that no longer has those thymine dimers, and this DNA has been repaired. The thymine dimers have been removed and replaced.

This here concludes our brief lesson on nucleotide excision repair and how this is able to repair these thymine dimers. This also concludes this video, and we'll be able to get some practice applying these concepts and learn more about other repair mechanisms as we move forward. I'll see you all in our next video.

Which of the following statements about nucleotide excision repair and base excision repair is true?

• A. Nucleotide excision repair fixes bulky, helix distorting mutations which encompass multiple nucleotides.
• B. Base excision repair fixes small, non-helix distorting mutations which only include a single, damaged base.
• C. DNA glycosylase proteins are used to fix the DNA in base excision repair.
• D. Thymine dimers are mutations which are commonly repaired using nucleotide excision repair.
• E. All of the above statements are true.

Photoreactivation

In this video, we're going to continue to talk about DNA repair mechanisms by focusing specifically on photoreactivation. Recall from our previous lesson videos that thymine dimers may be repaired using photoreactivation. Photoreactivation is a DNA repair mechanism that repairs thymine dimers, and it does so by using the light-responsive enzyme called photolyase. Only cells or organisms that contain this enzyme, photolyase, are able to repair their thymine dimers using photoreactivation.

If we take a look at our image down below, notice this is an image showing you photoreactivation. In the very first step here, we're showing you that the thymine dimer is going to form when the DNA is exposed to UV light, ultraviolet light. You can see that the UV light is being represented here by the sun, and it's causing the formation of this thymine dimer, which can cause complications in the cell. The thymine dimer must be repaired.

What happens in photoreactivation is the enzyme called, once again, photolyase, which in this image is represented by this big yellow structure in the back, is going to bind to the thymine dimer. The enzyme photolyase is actually going to break the covalent cross-link holding the thymine dimers together. Now the covalent cross-link has been broken and these thymine dimers are no longer dimers. They have been broken apart, and the cross-link that was holding them together has been broken, and now these thymines are normal thymines, as you see here.

At this point, the photolyase will then be released from the DNA, and the DNA has been repaired. The thymine dimer has been repaired. This concludes our brief lesson on photoreactivation. We'll be able to get some practice applying these concepts as we move forward. So, I'll see you all in our next video.

_________ is the enzyme involved in repairing thymine dimers during photoreactivation.

• A. DNA Polymerase.
• B. DNA ligase.
• C. Photoligase.
• D. Photolyase.
• E. DNA lyase.

Photoreactivation is able to remove what type of mutation?

• A. UV induced double strand breaks in DNA.
• B. UV induce thymine dimers.
• C. Mismatches in DNA.
• D. Single strand breaks in DNA.

SOS Repair System

In this video, we're going to continue to talk about DNA repair mechanisms by focusing specifically on the SOS repair system. Despite having many different repair mechanisms, an organism with extensively damaged DNA or with a lot of DNA damage is going to express the SOS repair system or just the SOS system. The SOS repair system is a complex repair mechanism that is activated by the cell when the DNA is extensively damaged. When there is a lot of DNA damage, the SOS repair system will be activated. The SOS repair system really acts as a last effort attempt, a last ditch effort attempt to repair the extensively damaged DNA. The SOS repair system involves the expression of several dozens of different genes, including a special DNA polymerase. This special DNA polymerase is actually somewhat error prone. So, it can cause what is known as SOS mutagenesis. SOS mutagenesis is really just when minor mutations or errors are caused by the DNA polymerase of the SOS DNA repair system. If we take a look at our image down below, we can get a better understanding of the SOS repair mechanism, which again is only implemented when there is extensive DNA damage. Lots and lots of DNA damage represented by all this fire here forming on the DNA. Enzymes, and many different enzymes are going to be implemented. The SOS repair system is only implemented when there is extensive damage. We can say that the DNA damage is extensive, basically meaning that there is a lot of DNA damage. Many different enzymes are going to come into play, represented by all of these different things that you see here, including a special DNA polymerase that is going to be error prone because it lacks proofreading activity. Notice that this special DNA polymerase that's implemented during the SOS repair mechanism, is saying here, "I can try to fix all this damage, but I can't really see." This is just an analogy to show you how the DNA polymerase here is, going to help repair a lot of this damage, but it is still somewhat error prone. The DNA polymerase is not going to be able to proofread. It cannot proofread. And so it is error prone. You'll see that the SOS repair system can repair most of the DNA. You'll notice that the DNA damage is not nearly as extensive as it was before. However, there still can be some mutations that are left over. Some damage that is left over, and this is what we refer to as the SOS mutagenesis. And that is just going to be mutations that are caused by the SOS repair mechanism. However, the SOS repair mechanism does help to repair most of the damage. It is a last ditch effort to repair the DNA when it is extensively damaged. This here concludes our brief lesson on the SOS repair system, and we'll be able to get some practice applying these concepts as we move forward. So, I'll see you all in our next video.

SOS repair is mediated by a ______________ DNA polymerase:

• A. Proofreading.
• B. Mutation-resistant.
• C. Single-stranded ongoing synthesis.
• D. Error-prone.
• E. Photoactivated.

When the DNA is extensively damaged the cell needs to repair the DNA with the SOS repair mechanism. What is the negative side effect of the cell using SOS repair?

• A. SOS repair mechanism can make errors in the DNA while attempting to repair larger mutations in the DNA.
• B. SOS repair mechanism consumes an extremely large amount of energy.
• C. SOS repair mechanism stops all other mechanisms in the cell from happening.

Here’s what students ask on this topic:

What is DNA polymerase proofreading and how does it work?

DNA polymerase proofreading is a mechanism that corrects mismatches during DNA replication. DNA polymerase, the enzyme responsible for synthesizing new DNA strands, can identify and correct errors by backtracking in a 3' to 5' direction. This backtracking involves the enzyme's 3' to 5' exonuclease activity, which excises the incorrect nucleotide. Once the incorrect nucleotide is removed, DNA polymerase adds the correct nucleotide, allowing replication to continue accurately. This proofreading process ensures high fidelity in DNA replication, although it is not perfect and some errors may still escape correction.

How does mismatch repair differ from DNA polymerase proofreading?

Mismatch repair is a secondary mechanism that corrects errors missed by DNA polymerase proofreading. It identifies and fixes mismatched nucleotides by distinguishing the newly synthesized DNA strand from the template strand through methylation. The process involves four steps: recognizing the mismatch, cutting the new DNA strand near the mismatch, removing a short segment of the new strand including the mismatch, and resynthesizing the correct sequence using DNA polymerase. Finally, DNA ligase seals the new fragment, ensuring the integrity of the DNA.

What is base excision repair and what role do glycosylases play in it?

Base excision repair is a DNA repair mechanism that targets and fixes damaged nitrogenous bases caused by chemical modifications. Glycosylases are enzymes that play a crucial role in this process. They identify and remove the damaged bases, creating an abasic site. An endonuclease then cuts the sugar-phosphate backbone at this site. DNA polymerase removes the damaged region and synthesizes a new DNA fragment, which is finally sealed by DNA ligase. This process ensures the correction of specific base damage, maintaining genetic stability.

How does nucleotide excision repair fix thymine dimers?

Nucleotide excision repair (NER) is a mechanism that repairs thymine dimers, which are covalent bonds formed between adjacent thymine bases due to UV light exposure. NER involves three main steps: an enzyme identifies the thymine dimer and cuts out a fragment of DNA that includes the dimer, DNA polymerase synthesizes a new DNA fragment to replace the excised section, and DNA ligase seals the new fragment into place. This process effectively removes and replaces the damaged DNA, restoring normal DNA function.

What is the SOS repair system and when is it activated?

The SOS repair system is a complex DNA repair mechanism activated when a cell experiences extensive DNA damage. It acts as a last-resort effort to repair severely damaged DNA. The system involves the expression of several dozen genes, including a special, error-prone DNA polymerase that lacks proofreading activity. This can lead to SOS mutagenesis, where minor mutations are introduced during the repair process. Despite its error-prone nature, the SOS repair system helps to repair most of the DNA damage, ensuring the cell's survival under extreme conditions.