DNA Repair Mechanisms - Video Tutorials & Practice Problems
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1
concept
DNA Polymerase Proofreading
Video duration:
6m
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in this video, we're going to begin talking about DNA repair by specifically focusing on DNA preliminaries proof reading. And so DNA preliminaries recall is an enzyme that is important for replicating or building D. N. A. And it has the ability to identify and correct mismatches in the D. N. A. And so when we're talking about mismatches, what we need to recall is the Watson and Crick base pairing rules where A. Is in the D. N. A. Always base pair with teas and G. S. And the D. N. A. Always base pair with sees. However a mismatch would be if for example a. T. Were to base pair with a C. Instead. And so this is not the correct match until we call this a mismatch. And so uh one thing to keep in mind here is that DNA preliminaries has this ability to identify and correct any mismatches. And these mismatches can occur naturally when it is synthesizing D. N. A. And it's able to correct these mismatches by the process called DNA proof reading. And so DNA proof reading as its name implies. Um It's going to proof read the D. N. A. And by proof read what it means. It's going to self correct. Um And so it's going to be able to check the DNA for errors and make corrections. And so proof DNA proof reading is a self correcting process of DNA preliminaries during DNA replication. And so just like you can proof read your english essay before you turn it into your english professor. Um and check your english essay for errors. DNA proof reading allows the DNA preliminaries to check the DNA for errors. And so essentially the way this works is that DNA proof reading is able to correct errors by backtracking in a backwards three prime to five prime direction. And it's able to x ice or remove the incorrect nucleotide. And we refer to this backtracking as a three prime to five prime xo nucleus activity. And this is referring to the cleavage of a nucleotide from the end of the DNA. To help remove or excites the incorrect nucleotide. And so once the incorrect nucleotide has been removed then the D. N. A polymerase can go ahead and add the correct nucleotide and replication can then continue as normal. And so if we take a look at our image down below, we can get a better understanding of DNA preliminaries proof reading. And so notice here what we're showing you is a DNA molecule that's in the process of being replicated. And so the pink structure that you see here represents the DNA preliminaries. And of course the DNA preliminaries builds the brand new strands in a five prime 23 prime direction. And so occasionally DNA polymerase can make mistakes as it is matching these base pairs. And so if it makes a mistake, as you can see here in this image where accidentally base pairs A T. With a C. Because remember teas are supposed to be based paired with a S and um sees are supposed to be based paired with Gs not with T. S. And so if it makes a mistake and incorporates A. T. That is something that it can occur occasionally. So it says DNA proliferates inserts the mismatched nucleotide during DNA replication. And so this is a mistake. However DNA preliminaries proof reading allows it to correct these mismatches. These mistakes. And so what can happen is the incorrect nucleotide is going to be removed from the new DNA strand. And so what you'll see here is that the T. Is being removed and this is all removed by the D. N. A preliminary races three prime to five prime Exxon nucleus activity. And so um once the incorrect nucleotide has been removed then the DNA polymerase can go ahead and incorporate the correct nuclear tie. And so the correct nucleotide is then inserted and DNA replication can continue. And so you can see here that A. G. Has been put in and this is creating a correct match. And so what we've seen here is that DNA preliminaries has the ability to proof read and correct errors that may have occurred mismatches that may have occurred. And while DNA preliminaries proof reading is very very effective occasionally DNA proof reading is not it is not perfect and it will not be able to correct these mismatches. And so the cell still needs to require other types of repair mechanisms in case the proof reading happens to miss a mistake if a mistake happens to pass through. And so this year concludes our brief lesson on DNA preliminaries proof reading, 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, so I'll see you all in our next video.
2
Problem
Problem
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'.
3
concept
Mismatch Repair
Video duration:
4m
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in this video, we're going to continue to talk about DNA repair by focusing specifically on mismatch repair. And so when proof reading by DNA preliminaries 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 old previous lesson videos that the D. N. A template strand can actually be distinguished from the newly built D. N. A. Strand via methylation. Uh The addition of a ch three functional group. And so recall that the old D. N. A template strand is going to be methylated, whereas the newly built D. N. A strand is not yet methylated. And so the methylation helps enzymes distinguished between the old template strand in the newly built DNA strand. Now mismatch repair occurs in a series of four steps that we have numbered down below in our image. And so uh this image is focusing on mismatch repair. And and the very first step of mismatch repair which will notice as we have the template strand is on the bottom here and notice that the old template strand is methylated. So it has these CH three 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 uh the incorrect nucleotide is going to be mismatched during D. N. A replication. And so notice here in the D. N. A. 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 based paired with sees, not with A. S. And so this is a mismatched nucleotide. So then in step number two, a specific enzyme is going to cut the new D. N. A. 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 three, this enzyme is going to remove uh a short stretch of the new D. N. A. Strand. And this is going to include the mismatched nucleotide. And so notice here that these 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 ah and 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 like this 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 repaired. 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.
4
Problem
Problem
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.
5
Problem
Problem
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.
6
concept
Base Excision Repair
Video duration:
2m
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in this video, we're going to talk about base excision repair. And so base excision repair is a DNA repair mechanism that is going to replace and repair damaged nitrogenous bases that may have been damaged through some kind of chemical modification to the nitrogenous base. And so basic decision repair is going to be using enzymes that are called like casa leases. And these glycogen palaces are able to identify the damaged bases and then they will remove the damaged basis. And so basic cision repair occurs in a series of three steps that we have numbered down below in our image. And so notice the image. Down below is focusing on base excision repair, which again, we know utilizes enzymes known as DNA like Castle Asus, which in this image is represented as this green circle that you see highlighted right here. And so the DNA like castles enzyme is going to identify the DNA distortion that's caused by the damaged nitrogenous base. And then after it identifies the distortion, you can see that the DNA backbone here is distorted. It will then remove the damaged nitrogenous base. And so here you can see that the damage nitrogenous base is this symbol that you see right here. It's the guanine that's chemically modified and so it is being removed as you see here by the DNA like hostels enzyme. And then another enzyme is going to come in and it is going to cut the sugar phosphate backbone where the damaged nuclear base used to be. And so here you can see the enzyme comes in and it cuts the sugar phosphate backbone. And then what happens is the DNA polymerase enzyme comes back into play and it's three prime to five prime Exxon nucleus activity is going to remove and then replace the damaged region of D. N. A. And then DNA like gates will seal it together. And so that you can see here is that here the new D. N. A. Has been, the D. N. A. Region has been removed and replaced. And so now there is the correct uh nitrogenous base has been implemented here. And so this year uh concludes our brief lesson on base excision repair and 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.
7
Problem
Problem
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.
8
concept
Nucleotide Excision Repair
Video duration:
3m
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in this video we're going to continue to talk about DNA repair mechanisms by focusing specifically on mechanisms that repair thigh ming di MERS including nucleotide excision repair. And so recall from our previous lesson videos that timing die MERS occur when covalin bonds form between adjacent timing nucleotides or thiamine bases and the DNA. And so these timing die MERS can cause issues because they can prevent replication and prevent transcription as it occurs normally. And so these timing diners must be repaired and they can be repaired into one of two ways they can be repaired, be a nucleotide excision repair or they can be repaired via photo reactivation. Now in this video we're going to focus on nucleotide excision repair and then later in a different video we'll talk about photo reactivation. Both are going to repair timing diners. And so nucleotide excision repair is going to once again repair thing. I mean die MERS and it does this by removing a region of DNA that overlaps the dime er and so nucleotide excision repair occurs in a series of three steps that we have numbered down below in our image. And so notice this image is focused on nucleotide excision repair which again is gonna repair timing diners. And so what you'll notice here is that in this image we're showing you the formation of thiamine dime. Er And so these I mean dime er will form when the D. N. A. Is exposed to UV light. Ultraviolet light. So for example here we're showing you the sun and the sun has radiation including UV ultraviolet light and that can cause timing diners to form. So notice that we have two adjacent demean bases and they are co violently bound and again this can cause issues and so these diamond diamonds need to be repaired and so nucleotide excision repair, what happens is an enzyme is going to identify the thiamine dime er and then it cuts out a fragment of the DNA that overlaps the dime er And so here you can see that the cut is happening here and over here and so it is removing this region of DNA that contains the timing diver and then uh DNA preliminaries enzyme is going to synthesize a new DNA fragment and the DNA like gates will seal it into place. And so you can see here the new DNA fragment is color coded here in red and so you'll see that the new DNA fragment replaces the old fragment that contained the timing dime. Er And so now we have the DNA that no longer has those timing diners and this D. N. A. Has been repaired. The timing diners have been removed and replaced. And so this here concludes our brief lesson on nucleotide excision repair and how this is able to repair these things. I mean die MERS. And so this here 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. So I'll see you all in our next video
9
Problem
Problem
Which of the following statements about nucleotide excision repair and base excision repair is true?
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.
10
concept
Photoreactivation
Video duration:
2m
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in this video, we're going to continue to talk about DNA repair mechanisms by focusing specifically on photo reactivation. And so recall from our previous lesson videos that timing die MERS may be repaired using photo reactivation. And so photo reactivation is a DNA repair mechanism that repairs timing die MERS. And it does so by using the light responsive enzyme called photo Elias. And so really only cells or organisms that contain this enzyme photo lies are able to repair their timing die MERS using photo reactivation. And so if we take a look at our image down below notice this is an image showing you photo reactivation and what you'll notice is that in the very first step here we're showing you that the timing dime er is going to form when the D. N. A. Is exposed to UV light, ultraviolet light. And so you can see that the UV light is being represented here by the sun and it's causing the formation of this timing dime er which can cause complications in the cell. And so the timing timer must be repaired. And so what happens in photo reactivation is the enzyme called Once again photo lies, which in this image is being represented by this big yellow structure in the back. The enzyme photo Elias is going to bind to the timing dime. Er as you see right here and then the enzyme photo lice is actually going to break the Covalin cross link between the timing holding the timing dymo together. And so you can see that now the Covalin cross link has been broken and these timing diners are no longer diamonds, they have been broken and the cross link that was holding them together has been broken. And so now these timings are normal timings um as you see here, and so at this point the photo lies will then be released from the D. N. A. And the D. N. A. Has been repaired. The timing dime er has been repaired and so this year concludes our brief lesson on photo reactivation and uh 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.
11
Problem
Problem
_________ is the enzyme involved in repairing thymine dimers during photoreactivation.
A
DNA Polymerase.
B
DNA ligase.
C
Photoligase.
D
Photolyase.
E
DNA lyase.
12
Problem
Problem
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.
13
concept
SOS Repair System
Video duration:
3m
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in this video, we're going to continue to talk about DNA repair mechanisms by focusing specifically on the S. O. S. Repair system. And so despite having many different repair mechanisms an organism with extensively damaged DNA or with a lot of DNA damage is going to express the S. O. S. Repair system or just the S. O. S. System. And so the S. O. S. Repair system is a complex repair mechanism that is activated by the cell when the D. N. A. Is extensively damaged. When there is a lot of DNA damage, the S. O. S. Repair system will be activated. And so the S. O. S. Repair system really acts as a last effort attempt a last ditch effort attempt to repair the extensively damaged DNA. And so the S. O. S. Repair system involves the expression of several dozens of different genes, including a special DNA proliferates. And this special DNA polymerase is actually somewhat error prone. So it can cause what is known as S. O. S. Muda genesis and S. O. S. Muna genesis is really just when minor mutations or heirs are caused by the DNA preliminaries of the S. O. S. DNA repair system. And so if we take a look at our image down below, we can get a better understanding of the S. O. S. Repair mechanism which again is only implemented when there is extensive DNA damage. Lots and lots of DNA damage represented by all of this fire here forming on the D. N. A. Okay and so what you'll notice is that enzymes uh many different enzymes are going to be implemented and the S. O. S. Repair system is only implemented when there is extensive damage. And so we can say that the DNA damage is extensive basically meaning that there is a lot of DNA damage. And so many different enzymes are going to come into play represented by all of these different things that you see here, including a special DNA preliminaries that is going to be error prone because it lacks perforating activity. And so notice that this the special DNA preliminaries that's implemented during the S. O. S. Repair mechanism and saying here I can try to fix all this damage but I can't really see and this is just an analogy to show you how the DNA preliminaries here is going to help prepare a lot of this damage but it is still somewhat error prone. And so the DNA preliminaries is not going to be able to prove right, it cannot prove it and so it is a rare prone and so what you'll see here is that the S. O. S. Repair system it can repair most of the D. N. A. And so you'll notice that the DNA damage is not nearly as extensive as it was before. However you'll notice that there still can be some mutations that are left over. Okay some damage that is left over. And this is what we refer to as the S. O. S. Muda genesis and that is just going to be mutations that are caused by the S. O. S. Repair mechanism. However, the S. O. S. Repair mechanism does help to repair most of the damage, and so it is a last ditch effort to repair the D. N. A. When it is extensively damaged. And so this here concludes our brief lesson on the S. O. S. 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.
14
Problem
Problem
SOS repair is mediated by a ______________ DNA polymerase:
A
Proofreading.
B
Mutation-resistant.
C
Single-stranded ongoing synthesis.
D
Error-prone.
E
Photoactivated.
15
Problem
Problem
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.
