BIOCHEMISTRY DISCUSSION 8
Biochemistry: A Short Course Fourth Edition CHAPTER 35 DNA Repair and Recombination
Tymoczko • Berg • Gatto • Stryer
© 2019 W. H. Freeman and Company.
Created by Brett Barbaro
So now we are going to talk a little bit about how DNA gets repaired when it’s damaged, and recombination plays a role in that. Yeah, that’s the same sort of recombination that occurs when a cell divides in meiosis.
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Chapter 35: Outline
35.1 Errors Can Arise in DNA Replication
35.2 DNA Damage Can Be Detected and Repaired
35.3 DNA Recombination Plays Important Roles in Replication and Repair
Created by Brett Barbaro
So first we’ll talk about some of the ways that DNA can be damaged. And then second, we’ll talk about how that damage is detected and repaired. And then we’re going to talk about recombination and its role in repair and replication.
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DNA Damage
DNA damage is inevitable, resulting from errors in replication or environmental insults.
DNA damage may lead to cell death or uncontrolled replication, as when normal cells are transformed into cancer cells.
Repair systems exist to recognize and repair damage to DNA.
Created by Brett Barbaro
So DNA damage is inevitable. And that’s kind of an important point. There’s a constantly changing environment inside the cell, and things get messed up! And so you need to have some sort of mechanism to fix it when it gets messed up - especially when you’re talking about DNA, which is your master blueprint for the cell. It’s supposed to stay intact. If it doesn’t get fixed your cell can die, but even worse might be it might just start replicating uncontrollably, and that’s what happens in cancer. And those cells form a tumor and can spread throughout your body, and that can kill the entire organism. So there are several different ways that damage to DNA is repaired in organisms.
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Section 35.1 Errors Can Arise in DNA Replication
The simplest source of DNA damage is the incorporation of an incorrect base during replication that escapes the notice of the proofreading capabilities of the DNA polymerases.
Other errors include insertions, deletions, or breaks in one or both strands, which may halt DNA synthesis altogether.
Special DNA polymerases, called translesion (or error-prone) polymerases, can replicate across the damage and generate a rough draft of the damaged sequence that can be at least partly repaired by DNA repair processes.
Created by Brett Barbaro
The first place that you might see some sort of DNA damage, or some sort of problem with your DNA, is if an incorrect base is incorporated while it’s being replicated. And the first line of defense against that is the proofreading capability of DNA polymerase - there’s an exonuclease part. But occasionally an incorrect base can slip in. You can also have problems with your DNA getting broken in one strand or both strands. You can have DNA get broken and recombine in the wrong way, and some of these things can halt DNA synthesis completely. So there is a special class of DNA polymerases that are able to replicate even if there is damaged sections, so that your DNA replication can continue. And then the damaged sections will get fixed by other mechanisms.
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Clinical Insight: Some Genetic Diseases Are Caused by the Expansion of Repeats of Three Nucleotides
CLINICAL INSIGHT
Some Genetic Diseases Are Caused by the Expansion of Repeats of Three Nucleotides
Genes that contain long sequences of trinucleotide repeats are sensitive to replication errors.
These sequences of repeats may expand during replication. In the case of Huntington disease, the sequence CAG, which encodes glutamine, is expanded, resulting in the pathological condition.
Because the arrays expand upon replication, children of parents with the disease may exhibit the condition earlier and more severely, a phenomenon called anticipation.
Created by Brett Barbaro
One common way that DNA gets messed up is when it has long sequences of trinucleotide repeats. And this is the case in Huntington’s Disease. The sequence CAG, which codes for glutamine, is repeated normally about 20 times. But if it gets expanded, and you get 40 repeats, then you start having some serious problems. And because these repeats can get expanded when the DNA is replicated, the situation can get worse, and children can have a more severe case of the disease than their parents, which is called anticipation. With every generation the disease gets a little bit worse.
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Diagram of Triplet-Repeat Expansion - BAD
Created by Brett Barbaro
Figure 35.1 Triplet-repeat expansion. Sequences containing tandem arrays of repeated triplet sequences can be expanded to include more repeats by the looping out of some of the repeats before replication. The double helix formed from the red template strand will contain additional sequences encompassing the looped-out region. The circle represents the replication machinery.
Now, this is a picture that’s in your book, or in the text, and it is incorrect because that’s not how the DNA looping occurs.
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One way that trinucleotide repeat expansion could happen:
Triplet-repeat expansion - GOOD
Created by Brett Barbaro
Bypass of a lesion. (Aa) The trinucleotide repeat (TNR) tract prevents polymerase passage on the leading strand template and it stalls (black circle), but the lagging strand can continue synthesis (green line). (Ab) To overcome the block, the fork ‘backs up’, forming a four-way junction resembling a ‘chicken foot’. (Ac) The leading strand polymerase uses the newly synthesized daughter on the lagging strand as a template to synthesize enough DNA to pass the long non-coding TNR tract block (dashed line). (Ad) TNR loops can occur during replication fork reversal or restart. In this example, a hairpin within the TNR tract (in green) is shown on the daughter strand of the lagging strand template, which is trapped to form an expansion intermediate. The template strand is in red; the nascent strand is in black.
This is a more accurate depiction of how DNA looping might occur. And it’s not completely well known, but there is a component of looping that’s involved. And in this case we can see, on the left hand side, we’ve got a “pause” spot where the trinucleotide repeats begin. And that tends to be a problem for replication for some reason. It stops for a minute, and then the replication fork can back up. And when that happens, there’s an overhang of DNA. Now that DNA is actually able to pair with itself {roughly} and form a stem loop. So when the replication of the DNA continues, as it does on the right, you will see that there is an extra few bases in there that weren’t there before. And that’s how your DNA gets extended, how the trinucleotide repeats become longer. {Replication Slippage Model was added as a more clear version of how this might happen.}
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Bases Can Be Damaged by Oxidizing Agents, Alkylating Agents, and Light (1/2)
Chemicals that alter specific bases after replication is complete are called mutagens.
Hydroxyl radicals oxidize guanine to 8-oxoguanine, which base-pairs with adenine instead of cytosine during the next round of replication.
Deamination can be mutagenic. Adenine can be deaminated, forming hypoxanthine, which pairs with cytosine instead of thymine.
Created by Brett Barbaro
But there are a lot of ways that the bases in DNA can be damaged even after replication is done. And this happens all the time. There are chemicals called mutagens that can damage your DNA, and also x-rays, and ultraviolet light.
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Diagram of Guanine Oxidation
Hydroxyl radicals oxidize guanine to 8-oxoguanine, which base-pairs with adenine instead of cytosine during the next round of replication.
Created by Brett Barbaro
Figure 35.2 Guanine oxidation. (A) Guanine, the base component of dGMP in DNA, can be oxidized to 8-oxoguanine. (B) 8-Oxoguanine can base-pair with adenine.
Here’s an example of how DNA can be damaged. And this is done by hydroxyl radicals. We talked about those during the part about oxidative phosphorylation. Those free radicals can damage DNA, and one of the ways that they damage DNA is by turning the base guanine into 8-oxoguanine. It’s a slightly different form, and it pairs with adenine. Guanine, of course, normally pairs with cytosine. So if you have a guanine that’s been changed to 8-oxoguanine, when the DNA replicates the opposite nucleotide that gets incorporated into the growing strand will be an adenine. So one of the daughter strands will have that mutation. And then, once that mutation is incorporated in the daughter strand it’s pretty much permanent, because there’s no way for the cell to know that that wasn’t supposed to be there.
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Diagram of Adenine Deamination
Deamination can be mutagenic. Adenine can be deaminated, forming hypoxanthine, which pairs with cytosine instead of thymine.
Created by Brett Barbaro
Figure 35.3 Adenine deamination. (A) The base adenine can be deaminated to form hypoxanthine. (B) Hypoxanthine forms base pairs with cytosine in a manner similar to that of guanine, so the deamination reaction can result in mutation.
A similar mechanism occurs when adenine is deaminated. A water can come in and replace the amine group on adenine with an oxygen, and hypoxanthine is created, which pairs with cytosine. So if a hypoxanthine exists in the DNA when it’s being replicated, it will be paired with a cytosine rather than a thymine, which is what adenine should be paired with, and then that problem will continue from there on. It’ll be a permanent mutation.
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Diagram of a Cross-Linked Dimer of Two Thymine Bases
Ultraviolet radiation covalently links adjacent pyrimidines, thereby blocking replication.
High-energy electromagnetic radiation, such as x-rays, may cause breaks in the DNA strands.
Created by Brett Barbaro
Figure 35.6 A cross-linked dimer of two thymine bases. Ultraviolet light induces cross-links between adjacent pyrimidines along one strand of DNA.
Ultraviolet radiation, like from the sun, will link adjacent pyrimidines - and that can block replication altogether. And that’s why the UV rays of the sun are dangerous. They can prevent replication from occurring and damage the DNA such that it begins to form cancerous cells. Another damage that can occur is from x-rays, which cause breaks in the DNA strands and that can interfere with replication as well. And that’s why you have to wear a lead vest when you go to the dentist to get your x-rays done.
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Section 35.2 DNA Damage Can Be Detected and Repaired
Learning objective 5: Explain the mechanisms that ensure the fidelity of DNA replication.
DNA repair systems follow the same mechanistic outline:
Recognize the inappropriate base(s).
Remove the inappropriate base(s).
Repair the resulting gap with a DNA polymerase and DNA ligase.
The first DNA repair mechanism occurs when a DNA polymerase proofreads the newly synthesized DNA and corrects mismatches.
Created by Brett Barbaro
But fortunately there are numerous ways that your cells can deal with damage to DNA. And the overall outline is that (1) you first have to recognize where the damage has occurred (what base is incorrect), then (2) that incorrect base has to be removed, and then (3) a new correct base has to be inserted, and that’s done with DNA polymerase I. And then the inserted base has to be connected to the remaining DNA, and that’s done with DNA ligase, such as we discussed in the last chapter. Now, the first line of defense against DNA mismatch is when the polymerase actually mismatches a base and that base does not fit properly with the other base that it’s been paired with. That causes the polymerase to pause because it can’t slide past that area because the bases don’t fit properly - it causes kind of a bulge. And then the nascent strand that’s being created will flop around and eventually hit that exonuclease site on the DNA polymerase where the incorrectly matched base will be removed. And then the polymerase can continue to do its work.
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Mismatch-Repair-Systems
Mismatch repair systems correct errors not corrected by proofreading.
In E. coli, two proteins are required for mismatch repair―one to recognize the error and one to recruit an endonuclease to cleave the DNA.
Direct repair corrects mistakes without having to remove any fragments of DNA.
Created by Brett Barbaro
But sometimes those mismatches just get glossed over. It takes a little bit more energy to get the polymerase past a mismatched base pair, but sometimes that energy is available. So you can have mismatched bases that have just been introduced during the process of replication. So there are several proteins that are involved in the repair of this type of mismatch. And in E. coli we have, first of all, a protein that recognizes a mismatch, and then another one that comes in to cut the DNA right where the mismatch has occurred. A different mechanism is to repair the problem directly without actually removing any DNA. And one example of that would be DNA photolyase, which can cleave the pyrimidine dimers that are created by ultraviolet light. It says here that DNA photolyase uses light energy, so I am going to guess that that’s more of a plant-related mechanism.
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Diagram of Mismatch Repair
Created by Brett Barbaro
Figure 35.7 Mismatch repair. DNA mismatch repair in E. coli is initiated by the interplay of MutS, MutL, and MutH proteins. A G–T mismatch is recognized by MutS. MutH cleaves the backbone in the vicinity of the mismatch. A segment of the DNA strand containing the erroneous T is removed by exonuclease I and synthesized anew by DNA polymerase III. [After R. F. Service, Science 263:1559–1560, 1994.]
Here’s a little schematic of what happens in E. coli. So you’ll see at the top that there’s a mismatch, a G paired with a T, which is not correct. And I am going talk right here a little bit about how…the cell knows which one of those is incorrect. If it comes across a piece of DNA with a mismatch, one of them is wrong - but which one? Well as it turns out, DNA in E. coli, and in many organisms, humans included, is marked with methyl groups. And these methyl groups are attached to the DNA and mark that that DNA has been around for awhile. When a new DNA strand is created, there are no methyl groups attached to it. So if you find a mismatch, the one that is incorrect is probably going to be the one that was just added, which is the one that is on the DNA strand with no methyl groups. So once that’s been identified, the MutS protein can find that sort of mismatch situation, and let’s say it’ll just attach to the most methylated strand of DNA where there is a mismatch. Then a MutL protein will come and attach to that. Who knows why that happens. There’s the MutH protein which comes in, and that’s an endonuclease - and an endonuclease cuts inside of DNA, whereas an exonuclease can only cut away bases from the ends of DNA. So the first cut needs to be made with an endonuclease, and then an exonuclease comes and removes a small portion of DNA. And now, this is a little bit of naked single-stranded DNA sitting there. And DNA polymerase III trundles along and polymerizes some more DNA in that area. That’s just what it does. So it’s basically redoing that area because something was messed up. And then of course, there’s ligase involved to make the final patch and connect the newly synthesized DNA to the previously synthesized DNA.
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Diagram of Base-Excision Repair
In base excision repair, modified bases are corrected by several enzymes. The enzyme AlkA removes the base. The site of the missing base is called an AP site.
The DNA backbone at the AP site is cleaved by AP endonuclease, and a phosphodiesterase excises the deoxyribose phosphate. The gap is repaired by DNA polymerase I and DNA ligase.
Base excision repair corrects the most common point mutation in humans, the deamination of methyl cytosine to thymine.
Created by Brett Barbaro
Figure 35.8 Base excision repair. The base excision repair process identifies and removes a modified base. Subsequently, the entire nucleotide is replaced. [After B. A. Pierce, Genetics: A Conceptual Approach, 3rd ed. (W. H. Freeman and Company, 2008), p. 493.]
A slightly different repair method (that occurs in humans as well) is called base-excision repair, where instead of removing the entire nucleotide and the area around it, you simply remove the incorrect base. Once that incorrect base has been removed, there’s an empty spot, which is called an AP site – which stands for apurinic (or pyrimidinic, but they both start with P, so they can just call it an AP site). And that excision is catalyzed by a glycosylase, which breaks the glycosidic bond between the base and the sugar.
Now, these empty AP sites are recognized by an AP endonuclease and a deoxyribose phosphodiesterase. The AP endonuclease will cut the backbone and the deoxyribose phosphodiesterase will remove the deoxyribose and the phosphodiester bond that are associated with that empty spot. So basically, just clearing out the backbone for that one single base. That gap can, then, be repaired by DNA polymerase I, and then the correct base can be inserted. And then DNA ligase comes along and fixes the break.
So this method is very similar to the method that we had just studied, where you take out several bases and it’s repaired with DNA polymerase III. But it’s mediated by a totally different set of enzymes. So if one of those systems isn’t working, then the other one can take over and do the repair. So there are redundant systems in these repair mechanisms. And this base-excision repair is one of the most common things because of the deamination of methylcytosine to thymine.
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Diagram of the Deamination of 5-Methylcytosine Forming Thymine
Created by Brett Barbaro
Figure 35.9 The deamination of 5-methylcytosine forms thymine.
Remember - I had mentioned that a strand of DNA that has been sitting around for a while in E Coli, and also in humans, is often modified with these methyl groups. And the base that gets modified here is cytosine. Well, the structure of cytosine, with a methyl group on it, 5-methylcytosine, is very similar to the structure of thymine. And if a deamination takes place, then the 5-methylcytosine can be turned into a thymine. Now keep this in mind for later - cytosine can be deaminated quite easily, that’s something that happens a lot. And if it’s not methylated, cytosine, when it’s deaminated, turns into uracil. But we’ll discuss that in a second.
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Nucleotide-Excision Repair System
If base excision fails to recognize the damaged base, the mutation may be corrected by the nucleotide excision repair system.
An enzyme complex recognizes the distortion of the DNA caused by the offending base. The UvrABC excinuclease cleaves the DNA at two sites, several nucleotides on each side of the distortion.
As usual, DNA polymerase I and DNA ligase close the resulting gap.
Created by Brett Barbaro
And the third system that we’re going to talk about is the “nucleotide-excision repair system”. This is very similar to the “mismatch repair system” in that it recognizes a problem, then cuts out a small piece of the DNA that has the problem in it, and then repairs it with DNA polymerase I and DNA ligase just like the others. This one is specifically used for repairing thymine dimers. So the first system recognized mismatches in the sequence; the second is more specifically for recognizing modified bases; and this third system is more the thymine dimer system. But together these three systems are the most common DNA repair mechanisms.
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Diagram of Nucleotide-Excision Repair
Created by Brett Barbaro
Figure 35.10 Nucleotide excision repair. The repair of a region of DNA containing a thymine dimer by the sequential action of a specific excinuclease, a DNA polymerase, and a DNA ligase. The thymine dimer is shown in blue, and the new region of DNA is in red. [After P. C. Hanawalt. Endeavour 31:83, 1982.]
So it’s essentially the same thing. There’s a mismatch {problem} that’s detected by a protein, and it recruits this uvrABC excinuclease, which takes out (this is the difference), it takes out specifically, a 12-nucleotide fragment of DNA. And then, that DNA is repaired by DNA polymerase I, and joined by DNA ligase.
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Quick Quiz 1
QUICK QUIZ 1
What property of the structure of DNA allows for the repair of bases damaged by mutation?
Created by Brett Barbaro
So this one should be a little obvious, hopefully. What property of the structure of DNA allows for the repair of bases damaged by mutation? Well, think about it for a sec.
The answer is that the two strands are complementary, so if you see a mismatch somewhere where they don’t belong, you’ll know that one of those is at least the correct one and then you can use that to repair the DNA.
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The Presence of Thymine Instead of Uracil in DNA Permits the Repair of Deaminated Cytosine
Thymine is used in DNA instead of uracil, which also pairs with adenine, to preserve the integrity of the genetic information.
Cytosine spontaneously deaminates to form uracil. If uracil naturally occurred as a base in DNA, cytosine deamination would lead an A–U pair replacing a G–C pair after the next round of replication.
Use of thymine instead of uracil allows the detection of deamination of cytosine.
If uracil is detected in DNA, it is removed by uracil DNA glycosylase and the resulting AP is repaired with the insertion of cytosine.
cytosine
uracil
Created by Brett Barbaro
So now let’s talk about the deamination of cytosine to uracil. Well, this is kind of an interesting one. It turns out that cytosine can be deaminated quite readily, happens with some relatively high level of frequency. And we’ve discussed how a methylcytosine can be deaminated to turn into thymine, but if you have a regular cytosine it gets deaminated and turns into uracil. And this is why DNA uses thymine instead of uracil. Because if the uracil is spotted in a DNA, then it’s obviously not supposed to be there. So if you had already used uracil as your base in DNA, then you wouldn’t know...which one of the two bases was incorrect. But since you’re using thymine instead of uracil, then whenever you see a uracil, it’s removed by the base-excision repair mechanism and replaced with cytosine.
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Diagram of Uracil Repair
Identical!
Uracil repair is an example of base-excision repair
Deoxyribose phosphodiesterase
Created by Brett Barbaro
Figure 35.11 Uracil repair. Uridine bases in DNA, formed by the deamination of cytidine, are excised and replaced by cytidine.
So Figure 35.11 here is pretty much a repeat of Figure 35.8. Except for that in figure 35.11 they've left out the deoxyribose phosphodiesterase, so I put that in there in blue for you. Uracil repair is in fact a form of base excision repair. It excises the uracil base and replaces it with a cytosine base. But let's pause for just a second to consider the question, "Why does RNA use uracil instead of thymine?" In fact, the 5-methyl group that distinguishes between them has no effect on their interaction with adenine. But it turns out that uracil costs less energy to produce than thymine. Perhaps there was more of it around when these systems were evolving. Now it is likely that uracil is necessary for all of the three-dimensional structures that RNA can form, and that thymine wouldn't do it. But one thing that thymine does for DNA is to increase its stability, and that is because of this spontaneous deamination of cytosine. So that is important for the stability of DNA. RNA does not have to be as stable as DNA because it doesn't stick around for as long. It's not used for long-term information storage. It has a rapid turnaround time. So do the cytosines in RNA get deaminated? Without looking it up or anything, I would tell you almost certainly. But it doesn't really matter so much. When DNA is transcribed, it creates multiple copies of RNA, hundreds of copies, thousands of copies. And if one of those copies gets corrupted, then there are usually plenty of other copies that are there to do the job that needs to be done. With DNA, however, you have one copy, or maybe two copies, of your DNA. So if one of those gets corrupted, that needs to be fixed.
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Clinical Insight: Many Cancers Are Caused by the Defective Repair of DNA
CLINICAL INSIGHT
Many Cancers Are Caused by the Defective Repair of DNA
Cancers are caused by mutations in genes that control growth.
DNA repair enzymes are often tumor suppressors.
If both copies of a DNA repair enzyme are mutated, cancer is more likely to develop, as illustrated by xeroderma pigmentosum.
Because tumors lack DNA repairs systems, damaging the DNA with chemicals such as cyclophosphamide and cisplatin is a strategy to prevent cancer growth.
Created by Brett Barbaro
As I mentioned previously, cancer is caused by mutations that lead to uncontrolled growth of the cell, uncontrolled replication of the cell and the DNA. Now, there are certain genes in the cell that control growth that prevent this kind of unbridled replication from occurring. Those are called tumor suppressor genes, and if those genes get damaged then uncontrolled growth can be a result. You know the cell is really trying to grow and replicate, but it can’t do it too much because that’ll cause problems - so there’s kind of a fight going on. And if these suppressor genes fail, then the growing side of the fight will win. So that's one of the reasons that you need to repair your DNA - so these tumor suppressor genes don’t get messed up. So DNA repair enzymes can also be considered tumor suppressors because they make sure everything is working properly. Now if you’ve got a problem, and your enzymes for repairing the DNA are mutated, then your DNA can get damaged and a lot of things can happen.
Now a lot of the time you damage your DNA, it’ll just kill the cell. And OK - not great, but that’s not so bad. The cell dies, gets replaced with other ones, life goes on. But if the mutation occurs that makes the cell divide uncontrollably, then you have a problem. Because, not only are the cells dividing, but they all have this mutation, so they will all continue to divide uncontrollably and that problem doesn’t just go away. That problem grows and grows and becomes a tumor, and that can kill you. So if you have a faulty DNA repair system, the most likely effect that you’ll see from that is cancer - because you won’t notice all of the cells that are dying so much as you will notice the few cells that survive and replicate like crazy. So - if you have a faulty DNA repair system, how could you deal with that? Well, you can damage the DNA further, and hopefully you’ll damage the DNA enough that the cells will start to die rather than continuing to replicate. Well, it’s a little bit tricky, but this method is used for chemotherapy. Drugs like cyclophosphamide and cisplatin will go in and damage DNA. Now, it damages DNA all over your body, just kind of anticipating that the healthy cells will be able to repair the damage that’s done. But the cancer cells won't be able to repair the damage that’s done and they will die. But you are doing damage to DNA all over your body, and that's one of the reasons that the side effects of chemotherapy are so bad, because you're actually killing cells all over your body. You’re just hopefully killing more of the cancer cells than you are the healthy cells.
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Section 35.3 DNA Recombination Plays Important Roles in Replication and Repair
Recombination is the exchange of genetic information between two DNA molecules.
Two daughter molecules of DNA are formed by the exchange of genetic material between two parental strands.
Recombination is useful for repair of extensive damage to the DNA, such as breaks in both strands of the DNA.
Created by Brett Barbaro
So now let’s talk about recombination. If you’ll recall, we have 23 pairs of chromosomes. And these pairs each contain the same genes. So if the gene on one of these...two elements of the pair, if the gene gets damaged, then it can be replaced with genetic information from its sister chromatid. That’s what’s called recombination. And sometimes that’s used to repair damage to DNA.
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Diagram of the Repair of Double-Strand Break by Using Recombination - BAD
Created by Brett Barbaro
Figure 35.15 Repair of double-strand break by using recombination. 1. A 5 exonuclease generates single-strand DNA at the site of the break. 2. Strand invasion takes place when the strand on the damaged DNA base-pairs with the complementary strand on the undamaged DNA, forming a displacement loop, or D-loop. 3. DNA synthesis takes place. 4. A second strand invasion takes place, resulting in the formation of two Holliday junctions. 5. The Holliday junctions are cleaved and ligated, forming two intact molecules of DNA.
Now, I don’t like the diagram in the textbook, so we’re going to go with a different diagram.
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http://www.nature.com/scitable/content/41523/10.1038_nrm2008-f2_large_2.jpg
Repair of double-strand break by using recombination - GOOD
Created by Brett Barbaro
Starting at the top, we can see that there’s a double stranded break in one of the chromosomes, but the other chromosome is intact. So if there’s a double stranded break, one of the first things that happens is that the 5’ ends of the DNA get chewed away, leaving the 3’ ends intact. This would be done by a 5’ exonuclease. The 3’ end then can pair with a complementary sequence on the other chromosome. A short stretch of DNA can then be polymerized by normal processes.
Now there’s two ways that this can go, actually, at this point. The way on the left, number b, is that the other 3 prime end also pairs with the sister chromatid, and DNA gets extended on that one as well. And those get ligated, and you have two junctions. And when those junctions, called Holliday junctions, get split, you end up with pieces of the opposite chromosome that have actually...traded places along with some newly synthesized DNA.
The other way that it can go, which is way c, is that if the DNA is created using the sister chromatid as a template, it can then be released and reanneal with a broken strand of the original DNA, which can then be repaired. So you end up with new DNA in the broken strand but no new DNA in the sister chromatid. But it is important to recognize that you have now the sequence of the sister chromatid that is in your new DNA, and sometimes those sequences differ a little bit. So that could introduce a new mutation in the genes, and hopefully not a bad one! If your sister chromatid is functioning properly, then the sequence in that sister chromatid should be perfectly good and everything should be working. But it’s like this that mutations get introduced into your DNA - and so this is one of the primary drivers of evolution.
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DNA Recombination Is Important in a Variety of Biological Processes
Recombination is a means of generating diversity in the immune system.
Recombination can be used as a powerful experimental tool to move, remove, or add genes to the genome.
For example, if the muscle regulatory protein myogenin is removed, or “knocked out,” of a mouse genome, the animal dies from a lack of functional muscle. Genes can also be added by “knock-in” techniques based on recombination.
DID YOU KNOW?
Meiosis is a special type of cell division that is required for sexual reproduction. In animals, meiosis results in the production of sperm and eggs.
Created by Brett Barbaro
Recombination will create diversity in your gene pool. It’ll slightly change the genes, and usually into a functional form, but maybe a slightly different functional form. That’s something that’s done in the immune system all the time. Your immune system has got to be prepared to deal with foreign invaders of multiple kinds. And so the antibodies that it creates to recognize these foreign invaders have to be very diverse. And recombination is one of the ways that that diversity is generated. Recombination in the areas of the chromosomes that produce these antibodies is something that’s occurring a lot, and all the time.
We also take advantage of recombination in the laboratory to change the genomes of creatures. Like, I worked on fruit flies a lot, and we needed recombination to alter the genetic makeup of these flies. It was just the easiest way to do it because it was already there. It was happening naturally. Recombination is something that happens every time {sexual reproduction} occurs because you’ve got two different chromatids that are being introduced with one another, and there is some mixing up of the chromosomes that occurs during that process. And that generates diversity, and leads to evolution, and the ability of the population to actually deal with unforeseen circumstances.
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