Transposons and Viruses - Video Tutorials & Practice Problems
On a tight schedule?
Get a 10 bullets summary of the topic
1
concept
Mobile Genetic Elements
Video duration:
2m
Play a video:
Hi in this topic we're gonna be talking about transpose sins and viruses. So the first thing we're going to talk about is mobile genetic elements which are defined as jumping genes. And these are small DNA segments that are found on every single cell. And so what they do is they actually insert themselves into any D. N. A. Sequence within a cell but they cannot leave. So it's not like they can sort of you know reproduce themselves and jump between cells. They're stuck in a single cell but within that cell they can jump all over the place within the genome. So surprisingly they make up a fairly large proportion of the genome about 50%. Um And even more surprisingly is that they really have no function. People call them selfish genes because they don't do anything other than just copy themselves and insert into the genome. And they can insert anywhere they can in certain genes they can insert in regulatory sequences. They can insert in centrum ears and telomeres and any chromosome they want to they can just sort of insert themselves. And so who discovered these? This is a name you're gonna want to know. Her name is barbara mcclintock. And she was actually studying corn. You may see this is maize for all you non farmers out there. That's just the type of corn. Um And she discovered them in the 19 forties. So she was really instrumental in finding these and that's probably a name that you may be quizzed about in the future. And so since then we found that there are really two types. There are D. N. A. Transpose sins, Your mobile genetic elements and retro transpose sins which instead of using D. N. A. U. R. N. A. And there are the two major families of mobile genetic elements. Now another type of mobile genetic element that you may hear about are actually viral genomes. Especially retro viral genomes retroviral very similar to the retro transpose since they use RNA. Um We'll talk about them more in different topics but viral genomes can actually insert themselves into the genome. Very similar ways that mobile genetic elements do and they have the ability to um sometimes occasionally move around especially when they're first infecting the cell. Can insert themselves in the genome kind of anywhere they want. So if we just look at this example here let me move out of the way. You can see here there's a transpose on and a gene and that transposon can move and insert itself into the gene. Now it doesn't always have to insert itself into the gene. It could it could have inserted. Well it's already there but it could insert it here. You can insert there. It kind of can insert anywhere but sometimes they do insert into jeans and that can cause some serious effects. So now let's move on
2
concept
DNA Transposons
Video duration:
3m
Play a video:
So in this video we're gonna talk about D. N. A. Transpose ions which is one of the types of mobile genetic elements. So um like I said type of mobile genetic element. And they actually moved through A. D. N. A. Intermediate surprising enough. So these are most commonly found in precarious and bacteria mainly because the eukaryotic DNA transposon have generally lost their ability to move so they no longer move anymore. But remnants of them still exist in the human genome. So about 3% of the human genome is just D. N. A. Transpose that really have no function now because they can't move. And so how do DNA transposon move in the genome? Well it's kind of just like cut and paste. Um So they're cut from one region and paste it into another. And so one of the side effects of this is that if it's actually cut during DNA replication then it can duplicate because it's already being replicated. And then if you replicate it and then cut it then that's going to insert into a new region of the genome. Which when it's replicated again We'll just be copied twice. So what's the structure of the DNA Transposon? Well it contains this very unique structure and has inverted repeats of 50 base pairs. So those are just repeated sequences on either end of the transpose on and the middle of the transposition sequence actually encodes for a gene actually codes for protein and that protein is a transpose ice. So what is the transpose ice while the transpose ice is responsible for cutting or removing the transpose on out of the D. N. A. Sequence. So the transpose X. Is kind of your scissors for the D. N. A. Transpose on. And um one of the really important aspects of this is we think cut and paste. Cut and paste their scissors there chopping things up. But this is important because it doesn't lose length when it inserts or when it cuts. And so because it isn't losing length it's still able to continue this cut and paste pretty much indefinitely throughout the lifetime of the cell. And so the transpose is responsible for cutting. But what's responsible for pasting? And that's actually this process called double strand break repair which you may have heard of. You don't necessarily need to know that term Right now we'll talk about it more and other topics. But if the transposes the Couser then the transposes the scissor then the double strike. Oh my goodness, I can't speak. The double strand break repair is the glue that sort of paste it back together. So if we're looking at a structure of A. D. N. A. Transpose on it has these inverted repeats here on either side. And this is a protein coding region. And what does this encode for this encodes for trans pose a space and that's kind of the scissors O. R. S. That can cut it out of its genomic location so that it can move to a different location. So now let's move on
3
concept
Retrotransposons
Video duration:
5m
Play a video:
Okay. So in this video we're gonna talk about retro transpose owns these are again they're mobile genetic elements. But instead of moving through D. N. A. They move through an R. N. A. Intermediate. So how does this happen? Well while they're in the genome there of course indiana chromosomes have D. N. A. So they have to be in D. N. A. So what happens is that they're actually transcribed into RNA and then process back into D. N. A. To insert. And so the enzyme responsible for taking our N. A. And sort of reverse transcribing it back into D. N. A. Is called reverse transcriptase. And the process of changing is actually called reverse transcribing. And that moves R. N. A. To D. N. A. So it's different than transcribing which uses DNA to RNA. So if we were to look at this what this looks like you have your D. N. A sequence here. There's a retro transpose on this. Remember is in D. N. A. Form. It is then transcribed and a portion of it is translated. Um And that allows for different complexes. The form you don't really need to know about this but eventually this is um it undergoes reverse transcription. So it changes from this RNA here back into A. D. N. A. And that D. N. A. Can then integrate right here into the genome in a new location. So that's kind of how retro transpose johN's work. Now there are a couple of different classes of retro transpose. Since the first one that I'm going to talk about our long terminal repeat retro transpose eons. And they make up about 8% of the human genome. Now they're called long terminal repeats because they have long terminal repeats. So these direct repeats are about 200 to 600 base pairs long. And like the DNA transposon they actually flank a protein coding region. Now there's a second class and these are non long terminal repeat retro transpose seasons. So again second class. Now there are two types of these. These are called lines is one of them and these are stand for long interspersed elements. Now lines are not commonly found in mammals and they're called long years long because they're about six killer base pairs long pretty long. And so um what you need to know about lines is that there are three classes um L one, L two and L three. Line one, line two and line three but only line one still works. And they actually make up a pretty large portion of the human genome about 21%. Um And so this is kind of surprising because they're not actually not commonly found in mammals but they're still present in large amounts in the human genome. Now most of these the majority of the overwhelming majority of these don't move. They're kind of dead. They just sort of sit there and they can't move anymore but they do still exist now the second kind um oh sorry like like the other transposing that we've talked about. They can take repeats followed by approaching coding regions in the center. Now. The second class is the short interspersed elements or signs for short. And these are the ones that are commonly found in mammals. Now they're called short because there are 300 base pairs long that's much shorter than the six killer base pairs that you see in the long interspersed repeats. So what you need to know about these is that the most common is the L. U. Or ALU element and this one is actively transposing in the human genome. So when me and you this can still happen moving around in the genome now this makes up about 13% of the human genome just signs in general. But the overwhelming majority 10% of it is actually these L. U. Um signs. Now these are a little bit different than the other transpose that we've talked about because they actually most of them lack approaching coding region and instead depend on the presence of other mobile mobile elements like lines or long terminal repeat retro transpose or even D. N. A. Transpose on to provide things like transposes and other proteins that are necessary for their jumping. So it's a little unusual because they're still present but they don't have everything they need to jump and so they depend on these other elements to jump but they are still one of the most moving um mobile elements in the human genome. A. L. U. Is kind of huge. So very much like you've seen in some of these other images that I've been showing you the structure of a line. It has these repeats here on the end. That's not a repeat. You don't actually need to know what this is. So ignore that. But it has these two protein coding regions uh right in the center, which is very similar to these other um transpose that we've talked about. So now let's move on.
4
concept
Viruses as Mobile Genetic Elements
Video duration:
5m
Play a video:
Okay so so far we've talked about different kinds of D. N. A. Elements that can actually jump around the genome. But viruses can do that as well. So viruses act as mobile genetic elements. And these this is because that some viruses can actually integrate their genome into the cell that they infect or the host cell. And so let's talk a little bit about the virus structure and then we can go into how they act and how they actually integrate and can jump around through the genome. So first viruses are really simple types of things. They just contain a protein coat that surrounds some type of genetic information. The amount of genetic information is just really small compared to other living organisms. Um And this genetic information can be D. N. A. Or RNA. Base. And I'll talk about a couple of different ways. Generally we're familiar with viruses because they cause disease but they're also very useful tools in a laboratory setting And so they can do more than just cause disease. Now there are different types of viruses of course depending on how they infect what kind of genetic material they have. And one really important type that we've mentioned before are bacterial pages. And these are viruses that infect bacteria. These can insert their genome into the host bacteria that they've infected. And so when they insert their genome that genome just gets inserted anywhere right? There's not normally not a very specific sequence. And so it can be in a gene it can be in a regulatory sequence, it can be you know nowhere important but where it inserts can have a drastic impact on the organism itself. So those are bacteria pages there are retroviruses and this is a really important class that we're going to talk about a lot. But retrovirus is are called that because they have R. N. A. As their genetic material and not D. N. A. And they use their R. N. A. As a template to produce D. N. A. So they start with R. N. A. It's sort of just this template and that is um in a process called reverse transcription, actually transcribe it into D. N. A. And because it's called reverse transcription, the enzyme that does that is called reverse transcriptase. And this is an enzyme that's not really found in humans or in the host cell for the most part but it's instead encoded by the virus itself. So the virus contains this gene for reverse transcriptase and that is what allows the virus to reverse transcribe that RNA and use it as a template to produce DNA. So here's just a structure of a retrovirus. It's not super important that, you know, you know, understand and be able to label this yourself. But the important thing here is that there's just this protein coat that is surrounding this um genetic material. And because it's a retrovirus, we know that's gonna be our N. A. Not D. N. A. So here's this RNA here and when this virus you know, is to infect something whatever it infects then that RNA will be used to reverse transcribe into D. N. A. Now the viral like I said before the viral genome is generally integrated into the host genome. And that's why we say these act as mobile genetic elements right? Because it has its own RNA or DNA. That is actually just inserted into the genome wherever it feels like. So it's actually this mobile genetic element that can jump around different places depending on where it's inserted at the moment. The virus infects now in order to insert it has to have some type of enzyme that's going to actually insert it very similarly to all the other types we've talked about. And this enzyme for viruses is Integrase which makes sense. Right? Aces the enzyme and then into Integrase is it's being integrated. It makes complete sense. And so this uh inserts the viral D. N. A. Into the host gene. Now remember this is DNA not RNA. Because if it if the virus has RNA that's going to be used as a template to produce DNA before it's actually integrated. So D. N. A. Is always integrated. RNA is not going to be integrated into the genome. So here's an example of the HIV genome and how it integrates in the hotel D. N. A. Now of course there's a lot of information here like for receptor none of this stuff you need to know just know here's the virus and here it is infecting a cell and you can see that it has this D. N. A. Or has A R. N. A. It's HIV is a retrovirus inside and then reverse the transcript face comes in and synthesizes it into D. N. A. So here we now we have D. N. A. Which is here, this gets into the cell nucleus and here's the viral D. N. A. And this dark black and you can see that it integrates into the host cell genome where the dark black is here. That's the virus and the lighter color is just the host cell. And so this is very common among especially retroviruses. It can be done through other viruses as well. But retroviruses this is a really common process. Um And that's why we say viruses can act as mobile genetic elements as well. So with that let's not move on.
5
concept
Evolution
Video duration:
3m
Play a video:
So in this video we're talking about mobile genetic elements and their role in evolution. So because mobile genetic elements are jumping all the time, you can very much imagine how they're playing this major role in evolution because each time they jump they're disrupting the genome. And so this is causing some kind of mutation. Whether it's a shift of a gene or inserting into a gene um these mutations can have huge effects on evolution. So um how often do these things jump? You know I've been talking about And is it that they're jumping every second? Or is it jumping there once every 10,000 individuals? Well that depends on the organism. So for bacteria this occurs once every 10 to the fifth cell divisions. Which for bacteria is actually fairly often. So it doesn't happen in every cell. But after all of these divisions which happened fairly rapidly it occurs. And this is actually an example of things that we hear about a lot in the news antibiotic resistance. Well that's a lot of times conferred through mobile genetic elements. So a gene that allows the bacteria to survive um you know or a gene that is dead with the antibiotic is affected by a mobile genetic element jump. Um for fruit flies, Joseph E. Lia that's about 50% of their spontaneous mutations occur from mobile genetic elements. Um for mice this is actually a big present. About 10% of total mouse mutations that exist in the current mouse genome Are due to mobile genetic elements. For humans this happens much less. Um one in every 1000 mutations which in humans mutations are fairly rare anyways. So this is I mean .1.2% of all mutations and but there has been one interesting example of a mobile genetic element actually causing a disease hemophilia in a patient that has no family history of it. So hemophilia is generally a genetic disease that is passed on in families, but this this one person came up with it and they were like, why do you have this? No one else has it. And the reason he had hemophilia was because a mobile genetic element had actually jumped into the disease gene causing hemophilia. Um And so you know that's kind of how often they happen. Um but they actually can have larger effects than just the gene itself jumping because sometimes when they move they actually can carry these sort of adjacent regions of the genome with them. So it's not just that they're moving themselves, they could be moving regulatory regions or you know, certain exxons of a gene to different places in the genome now. Um Throughout evolution there have been some really important um mobile genetic element jumps that have led to life as we know it today. So some important proteins include things like transcription factors which are really important in controlling gene expression and telomerase um which is an enzyme really important for maintaining telomeres. Um you don't necessarily need to know these terms. Now, we'll talk about them in future lessons, but just sort of know that some important proteins have come from mobile genetic elements, So not all of them are bad. Um And so just a couple of other final things in mobile genetic elements and evolution, they affect the expression of genes and proteins and they can be inherited. So if mobile genetic elements are in the germ cells and it jumps, that's going to be passed on to an offspring. Um So yeah, so that's mobile genetic elements and evolution. So now let's move on.
6
Problem
Problem
Which of the following is not considered a mobile genetic element?
A
DNA transposons
B
SINEs
C
Transposase
D
Retrotransposons
7
Problem
Problem
Which of the following transposons still jumps in the human genome?
A
L1 LINE
B
L2 LINE
C
L3 LINE
8
Problem
Problem
What is the name of the enzyme responsible for allowing the transposon to jump within the genome?