DNA Transcription

Hi in this video we're gonna be talking about DNA transcription. So in this video we're really going to be just doing a brief overview of some concepts that we need to know about transcription before we get into more nitty gritty details. So transcription is the process that changes DNA to RNA. And so how is that process catalyzed? Well that through enzymes known as RNA polymerase and RNA polymerase is the class of enzymes that tran scribe DNA. So I made this little table. Um This has you know RNA Plymouth race um what organism it's in and then also what it transcribed. So the first one which I've already highlighted is just called RNA polymerase. That's in pro cario and it does all pro carry attic RNA. Now you carry those are a little more complex. Um And so they actually have three which are very easily labeled RNA polymerase 12 and three. Um And they all work in eukaryotes. And but because there are three different classifications that means they do different types of RNA RNA polymerase. One focuses on our RNA. A. RNA polymerase two focuses on M. R. N. A. And R. N. A. Plumber. He's three focuses on T. R. N. A. Now we're gonna be talking a lot about transcription. Um And most of our focus on transcription will be focusing on M. RNA. And that's the RNA that forms proteins. So RNA polymerase two is going to be a big player. Um you need to know about the other ones really that they exist and they do other types of RNA is but we're not going to be focusing on them as much. So how does transcription work? Well transcription uses one strand of DNA as a template to produce a single stranded RNA. And so this D. N. A template can encode for one gene or it can encode for multiple. So for prokaryotes they're called policy straw nick meaning that a single um DNA that's transcribed into a single R. N. A. Can encode for multiple genes. Whereas eukaryotes are a term called mono sis tronic which means that the single RNA encodes for only one gene. So just an example of this down here, let me move out of the way you have your mono cis tronic here which encodes for one gene and your policies. Tronic here which encodes for multiple genes. And this is on a single RNA transcript. Now one thing to know is when we're talking about RNA transcription, we're talking about RNA polymerase and of course it's not perfect. Nothing in cell biology is just absolutely perfect. There are errors and these errors for RNA polymerase is about one mistake every 10 to the fourth nucleotides. Um which is not nearly as accurate as the D. N. A polymerase which is responsible for replicating D. N. A. Will be replicating and that's actually 10 to the seven. So it's actually much worse than the D. N. A polymerase that replicates DNA. But that's okay because it gets the job done. Um And so yeah that's transcription. So now let's let's turn the page.

okay continuing on this page, we are going to be talking a lot about transcription initiation. Now you're gonna have to bear with me is a lot of content and it's especially a lot of vocabulary but I'm gonna walk through all the vocabulary slowly but just sort of get ready. We're gonna we're gonna learn a lot of terms in this video. So the first time we're gonna learn is actually called the transcription start site. And the transcription start site is important because it tells RNA plum race where to start, which makes sense. It's its name. Um And so what is part of a transcription start site? Well, one of the things is called a promoter sequence and this is kind of a vague term and essentially it's just a specific set of nucleotides that RNA polymerase combined to in order to start. So these are the sequences that say, you know, bind here. This is where you need to start transcribing. So it's kind of interesting because you would think in order to start transcribing it can only you know, lie upstream but actually it can also lie downstream. And so I've given a couple examples of promoters here, we're gonna actually talk about these um in just a few minutes but just sort of as I'm introducing these names upstream or downstream Now um there can we talk mainly about upstream promoters because those are kind of the ones that make most sense. And there's also the most of those. And so there are two types of upstream promoters and these are proximal control elements and so these are elements of sequences that are located really close to the gene start side. So 100 or 200 nucleotides away. But then there's a second kind those are called enhancers. And these are located far away from the gene start and again these can be upstream or downstream. And so how do we determine what these sequences are? Are these sequences completely identical in every organism or every even between humans know they're not completely identical. So we don't call them conserved sequences because conserved sequences are practically identical but we can call them consensus sequences. So what is a consensus sequence? Well that is going to be a common version. So they're not completely identical. But we continually see these repeating patterns of sequences over and over again in these regions. And I'll show you an example of like that in just a minute. Now we have these sequences and that's great. But how does the preliminaries actually recognize these sequences? Well, the primaries can find the promoter, the promoter sequences because those sequences give the helical backbone of the D. N. A backbone unique features. So these can be unique properties or charges or polarity or structures. But the the these sequences provide these very unique backbone structures and the RNA plenary says, okay well that's where I've got to bind because that's the charge I'm looking for or that's the polarity I'm looking for. And so um we call this promoter has polarity which is a little misleading because we're not talking about its interaction with water but instead we're talking about the fact that the promoter can only binds the wench side. So the D. N. A. Is double stranded but the gene is really only on one side of the D. N. A. The other side encodes a completely different thing. And so when the RNA polymerase binds it has to bind to the correct strand. So we're saying that the promoter has polarity that promoter structure or sequence or charge or whatever is recruiting the RNA polymerase is only that way on one side. So it positions the RNA on only one strand in one direction. So if we're to look at what this would look like. So we're going to say this black thing is that chromosome sort of a section of a chromosome. What you see here is you have your gene whatever you're trying to transcribe and then you have proximal control elements here. These are close. So we call these the promoter with a proximal um elements. And then way over here you have your enhancers and these are really far away. And so you can see that the factors are in a prelim arrays for instance or other factors that we'll talk about in a second that are important for starting transcription. Get recruited to these sites and allow for transcription to occur. Let me back out of the way transcription. So like I said, these elements don't have to always be upstream and they don't have to be nearby. It can be far away and they can be upstream or downstream. Now let's come back we'll talk about some factors that are important for recognizing this promoter and binding to it and sort of recruiting this RNA plum race and allowing transcription to occur. Like I said a lot of vocabulary but just kind of bear with me and we'll go through it slowly. So the first thing is that pro carry outs are of course different than you carry out. So the important word that you need to know about pro carry attic transcription is called sigma factor and this is actually a region on the RNA polymerase itself and that is the region that binds promoter RNA. There are multiple types of signal factors. Each of them binds kind of different promoters. And so that's kind of how pro carry oats control which genes are going to be transcribed. It's kind of it's simple, it makes sense. You know you want to buy a different promoter, use a different sigma factor. But for you carry out of course it can't be the simple never is. So for eukaryotes we use things called transcription factors and what these do is these are proteins that bind the promoter and recruit RNA polymerase and so we need these factors to not only just sort of control gene expression but also to recruit RNA premise to the correct gene that needs to be transcribed because we don't need to be transcribing all genes at all times. Um So these transcription factors really give us control over gene transcription. So I've mentioned a couple of these before but we're gonna go through exactly what these sequences are and what they mean and what they do. So the first the two main sequences that are really important to control you know promoter binding and transcription initiation. One of them is called the Tata box or tata box or however you want to say it. But it essentially it's it's called that because that's what it is. It's a sequence of T. A. T. A. Um And this is bound by a transcription doctor known as T. F. I. I. D. Now there's a second one and this is the I. N. R. Initiation sequence. And you could use this or promoter RNA polymerase can use the sequence with or without the Tata box. So the tata box doesn't always have to be present. But the the I. And our sequence has is always present. So you're always gonna have this and this your most of the time but not always. And so um so what happens? So we have these sequences they are you know in the right position and they began recruiting transcription factors like I said this T. F. I. I. D. So um once the T. F. I. D. Is there it as a protein starts recruiting this other complex known as the transcription initiation complex. And this is a collection of proteins that need to be at the promoter to promote transcription and what the what's the what's the collection of proteins? Well I wish it were simple but it's not because it differs for every gene and that kind of makes sense because every gene needs to be regulated and transcribed differently. So of course you need to regulate that transcription with different collection of proteins. But just for simplicity sake we call all of these initiation complexes transcription initiation complexes And they contain a lot of protein sometimes. I mean over a 100 it's kind of it's kind of a complex process now. We've talked about T. F. I. I. D. But there's another one that gets recruited in this initiation complex called T. F. I. I. H. And this is really important because it contains approaching kindness. Which if you remember what approaching kindness is great if you don't, I wrote it down, it adds a phosphate. Um And that's really important because RNA polymerase has to have this phosphate before it can work. So if T. F. I. H. Is not there, it's not going to get phosphor related. Um and it's not ever going to activate. So it needs that. So we have all these. So I mean it's kind of hard to imagine. There's all these different terms. Like I said it was going to be a big on vocabulary. But you can kind of understand how this works. There's these sequences on these chromosomes. They recruit different transcription factors especially T. F. I I D. Once T F I. D. S there that recruits a bunch of other factors. And one of them T F. I. H. Is responsible for adding a phosphate to RNA polymerase which says go ahead, get started ready to transcribe. And so once transcription begins it makes sense the transcription factors are no longer needed. And so they actually, whoops let me not highlight that leave the promoter. So this all is sort of in a stepwise process. We're going to go over a lot of steps in cell biology. So we're just getting started here now there's another vocabulary word. Of course. Not that easy and not done yet. Um And this is called a mediator or mediators. And this is just another group of proteins. Or another set of proteins that are found in this transcription start area and they communicate between RNA polymerase and different transcription factors and transcription. Um you know mediators to really just sort of get everything communicating together. So transcription can be activated. So a lot of lot of processes here. Now this is all for RNA polymerase to do you remember was the one I said that we were going to be talking a lot about but there are RNA polymerase one and RNA polymerase three as well. And of course this process differs from them. Um and they have different promoters and different transcription factors that really drive this process. But for now we're going to focus on RNA polymerase too because that's really important and that's the one that drives everything we're gonna care about. Um At least for the most part at least for this part of cell biology. So they back up and I'll show you this example. So this is a promoter element um and consensus sequence which I said I was going to show you on a. D. N. A. Region. So let me walk through this for a second. So here you have numbers. So what do these numbers mean? These are positions of nucleotides to the gene. So you'll notice here that the gene isn't anywhere on here but it's just all these control regions. So the number tells you where the gene is gonna lie. So it's gonna lie at zero. That's going to be the start site. So if I was adding the gene here, the gene would start here and go that way. Now you'll notice that one of the important um transcription initiation sites or promoter sites is the initiator. And it actually overlaps with the gene. Um And this is true for most initiation sites. Um And so you'll also see here that this gene particularly has the tata box. It also has this other element that we didn't talk about. But it just giving you example we didn't talk about every promoter that there is um just a couple of the important ones, but just know there's all these other ones. And just for good measure here's a downstream promoter element which is actually downstream of the gene. Now the consensus sequences here and you'll see that this isn't um a conserved sequence because it's not exactly the same in all organisms. But what you can see is that there's this consensus, you know, it's either going to be a gRC, it's either gonna be a G. R. A. It's either going to be a G. A. Or C in this position, so it's not identical. There is this flexibility that exists in consensus sequences that aren't there in conserved sequences. So promoters generally have consensus sequences. So with that let's now move on.

Okay, so now we've talked about transcription initiation but let's talk about transcription elongation. So after RNA polymerase get started it's got to transcribe the whole thing. So it has to actually work to continually stay on and elongate the RNA transcript so that the entire gene is transcribed. So how does it do this? Well there are proteins that actually travel with RNA polymerase sort of bind to the RNA plum rice and continually open up the DNA strand so that RNA polymerase can continually transcribe the gene that it's transcribing. So one of these we've already talked about this is T. F. I. I. H. It continually travels and it's the one responsible for opening around 12 to 14 base pairs at a time. So RNA polymerase can continue down the strand Now. How does RNA primaries actually transcribe DNA to RNA? Well, it is responsible for catalyzing um bosco di ester bonds between rival nucleotides during transcription. So if you remember back to some of our earlier topics, phosphate ester bonds and the bonds that form between that form between RNA and DNA and different nucleotides. Um And so RNA polymerase is the enzyme that has to actually inform those bonds. And so these reactions don't require energy and input of energy because they are energetically favorable. It ends up releasing two phosphates. You don't necessarily need to know the two phosphates. Just sort of know these are energetically favorable reactions don't require energy but it is kind of this kind of overwhelming process. You think of how many nucleotides are in every single gene, These nucleotides are added one at a time. But very quickly, probably around 1000 nucleotides a minute. Which is a huge amount of nucleotides to even think about processing in a minute. And so um like I said, these factors move along with the RNA Plymouth race. Help keep it attached, help keep it catalyzing, help open the D. N. A. So it has access to it. And all these factors we call elongation factors because they're helping the RNA polymerase to elongate the transcript. So just as a quick reminder what bosco di ester bonds are. So here we have different nucleotides and you can see here the phosphor di ester bonds forming between them. So this is what RNA plum rice does. Now another thing that RNA polymerase does is RNA plumb arises catalyze is RNA transcription in a five prime three prime direction. So if you remember um D. N. A. Is uh you know they're different directions of the DNA backbone on each strand. And so you can actually see this here, you have your D. N. A. Oh God, your D N. A. A five prime three prime and its other strand is five prime, 23 prime. Now here you have this sort of the transcription factors or the transcription initiation complex and you have your are in a race which is here. Now, what this means is that it transcribes in a five prime 23 prime direction means that it actually has to bind on the three prime side, which you can see here. And it transcribes this way until it's done and it leaves. But what you get you get an RNA transcript that is going five prime 23 prime. But just remember in order for this to transcribe in a five prime three prime, it actually has to bind to three prime end so that it can transcribe the appropriate way. So that was transcription elongation. Let's move on.

Okay, so now we're gonna talk about transcription termination. So so far you know RNA polymerase has been chugging along, it's been transcribing elongating the transcript but it's done. And so um how does it know it's done? Well it knows it's done because it reaches a terminator which is generally just a stop site, a stop sequence for transcription. So when it reaches this this terminator, what happens is the phosphates on the tail are removed. So if you remember in order for RNA polymerase to initiate, it had to be had to have a phosphate on it. And so in order to stop that phosphate has to be removed. And so that gets removed by protein phosphate. Asus which are enzymes that remove phosphates. Now the newly de phosphor related or the protein or the enzyme without phosphates um is free to go somewhere else. Go to a different gene become phosphor related again and start again. Doesn't need any kind of extra things. As soon as it's done it can start all over. So if we're to look at this um let me move out of the way you've seen a similar picture to this before where you have RNA polymerase but now I've added a phosphate. You can see here, so it's transcribing this way and it eventually reaches some kind of termination sequence of terminator and that sequence releases on a plane arrays from its phosphate and then that is free to go transcribe somewhere else wherever it wants to. So that's transcription. So now let's move on