Biology: Transcription: Form RNA from DNA Template

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It's time to spiral in. It's time to take a look at how DNA is going to make RNA. What events do we know about? Without turning this into a molecular genetics course, which I highly recommend you take, because that stuff is amazing. But let's see how much of this we can do.
First of all, we're talking about the process of transcription, which means that DNA is making RNA. Now, let me give you just a couple of quick reminders of the difference between DNA and RNA. Remember that RNA is made out of ribonucleotides. And ribonucleotides, like deoxyribonucleotides, consist of the 5 carbon, ribose. Now there's a difference right there. Notice I said ribose. Whereas deoxyribonucleotides consist of deoxyribose. So what we have are two OH groups instead of just the one OH group in deoxyribose. And just like the DNA molecule - we have that whole analogy of the house with the pool and the driveway. And this driveway can be one of four bases - nitrogenous bases. It can be adenine, guanine, cytosine, but not thymine. Okay, in RNA, thymine is replaced by uracil. There is no thymine in RNA. But other than that, it's all similar.
So that's RNA. Because of that bonding - because of that OH group - what we find is that RNA will not form a helical structure. You will not get the double-bonded hydrogen bonding holding these nucleotides strongly together that happens in DNA. So we don't get a double helix in RNA. RNA is single stranded. Now sometimes it does, in some of the RNAs like transfer RNA, form a secondary structure. And ribosomal RNA becomes very complex with all of its interactions. But the bottom line is RNA is single-stranded at its outset.
So let's make some RNA. Well, we've got to go to DNA to make some RNA. And we're going to start with something called the transcription unit. Now the transcription unit on DNA - we'll just make a crude line of DNA here - and let's just say that the transcription unit - the thing we want to transcribe - is right here - the transcription unit. Okay? And here's the thing. In order to make RNA, you need an enzyme. There are actually three of these RNA polymerases. The one we want to concern ourselves with is RNA polymerase 2. We won't worry about 1 and 3 right now. And I'm just going to refer to it as polymerase.
So polymerase - RNA polymerase, in this case, rather than DNA polymerase - is going to come on here. And RNA polymerase is going to land on the DNA strand. Now, you're going to hear me a lot, over this unit, comparing bacteria prokaryotic cells with eukaryotic cells. Prokaryotic cells are simple - often much simpler. In prokaryotic cells, RNA comes on, recognizes what is going to be called a promoter sequence. In prokaryotic cells, you're going to get this promoter sequence. The RNA polymerase is going to land and start to read. I'll tell you how it reads in a second. That's not what's going to happen in eukaryotes. In eukaryotes, we do have a promoter sequence, but now we've got to add some things. Right?
So let's draw my DNA strand still one more time. There's my transcription unit and I'm going to put in my promoter sequence. Now how big is a promoter sequence? A promoter sequence is about 15 to 300 bases, or nucleotides. Please note, I do use that word bases and nucleotides almost synonymously, because remember, every nucleotide has a base - the nitrogenous base. And we often refer to the nucleotides as the base, because remember, A, G, C, T or U is the base. So we kind of throw those terms around randomly. But I tend to use the word "nucleotides" but you'll often seen them referred to as bases, so don't get nervous about that.
Eukaryotes, RNA polymerase can't recognize this. And so you need some help. What's the help? Well, here we go. If this is a transcription unit - I'm going to refer to "upstream". Now we'll talk about directions and 5 prime and 3 prime in just a second. Okay? But "upstream" of the promoter sequence is going to be something called a TATA box. What is a TATA box? A TATA box is - now, all right, I'm going to tell you guys about direction of reading.
Do you remember that DNA polymerase reads 3 to 5? Guess what? So does RNA polymerase. Isn't life wonderful? We don't have to learn anything new. RNA polymerase is going to read 3 to 5, add 5 to 3, just like that. So if the strand to be - the strand that is going to be read - is this one, because I've already made it this one, then this is the strand that's going to be read, I'm going to put 3 prime here and 5 prime here. Remember, this is a DNA molecule. We're starting with DNA. So this is going to be 5, 3. If this is the transcription unit, just by convention, we refer to the TATA box on the non-transcribed strand. Don't get overly nervous about that. I'll say it one more time. Just by convention, we say, when I refer to the TATA box - T-A-T-A and then several more nucleotides - actually, we'll throw those in, A-A. When I refer to that TATA box, literally, I'm talking about it on the non-transcribed strand. So, again, save your neuroses for more important things.
So there's the TATA box and, as you know, there's a complimentary sequence here - the ATAT box, if you will. Okay, so we've got TTT. Nobody but me ever calls it the ATAT box, so please don't. That's between you and I. So here's my TATA box, and it's my TATA box that's going to be important in eukaryotes, because here we are. Here's what happens.
Number one, we have the TATA box. Number two- we have the promoter. Number 3, we have what are going to be called transcription factors. Transcription factors - proteins - transcription factors. Without these proteins - and trust me, you don't want to get into a lot on transcription factors now. Take a good molecular genetics course. But transcription factors are proteins without which transcription cannot begin. So we're going to have these transcription factors that are going to allow the RNA polymerase to land. So without transcription factors, we're not going to have that. But when we get the transcription factors landing at the TATA box, then RNA promotion can begin and we are going to get what is going to be called a transcription initiation complex. Sometimes I think that's a disease molecular biologists have. But it's going to be called a transcription initiation complex.
So what do we have? Transcription factors, RNA polymerase - transcription can begin. Let's take a look at this. Here is my start point. There is the beginning of what I want to transcribe. Here's my TATA box - my 5-prime and 3-prime strand. Here's the strand I want to transcribe. Well, without with the transcription factors, my RNA polymerase cannot land. So along come my transcription factors. They land at the TATA box and on the promoter region. And now, we can get the beginning of what is called the transcription initiation complex. And there it is.
Now you see what's happening here. This is kind of cool and this is the next factor. What's going to happen is, just like in DNA polymerization, we're going to open up a bubble - a much smaller bubble - about 20 nucleotides or bases at a time. And the RNA polymerase is going to proceed reading the strand like I told you it's going to read it. So it's going to read the 3 to 5 prime strand, but it's going to add 5 to 3. Remember how that works, okay? And so now we can see that it's going to elongate and polymerization is going to occur. And like DNA polymerization, RNA polymerization cannot occur without RNA polymerase.
Let's just take one quick look at this whole idea of 3 prime and 5 prime - just one more time so you feel good about it. Here's my DNA strand, and I'm not going to put any A's or T's or G's or C's on here, but I'm going to show you why we say this 3 to 5 thing. And here's my RNA and that's my ribose. And once again, what's going on? Well, we know we have a base coming off of here that's going to be the matching base here. All right, I'll put A's and T's in here. Remember, DNA can have a T, right? This is DNA. So I've got a T there. I'm going to have a ribonucleotide with an A there. Remember what's going to happen. What can only happen? One, two, three, OH group and of course there's an OH group there, because this is ribose. Here's the only thing that can happen. As this thing bonds here, in order to polymerize this thing, I have to take and make a phosphate backbone, don't I? And that's going to come off of my number 5 carbon from this one, which will make - let's say this is a G. We'll make this a C. So therefore, for this polymerization to occur, for RNA to polymerize RNA polymerase, we have to do a bond right here. And so we have to add my 5 to my 3. It reads 3 to 5. It adds 5 to 3.
When you're done, you have an RNA strand. What are you going to do with that RNA strand? Stay tuned, you'll find out.
Molecular Genetics
Transcription
Transcription: RNA Formation from the DNA Template Page [1 of 2]