Biology: Translation/Elongation: Initiation

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Let's recoup. Let's take a look and see what's going on with our initiation complex and once we're initiated, let's get down to making some polypeptides. We started out with a messenger RNA molecule. The messenger RNA molecule was an edited version of what came right off that DNA template in the nucleus. Remember, we had to cap it on both ends. We had to chop out some introns. We had to get that baby ready to go. Boom, out it goes into the cytosol. Out into the cytosol, though, is no guarantee of success unless you can find those components of protein synthesis that are going to allow the beginning, the middle and the end of this whole synthetic process. And so we found out that, indeed, our mRNA strand had to find other components to start the initiation process. One of the first things that happened to our mRNA - and here's our green mRNA strand there - is that it had to hook up with the small subunit of a ribosome. That's step one.
In addition, that 5' site with its leader had to bond to that ribosome. It's what attracted it. And if you think back and look back at those earlier lectures, you remember that 5' cap said, "Here I am. I'm ready to translate." And indeed, what was that signal to? To the lower subunit of the ribosome. But that's not all. Then, along had to come a tRNA to bond into this mRNA, but not just any tRNA - a charged tRNA molecule. What's that mean? That means that it has already gone through this whole idea of getting a high-energy phosphorylated bond between the amino acid - in this case methianine - and the tRNA through the interaction of ATP. Thus phosphorylated intermediates become a key, and of course, that's all enzyme-driven.
Well now that we have this, we're almost ready to start the initiation of this protein synthesis. And so along came the rest of the ribosome and it sat over this tRNA. Now you'll notice that I deliberately put that tRNA in what is called the P site. And there's an E site - and I'll tell you right now that just stands for "exit". A lot of books don't even refer to the E site, but it's a reality - it's there - and you'll see what it does in just a few minutes. And then the A site, and that's going to be an important site because that's what's coming once we get to elongation.
Now before we do that, though, I want you to look at this and I want you to start thinking about ribosomes. Ready, think. I should tell you what to think. I want you to think about the functions of ribosomes. You see if you'll look at the ribosome and get a feel for what it is and what it does, you'll get an idea for structure and function. I want to make you realize two crucial roles of that ribosome - of that thing made out of ribosomal RNA and protein. Function number one - it is going to catalyze peptide bond formations between, literally, high-energy bound tRNA molecules, one to another. Now, that's a clue of what's coming. I have an amino acid here. To make a polypeptide, what do I need? Another amino acid. In order to put two amino acids together, what do I need? I need to somehow form a peptide bond. So I want you to think of this ribosome almost as a giant enzyme. It's much bigger than an enzyme. An enzyme's a molecule. But nevertheless, this thing is a collection of proteins and RNA. So your picture of it is something that's going to bring molecules together, enzymatically, so to speak, is very important.
In fact, if you know a little bit about evolution, you know that we talked about something called ribozymes, that RNA can self-catalyze. Remember ribozymes and the fact that there are some introns that can actually catalyze their own removal by RNA acting as a catalyst. You know the discovery of these things set biology on its ear because we had to change our definition of catalysts. Up until we realized about ribozymes, we thought catalysts were always proteins. It turns out that RNA can be a catalyst too. And that, if you think back to the heterotroph hypothesis, that's why we think RNA may have been the first nucleic acid to form, but that's another story. I just had to lay that out on you because that's cool stuff anyway.
So I want you think of the ribosome as like a ribozyme - a kind of an enzyme that's going to catalyze things. The second thing I want you to think about, when you think about the ribosome, is this, that it's eliminating any possibility of ambiguity. Notice, AUG - this codon fits into that site and only that codon. And if you look at the next group - and let's just enlarge the bottom of this ribosome so you can see it. If we have a codon that fits in right here - one, two, three - this site is the same size, so the next codon that's going to fit in - one, two, three. So you, literally, are using this ribosome as a reading frame reference. That's the thing that's going to say, "My first word has three letters in it. My second word has three letters in it. And you'll see my third and my fourth and my fifth." So it's also eliminating ambiguity. This is a conceptual thing about the ribosome, but if you get it, you'll understand what's about to happen. So it eliminates ambiguity.
If you guys have it up to here, it's easy. Because here on in, I think you could almost predict what's going to happen. Let's see. So I'm going to make a little drawing here and then we'll look at probably a little bit better drawing than mine. Okay, so what we have, therefore, is we have this mRNA strand and we have the very first AUG codon. We'll do a ribosome here and we've got to divide. That's going to be my UAC and that's going to be in my P site. And that, of course, is going to have this tRNA on it and the tRNA is going to have methianine. All right, now let's zoom in and take a closer look at that.
And what we'll do is we'll make that ribosome bigger still. We'll make those sites bigger still, and I will put my AUG here. The next step is called elongation, and it's the elongation of the protein. When we do protein elongation, we have to start making bonds, and here's what happens.
You remember this is one big mRNA chain. That means that there are three more nucleotides right here. In my hypothetical mRNA strand, I'm going to put AAA. Why did I put AAA? I just - that's what's going to come next. Now here's the thing. We have a tRNA that's sitting right here and we know that that has methianine in it. Well guess what? By virtue of a few factors called, number one, elongation factors, elongation proteins, and an energy source - yes, an energy source. This is endergonic. We have to add energy - GTP. With all of these things coming into play here, what's going to happen is we are now going to bring a second tRNA and usher it in to this site. Look at this - AAA. Which tRNA is going to come in here? The tRNA that comes in there is going to have the anticodon UUU. Now, we take out our chart. Slide that away for a second. We look up AAA on my codon chart and that's lysine. That means that this tRNA is going to bring in lysine. Upon bringing this right in here, what we are going to get is a bond. And that bond is going to happen between the methianine and the lysine. And so it's going to occur like that. What kind of bond is that? You know this. It's a peptide bond. And now, once this peptide bond occurs, the elongation pattern can begin. Let's take a look at it in a little bit better diagram than I have.
Okay, so here's what's going to happen. What's going to happen is this. In a growing RNA strand, here is a chain of amino acids. So we are going to go about halfway down the chain. It can be the first one. It can be the fiftieth one. In comes a tRNA that's charged. That tRNA that's charged is going to bring an amino acid. Here's what's going to happen. Look, right here - peptide bond formation. Now, this entire chain of amino acids will be transferred right there. So this tRNA in the A site now has the polypeptide chain and it's hanging on for dear life, because guess what? The tRNA that was in this site is going to move over. It's going to move into the exit site.
But how does this occur? How does this tRNA that's here move into the exit site? How does elongation continue? Well, here's what we're going to do. I want you to picture that ribosome sitting over these six nucleotides. Think about it. If I move that ribosome over three, what's going to happen? Simple - the three that are in the P site are going to do what? They're going to move this way. The three that are in the A site - they're going to move this way. And the three that are out here - where are they going to go? Into the A site - shifting one or three by three by three - allowing the beginning of the elongation of our chain. How does the chain keep elongating and finally, how does it end? That's another story.
Molecular Genetics
Translation
Translation/ Elongation: The Initiation of Elongation Page [1 of 2]