Translation

Hi in this video we're gonna be talking about translation. Okay so translation is the process of turning in the RNA into a protein. And so there are three steps the initiation, the elongation and the termination. So this video we're gonna focus on initiation. The next one will focus on elongation. And then the last or one of the last ones we'll talk about termination. So when we think about translation initiation we need to think about two ways that that's initiated. The first is how pro carry optic cells do it. And the second is how eukaryotic cells do it because it's different of course. So pro periodic sell translation initiation requires specific sequences. So what are those sequences? Well the main one is going to be the Shine del Garneau sequence and this sequence is going to be upstream. So right before the code on the initiation code on the one that's going to start translation. And so and what it is is when the initiator T. RNA, which we're going to talk about soon. So T RNA is going to be really responsible for recruiting the ribosomes and all sorts of things. So so the initial there's a really special one called an initiator T. RNA. And it binds to the shine or it binds to the starch coat on but it knows where to bind because of the Shine del Garneau sequence. So the Shine del Garneau sequences saying, hey initiator. Trn a your start code ons here. And so it says okay I'm coming let me go to the start code on. So the Shine del Garneau sequences letting the T. RNA know where it needs to go. So another factor that is required are proteins of course. And in um pro chaotic cells these are called initiator factors. You may see them as I. F. For short and there's I. F. One, I have to I. F. Three. And these proteins just sort of settle everything in. They say initiation is going to start here. Let me get everything oriented correctly. That's what those proteins do. So that's pro periodic transcript translation with the Shine del Garneau sequence. Eukaryotic translation initiation requires much more many more proteins than pro periodic. So the first thing is is that in eukaryotic translation, the M. R. N. A. Isn't just so in pro periodic cells when the M. RNA is transcribed, it's translated pretty immediately after in eukaryotic cells. That's not the case when the M. RNA is transcribed, it didn't undergo some processing before it ends up being translated. And so the M. RNA for eukaryotic cells exist in the cytoplasm. And because it's just been sitting out there for a little while, it's gone through some processing, it's kind of folded in on itself and a bunch of proteins has bounded. So already it starts out more complicated because there's a ton of proteins. There's the secondary structures where the M. RNA is folded in on itself. And so when translation initiation begins, there's already a lot of proteins there and those proteins either need to be removed or reoriented. So translation can occur. So some of the first things that happen in tran translation initiation for eukaryotic cells are initiation factors now in pro chorionic cells those were called I. F. But in eukaryotic cells is called E I F. So you add that E. For eukaryotic and instead of 12 and three in eukaryotic, it's four A B N C. Or A B. And G. So E F F four E I F E I F E E I F G. And so what these initiation factors do is they say, hey that M. RNA needs to be translated. So what do I need to do? I need to bind to the five prime cap. Remember that the RNA has been processed with that cap? So they come in, they bind to that cap. They say hey all you other proteins need to leave because I gotta we gotta get translation started. So it kicks all these other proteins off and it exposes the M. RNA. And it says okay we're getting you ready for translation. So you don't need to be folded in, you don't need to be covered with protein. So let us come in clean you up, get you ready. So then whenever those initiation proteins have come in they've cleaned up the M. RNA, they've gotten the proteins off. What happens is we get an initiation complex which comes in attaches to the M. R. N. A. And looks for where translation is going to start and where translation starts is the start code on the A. U. G. Start code on. So we started out with that like complex M. RNA. That was covered in proteins. The initiation factors came in, cleaned it up the initiation complex bound to it and starts running across it. Looking for the A. U. G. Start caught on. And um when it finds it it can start initiating. Now there's one more sequence you need to know about for a eukaryotic initiation. And that's the Kozak sequence. So the Kozak sequence is a consensus sequence. Remember a consensus sequence isn't conserved. So it's not the exact same between different organisms but it's fairly similar between different organisms. So it's it's a really important sequence. It's been around for a while. So the Kozak sequence sits around the start code on and increases translation efficiency meaning that without the Kozak sequence your translation is just like gonna be half hazard about it. It's just gonna be like whatever when I get it done I'll get it done. Um But a Kozak sequence that is when it's there it is like ready to go it says I'm ready to translate. And so um I guess you can kind of think of the Kozak sequence is clutch if you're using clutch you're like ready to learn. And so the Kozak sequence is you when you're using clutch. So that's translation initiation. So we start out with that M. RNA folded. It gets cleaned up with the initiation factors. The initiation complex comes on, binds to it finds that start code on. And when it finds that start code on the initiator, T RNA is going to initiate translation. So what is the initiator? T. RNA? And how is it different? Well the initiator T. N. A. Is obviously going to start translation. And it's different between pro carry oats and you carry outs in pro carry oats. The T. RNA is attached to this chemical, the informal matthias me. So matthias nine here this word here, this is an amino acid and it is the amino acid associated with the start code on. So every protein always starts with a tiny but the initiation TR N. A. Is different because in pro carry out it starts with informal Metheny which is a special type of Athenian that's only used for initiation. And then you carry oats that T. R. N. A. Is attached to again a specialty RNA. But it looks like this, it's not the informal it's um a thiamine but it's a special initiator methionine which is where that like tiny little I comes in. So whenever the start coding has been found whether through this initiation complex and you carry oats or through the shines Garneau sequence. And pro carry outs when the initiator T RNA comes on, it initiates translation by adding this meth find special initiation Metheny. So here we have this is an example of you carry outs we know because it says E. I. F. So that's you carry out. So here we have our M. R. N. A. And our initiation factor has come in and it's helped clean up the M. R. N. A. We have our initiation complex that binds the M. RNA. Once it's been cleaned up and it scans looking for the A. U. G. Start code on. When it finds this, the T. R. N. A. Containing the special initiation Mazzini will come on and initiate translation. So that translation initiation, let's turn the page and get the translation elongation.

Okay so now we're gonna talk about translation elongation. So when we left off before we were at the AU. G. Start code on. So the initiator tr N. A. Had come in. The A. G. Start caught on has been identified. The initiator T. RNA was there. The ribosome came and they're ready to get started. So the initiator T. RNA sitting in the ribosome and it's ready. But what happens is when it gets ready it just pauses for a second and then the ribosome is released and then it elongates and whenever it's released it goes it goes quickly. It's booking it down that M. RNA translating really as fast as that little ribosomes can go just go go go go go go go. So what do we need to know to talk about the elongation step of translation? Well the first thing we need to know that ribosomes have sites in them which we've talked about in other videos. They have the A site, the P site and the E site and they have different functions and we'll talk about which elongation steps in each function. And then there's a second group of proteins called elongation factors to really important ones are E. F. Two and E. F. G. And these factors they get their energy from GTP. So they come they break down GTP. They get their energy and what they do is they associate with the ribosomes they associate with the T. R. N. S. They associate with the M. RNA and they help this process. So they're just helper proteins that are like hey ribosomes I see you're translating, you're going pretty fast you need any help. And the ribosomes says yes and so they come in and help. So let's go through each of the steps. So we already have the initiator. Matheny and it's already on the initiator. Does has done its job and it's gone. So now what's the next T. RNA doing? So the next T RNA is binding to an elongation factor EF two which is bound to GTP that's where it gets its energy and that T. R. N. A enters into the a site of the river zone. When that T. R. N. A enters into that a site we get GTP is hydrolyzed and that means that it turns into G. D. G. D. P. That extra P. Is released and the E. F. Two is also released. So we had the T. RNA coming in with the elongation factor. The elongation factor helped it get in. Then once the T. RNA was there that the elongation factor didn't need to help it anymore. So it hydrolyzed its GDP and left. Then the T. R. N. A. Moves to the P. Site and this is where the amino acid is attached to the polyp peptide chain that's growing so it entered with the F two F two left, it moved to the p site it attaches its amino acid and then whenever it's in the P site the other elongation factor comes in and binds E. F. G. Says hey you need help getting out of the P site and the T. R. And I said yeah can you help me get out of this P site. And so the F. G. Says sure let me hide relies this GDP or GTP and then I'll get you to the E. So that's what it does. The E. F. G. Comes to the P. Site it hydra lies is its GTP. And that energy moves the T. RNA to the, so these elongation factors are binding to these T. RNA. Is there helping the trn a move from site to site? So the EF two helps to get into the A. The GTP hydraulic sis releases it. It moves to the p site when it's in the p site it needs to get to the E. Site. So the E. F. G. Comes in. E. F. G. Releases its energy and then it moves the T. RNA to the E. Site. So here we have an example, here's our rib zone with our sites, we have our T. N. T. RNA. Sitting here in the two different sites. This one's gonna be the p site because of the new polyp peptide chains. And these um E. F factors are gonna come in. They're gonna bind to the T. N. A. T. RNA at any kind of step and help it get to the next one. So for E. F. Two it's helping it get into the A. For E. F. G. is helping get to the so with that let's move on determination.

Okay so translation termination. So where we left off is those T. R. And S. Are being fed through those ribosomes sites and now we're ready to terminate. And so how do we tell the ribosomes to stop translating. I mean that ribosomes just going and it's just having a great time. It's just going we I'm translating but we want to stop it. And so termination is controlled through stock code ins and proteins called release factors. So we know what stop code ons are. We talked about them before they're these ones here and that. I'm highlighting what our release factors. We'll release factors are proteins that can recognize stock code on. So they kind of like survey the M. RNA and they say oh where's the stock code on And when they find 21 what happens is a release factor binds to that stock code on. So now we have a release release factor is a protein it's bound to that stock coat on and our rivals um is just translating. It's just go and go and go and go and go on. But eventually it's gonna hit a stock coat on. And what happens when it does that release factor is there then um the release factor comes in and it binds to the ribosomes and blocks the T. RNA from getting in. So if it's and they can't get in the zone and a release factor is then the ribosomes says hey this is a release factor. I don't need to continue anymore. And through GTP hydraulic sis for the energy for this process. It terminates. It says okay translation stops. I'm not going to worry about this. There's a release factor here. I don't need to continue. So that's exactly what happens. So here we can see there is a river zone here. You can see that it's coming in and this release factor was on the stock coat on and that's the ribosomes said, Hey, I don't need to be here anymore. So I'm just gonna release and that is how translation is terminated. So with that, let's move on.

Okay. So now I want to talk to you about the wobble hypothesis. Now this is something that you may have heard about before in an intro biology class. But I want to mention again here in case you've never heard of it. And what the wobble hypothesis says is that the third nucleotide in a code on. So we have our 123. So this one here This one is less rigid than the first two. So what does that mean? It means that this is a code on. Right. And it encodes for an amino acid right? And A. T. RNA. And it does this because A T. RNA comes in says I can recognize I have an anti code on that's gonna bind to this code on and that and then I will give you my amino acid. But actually the wobble hypothesis says that the T. RNA is really concerned with the first, the first nucleotide and the second one. But the third one has a little bit more wiggle room or wobble room I guess. So the T. RNA comes in and it says and it says oh my first nucleotide matches perfectly. My second nucleotide matches perfectly. But we don't match with my third. The T RNA says good enough that's fine. So let me add my amino acid. And so the T. RNA compare with one more than one M. RNA sequence. As long as the first two nucleotides are a pair with the T. R. N. A. The third one doesn't always have to. Um and so why do we do this? Well because it allows for multiple cottons to code for the same amino acid because A T. RNA combined to say A. T. G. And A. T. C. Right? And that gives the same code on. Now I don't know off the top of my head if that's true. But this is just an example one that is true. Is this where G. A. G. Is the T. RNA. The anti code on. And the M. RNA is C. You see. Now this is a perfect pairing. Right? And that's going to allow for the amino acid losing to be given to the growing polyp peptide chain. But this one say the M. R. N. A. Is. See you you well this is not a perfect pairing G will not normally pair with you. Right? But that's okay. The T. RNA doesn't care and it still can provide lucy. Now one of the questions I get asked a lot with this is is can this third nucleotide be anything? And the answer is no there's actually specific complicated rules of what this third nucleotide can be to allow the T. RNA to bind. Um But I'm not it would take me like three hours to describe all the rules. So I'm not gonna go into all those rules but just know that there is some flexibility. Not 100% flexibility but there is some flexibility to this third nucleotide. And that the T RNA doesn't always have to match all three nucleotides perfectly. Just the first to the third one is sometimes a little bit more wiggly. So with that, let's move on.

In prokaryotes, which of the following sequences is responsible for initiating translation?

• A. Kozak sequence
• B. Initiation sequence
• C. Shine-delgarno sequence
• D. Elongation sequence

The methionine used to initiate translation is the same methionine used during translation elongation.

• A. True
• B. False

Which of the following chemical reactions provides the ribosome with the energy required to complete translation?

• A. ATP hydrolysis
• B. GTP hydrolysis
• C. Protein lysis
• D. H2O hydrolysis

Which of the following represents the wobble hypothesis?

• A. CUC and CUA encode for different amino acids
• B. CUC and CUU encode for the same amino acid
• C. tRNA is specific for only one codon
• D. CUC and CUG encode for stop codons