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MSU BMB 401 - 0Biochemistry 401 Lecture 39 transcript

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BMB 401 Lecture 39 Biochemistry 401 Lecture 39Today, we’re going to talk about translation in bacteria and in eukaryotes. So, let's get started. Now there are many differences and similarities in translation in prokaryotes and eukaryotes. Translation is the synthesis of protein from an RNA template. Both translation in prokaryotes and in eukaryotes use ribosomes, universal code and tRNAs, but there are many differences. In prokaryotes translation occurs at the same time and in the same place as transcription. There's no delimiting membrane that isolates the genome from the ribosomes, and so transcripts that are being synthesized may be bound by ribosomes that are actively translating the message, even before the message is fully made. In prokaryotes as in eukaryotes, there is an initiator methionine, however in prokaryotes this initiator methionine is formylated. There is a formyl group attached. In prokaryotes, the RNA message is generally polycystic. This means that this messenger RNA has multiple coding regions, each with its own attachment site for ribosomes. This is a region that is purine-rich, and isknown as the Shine-Delgarno sequence. This sequence is recognized by 16S ribosomal RNA in the small subunit of the ribosome. Now in eukaryotes, there is a circular messenger RNA that contains one message. This messenger RNA is recognized by the ribosome by both the five prime cap, and the three prime polyadenylate tail. The ribosome binds at the cap and scans for the first AUG codonSo in which direction is the message read, five prime to three prime, or three prime to five prime? Well, when a specific sequence of messenger RNA was made, a poly-adenylate message, with a cytydylate at the three prime end, what was synthesized was the poly-lysine with an asparagine on the end. By giving the ribosomes a specific RNA sequence, it was determined that the RNA was read five prime to three prime. If the message were read in reverse, an entirely different peptide would be made, and so the message is read five prime to three prime. This also has great implications for prokaryotic translation, because, since the message is read five prime to three prime, this means that as soon as the message is synthesized, it can be immediately bound by ribosomes that can immediately begin translation, even before the RNA transcript is fully synthesized. If the message wereread in the opposite direction, this would not occur. It would be necessary for the whole RNA transcript be synthesized, before translation could start. 1BMB 401 Lecture 39 Amino acids are activated by attachment to a transfer RNA. They’re brought to specific regions of the ribosome and once they're in position, the amino group makes an attack on the ester carboxyl group. This forms a tetrahedral intermediate that then collapses to form an empty transfer RNA, and a peptide chain that's increased in length by one amino acid. It's important to note that the incoming tRNAthat’s shown in green is also going to be the tRNA that accepts the growing chain, and so there is a transfer of the growing peptide chain from one tRNA to the new incoming tRNA, and it is the old tRNA that's left empty. Let's take a look at prokaryotic ribosomes. Now when we talk about ribosomes we do so Svedberg units. This refers to how the proteins sediment, and so we have an E. coli ribosome that is 70S, and it's comprised of two subunits, 30S and 50S, and again, the S refers to how these proteins sediment under specific conditions. Now each of these subunits are made up of ribosomal RNA and protein, and if you look at the 50S subunit that’s shown here, you can see that the majority of the ribosome is actually made up of ribosomal RNA. That’s shown in yellow. The protein is shownin red, and it's thought that the protein provides structural stability, but the ribosomalRNA is actually the catalytic portion of the enzyme. The 50S subunit is called the large subunit, and it contains the 23S and the 5S ribosomal RNAs and several proteins. The 30S subunit contains 16S ribosomal RNA, and it's this 16S ribosomal RNA that makes contact and recognizes the start site of translation, by recognizing a particular sequence in the messenger RNA. The small subunit and the large subunit fit together, and the messenger RNA will sit in the interface between these two subunits. In the small subunit, the RNA is shown in green, and the protein is shown in blue, and again you can see that the majority of the enzyme is made up ofribosomal RNA, rather than protein, and again the protein provides structural stability to the RNA. Now here we see a eukaryotic ribosome. This is an 80S ribosome. The entire thing is 80 Svedberg units. 'It is made up of a large subunit that’s called the 60S subunit and a small subunit that is called the 40S subunit. The large subunit contains 5S rRNA, 5.8S rRNA and 28S ribosomal RNA. Well, the small subunit, the 40S subunit,contains 18 S ribosomal RNA, and this 18S ribosomal RNA serves a similar purpose in eukaryotes that the 16S ribosomal RNA does in prokaryotes. It's used for identification and binding to the messenger RNA. 2BMB 401 Lecture 39 So let's look at what's going to happen. We have the ribosome with the messenger RNA in the interface between the small subunit and the large subunit and there are three specific sites in which transfer RNAs are positioned. The E site, the P site, and the A site. the E site stands for exit site, P site stands for peptidyl site, and this is the place in which the peptide bond will be formed, and A stands for the aminoacyl site. This is the place where the new transfer RNA that's charged with an amino acid will enter. So what's going to happen is there is an empty tRNA that's discharged. It's lost its amino acid in the formation of the peptide bond, and so it's inthe E side – E for exit. The next step is that it will be kicked out. Now in the P site there is a transfer RNA that contains an amino acid that's going to be attacked by the amino acid that's attached to the transfer RNA in the A site. As this happens, thepeptide bond is formed. The next thing that’s going to happen is the messenger RNA is going to ratchet toward the five prime direction, and the transfer RNA in the E site is going to be ejected. The transfer RNA that’s now empty that was in the P site will now be in the E site, and the transfer RNA that was in the aminoacyl site willnow be in the peptidyl site, and a new transfer RNA that's


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