Hey, all you Goobers! Hope you’re having a good evening! Today, on the eve of my biochem test, I will be bringing you many posts about things that you probably don’t care about. First on the list is something that’s actually really important: the process of translation!
In yesterday’s post, I talked a bit about how mRNA manages the impressive task of coding for very specific proteins. However, I mentioned, in that post, that there was more to it than just that—there’s a whole process we have to take into account. That process, usually lumped together with transcription in high school biology books, is called translation.
You see, cells have these things called ribosomes. These things make proteins. In prokaryotes, they’re made of two different subunits: a 50S subunit and a 30S subunit. The ribosome is composed almost entirely of rRNA, with a few proteins tossed in that, interestingly enough, aren’t actually required for it to do its thing. (In other words, we’re talking about an RNA enzyme here!)
Ribosomes, unsurprisingly, have a very specific shape. Notably, each ribosome has, among a lot of other features, a decoding center (where decoding occurs) and a peptidyl transferase (peptide-transferring) catalytic center. Even more notably, although all organisms have ribosomes that are very structurally similar, sequence homology isn’t really a thing. (In other words, our ribosomes all look the same, but they don’t have the same RNA sequences.)
So, we’ve got ribosomes, we’ve got a transcript, and we’ve got charged tRNAs. Seems like we’ve got all the right ingredients, but how do we mix them up? Well, as with just about everything else that we’ve looked at so far, translation is a process with three steps: initiation, elongation, and termination. Let’s look at them in prokaryotes first, shall we?
In prokaryotes, initiation requires a special kind of tRNA called f-Met-tRNA. This holds a formylated methionine amino acid, which looks kind of like normal methionine with a “peptidy” group sticking off of the end. The tRNA associated with this amino acid recognizes the start codon for a sequence, seeking out AUG (or GUG or UUG).
However, before we can bind to mRNA, we have to have mRNA in the right position on the ribosome. This occurs by the binding of a pyrimidine-rich sequence on the rRNA to a purine-rich sequence on the mRNA. This sequence, called the Shine-Dalgarno sequence, puts mRNA in the right place to be translated.
Now that we’ve got everything situated, here’s how initiation goes down: a 30S subunit with Initiation Factors 1 and 3 (IF-1 and IF-3) bound to it binds a complex of IF-2, f-Met-tRNA, and GTP. The f-Met-tRNA finds its codon, and GTP is hydrolyzed in a step that is characterized by the release of IF 1 and 2 and the binding of the 50S subunit.
Once we’ve got that down, we can start elongating our protein. This involves the ribosome moving (“translocating”) along the transcript while tRNAs move from one “site” of the ribosome to the next. The ribosome has three sites: the A site, where charged tRNAs are accepted, the P site, where the tRNA holding the peptide chain resides, and the E site, where spent tRNAs exit.
First, EF (Elongation Factor)-Tu binds a tRNA and GTP. This then enters the A site. The GTP is hydrolyzed, causing a conformational change that puts the aminoacyl part of the charged tRNA in the right spot in the peptidyl transferase site.
The actual formation of the peptide bond between the incoming amino acid and the existing peptide chain actually takes no energy input. As it is, the PTC (peptidyl transferase center) is just there to make sure that everything’s situated properly in order for the chemistry to occur.
Now an EF-G:GTP complex binds to the ribosome. By hydrolyzing its GTP, EF-G causes a conformational change that results in movement of the ribosome. The tRNA in the A site, which contains the peptide with its new amino acid, is moved to the P site. The “empty” tRNA in the P site is moved into the E site. The ribosome is lined up to another codon. Everyone’s happy.
Termination of the whole mess employs the use of release factors. Once the protein has been completely decoded, the end of the transcript will be reached. This is marked by a “stop” codon, a nonsense codon which doesn’t code for a tRNA. Release factors bind, creating a 70S ribosome:RF-1/RF-2:RF-3:GTP complex. The peptidyl transferase hydrolyzes the peptide chain from the last tRNA, and the release factors are ejected. Ribosome Recycling Factor (RRF) pulls the resulting mess apart, disassembling the ribosome and the mRNA and tRNA left inside.
That’s not too difficult, but what if you’re a eukaryote? Painful life experience has taught us that eukaryotes rarely do things with the same simplicity that prokaryotes. So, how does eukaryotic translation differ from prokaryotic?
Well, actually, the differences aren’t too staggering. In initiation, some eukaryotic initiation factors (eIFs) bind to the ribosomal subunit before mRNA, providing a scaffolding for the mRNA and its accompanying proteins. The initial Met-tRNA (not formylated) binds before the mRNA. Then mRNA is bound to the subunit through the help of the eIF4 group (containing a “cap-binding protein”) and (poly)A-binding protein (PABP). Scanning then occurs, wherein the ribosome finds the start codon on the mRNA. GTP is hydrolyzed, and the IFs are then ejected.
Elongation is pretty similar, excepting the use of eEF1 and eEF2 in the place of EF-Tu and EF-G. Then, when a codon is reached, a single release factor (!!), with GTP attached, binds to the ribosome. The GTP is hydrolyzed, the peptide is released from its tRNA, and everything pretty much goes to pieces.
All right! So far, so good! We’re making a good amount of sense, right? Well, lucky you, it only makes more sense from here on out. Now that we’ve made our proteins, we have to do stuff with them, right? Well, before we can figure out how proteins work, we have to know their structures. Sounds like fun, right?
Brb, physics lab is a thing that exists.