The next thing we want to do is understand how the information in DNA is actually turned into a protein that's going to do the work of the cell. And in order to do that, I want to break this up into a couple of pieces. I want to talk about the components of translation, the pieces that the cell needs to get that done.
And then we'll talk about process, including another animation for you to review. The first thing I want to talk about are the different kinds of RNA. I have really focused just on messenger RNA.
So we've talked about the DNA being opened up, RNA polymerase finding the promoter, synthesizing a gene, right? The messenger RNA is going to come from a specific gene in the DNA, and then detaching from the DNA. The DNA rewinds and the messenger RNA goes out and finds a ribosome.
There are actually two other kinds of RNA to get made by RNA polymerase. So one of those is ribosomal RNA, and that's actually a structural component of the ribosome itself. It's part of the ribosome.
It makes up the bulk of the structure as well as function, has enzymatic function in the ribosome. The other RNA that is made is called transfer RNA. And transfer RNA actually brings amino acids to the ribosome so that the ribosome can build proteins from those amino acids. Now, if you look at a messenger RNA molecule, it's divided up into something called codons.
And so we know that there are three bases that are required for each amino acid. And we'll talk more about that in the next slide. But for now, each of these three bases is a codon. And you can see that we have three codons so far that have been labeled here. So here's the first one.
Here's the second one here. And here's the third one. And so the first codon, AUG, that tells the ribosome that it needs to bring a methionine.
That's the amino acid that's going to start this protein. Actually, methionine is always used at the beginning of proteins. So AUG is always the beginning of a protein. That's something that's useful to know. Notice that...
What's bound to it is this transfer RNA molecule and it has a complementary sequence that's called the anticodon. The anticodon, it binds to the codon in that messenger RNA and it's going to have a complementary sequence so UAC is complementary to AUG. And this transfer RNA with the anticodon UAC will always bring a methionine to the ribosome. The second codon. in the messenger RNA is UUC.
Its complementary anticodon is AAG, and AAG anticodon on a tRNA will always bring a phenylalanine to the ribosome to build proteins. And then the third one that's labeled here has a codon of AAA in the messenger RNA, and it binds exclusively to the anticodon UUU. the transfer RNA with the anticodon UUU will always bring a lysine to the ribosome. And as these are brought to the ribosome, the ribosome actually forms a peptide bond between these amino acids and begins creating a protein. And this is the primary structure from these amino acids.
One of the interesting stories is just how scientists figured out the genetic code. They've called this the Rosetta Stone of biology because after Watson and Crick published their paper describing the structure of DNA, it was pretty clear that the sequence of bases was informing the cell what order to put amino acids into proteins. But at that point, they didn't know what that code, how to read that code.
And so they did some experiments. some of them were thought experiments. So for example, we knew that there were 20 amino acids that were found in proteins. And if you had one amino acid per base, that would only allow you to encode four amino acids.
So they were confident that it couldn't be just four, it couldn't be a direct relationship, you know, adenine was one amino acid and thiamine was another, it had to be more complex than that. If you, if the... If each amino acid was encoded by a two base sequence, that would give you 16 combinations.
Four to the two is 16. And that's not enough, right? 20 is more than 16. So they figured it might be three because four to the third would give you 64 combinations. And that would be certainly enough for 20 amino acids. And the kinds of experiments they did was they would make synthetic messenger RNA with only U's, and they would find that you always got phenylalanine when you made only U's. And if you made only A's, you got lysine.
And then they would do little segments where they would do UUA, UUA, UUA. And they did experiments like that until they had cracked the whole code, and they figured out exactly what the sequence was for every amino acid. And some amino acids...
are encoded by more than one codon. So for example, phenylalanine is encoded by UUU and UUC. And there are some with four. Proline is actually encoded with all four of these sequences. Now, how do you read a code like this?
Well, this is first position. So if you know that your codon starts with a U, then you would go to this particular row. If your first position was an A, you would read from this row. The second position is here, right?
And then the third position is along this particular row. So for example, if I wanted to find the amino acid that was encoded for CAC, I would go down to C, and then I would go down to A, and then I'd go across to C, and I'd find it right here. And I'd notice that it was histine, okay?
So histidine, actually, is the, I said that wrong, it's histidine. So that's how you read the genetic code. A couple of other things that are really important. I said on the last slide that AUG always encodes methionine, and that's always the start codon. So whenever you're looking for the beginning of a protein, you want to look for that first AUG, because that's usually the beginning.
And then there are three sequences that don't encode any amino acids, and these are our stop codons. So UAA, UAG, and UGA are stop codons. You do not need to memorize any of these because you can look them up on your phone if you ever needed it, right?
It's not that critical. If this was ever going to be on a test, I would provide you with a genetic code, but I would expect you to be able to read the genetic code. So if I gave you a sequence and I said, you know, what amino acid is encoded by the codon GAA, I would expect you to be able to go here and read it and tell me that it's glutamic acid in this particular case. At least give me the three-letter code that's there, the GLU. Okay.
So another interesting thing is just the structure of transfer RNA. I told you before when we talked about RNA structure that RNAs can base pair with themselves. We call that intramolecular hydrogen bonding.
And so transfer RNAs are kind of a classic. Here is an example. It's a single molecule of RNA, but you can see it base pairs with itself here and here and here. And it forms this really nice cloverleaf shape.
And at the base... Of the cloverleaf here is the anticodon, and we said that matches up with a codon in mRNA. If you wanted to look at this in a more molecular space-filling model method, you'd kind of see it looks more like this with the amino acid attachment site, which is shown here, right here. So the amino acid is hooked here, or if you look at it kind of in a, it looks like a question mark a little bit if you want to draw this without the space-filling model. So the anticodon is at one end, essentially, and the amino acids are attached.
the other end of the transfer RNA. There is a specific enzyme called an amino acl tRNA synthase that charges transfer RNAs and what do we mean by charging? Well this particular enzyme is responsible for adding amino acids to the transfer RNAs and getting them ready for protein synthesis. So here's the enzyme.
And what's going to happen here is the first thing is this isn't free. It's going to cost the cell some energy. Okay.
So what we should see, I hope, maybe I'll have to set it to the slide again. So it will go. Come on little animation.
Okay. I've gone back a slide and I think I figured out how to get this. gift to play again.
It seems to do it one time and then stop instead of playing over and over again. So I'm going to go a minute forward in the next slide, and then we're going to go through this gift kind of quickly. All right, so what's happening with this enzyme is it's taking the amino acid, which is valine, and it's not going to be free. So this is an ATP. So it's going to release two phosphates.
It's got energy. It's added the phosphate to the valine. Here's our uncharged tRNA.
It's going to lose that high energy bond and then now we have the aminoacyl-tRNA with the valine on it and it's ready to go and participate in protein synthesis. So each time one of those transfer RNAs drops off an amino acid. it's going to go back to the enzyme that charges it and get another amino acid, and then it can go back and participate again in the process of protein synthesis. But you can see how each time this happens, it costs the cell some energy, and ATP gets used up.
So when we talk about catabolism and anabolism in the cell, we say, you know, anabolic pathways require energy, generally speaking. This is an example. Here we are building a protein, and we're using an an ATP for every amino acid that gets put on a transfer RNA. So this is just a nice illustration of how cells need energy to do things, right? It's costing the cell energy in order to charge these tRNAs with their amino acids that they need to bring to the ribosome.
Okay, so the next thing I'm going to show you is an animated overview of translation, and then I'm going to go through the steps with you one by one as well.