Gene Expression (Part 2): Translation in Eukaryotes

ElersonGL — Sat, 31 Oct 2009 22:40:26 +0000

Do you remember that we decided that DNA and RNA are two separate languages? Transcription factors read “TATAAA” as “park here.” There are hundreds of other examples of how enzymes recognize only certain sequences, but we’re gonna keep it simple for now.

Well during translation, Dr. Ribosome and his tRNA graduate students “translate” the mRNA into yet ANOTHER language: polypeptide. Ok, after some thought, that’s too cheesy even for me. But since it gets the point across, I’ll leave it at that.

Once the mRNA strand has left the nucleus and entered the cytoplasm (or “cytosol” to some people), it is fair game for ribosome binding. That 5′ cap is EXTREMELY important here because it marks the location for the ribosome to bind.

WAIT! I want to add a little sidenote here that would have REALLY aided me in getting the concept of why all the little proteins are necessary. Remember how we needed transcription factors to start transcription? We’re gonna need translation initiation factors in order to start translation as well. But what’s really the point? You’ll have to read that article to find out, but for now, read on.

SO, the ribosome uses initiation factors to bind on the RNA, more factors find the AUG start codon, then the ribosome uses factors to bring the tRNA molecule with Methionine to the AUG Start codon… WHEN DOES THE RIBOSOME ACTUALLY DO SOME WORK BY ITSELF!?!?

Ummmmmmm, pretty much after that first methionine. You see, once everything is set up, the rest is automatic. If you look at the picture above, you’ll see that there is an “A Site,” a “P Site,” and a tRNA molecule floating away. The “A Site” is short of aminoacyl site, or “amino ACID” site. This is where tRNA molecules land if their anticodon matches the codon that is showing.The “P Site” is short for the peptidyl, or “PEPTIDEyl” site. This is where the amino acids bound to the tRNA molecules are added to the growing protein using a peptide bond. Finally, there is the exit site, where the empty tRNA molecule is allowed to float off and become recharged with another amino acid (of the same type).

In the case of the methionine start codon, the ribosome was moved so that the AUG codon was the only one that was showing in the Aminoacyl site. Once the methionine tRNA was bound, the RIBOSOME MOVED (not the tRNA molecule) and this pushed the tRNA molecule over to the Peptidyl site. This left an empty A-Site for another tRNA to enter and bind, causing the ribosome to move again. This time, the methionine tRNA is pushed into the exit site and ejected from the ribosome.

This move-eject-bind procedure will go on until the ribosome encounters a stop codon. If you look at the chart above, you’ll see three different combinations that will result in a stop. This happens because there’s a special molecule that possess and anticodon but NOT an amino acid. When this molecule moves into the P site, the ribosome will attempt to move the growing amino acid chain to bind with the new amino acid. The only problem is that with this special molecule, there is no amino acid. So the protein just floats off, and the ribosome falls apart, thereby ending translation.

Short Version

Factors bind ribosome to mRNA
Methionine tRNA initiates reading
Move – peptide bond/eject – Move – peptide bond/eject
Stop codon ends it all

Best of Luck,

Grey

Gene Expression: (Part 1) Transcription in Eukaryotes

ElersonGL — Sat, 31 Oct 2009 21:03:29 +0000

Have you ever baked cookies? Ok, so that’s a dumb question. But how about this one — did you use a cookbook? Unless you’re one of a seriously small percentage of humans with a photographic memory, then chances are that you did. So, making cookies was a 2 step process: writing the information down and deciphering that information into a different language.

I know it’s corny, but just go with it… for the sake of education.

From that awful analogy, have you figured out that there are 2 separate forces at work here? There’s the information-writing party and the information-reading party. In your case, the cookbook writers were… oh, you get it.

So, lets take what we now know and apply it to cell biology. In THAT case, the information-writing party would be anything involved in transcription, and the information-reading party would be anything involved in translation. Since this particular article is supposed to be about transcription, let’s go into a little more detail, but always keep in mind that everything in this process is about writing information down so that it can be read later.

Think of the genome as a library, full of cookbooks. This entire library is in the DNA language, and the ribosomes (the information-reading party) don’t speak DNA. There’s a wealth of information there for making all kinds of proteins, but the ribosomes just can’t read it, so it’s necessary that the information be translated into RNA, the ribosome’s native language.

The obvious place to start is in the nucleus at the gene of interest. We know from my post on the parts of a gene that there is a part called the promoter. I’ve heard the promoter referred to as everything from an on/off switch to an airport landing strip, and they all make sense. The promoter is the part of the gene that says “HEY! Bake THIS recipe!!”

There is a specific word in the DNA language that transcription factors, proteins that do speak DNA, understand as meaning “park here.” We refer to this word as a sequence called the TATA box. These transcription factors (there are many of them that work together to start transcription) act as a pit crew for RNA Polymerase. Their job is to find the starting line, get the RNA Pol in the right spot, and then give it any starting push that it may need (from stored energy, like ATP).

The RNA Polymerase is the only enzyme that is actually bilingual. Once it is given the proper push by the transcription factors, it glides along the DNA template strand, reading the DNA words and translating them into RNA. The two languages are very similar, in fact that only difference is that whereas the DNA alphabet is A, G, C, and T, the RNA alphabet is A, G, C, and U.

At this point in the process, we have RNA sliding down the DNA template strand translating the directions from DNA into RNA. So, what next? There must be something programmed into the system to stop it at the end. Nope. In fact, transcripts don’t even make it to the end 100% of the time.

The RNA Polymerase glides along the top of the DNA strand in much the same way as a kid running down the curb on a street. It doesn’t take much force to knock the kid off the curb, and it takes even less to knock the RNA Pol off the DNA. There are no strong magnetic forces acting that hold the RNA in place, and the enzyme itself fits over the DNA like a horseshoe on a string. Sometimes, the transcript lasts all the way to the end of the coding sequence, sometimes it doesn’t, and sometimes it may go on for many thousands of base pairs after the gene has ended. Obviously, though, enough transcripts last until the end of the coding region, or else this system wouldn’t work.

You would think that, logically, as soon as the RNA Pol falls off the template strand, the new mRNA molecule would be finished and the process would be over. However, grammar is always important. I’m sure you can think of a few instances in which bad grammar made something hard to read, or even completely unreadable. Cells use a type of grammar as well, but we call it “post-transcriptional mRNA modification.” I know it’s a big scary term, but it simply means that after the RNA Pol does its job, the cell changes the molecule a little bit.

This modification consists of three very important parts: A 5′ cap, 3′ polyadenylation, and intron excision. These are all rather simple as well, but terms can be scary. When I say 5′ cap, I mean that the cell contains a host of enzymes that add a protective molecule onto the transcript at the 5′ end that signals the ribosomes to do their job later as well as protects the transcript from being sliced up by exonuclease enzymes. The 3′ polyadenylation, which means “lots of Adenosines on the 3′ end,” also protects the mRNA from exonuclease shredding. Intron excision, however, it probably the most important. In this process, chunks of DNA words that don’t actually mean anything are taken out of the directions in the mRNA.

Why these stinkin things are even there, we don’t know, but we DO know that if they aren’t taken out of the mRNA transcript, there will be no cookies later on. You see, in the DNA language, it is customary to take chunks of sentences and overlap them with each other. In order to read the original sentence, we must remove the chunks of other sentences. We call the original sentence chunks “exons” because we want to EXPRESS them, and the INTERVENING sentence chunks are called “introns.”

Once the cell has written down the recipe in a language that the ribosomes can understand and put it in the correct grammatical format, then the mRNA transcript can leave the nucleus and move on to the second step in protein expression.

The Short Version