Did you know that some biologists believe that there was once a time when DNA and proteins didn’t exist, and RNA did all the work of genetic material AND enzyme? There are many reasons to argue both why this could have been the case and why the cells of the world decided that protein and DNA were the “wave of the future,” But that’s an article for another time. It’s called the “RNA World Hypothesis,” and if you’re interested let me know. If there is enough interest, I’ll write a little introduction for your investigation on the topic.

Anywhoo, One reason for this hypothesis is the fact that there are so many different types of RNA that range in duties from genetic material to enzyme even in today’s cells. In fact, I can promise that there are hundreds of RNA molecules doing both of those jobs in YOU RIGHT NOW. I think it’s not only important to be familiar with the different types of RNA, but also to be familiar with the hypotheses as to why they work why they do. But without further hold up…

THE GREAT RNA LIST:

1. mRNA – Messenger RNA is a photocopy out of the library reference section (nuclear DNA). It carries all the same information as the DNA original, but the DNA remains in the nucleus and the ribosomes are in the cytoplasm. Just like you cannot check out a book from the reference section in a library so that it can be both ACCESSIBLE to another individual who wishes to use it and so that it can REMAIN PROTECTED, a cell cannot allow the genetic material to leave the nucleus. So mRNA acts as the photocopy. Here’s something to think about as well: mRNA is the only type of RNA that codes for protein. Everything else has some sort of regulatory function.
   
2. rRNA – Ribosomal RNA is a modern day example of RNA acting as an enzyme. If you read my article on translation, then you already know that the ribosome is the site of protein synthesis. It “translates” the information from RNA to Polypeptide. But what you didn’t know is that the ribosome is made of RIBOnucleic acid (and some protein, but mainly RNA). It catalyzes the peptide bond between amino acids, forming the polypeptide. When RNA acts as an enzyme, scientists refer to it as a “ribozyme.”
   
3. tRNA - think of Transfer RNA as an envelope that delivers amino acids. When you send a letter in the mail, you can’t simply drop the letter in the mailbox and expect it to go where it needs to. The tRNA molecule is the envelope that carries the amino acid molecule to the ribosome.
   
4. tmRNA – Transfer/Messenger RNA is a really cool RNA molecule. I had never heard of it before I started writing this article, but I wish I had. tmRNA is only found in bacterial cells, but in those cells, it acts like the refferee for translation. Check this out: When a ribosome gets stuck on an mRNA molecule for some reason, the tmRNA molecule (and some other proteins) unstuck the ribosome, put a marker on the unfinished protein so it can be destroyed, and destroy the mRNA molecule so that this doesn’t happen again. It breaks up the fight.
5. snRNA – From what I’ve found, there isn’t a lot that’s known about Small Nuclear RNA, other than that it’s composed of short RNA strands that can be found in the nucleus… who woulda thunked it? However, scientists have shown that this type of RNA molecule is involved in the splicing (cutting out) of introns from mRNA transcripts as well as the regulation of some transcription factors.
6. snoRNA – Small Nucleolar RNA is not to be confused with snRNA; it is found in the NUCLEOLUS, rather than the nucleus. In vertebrates, snoRNA is made from those introns that get spliced out of the mRNA transcript during transcription. They modify RNA nucleotides and they mark the length for rRNA molecules that are being synthesized to form ribosomes.
7. miRNA – MicroRNA molecules are usually only 19-25 bp in length – unusually small for a nucleic acid transcript. They play very specific roles in the cell, though. I’m sure you’re already well aware of the fact that stem cells can become any type of cell, and that the type of cell that they become depends on which genes become expressed in that cell. MicroRNA molecules can assist in this differentiation process by binding to the 3′untranslated region (UTR). MicroRNAs bind to regions on the mRNA transcript that match exactly, and they block translation. The cool thing about miRNAs is the fact that one miRNA can bind the 3′UTR of hundreds of genes, so the expression of a few miRNAs can block the ability for a cell to express the genes to become all but one type of cell.
   
8. siRNA – Small Interfering RNA molecules are much like miRNA molecules in that they are very small (~21 bp) and that they keep mRNA transcripts from being expressed. However, siRNA molecules come from outside RNA. Cellular RNA only exists as one-stranded molecules. When a cell encounters double-stranded RNA (viral), it chops it up into ~21 bp lengths (~2 twists of helix). It then attaches one strand (antisense) of the molecule to a protein called DICER. Using this siRNA as a template, DICER floats around the cytosol looking for mRNA molecules that are complementary. If it finds one, then that mRNA molecule is probably viral, so the cell destroys it. Cool Stuff!
   

Simply for the sake of ease, I put the most commonly taught RNA molecules in BOLD font. These are the likely suspects that your teachers will want you to know in introductory biology.

Guess what. These 10 don’t even scratch the surface. There are hundreds more classes of RNA out there, but you’re gonna hafta do your research if you want to know anything about them. But if you wish to be a kind soul, you could go look some up and post the name and description as a comment below. I’m sure your fellow nerds would be very appreciative.

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Best of Luck,

Grey

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.

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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

1. DNA attacked by Transcription Factors that recognize the TATA box
2. RNA Polymerase binds to Transcription Factor complex, then begins to synthesize mRNA strand complementary to the DNA template
3. 5′ Capping, 3′ Poly-A tail, Intron Excision
4. Move out of Nucleus

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Best of Luck,

Grey