DNA itself does not actually leave the nucleus of the cell. However, we learned that ribosomes, the organelles involved in protein synthesis, are also not inside the nucleus. Somehow, the instructions have to leave the nucleus and travel to the ribosomes to initiate protein synthesis - but what will carry the instructions we need? The answer to that is mRNA, or messenger RNA. mRNA is created in a similar way to that of DNA replication. An enzyme called RNA polymerase binds to a strand of DNA. RNA polymerase pulls and unwinds the two DNA strands apart and adds nucleotides to one strand, called the template strand. The nucleotides added are RNA nucleotides (A,C,G,U), and as RNA polymerase progresses, the growing strand trails behind. RNA polymerase then rewinds the DNA together. This process is actually really funny, because RNA polymerase binds to a sequence of DNA called a promoter. After binding, it starts transcribing everything in front of it. It doesn't stop after the protein coding sequence is complete - it keeps going until it reaches a sequence of AAUAAA. This calls several proteins to bind to RNA polymerase and chop off the tail 10-35 nucleotides later. However, this doesn't stop RNA polymerase. It still produces RNA, even through the RNA is degraded immediately by enzymes since it has no protective cap (I will explain later). RNA polymerase keeps going until the enzymes that chase it catch up and take it off the DNA. I have no idea why, but I think that is so cute. Imagine the RNA polymerase is named Bob, and Bob does his job but forgets to stop doing it, so a bunch of his friends chase him down going "Bob! Bob, you're done!" This is how it works in eukaryotic cells, anyway. Bacterial RNA polymerases are a bit smarter. They have a termination sequence where the RNA polymerase detaches. 

One incredible thing about this process is that the mRNA is not finished! It is actually pre-mRNA right now, since it still has to go through some processing before it can be kicked out of the nucleus. The pre-mRNA has to have a cap added to it at the beginning 5', made of modified guanine. The end is added a tail of 50-250 adenine nucleotides at the 3' end. But, we're still not done. The actual protein-coding segment region of mRNA has certain parts that are not actually needed to code proteins - called introns, and certain parts that are needed, called exons, that code for different domains (sections) of proteins. The introns must be spliced out of sequence and the pre-mRNA must be reattached together. This is done by a protein complex known as a spliceosome. We don't even need to splice mRNA in a bacterial chromosome, though, as there are no intron parts and the mRNA can immediately be translated. We are still trying to figure out what the introns in our DNA are meant for.

This process is incredible because it helps limit the amount of genes needed in a cell. If you just splice different introns out, you can get many different kinds of proteins from the same pre-mRNA molecule, which means you don't need as much DNA for everything. This is called alternative RNA splicing, and we believe it is this process that allows humans to function with about the same number of genes as a nematode (roundworm). Amazing, isn't it? This process is one of my absolute favorite parts of biology, but we're only halfway through the process. 

Now that we have our finished mRNA, we can start translating it. A picture of finished mRNA (before and after) is shown to the right. In order to better grip onto the ribosome, mRNA also has sequences of UTR repeated over and over again on either side of the protein-coding segment that go untranslated.

But how does the protein-coding segment code for proteins anyway? We know there are 20 amino acids whose order matter, so how are four nucleotides supposed to code for that? Nature came up with an ingenius solution - make a code for each amino acid with sequences of three nucleotides, called codons. The reason we use three nucleotides is simple. We obviously cannot use one, as that leaves only four combinations of nucleotides. We cannot use two as it leaves 4^2 = 16 combinations, and that is not enough for all 20 amino acids. So, we can use sequences of three nucleotides, creating 4^3 = 64 possibilities, more than enough for all 20 amino acids. To the right, I have also added a picture of the table that details the amino acid code. For some acids, more than one sequence can apply. There are also stop codons that do not code for an amino acid, but rather code to stop the chain. Since there are stop codons, there is also a start codon, which actually does code for an amino acid. In many cases, this code is AUG, which codes for the amino acid Methionine, abbreviated Met.

Translation actually involves three different kinds of RNA. You already know about one of them: mRNA. But the other two, tRNA, and rRNA are also very helpful in the process of translation. rRNA is ribosomal RNA, and it helps read the order of amino acids and linking amino acids together. tRNA is transfer RNA, and it is what brings the amino acids needed to construct the protein. Each tRNA has an anticodon on it, and its corresponding amino acid. When the anticodon binds with its codon, the correct amino acid can be attached to the polypeptide chain. So basically, tRNA has a specific anticodon with a specific amino acid that enables it to bring the correct amino acid for each codon on the mRNA, allowing for construction. Now, we can start the process of translation.

The mRNA binds to the ribosome, which has three sites: the P-site, the A-site, and an exit site. The first tRNA, which is usually Met, goes into the P-site and starts translation. Another tRNA goes into the A-site with its amino acid, and the amino acids bind together. The one in the P-site exits using the exit site. The tRNA in the A-site slides into the P-site, also sliding the mRNA over. This goes until the polypeptide chain is complete, creating a new protein.