RNA to Protein

Ribosomes

So here we have a ribosome. It is a two-part organelle. And the two parts the large subunit and the small subunit float around the cytoplasmThe gel-like substance within a cell that contains organelles and cytosol. unconnected. The parts only assemble as a ribosome when they are ready to sandwich an M RNA between them. They then begin the translationThe process of converting mRNA into a protein. of a protein. Let’s look at the structure of ribosomesSmall structures responsible for protein synthesis, either free-floating or attached to the rough ER which contain rRNA(ribosomal RNA) – RNA that forms part of the ribosome and helps in protein synthesis..

The small ribosomal subunit has what are called M RNA binding sites. These are places where the small subunit will clamp down upon M RNA and secure it. The large ribosomal subunitThe larger part of a ribosome that helps form peptide bonds during translation. has what are called T RNA docking sites. I think of these docking sites kind of like stages on an assembly line. There are three of these stages or docking sites.  Docking site a is where T RNA moleculesGroups of atoms bonded together. first find to the large subunit. They are moved to docking site P. It is there that they complete making a peptide covalent bondStrong chemical bonds formed by the sharing of electrons between atoms. between amino acids.  Once they’re done in docking site P they move to docking site E where they prepare to exit the large subunit. Of course, while one tRNA moves through the three docking sites, other tRNAs occupy the docking sites. They move through the sites in order. Let’s look and see what a tRNA is.

The Translator

Before we get into the machinery, let’s meet the translator.  tRNA is the molecule that can both interact with a nucleic acidA substance that releases hydrogen ions (H⁺) in solution. and with an amino acidThe building blocks of proteins, consisting of an amino group, carboxyl group, and side chain..  This picture on the left is a pretty realistic picture of tRNA.  It’s just a strand of RNA, or a sequence of nucleotidesThe building blocks of nucleic acids.. It has a messy shape. However, it has two places on it that are very important.  On tRNA there is a site called the anticodon.  This anticodon has a sequence, say UAC, and matches up with a corresponding colon on the mRNA.  Codons on mRNA, anticodons on tRNA.  Interesting.  Also, the tRNA has a site on it that will also match with an amino acid.  Which of the 20 amino acids?  Well, that is predetermined, but each tRNA has a specific amino acid.  They only connect to one.  For example a tRNA that has an anticodon that is UAC will always carry an amino acid called methionine. I was just about to say that this picture on the right is a more realistic picture of T RNA’s. I don’t know. Now that I’m looking, I feel like the picture on the left is easier for me to understand. Alright. Just before we’re moving on, tRNA is like a decoder ring. It’s a translator, something that knows the genetic codeThe set of rules by which DNA sequences are translated into proteins..

The Genetic Code

Students notice a specific match in the translation process. It goes from codon on DNA to anticodon on mRNA. Then it moves to amino acid in the protein.  Yes.  In factA statement based on direct observation that is repeatedly confirmed., this relationship is set in stone and reflected in this strange picture.  I encourage you to find other pictures of the genetic code. If this one does not speak to you, consider its circular form. There are tabled or grid like representations of the genetic code.

You may notice that thymine is not present. This picture is restricted to representing the nucleotides that are present in RNAs.  Actually, these are going to represent nucleotides on our mRNA that we made in transcription.  What this picture does is connect each codon, or three-nucleotide sequence of mRNA with a specific amino acid.  Let’s do an example.  Let’s say that on the mRNA, there is a sequence of three nucleotides, a codon, of A U G.  Let’s start at the middle ring of this diagram. Choose A in the red, on the bottom left of the inner circle.  Now let’s move outward one circle and choose U, in green , almost at the bottom of the circle.  Let’s move outward one more ring and choose G in blue.  The amino acid that corresponds to AUG is Met or methionine.  In our class, it is only necessary that you use the 3-letter abbreviation. 

Do another.  GGG.  Pause this video and do it now.  Did you get Ser?  No, Good!  Because that’s not it.  I just didn’t trust you to pause the video quick enough.  The GGG codon matches with Gly.  Try UGG.  It matches with tryptophan, the sleepy stuff in turkey.  One more, an important one.  UAA.  This codon UAA, along with UAG and UGA are called stop codons.  They do not correspond to an amino acid.  What they do is they make the ribosome spit out the mRNA and stop translation.

So, this decoder ring here is the English to Swedish dictionary I needed to translate my cook book.  What’s cool about this is that one codon will only have one amino acid to match it. However, one amino acid can match to a few codons.   This provides the ability to create an unlimited number of proteinsLarge molecules made of amino acids with various functions in the body. for life. This is remarkable given we only have 5 different nucleotides and 20 amino acids.

Translation
Initiation

Let’s look at the process of translation.  We can see the large and small subunits of the ribosome coming together and sandwiching the mRNA between them. The small ribosomal subunit locates the codon Aug. It ensures that this codon is loaded in the middle M RNA binding site. The large ribosomal subunit finds a tRNA. This tRNA has methionine attached to it. It loads that tRNA into the pee docking site on the large ribosomal subunit. This is how every single protein begins because there is only one start codonThe codon (AUG) that signals the beginning of translation. AUG. This also means that methionine is the first amino acid on every amino acid chain. However during folding and splicing methionine may be cleaved off of the final protein shape. The mRNA is bound to the small ribosomal subunit. The tRNA is bound to the large ribosomal subunit. Now we can begin the elongationThe phase of DNA replication, transcription, or translation in which the molecule is lengthened. process of translation.

Translation
Elongation

In this first picture here on the left, we can see another tRNA. It is coming over to the a site on the large ribosomal subunit. This tRNA has an anticodon of CHG which matches the codon of GUC on the M RNA. Once docked into the a site, the tRNA aids in bonding. The amino acid from the PC site bonds to the amino acid on the a site. This bond is a covalent peptide bond. Examine this diagram carefully. Confirm that the codon on the mRNA matches the anticodon on the tRNA.

The second picture here shows you the 1st and the second tRNA’s moving over one docking site. The tRNA now lacks an amino acid. It moves over to the E docking site to get ready to exit the ribosome. The tRNA that has the two amino acids attached to it now moves into the P docking site. This leaves the a docking site open and capable of attracting the next tRNA. The next tRNA has an anticodon of Aug and matches the code on on the mRNA of UAC. So these little tRNA’s are actually floating around in your cellsThe basic structural and functional units of life. all over the place. They’ve been produced by you breaking down the DNA of the other organisms that you eat. These tRNA’s all day long go to your digestive system to pick up an amino acid. Then they go to some cell and drop off their amino acid. They return to the digestive system and pick up an incoming amino acid. They go back to a large ribosomal subunit. So tRNA’s are like taxis for amino acids. The third picture here shows our very first tRNA leaving the large ribosomal subunit without its amino acid. The third picture also shows us that the two amino acids from the P docking site are now attached. They join with the amino acid in the a docking site. And so we continue this process matching tRNA’s to the mRNA and forming peptide bondsBonds that link amino acids in proteins. between amino acids.

Translation
Termination

The last thing that happens in translation is a process that we call termination. This is when the text one of those stop codons in the mRNA binding site.  The stop codonA codon that signals the end of translation (UAA, UAG, UGA). will trigger the amino acid chain in the P docking site to be released from its tRNA. When the amino acid chain releases, the ribosomal subunits break free. The mRNA is now free floating in the cell.  It can be degraded by enzymesProteins that speed up chemical reactions in the body. because it was a disposable copy.  We now have an amino acid chain but that in and of itself is not a finally functional protein. Remember that proteins have levels of structure that reflect the folding and stabilization of folds by hydrogen or intramolecular bonding. However the folding of proteins is done by other proteins and that is another process for another PowerPoint. But now knowing that proteins are folded by other proteins you should be asking what folded the first protein.