Translation

Translation

From the video on transcription we realized that we’re at this point where the disposable M RNA copy is floating around in the cytoplasmThe gel-like substance within a cell that contains organelles and cytosol. looking for a ribosome. Ribosomes are a two part organelle that can be attached to the endoplasmic reticulum or they can be free floating in the cell. Ribosomes are the location of the process called translationThe process of converting mRNA into a protein.. Ribosomes have a large subunit and a small subunit.  They actually float around the cytoplasm separately and only come together when they meet an mRNA. The mRNA is positioned in such a way that the nucleotidesThe building blocks of nucleic acids. are all facing into the big subunit.  This is because the codons, sequences of 3 nucleotides on the mRNA, will now be matched with the anticodons, sequences of 3 nucleotides on the tRNA.  The large ribosomal submit is kind of like a garage with three bays.  Wait, no.  It’s more like a car wash where all the machinery is stable and the cars move through it.  The ribosome is the machinery and the tRNAs are like little cars moving into and out of the car wash.

The Translator

So now we have a processed mRNA transcript at a ribosome and ready for translation.  Let’s meet our interpreter. 

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..  A tRNA molecule has a part of it that is made up of nucleotides and a part of it where an amino acid can connect.  In this way, tRNA is a translator that can interact with a nucleic acid or with an amino acid.  It knows both languages and be a go between.  Thinking about our already-existing mRNA, the tRNA molecule could somehow match with mRNA and made then string along the amino acids?  Maybe?  So, also, where are tRNAs located?  Everywhere?  Blood, cytoplasm, fluids around the cellsThe basic structural and functional units of life..  Yes.  All.  tRNAs have a simple task which is to run to the digestive system and pick up incoming amino acids and then to run back to some cells that are making proteinsLarge molecules made of amino acids with various functions in the body. and drop off the amino acids.  Once that is done, they go back to the digestive system and continue this cycle of pick up and drop off.  So, much like free nucleotides floating around everywhere, so are tRNAs.  The big difference is that tRNAs are big enough that hey can’t get into the nucleusThe control center of the cell that contains DNA and directs cellular activities..  But, they are needed there.  Translation takes place in a ribosome, not a nucleus!

This picture on the left is a pretty realistic picture of tRNA.  It’s just a strand of RNA, or a sequence of nucleotides, it has a messy shape, but 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 GAU, 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 taught from a book along time ago that had this picture of tRNA on the right here.  I like it.  By using this cylinder, we can clearly see that one side connects with an amino acid and the other side has that anticodon.

Translation

Let’s look at the process of translation.  This blue blob here is a ribosome.

The ribosome has a three sites in it.  The A site allows a tRNA to enter and the E site on the other side allows a tRNA to leave the ribosome.  So, tRNAs are always in motion through the large ribosomal submit.  A tRNA enters, drops off its amino acid, and then it leaves destined to go get another amino acid and return. 

Let’s start.  We have the first codon on our mRNA as AUG.  The ribosome reads this codon and kinda calls out: I got AUG, anyone match with AUG?  Somewhere out in the cytoplasm, there is a tRNA that has the anticodon UAC and it says: oh! Me! I can match that!  The tRNA comes over to the ribosome, and we get started with the first amino acid in the protein chain.  Just as a hint…all amino acid sequences start with MET and all mRNA sequences start with AUG.  The first tRNA will always have the UAC anticodon.  Now, upon folding, that MET amino acid might get clipped off, but every single mRNA transcript starts with AUG. 

Notice how the second and third codons are also matched to their anticodons and in this picture already have their matching tRNA moleculesGroups of atoms bonded together. in place.  Once all three of these bays in the ribosome are full, now we start moving tRNAs through like a car wash.  Notice the tRNA on the left without its amino acid – it’s leaving.  Notice the tRNA with its amino acid on the right – it’s approaching.  So, this picture, although old, blurry, and slightly fuzzy, it has motion in it.  This static picture represents this really fluid process of the movementA fundamental property of life involving motion of the body or its parts. of the tRNA and the growing length of the amino acid chain as more and more tRNAs cycle through.

Once we have this in motion, surely it will end.  Yes.  There are three codons on mRNA that will stop this process: UAA UAG UGA.  When the ribosome calls out these codons on the mRNA, no tRNAs respond.  They are all like, “We don’t know who you mean.  No one in our group goes by those names.”  So, the ribosome processes the last tRNAs out and stops or terminates translation.  It’s important to note that no proteins are added to the growing amino acid chain after a stop codonA codon that signals the end of translation (UAA, UAG, UGA). is read.  At that point, the amino acid chain is complete.

The Genetic Code

How do you know what codon matches to what amino acid?  Those relationships are set in stone and are also all explained in this chart above, which is called the genetic codeThe set of rules by which DNA sequences are translated into proteins..  What you first notice if the fidelity and infidelity of codons and amino acids.  It’s not an equal relationship.  Every single codon matches to only one amino acid.  This means that every anticodon matches only one amino acid and therefore every tRNA can attach to only one amino acid.  AUU will always attach to isoleucine.  Nothing else.  The opposite is true for amino acids.  They don’t commit to one codon.  A few match with two, a few moe match with three and there are even some amino acids that will match with 4 different codons.    These qualities of the genetic code are called ambiguity and

In looking at this process of translation, it occurs to students that there seems to be a very specific match from codon on DNA to anticodon on mRNA and then 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 grid here.  This is the genetic code.  It is a list of mRNA codons and the amino acid to which they match.  For example, on the first codon in our example, we have AUG, which ultimately brought methionine to our protein chain.  How did I know that, well it’s highlighted in green on the grid, but also, I noted that there are labels on the sides and top of this grid.  Looking along the left side, I find the row with all the codons that start with A.  OK.  Now, I look along the top of the grid and find the column with  all the codons that have U as their second letter.  I find where that row and column intersection and then I can look at that short list of 4 codons to find mine.  AUG – methionine. 

The grid here is the English to Swedish dictionary I needed to translate my cook book.  What’s kind cool about this is that, if you can see, even though one codon will only have one amino acid to match it, one amino acid can match to a few codons.  This allows the flexibility to create an unlimited number of proteins for life even though we only have 5 different nucleotides and 20 amino acids.

DNA to RNA to Protein