The Genetic Code

Good evening, all! I hope you’ve had a decent month since I last checked in. I know I promised several posts on various specific aspects of transcription, but to be perfectly honest, they ended up sounding disjointed and uninteresting. (I was really freakin’ tired when I wrote them, so…) Perhaps I’ll go back and edit them, but in the meantime, I’ve got something more interesting to offer you: translation! Doesn’t that sound like fun?

Cells put a lot of effort into making RNA transcripts. That much is apparent, if only from our past study; the process is long, complicated, and very tightly controlled at more levels than we, as students, really want to thing about. The reason for this is one that we’ve known since we were in high school: cells take these mRNA transcripts and turn them into protiens. (That’s, you know, what makes DNA a so-called “blueprint.”)

That’s great and all, but how do we get from Point A to Point B? Somehow, we have to take a seemingly random sequence of nucleotides and turn it into a very specific sequence of amino acids. Obviously, there has to be some kind of go-between, something that bridges the gap. But what could that be?

Enter tRNA! In the past, we talked about tRNA, and how aminoacyl-tRNA synthetases love to attach amino acids to them (a process called “charging”). There’s one vital piece of the puzzle: we’re linking an amino acid to something made of nucleic acid. So far, so good.

The next logical step is to suppose that, if the amino acids attached to each tRNA are specific for that tRNA, there has to be a way that the protein-building machinery of our cells (ribosomes) can tie that tRNA to a bit of genetic information. This is accomplished in a very simple and elegant way, through the use of a genetic code of triplets.

In mRNA, each sequence of three bases (a “triplet”) constitutes a piece of information that codes for one amino acid. This bit of information is called a codon. Codons correspond to complementary sequences, called anticodons, on the tRNA molecules attached to their specific amino acids.

Codons are arranged on an mRNA molecule in a non-overlapping way, and their code isn’t punctuated. The sequence is read from 5′ to 3′ direction, one triplet after another, according to the reading frame of the molecule. Therefore, if you shift the machinery’s reading frame a base forward or backward, you end up completely messing up the code.

Each codon has a meaning, and all except for three (the three “nonsense,” or “stop” codons) code for an amino acid. Most amino acids (excepting Met and Trp) are coded for by multiple codons, but multiple amino acids are not coded for by the same codon. (This is called degeneracy.) Because of this, changes to bases in the genetic code don’t always alter the protein—as long as the altered codon is still one of the codons that corresponds to the amino acid specified by the original sequence, there’s no harm to the protein itself.

Additionally, amino acids with similar properties are coded for by similar codons. In other words, even if you manage to turn a codon for A into a codon for B, chances are that B will do about the same thing in the protein as A would have. This is another protection against harmful mutations.

So, I probably know what you’re thinking right about now. “Wait just a darn minute. You just said each codon specifies an anticodon through complementary base pairing. How the heck can multiple codons code for the same amino acid, then? Does each specific form of an amino acid’s codon only get the specific anticodon that it’s complementary to? If so, that’s dumb. What’s the point in that, besides making things more complicated?”

I’m gonna stop you right there, because the answer is simpler than you think. The truth is that one codon can, in fact, code for multiple anticodons! That’s pretty thrifty, if you think about it, but it also probably makes you feel cringy. After all, didn’t we just put a lot of effort into keeping this code as pristine and unaltered as possible? Does it even matter anymore? [cue existential crisis]

Well, it does matter, because even the not-quite-right pairing follows specific rules. More specifically, a codon can only code for anticodons that have a different base in their third position (incidentally, this is where all synonymous codons differ). This position, the position of “meh, whatever,” is called the “wobble position.” If you’ve got a U in this position, the protein-making machinery can squeeze either an A or a G in there. If you’ve got G, you can get C or U. If you’ve got I, heaven help you—U, C, and A are free game.

That being said, certain organisms favor certain codons for an amino acid over others. This “codon bias” accounts for the different base compositions of different genomes. For example, while E. coli and humans both need to code for proline, E. coli’s favorite codon for this is CCG, while ours is CCC.

All right, so we’ve basically pieced together how our cells piece together our proteins, but we’re still missing something vital. How the heck does this actually happen? Well, dear reader, that’s the subject of another blog post—come along with me, and we’ll enter the mystical, magical world of translation.

Questions? Comments? Want to rant and rave about how wonderful biology is? I hear you!


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