My Favorite Enzyme

All enzymes are great. So by saying I have a favorite, I don’t mean to denigrate the others in any way. All enzymes are just great at what they do, and most of them simply couldn’t possibly do their jobs better than they are doing them.

Having said that, I do indeed have a favorite, and I will explain why. But first, you might be asking: what is an enzyme? Enzymes are proteins, meaning they are strings of amino acids linked in long chains. More specifically, enzymes are proteins that function as catalysts. And you know what a catalyst is, right? A catalyst is a chemical that makes a chemical reaction go faster than it would go otherwise but isn’t part of the reaction itself, so it doesn’t get used up.

Enzymes are the best catalysts known. Lots of metals can act as catalysts for chemical reactions used to make stuff, and cars have a catalytic converter that helps eliminate air pollution. But enzymes are thousands of times more efficient and more specific than any other kind of catalyst. Life could not exist at all without enzymes (or some kind of catalyst), because the chemical reactions that make life work must go on very rapidly, and without catalysis, those reactions could take hours or weeks.

Enzymes work so well as catalysts because they are large molecules that are perfectly shaped to bind to the molecules that need to react, and then they encourage, simulate, and… well, catalyze the reactions by moving the reactants closer together; by using some of the chemical properties of their amino acids; by providing energy to some reactions; and by making sure only the exactly correct chemicals react with each other (and not some closely similar chemicals).

Enzymes are so close to being perfect at their job because it’s the enzymes (mostly) that are the targets of natural selection and evolution, so after a couple of billion years of trial and error, most enzymes have become really good at what they do.

And that brings me to my favorite enzyme. My favorite enzyme has a terrible name, so let’s call it Syzase, as a nickname. Its real name is Aminoacyl tRNA Synthetase, so you see why I prefer Syzase.

Syzase is the most important enzyme in the most important biological process in evolution – and in life in general. The process is called protein synthesis or translation, and it’s the way that proteins (including all the enzymes, including Syzase itself) are synthesized. You might have already learned that the exact sequence of the amino acids in a protein (which is the critical feature that allows them to act as very specific catalysts for specific reactions) is determined by the sequence of the nucleotide bases in a gene made of DNA.

So the DNA sequence determines the amino acid sequence. That seems fine, unless you happen to know some chemistry. Because, chemically, there is no way that the nucleotides in DNA can interact with amino acids to produce a protein with a specific sequence. Amino acid chemistry and nucleic acid chemistry just don’t go together.

So how does it happen? The answer is why I love Syase. The code in the DNA sequence needs to be translated into amino acid chemistry. Translation is in fact the name of the process, and it’s probably the most complex chemical process in the universe. And my favorite enzyme, Aminoacyl tRNA Synthetase, is at the very center of the process and might even be considered the actual translator, the chemical entity that speaks two languages, nucleotidese and amino acidese, and can translate each into the other.

But this post is getting too long, so I will post the amazing details of how my beautiful, favorite enzyme does its job so spectacularly well in the next post (coming very soon, I promise).

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6 Responses to My Favorite Enzyme

  1. Great post Sy. I found enzymes fascinating when I came across them in my biology class. You’ll be happy to know that I’m doing really good in that class (my favorite thing so far has been the Chi-square statistics tests to accept or reject the null hypothesis; gotta love those Mendelian genetics). You’ll be even happier to know that this class wasn’t enough biology for me and that I plan on taking the biology course for actual science majors next year. Bring on the in-depth stuff.
    Peace of Christ

  2. You have my attention with this one. After an initial read of this, I’ve spent several hours going through anything I could somewhat understand regarding Aminoacyl tRNA Synthetase. I see that there are 20 variants with regard to each “standard” proteinogenic amino acid (and that the last two can be made by some hat-trick). What about the 64 codons on the other end (are there variants for each)? Stops just not interpreted?

    Very interesting. The way I see it, this (or something that performed the same or a similar function) is the actual origin of “life”. I recall once suggesting to you that the interpretation may be more important than the text… a reading reflecting an **impetus** to interpret things in a self-organizing manner? “Syzase”… indeed.

    • Yes, there are 20. I am in the middle of writing the sequel which will answer some, but not all of your questions. Thanks for your comment, and I fully agree that this process is the true beginning of life as we know it.

  3. SheilaDeeth says:

    Wow! By a quirk of the English education system i missed out on learning any of this. And now I’m hooked! Eagerly awaiting your next post. Thanks.

  4. Pingback: My Favorite Enzyme, Part 2 | The Book of Works

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