The Book of Works

OK readers, here we go. Now that you have the basics, let’s get back to the hero of this series, my favorite enzyme, Aminoacyl tRNA Synthetase (usually referred to as aaRS, not Syzase). Remember that the task of the enzyme is to join the right tRNA with the right (cognate) amino acid. The tRNAs each carry one amino acid to the ribosome where their cargo (the amino acid) is added to the growing protein chain in the correct order. This happens because the tRNAs, using their anticodon triplets, bind in turn to the codons on the mRNA, which have been copied from the master code sheet, the DNA.

Amino acids and tRNAs cannot recognize each other because they are parts of different chemical systems, so there is no way that the correct amino acid (matching the tRNA anti codon) could ever get matched with its tRNA without help. It would be like an English-only speaker having a conversation with an Italian-only speaker. They need a translator. And the helper/translator is aaRS. That’s why I consider this enzyme to be at the heart of the entire translation process.

How does the enzyme do this? First, each enzyme has a binding site for its specific amino acid. So alanine aaRS has an alanine binding site. It also has a binding site for each of the 4 tRNAs that carry one of the 4 anticodons for alanine. Once this very large enzyme has alanine bound in one site and an alanine tRNA bound on the other site, the protein conformation (the protein’s shape) shifts in a way so that the end of the tRNA and one end of the amino acid are close. The enzyme then catalyzes a chemical reaction (requiring energy) between the two molecules, and the result is a strong chemical bond between tRNA and amino acid. The process is illustrated in the following figures.

Imagine the interpreter saying “Mr. Smith, let me introduce Mr. Russo; Signor Russo, le presento il Signor Smith.” And the two men shake hands. Only in the chemical case they don’t let go; they are bound.

So the enzyme has done its job. It has taken its amino acid and matched it with the right tRNA so that the amino acid will be put in exactly the right place determined by the DNA sequence. Once this is done, the new bonded tRNA-amino acid complex can leave its binding sites, and as a tightly bound couple navigate its way to the ribosome, where the two molecules will part company, the tRNA to go back to finding another aaRS (or maybe the same one), and the amino acid to live the rest of its life as part of a protein.

But wait, we aren’t done. If this were the whole story, it would be amazing and exciting, but there’s more. You see, the entire process of translation really needs to be very accurate. If the wrong amino acids get attached to the wrong tRNA, the protein sequence will not be what it’s supposed to be, and the protein might not work. In fact, the entire translation process, including the work of the aaRS, is extremely accurate, with one mistake in over 10,000 trials. To reach that level of accuracy, the binding and matching I described above just won’t cut it. Many amino acids are very similar to many other amino acids (just ask a biochem grad student), and mistakes can definitely be made. A leucine might just fit into the binding site on an isoleucine aaRS, and that wouldn’t be good. And alanine is only slightly bigger than a glycine, and it would take an amazingly well engineered binding site to be able to distinguish the right from the wrong amino acid with 99.999% success.

So the enzyme has some tricks to make sure it hasn’t screwed up. Once the amino acid and tRNA are bound, the happy couple are shunted to another site on the enzyme called the editing site. This site is shaped in a way that will allow almost any amino acid and tRNA to get in, except the right ones. That particular amino acid tRNA just doesn’t fit. It’s especially good at admitting smaller amino acids while excluding the right one. So if everything is correct, the amino acid tRNA does not (cannot) bind in the editing binding site, and it breaks free from the enzyme to go on its merry way toward the ribosome. But if a mismatch or some other error had taken place, and the mistakenly bound couple does fit into the editing site, it’s cut into pieces by the action of the enzyme and never gets close to the ribosome.

So not only does my favorite enzyme recognize the proper amino acids and from 1 to 6 proper tRNAs, and not only does it provide the energy and mechanical means to link the two together, it also makes sure it got it right and deals a death blow to any erroneous products. Pretty neat, eh?

And I should mention that every cell in every living thing on this planet has the same system and has had it as far back as LUCA. In fact, we have no idea what came before and how the present universal system evolved, since it’s this system that is the biochemical key to evolution. But we can discuss this another time. For now I hope you will agree that aminoacyl tRNA Synthetase should be everyone’s favorite enzyme.

My favorite enzyme (see previous post about enzymes in general, and why I have a favorite) has a very specific job, as all enzymes do. But my enzyme, Aminoacyl tRNA Synthetase (or Syase for convenience) has a job that is both extremely difficult and absolutely crucial to all life.

The job is to link up two chemicals that otherwise would have no chance of getting together. The sad fact is that most chemical molecules are very unreactive, and only very few sets of molecules will react with each other to form new compounds or even a complex from the two joining together. In this case, one of the molecules is an amino acid, and the other is an interesting RNA molecule called transfer RNA or tRNA. Because of the very different chemical nature of these molecules, (they belong to very different chemical families) spontaneous, uncatalyzed combination of the two would simply never happen.

As you know (or you should), there are 20 amino acids, and about 60 tRNAs, so this is an impossible job to get right for one enzyme. Luckily, it turns out my favorite enzyme is not one enzyme but a collection of 20, one for each amino acid.

To explain why there are 60 tRNAs and not 20, we need a small diversion to discuss the genetic code (and yes, it is a code!). The genetic code works  much like written language, a code we know well, does. In English, for example, meaning is assigned to words, and there are 26 letters to construct these words (which can be of any length). A word is a collection of the letter symbols in the correct order that means something different from its physical nature (which is simply a collection of shapes).

DNA operates the same way, with some important differences. First, there are only four “letters,” which are actually molecular entities, but they function as symbols. Since their importance is in their symbolism, we generally designate them by the first letter of their names, A (for adenine), C (for cytosine), G (for guanine), and T for (thymidine). The word length is constant: three letters are a code word. For example, ACC is a code word for threonine, and CAA means glutamine.

So, why three, and not four or two? Well, two-letter words would allow for 16 permutations, not enough for the 20 amino acids. Four letters would give far more possibilities than needed and would cause confusion and chaos. So three letters, which gives 64 possible arrangements, is what we have. What this means is that there are synonyms, more than one word (or codon in Biologese) for each amino acid. Thus ACA, ACG and ACT also mean threonine, and CAG also codes for glutamine. Some amino acids have as many as 6 synonyms.

I am not going to discuss the details of how the proteins are built on the ribosome (see Figure 1 and online videos), but I need to tell you that the key step in making the right protein (meaning having the right amino acids in the right order) is for each tRNA/amino acid complex to bind to the codon copied from the DNA onto a long RNA strand called messenger RNA (mRNA). Now, if you read the post on how to be a molecular biologist, you will remember that the secret is that A always and only binds to T, and C only and always to G (even though this not actually true, but see the post if you forgot why).

Figure 1.

The point is that the tRNA for each amino acid contains a three-letter sequence designed to perfectly bind to the codon. That sequence is the complementary sequence of the codon, called the anticodon. So for the codon ACC, the anticodon is UGG. And for CAA, the anticodon is GUU. (One little detail, in RNA we use U instead of T. Doesn’t matter why.)

Now, since there are anywhere from 1 to 6 different codons for each amino acid, there are from 1 to 6 different tRNAs for each amino acid, each with its own anticodon. And each of the 20 Sysases must be able to attach its specific amino acid to each of the different (up to 6) tRNAs that have the correct anticodon.

I should apologize for oversimplifying this whole thing. The reality is far more complicated, and you will notice that I haven’t even gotten to describe what it is that my favorite enzyme actually does. But I thought it was important to set the stage, as it were, and explain what the task it must do entails. Now that we have that all straight, I should (hopefully) get to how Syzase does its job (and if you think this is hard for you to understand, imagine how a poor senseless molecule feels!) in the very next post. I promise (sort of).

In a recent post I said that the replication of cells is required for evolution and the origin of modern life as we know it. While it’s true that the daughter cells of a parent dividing cell end up containing all the elements and features of the parent (assuming replication accuracy is very high, as it is in all life forms), the fact is that cells don’t actually replicate all of their components. In other words, each protein doesn’t produce a faithful copy of itself, and neither do membranes, filaments, flagella, or ribosomes. There is only one component of living cells that is replicated with high accuracy, and that is the DNA molecule. The reason that works is that DNA is not only capable of being copied almost exactly, it is also the part of the cell that is responsible for guiding the production of all the other components of the cell – all the proteins, enzymes, membranes, and cell organelles. (One exception is the energy-producing mitochondria in eukaryotes, but we won’t go there now). This means that if the DNA of the parent cell is faithfully copied, then the entire cell will be faithfully copied in the two daughter cells.

There is a scientific consensus that the modern life system of DNA replication and DNA control of the synthesis of all subsequent cellular components is so complex that it could not have been present in very early life forms. The idea that earlier life forms might have used RNA (similar to DNA) as the original replicating molecule has become known as RNA world. This RNA world is proposed to have predated our current DNA world (along with LUCA, the last universal common ancestor of all life today).

RNA can probably be copied (although the details of how this happens are not yet completely worked out. See previous post). In addition, RNA can act as a catalyst, so all the protein enzymes present in modern cells might not be needed. How RNA world turned into DNA world is a question that has not yet even been addressed.

Aside from the existence of some kind of replicator molecule like DNA or RNA (there are one or two other possible candidates), there is no known possible mechanism for a cell to replicate itself into two daughter cells that are just like the parent. This is the reason that replicator-first proponents insist that cells that have plenty of metabolism but no replicators could never evolve to produce anything like the life we know.

But even if primitive early cells had replicators that were able to manage the production of an accurate copy of the parent cell phenotype (meaning all the components and characteristics of the cell), there is a potential problem that has only rarely been addressed. That problem can be stated simply: How did the accuracy of replication become so high?

One would expect lots of errors in primitive replication systems, no matter what chemical composition they had. It’s likely that replication became more accurate over time thanks to the only biological process we know that makes things better over time – evolution. But wait, if accurate replication is required for evolution, and evolution is required for accurate replication…? We have a problem.

And that is the problem I have been working on. I will present some preliminary results in Part 3. Stay tuned.

In the transition from chemistry to biology, many new features had to emerge from an increasingly complex chemical system. Examples include some form of membranous enclosure to allow for appropriate concentration of reactants, thus defining the borders of a living cell; the inclusion of catalysts to allow for rapid reactions; the ability to derive energy from molecular reactions and to synthesize useful chemical end products and structural components; and many more. Most of these features, while remarkable can undoubtedly arise spontaneously given a sufficiently large pool of soluble chemicals and time.

Membrane enclosed vesicles containing rapid and complex chemical reactions that will allow for such vesicles to survive for long periods (days or longer) could be considered to be living cells. This assumes we define life in the most elementary way – an enclosed cell in which chemical reactions allow for the cell to grow to a size at which it spontaneously divides in two.

But that is not the kind of life we know. All living forms on earth are indeed composed of cells that carry out extremely complex catalyzed chemical reactions, and such cells do grow and divide. But living terrestrial cells, going all the way back to the first cell from which all modern life evolved, the Last Universal Common Ancestor (LUCA), do more than that – they evolve.

The primitive protocells that I described above cannot evolve, and they will eventually die out. The reason is that the simple division of cells, whereby a cell splits in two, is not what life does. Living cells, since before LUCA, don’t just divide – they replicate. And it’s cell replication, not cell division, that allows for evolution.

Cells replicate themselves by making close to identical copies of themselves when they divide. When one cell becomes two cells, the new cells (usually called daughter cells) are close to identical to each other and to the original (parent) cell. The new cells contain the same ingredients, catalysts, subcellular systems, and all features of the original cell. Simple division of a cell into two parts cannot do this, since there is no copying mechanism to make sure that every feature of the original cell is shared by both daughter cells. With replication, however, everything within the cell is duplicated and then equally distributed in the two new daughter cells after division.

Nothing else outside of life does this. Crystals grow in ways that replicate the starting structure, but crystals do not make copies of themselves. Neither do stars or storms, galaxies or glaciers, mountains or molecules (outside of life). Nothing does.

The ability for a single cell to make a perfect or near-perfect copy of itself is the actual beginning of life as we know it. Non-replicating cells might appear to be alive, but they cannot last beyond a short time span. To become truly alive in the sense that cells can survive and reproduce for years or millennia, evolution is essential. Evolution allows primitive cells to become more stable, more fit, more able to do what they need to do in order to survive. And evolution requires actual replication, not simply division.

To see why that is true, imagine a cell that by lucky chance has incorporated a catalyst that allows it to perform a very useful chemical reaction – say, one that generates energy. The cell now has a higher fitness (defined as the probability of survival until division). When this lucky, very fit cell does divide, the chemical catalyst it found goes into one of the daughter cells, but not the other. So one of the new cells has inherited the higher fitness of the parent, but the other has not. It isn’t hard to see that as time goes by, the more fit cell becomes more and more of a minority, and while its probability of survival might be higher than its relatives’, it’s still not very high, so eventually one of the descendants of the original lucky cell containing the new catalyst will die and that’s the end of that. No evolution has taken place.

On the other hand, if the original cell had replicated the new catalyst so that both daughter cells had inherited it, then a new population of cells with higher fitness would have developed and survived to continue to improve its fitness, leading to evolution of a strong population of living cells.

So the central question of the origin of life becomes clear:
how did accurate cell replication originate?

There are some fascinating theoretical offshoots of this question, and I have started working on them using statistical modeling. There are strong implications for the origin of life, and I will explore some of them in future posts.