The biochemistry happening on a molecular scale every second in every organism on the face of the planet is extremely complicated. I’m not a fan of bench work and chemistry to begin with, so add an “organic” to the front of the subject field and you’ll find me running for the physics lab. I’d rather take advanced calculus differential equations or compressible fluid flow aerodynamics than OChem. Actually, now that I think about it, that’s exactly what I did in college.
Although the specifics of the molecular chains and bonds that drive the engine of life are beyond me, the basic gist of what’s going on isn’t that difficult to understand. You’ve got DNA that is basically the blueprints of the proteins you want to build. You’ve got messenger RNA (mRNA) that reads those blueprints and carries the instructions to the workers, sort of like a foreman. You’ve got transmission RNA (tRNA) that – on the orders of the foreman – goes out and gets construction materials. And finally you’ve got ribosomes that are both the workers and the factory that assembles the materials. The end results are proteins that do things throughout the organism that makes the whole process possible to keep chugging along.
That’s life in a nutshell. Every single complex bit of it. Not all that difficult, right?
A group of researchers from the University of Illinois recently had an interesting question; which pieces of the manufacturing puzzle are the most ancient? Evidence has already supported the insight that life was chugging along well before DNA came on the scene, but what parts of the RNA juggernaut came first?
The scientists answered this question by cataloguing the different gears, springs, and motors that work together to keep the machinery running along. Called domains, these distinct subareas of the foremen, runners, and messengers can vary from organism to organism. The scientists figured that if only a few branches on the tree of life have a particular widget, then it probably cropped up fairly recently. But if every branch of the tree of life, including the trunk, has a specific cog, then it’s probably been around a long, long time, and has been passed down through the ages from the most basic forms of life.
They found that the most ancient pieces are found on tRNA synthetases, enzymes that “read” the genetic information embedded in the “materials list” and attach the appropriate building blocks. Specifically, the code that activates the attaching – and the deleting of mistakes – has been around the longest.
This indicates that these bits of machinery are even older than the genetic code. Millions of years ago, these molecular machines were busy attaching building blocks together based on free-floating instructions – there were no central blueprints that long ago. And in support of this fact, their structures are very similar to enzymes in existence today that put together proteins completely independent of DNA instructions.
So what were they doing if they weren’t reading DNA?
According to the researchers, these free-floating enzymes were busy forming dipeptides in some of the first proteins ever created on Earth. What’s more, these dipeptides are only found in rigid regions of proteins. So chances are that ancient proteins were not flexible and had much less functionality than today’s decedents, which can fold themselves into many different configurations to complete many different tasks.
Continuing down this path of logic, ancient proteins must have been made up of only rigid dipeptides, hindering their ability to perform multiple functions. Once DNA came along, however, having a master plan allowed RNA to begin building flexible protein pieces. Thus, the origin of DNA can be associated with protein flexibility.
“Our study offers an explanation for why there is a genetic code,” said Gustavo Caetano-Anollés, professor of crop sciences and bioinformatics. “[Genetics allowed proteins] to become flexible, thereby gaining a world of new molecular functions.”
The paper, “Structural Phylogenomics Retrodicts the Origin of the Genetic Code and Uncovers the Impact of Protein Flexibility,” was published in the Proceedings of the National Academy of Sciences by Caetano-Anolles, Derek Caetano-Anolles, and Minglei Wang, all of the University of Illinois.