Feynman’s Flower

The purpose of life is for ribosomes to make more ribosomes, said my college biochemistry professor, and later friend, Harry Noller.

The award of the Nobel prize in chemistry for the structure of the ribosome gives me a happy excuse to describe the wonderousness of this molecular machine. The central dogma, the genetic code, and the ribosome itself inspire a fountain of awe within me. These are proof that understanding the mechanisms behind the beauty we see in the world gives our experiences more depth, not less as some people fear.

Ribosomes are found in all cells. You may remember them from high school biology, like I do: a bunch of tiny dots under the light microscope. This coarse view belies their complexity. Even bacterial ribosomes have 3 RNA molecules and over 50 proteins. They are made from two parts that assemble together around a messenger RNA. Ribosomes travel along the mRNA, decode the message, and make a specific strand of protein denoted by the genome.

All cellular life has ribosomes. That means that the last common ancestor that gave rise to all life that we have ever observed on this planet used ribosomes. And no wonder, since they make the enzymes that fulfill all life processes.

DNA->RNA->proteins. James Watson named this chemical flow of information the Central Dogma of life. Genes coded by in DNA are transcribed into its chemical sister RNA. The DNA stays in the nucleus, a couch potato, while the messenger RNA goes out into the cell to communicate the genes’ information. The messenger RNA ends up at ribosomes, which decode the messages and construct proteins following the instructions in the mRNA. These proteins are often enzymes, the cellular workers.

The DNA->RNA->Protein flow is so elegant, and yet contains an intriguing paradox. DNA requires proteins for its replication and maintenance. So how did this system come to be? A classic chicken and the egg problem: which came first, DNA or proteins? This is one of the deepest puzzles of the origins of life.

Perhaps, some scientists wonder, at one time this was an RNA World. Because RNA does DNA’s job of holding information in some viruses and because it performs some enzymatic tasks, like proteins, perhaps there was a time–a time way back before the last common ancestor–when all these tasks were accomplished by RNA. Then DNA, which is more stable, took over the information storage and proteins, which are more chemically diverse, took over the enzymatic functions.

When Harry Noller’s lab at UC Santa Cruz realized their experiments suggested the RNA was at the heart of the ribosome’s activity, some scientists just couldn’t believe it. Such a complex reaction! Proteins must be doing it! But, as biochemical and structural experiments have now proven, the ribosome is at its core a ribozyme. A ribozyme with dozens of protein helpers, that is. This is one of the reasons why getting the molecular structure of the ribosome was such a big deal and why (my former PhD thesis committee member) Tom Steitz is now a Nobel laureate.

What is still unknown is whether the ribosome is a remnant of an ancient all-RNA cell. I like to imagine it is. I envision a very simple cell where RNA is the genetic material. It replicates itself and it makes small protein chains to help out. Other people have the same notion and some are trying to create such a cell in the lab, like another 2009 Nobel laureate - Jack Szostak.

Oh, shoot. I haven’t quite gotten around to mentioning the amazing and mind-boggling nature of the genetic code. That will have to wait for another time.