Molecular Biology Survival Guide for Chemists — V: The Ribosome

The ribosome is where the rubber meets the road (in the protein-centric view of the cell).  It is a monstrously large molecular machine 200 – 300 Angstroms in diameter.  Remember that the diameter of the double helix is only 20 Angstroms.   It takes messenger RNA (mRNA) and, using it as a code translates the sequence of nucleotides into a sequence of amino acids (e.g. a protein).  Get a copy of the 16 December ’11 issue of Science, and stare at the cover for a while.  It’s a picture of the eukaryotic (yeast) ribosome in all its glory. The details are to be found [ Science vol. 334 pp. 1524 – 1539 ’11 ].  If you have an issue hanging around. around also look at pp. 1509 – 1510, as some ribosomal background is required before a post on that subject.

The article gives the structure of the Saccharomyces cerevisiae ribosome at 3 Angstroms resolution.  Quite a feat.  It comes in two parts, a large subunit which sediments at 60 Svedberg units, and a ‘small’ one at 40S.

The large subunit contains 3 RNA molecules and 46 proteins, the small one contains 1 RNA and 33 proteins.  Total molecular mass is around 2.5 megadaltons.  It’s maddening, but I can’t seem to find out just how many nucleotides our ribosomal RNAs (rRNAs) contain in toto.  It is well over 5,000 however.   So the number of atoms in the RNAs alone is over 200,000.  There must be many more atoms than that contained in the associated proteins, as the phosphates have a mass of 98, the ribose 115, the pyrmidines around 100.  So they don’t account for more than 40% of the total ribosomal mass.  If anyone can give me exact numbers, I’ll update this.

The actual catalysis is not accomplished by the 79 proteins, but by the RNAs themselves.  This is thought to be a living relic of an RNA world where life actually began.  The proteins are mostly found on the surface of the ribosome.

There are a gigantic number of things to say about the ribosome, but I’m just going to put in the facts needed so pure chemist types can read other posts. This post will be expanded as necessary when further background is needed.

Amino acids are linked together (the rate is only 2 – 6 per second) by the beast. This is OK as the average cell has over 10 million ribosomes (neurons probably have more).  The article above notes that most of the changes between the ribosome of bacteria and that of celled organisms (eukaryotes) make our ribosomes bigger.  The proteins are bigger, the rRNAs are longer.

The actual synthesis of proteins takes place deep in the center of the ribosome, where the two subunits come together.  How does the protein get out?  It is extruded (like sausage) through the exit tunnel, which is 100 Angstroms long in the E. Coli ribosome, where it’s diameter varies between 10 to 20 Angstroms.  Since the alpha helix is 11 Angstroms wide, this means that little if any other secondary structures (beta turns, beta sheets) and no tertiary structure at all can form within it.  It’s probably longer (and possibly wider) in our ribosomes.

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