December 1, 2005 | David F. Coppedge

Cell Ribosome Assembly Is Like Throwing Car Parts Together

Ribosomes are the protein-assembly machines in the living cell (11/24/2005, 07/26/2005, 01/19/2005).  A bacterium can have thousands of them.  They are composed of two large RNA complexes; the smaller one has 20 unique proteins that fit snugly in various parts of the apparatus, and the larger complex has even more.  How do the parts all come together?  That’s an area of intense study, reports Sarah A. Woodson in Nature:1

Many of the biochemical events that occur in a cell are performed by huge complexes of proteins and nucleic acids.  A cunning approach promises to show how the components convene to make a functioning ‘machine’.
    The cell’s macromolecular machines contain dozens or even hundreds of components.  But unlike man-made machines, which are built on assembly lines, these cellular machines assemble spontaneously from their protein and nucleic-acid components.  It is as though cars could be manufactured by merely tumbling their parts onto the factory floor. (Emphasis added in all quotes.)

Clearly there is more to it than that, because the parts all fit together in the right places, at the right times.  Woodson describes how researchers are trying to observe whether the assembly steps are strictly determined in a predefined sequence, or whether the parts can arrive via alternative paths, like band members in a scatter formation.
    Whatever happens, it needs to be reliable and energy-efficient.  All the parts “interact through highly specific interfaces,…” she explains.  “Actively growing cells demand many thousands of ribosomes, whose synthesis consumes a large fraction of the cell’s metabolic energy.  So ribosome assembly must be efficient as well as precise.”
    Unlike car parts, protein and RNA parts have some flexibility.  In a process called induced fit, they snap together snugly, like rubbery puzzle pieces:

In the soft world of biological materials, cooperativity and specificity are achieved by the induced fit of molecular interfaces; that is, as two or more components come into contact they mould around one another to create stronger, more specific junctions.  The idea that ribosome assembly can follow more than one path is consistent with redundant cooperative linkages in the assembly map.  These cooperative linkages ensure that individual complexes are assembled completely.  They also create alternative kinetic paths that make the assembly process itself more robust.

Woodson spoke of machinery and machines five times, but only mentioned evolution twice, neither time explaining how the machinery and its precision assembly process came about.  In her introduction, she merely said, “Knowing how cellular complexes organize themselves is crucial for understanding molecular evolution and for engineering materials that can mimic their properties.”  The other mention of evolution was in her last sentence: “In the ribosome, these interactions have been fine-tuned through billions of years of evolution, providing a clear window into the world of cellular machines.”

1Sarah A. Woodson, “Biophysics: Assembly line inspection,” Nature 438, 566-567 (1 December 2005) | doi:10.1038/438566a.

And for that classic line, Woodson earns Stupid Evolution Quote of the Week.  We’all just throw a bunch of car parts on the factory floor for billions of years, and when they get it right by chance, presto: we can expect a fully operational vehicle.  This article, therefore, gets listed in both the Amazing and Dumb categories.  It can be considered typical of references to evolution in scientific papers: nobody tells us how such things could have evolved by mindless, directionless chance processes; they just claim they did.  You call this science?  Read Gerald Schroeder’s editorial on AISH.  He examines the probability of such accidents occurring naturally, showing that the argument of our online book is still valid.  Any scientists who can believe that chance could perform miracles on this order should be called People of Frothy Faith.

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Categories: Cell Biology, Dumb Ideas

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