January 19, 2005 | David F. Coppedge

Ribosome Unties the Messenger-RNA Gordian Knot

Cells needing to translate their DNA into proteins have a problem.  The messenger RNAs, the molecules that carry the genetic code from the nucleus to the translating machine called the ribosome, get tied up in knots.  How does the ribosome untie them before they can begin translating?  Takyar et al., writing in Cell,1 explored this problem and found that the ribosome has a novel solution.
    If you have seen the film Unlocking the Mystery of Life, you watched a messenger RNA molecule, nice and straight, exit the nuclear pore complex and neatly enter the ribosome, like a man reclining in a barber chair waiting to get a haircut.  Unfortunately, things are not so simple.  Because of chemical affinities between the bases of the RNA molecule, the bases attract other bases (base-pairing) or else fold over on themselves, forming amorphous lumps (secondary structure).  Untangling this mess would be like straightening out a chain of several hundred magnets that has clumped together.
    The untangling problem is not unique to messenger RNA (mRNA).  DNA in the nucleus also has to be unwound.  Each of the processes of “replication, DNA repair, recombination, transcription, pre-mRNA splicing, and translation” have their own specialized enzymes, called helicases, that latch onto the nucleic acids and work their way down the helix, unwinding them for whatever subsequent operation is necessary.  Until now, though, no helicase was found associated with the ribosome.  It turns out the helicase activity is built-in.
    The ribosome has an entry tunnel and exit tunnel.  As the mRNA strand enters, specialized proteins named S3, S4 and S5 are precisely placed to form a ring around the mRNA helix.  They grab the phosphate groups on the side chains and separate the base pairs.2  There’s only room in the tunnel for a single strand.  As the interior of the ribosome pulls the mRNA through, this entry-tunnel helicase, built into the walls of the tunnel, effectively “melts” the double strands, sending in a clean single strand for the translation machinery to work on.  And how does the ribosome pull it in? 

In their studies of ratcheting of the two ribosomal subunits between the pre- and posttranslocation states, Frank and Agrawal (2000) observed a reciprocal expansion and contraction in the diameter of the upstream and downstream tunnels, suggesting that these two features may alternately grab and release the mRNA during translocation of mRNA.  This dynamic behavior in the downstream tunnel could also be related to its helicase function.
  (Emphasis added in all quotes.)

The action seems analogous to those old Dymo labelmakers people used to use for labeling household items.  You remember: as your hand clicked the machine, the tape came in one tunnel and out another.  In the case of the ribosome, the entry and exit tunnels alternately expand and contract, forcing the mRNA molecule to ratchet through the system.  The ratchet prevents backward motion and also is delicate enough to prevent breakage of the single strand during the unwinding process.
    The placement of S3, S4 and S5 in the tunnel is critical.  The researchers found that when they were mutated, the helicase activity stopped.  Because it latches onto the phosphates, which are universal to RNA molecules, they can unwind any strand, regardless of the sequence of base pairs.
    The authors do not speculate on how this helicase system, which is unique to the ribosome, evolved.  They only note that if it did, the unwinding puzzle needed to be solved by the very first living cell:

The inescapable presence of secondary structure within mRNA coding sequences must have been one of the first problems encountered in the transition from an RNA world to a protein world and may have resulted in coupling of ribosomal helicase activity with the fundamental mechanics of translocation.

How this was accomplished by a sequence of random changes, they do not explain.

1Takyar et al., “mRNA Helicase Activity of the Ribosome,” Cell, Vol 120, 49-58, 14 January 2005.
2It was not clear to the authors whether the helicase pulls the bases apart with the expenditure of energy.  It may be that the helicase can take advantage of spontaneous separation.  Base pairs tend to “breathe” as their weak hydrogen bonds stretch.  The helicase may be able to latch onto the nucleotide during its spontaneous separation, as if saying “Aha!  Gotcha!” and prevent the hydrogen bond from re-forming.

Again, we see an elaborate system, with only a wave of the Darwinian hand to explain it.  It is a cardinal sin of evolutionists that they merely assume evolution can solve any problem the realities of chemistry, physics and the environment throw at life.  They invoke hypothetical lucky mutations, never observed, that somehow appeared at the right time and place to produce irreducibly complex structures like ribosome helicase.
    Take off the funky Darwin glasses and what do you see?  Evidence of exquisite, effective design.  The authors take note that this helicase activity is very efficient and works rapidly: “The ability of the ribosome to unwind a long, highly stable helix shows that it is a highly processive helicase, capable of successive disruption of many base pairs without dissociation from the mRNA.”  Materialists decry miracles, yet they want us to believe nature solved this problem so exquisitely all by itself.  Come, let us reason together.

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