November 11, 2008 | David F. Coppedge

Scientists Marvel at Enzyme Efficiency

Many chemical reactions occur from simple collisions.  One atom may have spare electrons, another may need them.  Attracted by each other’s valences, the atoms collide and bonds form.  Not so with biological enzymes: these molecular machines owe their efficiency to their three-dimensional shapes.  Made up of hundreds of amino acids, enzymes have “active sites” where precise interactions occur.  Some even have moving parts that guide the molecules into the active site (e.g., 07/31/2004).  The substrate leaves the enzyme unchanged, ready for its next customer.  Scientists are finding that the precision of these machines is finely tuned.  Here are some astonishing examples from recent papers:

  1. The ultimate:  Man-made catalysts can’t match natural ones, said Anthony J. Kirby and Florian Hollfelder in Nature.1  One enzyme another team had measured, ketosteroid isomerase, is so precisely fitted to its substrate that a change of 10 picometers (where a picometer is 10-12 meters) is enough to decrease its efficiency.  The active site holds onto the substrate while another molecular switch transfers a single electron.
        “Available tools for protein engineering clearly lack the subtle touch that is required to prepare effective designer enzymes,” they said.  Our fumbling attempts at engineering protein catalysts are like trying to thread needles with boxing gloves on.  The best reaction rates of artificial enzymes we have designed, they said, are “still tens of billions of times smaller than those of many enzymes.”
  2. Gate police:  The ribosome, where proteins are assembled from RNA, is a kind of super-enzyme: a molecular machine where systems of enzymes work together to build proteins.  A paper in PNAS2 discussed the guard at the exit gate: how proteins coming out the exit tunnel are recognized and authenticated.
        First, a word about why this matters: “The ribosome is a large complex catalyst responsible for the synthesis of new proteins, an essential function for life,” they began.  They determined that the exit tunnel contains sensitive probes that “feel” the side chains of amino acids on the emerging protein.  There are little binding crevices and barriers that the substrate must pass by.  The transport experience coming out the tunnel could be different for different amino acid species, they said.
        One thing they found involved moving parts.  There is a kind of gate and latch mechanism; a turnstile, perhaps?  They tried to describe it: “we find rare events in which most of helix 24 [the gate] sways away from the tunnel’s entrance for a few picoseconds [trillionths of a second], leaving the exit clear, and promptly returns to its capping state as a valve that is closed but momentarily opens.”  Maybe this is doing a final checkout or keeping contraband from getting inside.  Whatever is going on, they thought it must be important: “we propose that ribosomal features at the exit of the tunnel can play a role in the regulation of nascent chain exit and ion flux.”  This exit tunnel is no concrete tube: it’s a “protein-sensitive channel” that aids in ensuring the product comes out right.
  3. Super slo-mo:  One enzyme reported in Science Daily can speed up a chemical reaction by 12 orders of magnitude.  On its own, the reaction would take 2.3 billion years3 – a good part of the assumed age of the earth.  With the enzyme it happens in milliseconds.  This sets a new record for enzyme efficiency: their previous record-holder, an enzyme “absolutely essential” for binding RNA and DNA, speeded up a 78-million year reaction into thousandths of a second.
        The current enzyme under study is “essential for both plant and animal life on the planet,” Richard Wolfenden [U of North Carolina at Chapel Hill] said.  “What we’re defining here is what evolution had to overcome, that the enzyme is surmounting a tremendous obstacle, a reaction half-life of 2.3 billion years.”

A major puzzle from the third article was how the enzyme could have originated in the first place:

Without catalysts, there would be no life at all, from microbes to humans,” he said.  “It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction.

He may not have the answer, but studying such enzymes “allows biologists to appreciate their evolution as prolific catalysts, Wolfenden said.”  See also the 05/06/2003 and 02/13/2004 entries.


1.  Anthony J. Kirby and Florian Hollfelder, “Enzymes under the nanoscope,” Nature Vol 456 No 6, November 2008, pp. 45-46.
2.  Paula M. Petrone, Christopher D. Snow, Del Lucent, and Vijay S. Pande, “Side-chain recognition and gating in the ribosome exit tunnel,” Proceedings of the National Academy of Sciences USA, published online before print October 22, 2008, doi: 10.1073/pnas.0801795105.
3.  This is the “half-time,” the time for half the substrate to be consumed.

This is such wonderful science – it is astounding that scientists can even measure such tiny structures working at such infinitesimal speeds – and to think that these molecular machines have been there all this time with their jaw-dropping performances is a great thrill.  You can just feel the evolutionists’ pain, can’t you? (or gullibility; see 01/12/2004).  Wolfenden struggles to imagine how natural selection could have produced an enzyme for an essential biological reaction vital to all life that speeds up a reaction from 2.3 billion years to milliseconds.  He can’t imagine how the protein “got off the ground as a primitive catalyst for such an extraordinarily slow reaction.”  One thing we know about the ground: things fall down onto it; they don’t spontaneously get up from it and go to work without directed energy and purpose.  At this stage of chemical evolution, remember, there is no natural selection (see 01/26/2008).  NS requires replication – accurate replication.  Without intelligent design, Wolfenden and other evolutionists have no recourse but chance.
    The movie Expelled has a funny cartoon showing Richard Dawkins trying to win the cell lottery.  He’s at a slot machine that he can’t get to come up with the winning combination to create life.  As he is kicking the stupid machine in frustration, the camera pans out to a room filled with hundreds of slot machines vanishing into the distance where, to win, he must get them all to succeed together.  As our online book shows, that cartoon is an understatement!
    So pity the evolutionist.  Not only will he never win, he can’t really enjoy the wonderful feeling of appreciation that comes from honoring the Creator of technologies like these.  Do you?

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