October 27, 2005 | David F. Coppedge

Cellular Black Box Reveals Precision Guidance and Control

Amazing discoveries about the cell are being made each week.  It’s a shame more people don’t hear about them.  They are usually written up in obscure journals with incomprehensible jargon, but when explained in plain English, the findings are truly astounding.  Not long ago, the cell was a “black box,” a mechanism of unknown inner workings that somehow survived and reproduced.  Only recently have imaging techniques allowed us to peer inside the box at the nanometer scale (one nanometer is a billionth of a meter) and see what is going on.  Prepare to be astonished.
    A fundamental shift in thinking about cellular processes has occurred since the structure of DNA was elucidated in the 1950s, and has been accelerating ever since.  What used to be mere chemistry is now mechanics; what used to be imagined as fluids mixing in a watery balloon is now programmed robotic machinery.  Cells don’t just perform chemical reactions like we did in high school, pouring mixtures together and seeing if they explode or not.  It’s more like robotics, and is properly known these days as “biophysics.”  Cells are not just tossing ingredients together, but guiding them into place with motors, pivots, guardrails and inspectors.5  The cell is engaged in precision manufacture with molecular machines and motorized transport.  The coolness factor of these molecule-sized gadgets would blow away any competition in Popular Mechanics if they could be appropriately visualized and described.  Let’s try with some recent examples.

  1. tRNA: Guided Trackways:  A paper in PNAS1 took five pages describing one tiny segment of the DNA translation process: the moment when transfer RNA (tRNA) enters the inner sanctum of the protein-building machine, the ribosome (see also summary on Science Now).  If you have seen the animations in the film Unlocking the Mystery of Life, you probably remember the climactic scene of tRNAs lining up in assembly-line fashion as their attached amino acids are fastened together.  Stunning as that animation was, it was vastly oversimplified.  The ribosome actually contains a precisely-molded entrance tunnel where each tRNA is inspected and guided into place before allowed into the active site.  Each tiny movement along the track is authenticated by contacts with specific atoms at checkpoints along the way.  A Los Alamos team achieved the highest-resolution images yet of this process and found that parts of the tRNA and the tunnel turnstiles actually flex as much as 20° as part of the guided entrance, called accommodation.  Their diagrams show multiple precision contacts all along the four specific stages of accommodation they investigated.  Whether able to follow their dense jargon-laden description or not, the reader is sure to get the sense that something incredibly precise is going on.  And then to learn that it all takes place in two nanoseconds is almost too much to handle.
  2. DNA Copying: Tight Fit:  Another paper in PNAS2 explored the fit of DNA bases in the copying machinery at the sub-angstrom level (an angstrom is 10-10 meter, about the width of a hydrogen atom).  Stanford and MIT scientists investigated how thymine fits into DNA Polymerase I as the genetic code is transcribed.  As in the tRNA case above, the fit is precise and guided.  They were surprised to find a little bit of margin inside the active site, which they speculated might “allow for an evolutionarily advantageous mutation rate.”  Nevertheless, their “results provide direct evidence for the importance of a tight steric fit on DNA replication fidelity.”  The tight fit ensures that illegal interlopers cannot make it into the active site.  They also found that simple Watson-Crick base-pairing was not sufficient: the machines actually force the bases together in a coordinated way with error-checking.  They remarked that this authentication and guidance system is speedy: “This choice, which occurs dozens of times per second, involves the selection of one nucleotide among four for insertion into the growing primer strand, opposite each DNA template base as it is addressed in turn.” (Emphasis added.)
  3. Unzipping Acrobatics:  A paper in Nature3 investigated helicases, the molecular machines that unwind and unzip DNA strands.  “Helicase enzymes can move along DNA or RNA, unraveling the helices as they go,” said Eckhard Jankowsky in an analysis of this paper in the same issue.4  “But simply traveling along a nucleic acid in one direction seems not to be enough for some of these molecular motors.”  They discussed how helicase repeatedly bends over, forms loops, and snaps back into position during the operation.  These acrobatic machines don’t just plod along in one direction but undergo a complex choreography with moving parts as they consume ATP for energy.  The “repetitive shuttling” the authors described has a purpose, possibly for “keeping the DNA clear of toxic recombination intermediates.”
  4. Cellular Oarsmen:  Three German researchers imaged eukaryotic flagella with twice the resolution of previous attempts.  The whiplike propellers, which beat with back-and-forth motion (unlike the rotary flagellar motors of bacteria), contain a 9+2 arrangement of microtubules that are tied together with motors and spokes.  “Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella,” they wrote.  Their paper in PNAS6 includes a stereo pair image that provides a 3D look down the flagellum shaft.

The literature is filled with examples like these.  They usually say little or nothing about how these machines evolved; in fact, more often, they are likely to mention that the machines are “highly conserved” (i.e., unevolved) between the simplest one-celled organisms and humans.
    Though the articles valiantly attempt to describe what happens at these submicroscopic levels, the subject matter would greatly benefit from top-notch animation.  Microscopic imaging technology keeps improving, though; some day soon, it may be possible for scientists to watch the machinery of the cell at its own nanometer scale in real time. 


1Sanbonmatsu et al., “Simulating movement of tRNA into the ribosome during decoding,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0503456102, published online before print October 25, 2005.
2Kim et al., “Probing the active site tightness of DNA polymerase in subangstrom increments,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0505113102, published online before print October 25, 2005.
3Myong et al., “Repetitive shuttling of a motor protein on DNA,” Nature 437, 1321-1325 (27 October 2005) | doi: 10.1038/nature04049.
4Eckhard Jankowsky, “Biophysics: Helicase snaps back,” Nature 437, 1245 (27 October 2005) | doi: 10.1038/4371245a.
5This is not to say that biomolecular machinery looks like human machinery.  Straight lines and geometric shapes are rare; tRNA entering a ribosome looks like spaghetti in a blender to an untrained eye.  In addition, at the nanometer scale, molecules are subject to the random vibrations of Brownian motion.  It has taken decades of careful research to tease out the order and intricacy of the cell’s moving parts.  Nevertheless, the language of motors and machines in the literature is apt and ubiquitous, as is the language of physics (piconewtons of force, thermodynamics, translational motion in nm/s and rotational motion in Hz or rps).  Human engineers are trying to emulate some of these machines in the new science of nanotechnology.
6Nicastro et al., “3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0508274102, published online before print October 24, 2005.

These are just a few of the reasons students should be allowed to hear about intelligent design.  Darwin?  He was just an old Victorian who didn’t know anything about this.  If he had, he might have decided to stick with his training to become a country parson after all.  This is the 21st century, folks: the age of nanomachinery and biophysics.  Enjoy!

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Categories: Physical Science, Physics

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