November 13, 2013 | David F. Coppedge

Cool Tools in your Cellular Toolkit

Biochemists can’t help using familiar tools to describe what they are finding in living cells.

Swiss army knife:  RNA polymerase 1, a molecular machine that builds the ribosome protein factory, is your “Swiss-army knife,” Science Daily says.  That’s because researchers at the European Molecular Biology Laboratory have found “it incorporates modules which prevent it from having to recruit outside help.”  The components it needs are all built in.  Even though that makes it bigger, it also makes it efficient; “Because everything is already assembled, there’s no time delay,” a team member remarked – which is good, because this Swiss-army knife keeps very busy.  It even has built-in regulators, removing the need for external regulatory elements.  Another Science Daily article says RNA polymerase 1 is a “very large and highly complex molecular machine” and calls it “a crucial cog in the machinery of all cells.” as well as a “central pacemaker for cell growth.”  See also Nature News for word about the latest mapping of the enzyme.

Samurai sword:  The sword in your toolkit is katanin, an enzyme actually named for a katana, a Samurai sword.  PhysOrg describes how this enzyme cuts microtubules with precision to keep the cell’s “skeleton” just right.  Just as our bodies would fall limp without bones, “without our cytoskeletons, our cells, which come in roughly 200 different shapes and sizes, would all become tiny spheres and stop working.”  Researchers at Washington University at St. Louis found that without katanin, the microtubules became disorganized like cobwebs.  Katanin acts like a pruning shear that cuts microtubules when they cross over one another, keeping the cytoskeleton ordered and functional.  It also creates the “array patterning” that arranges the microtubules into “parallel bands like barrel hoops around the cell’s girth,” giving the cell strength.  Since there are typically “hundreds or thousands” of microtubules in a cell, a whole army of Samurai swordsmen remains at the ready.  See more about katanin in a Science Daily article that shows how it helps sprouted seedlings grow.

Stretch sensorsPhysOrg described integrins, machines that sense the cell’s external environment.  They do this by making “catch bonds” that can measure stiffness of the outside world.  The more the catch bond is pulled, the stronger it becomes.  “The cell therefore has a very useful instrument,” the article says. “An internal measurement unit – the number of bound catch bond integrins – proved to be a direct measure of the mechanical stiffness of the external environment.”  Another PhysOrg article described other machines that “feel” the environment, acting as “molecular muscles” that notify the cell when it needs to change shape, such as when it needs to squeeze through a narrow opening.

Cargo carts:  A paper in Current Biology describes the motorized cargo carts that carry tubulin proteins up the cilium to the growing tip.  “The kinesin-2-driven anterograde transport of intraflagellar transport (IFT) trains has long been suspected to deliver cargo consisting of tubulin subunits for assembly at the axoneme tip,” the summary says. “Important new work identifies the tubulin binding site on IFT trains that is responsible for this cargo transport.”

Clock drive:  Different proteins need to be made at different times of the day and night.  A paper in PLoS Biology describes how the circadian clock, the timekeeper in cells, regulates protein synthesis.  Researchers found that mid-day and midnight are key times for activity.  “Our work also finds that many clock cell processes, including metabolism, redox state, signaling, neurotransmission, and even protein synthesis itself, are coordinately regulated such that mRNAs required for similar cellular functions are translated in synchrony at the same time of day.

If there is any field of science that has revolutionized our view of life, it is the discovery of factories of molecular machines in living cells.  Look at them!  They are doing precise, coordinated work involving thousands of parts working together, all the time, even in our sleep.  When you realize that these discoveries have occurred in the lifetimes of many people alive today, and continue to accelerate each year, you realize how privileged we are to see this nano-miniaturized manufacturing phenomenon keeping us and every living thing alive.  This short article doesn’t tell the half of it, or the hundredth, of what new imaging techniques have revealed in the last 20 years.

One can only wonder if Darwin would have dared to put forth a speculation that blind, unguided processes are responsible for life, had he known what we know today.  Think back also to the scientists and philosophers of earlier centuries, back to the Romans, Greeks and Babylonians.  If they had known what we know, how different a world might it have been?  How different would have been the religious, cultural and philosophical traditions of the nations?

The modern world coasts on Enlightenment and modernist assumptions about life and its simplistic Darwinian notions.  The implications of this scale of complexity at the basis of life – the cell – have not yet had time to percolate into the culture.  Take time to think through those mind-boggling implications.  They are life changing!  Only intelligent design has a vera causa adequate to explain what biochemistry has revealed, and only biblical creationism has an adequate Designer.  Leeuwenhoek, the creationist father of microscopy, was astonished and delighted with what he saw through his crude instruments.  Oh, to be able to show him what we see now!  Play that role for him; don’t ever let the wonders of Swiss army knives, Samurai swords, clock drives and all the rest become mundane news.  This is epochal.  This is monumental.  This is world-changing.

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