October 5, 2013 | David F. Coppedge

Marvelous Machines That Keep You Running

Here are just a few of the recent reports describing the intricate biological machines on which life depends.

Roundup and separate:  Take a look at the diagram in an article on PhysOrg, then watch the embedded video clip.  Every time a cell divides, that elaborate machinery organizes and coordinates hundreds of intricate, sequential operations, generating physical force to “reel in” the chromosomes.  “At the cellular level, the mitotic spindle apparatus is arguably the most complicated piece of machinery in existence.”  The video clip shows how six feet of DNA is coiled, recoiled, supercoiled, and coiled again to fit into chromosomes on which the mitotic spindle operates.  “The group chose to simulate budding yeast cells because their entire spindle is comprised of only around 40 microtubules (MTs), compared to 100 times that amount in mammalian cells.”  The article is based on a paper in Current Biology. A paper in Nature described one of the many players in the elaborate choreography, an enzyme named Cyclin A that promotes “faithful chromosome segregation” each cell division, to maintain “robust error correction” in this critical process.

Energy pumps and batteries:  Did you know that about 40 percent of the energy in your body goes to operate pumping machinery?  Science Daily describes the sodium and potassium pumps that are at the forefront of action for nerves and muscles.  The sodium pumps are able to permit sodium ions, while blocking the slightly-bigger potassium ions.  “The pump is constantly doing its job in every cell of all animals and humans,” the article explains.  “It works much like a small battery which, among other things, maintains the sodium balance which is crucial to keep muscles and nerves working.”  A team at Aarhus University says they have achieved resolution at 0.28 nanometers to look at these amazing machines that are embedded in cell membranes, allowing them to “actually see the sodium ions and observe where they bind in the structure of the pump.”

Powerhouses with triple redundancy and bouncers:  “No less than three” signaling pathways are involved in regulating mitochondria, the powerhouses of the cell, Science Daily says.  These essential organelles do not operate independently from the rest of the cell, as once thought.  Families of special machines control traffic into the inner and outer membranes, called TIM and TOM (transporter in the inner membrane, and transporter in the outer membrane).  They act like bouncers, the article says:

Mitochondria resemble a cell within the cell: Separated by two membranes from the rest of the cell and with their own genome, they were long thought to be regulated for the most part independently of the nucleus. However, most mitochondrial proteins are read off from the DNA in the nucleus and need to be transported to the mitochondria following their synthesis in the cytosol, the liquid surrounding the cell components. The mitochondrial proteins need to be sorted precisely according to their destination. Not just anything is allowed to pass through the membrane of the cellular powerhouses: Only with a molecular mailing address can a protein pass though the central entrance gate in the outer mitochondrial membrane, the TOM complex. In addition to the molecular pore Tom40, the complex contains receptors like Tom22, which decides in the manner of a bouncer at a nightclub which proteins can enter and which can’t. The right “outfit” for admission is a particular molecular structure.

Remember this:  Long-term memory is thought to be stored in neuronal proteins in the brain.  PhysOrg reported that proteins are “made to order” at the synapses, the junctions between dendrites (extensions on neurons), where biochemical signals are transported to other neurons.  Thousands of messenger RNAs (mRNA), manufactured in the nucleus, aid in the “local” manufacture of proteins where they are needed.  The manufacturing occurs by splicing of translated mRNA subunits, called exons, in various ways.  Usually, splicing occurs in the nucleus, but the tips of neurons (dendrites and axons) can be far removed from the nucleus.  For efficient production, proteins can be spliced locally at the tips.  Work at the U of Pennsylvania School of Medicine shows that the ribosomes that translate messenger RNA react differently at “translational hotspots,” providing local response and diversity essential for memory storage.  “Our results suggest that the location of the translational hotspot is a regulator of the simultaneous translation of multiple messenger RNAs in nerve cell dendrites and therefore synaptic plasticity” (i.e., flexibility), a representative said.

Transformers robots:  Speaking of splicing, the spliceosome in the nucleus is an amazing splicer and dicer.  Science Daily described it as “a complicated complex, made up of four major parts and more than 100 accessory proteins that come together and break apart throughout the splicing process.”  The press release from Brandeis University invited readers to “Think of the spliceosome as an old Transformers robot — it has individual pieces that operate independently but can also come together to form a larger structure.”  The “highly ordered process” of splicing is both “flexible” and “sensible,” the article said – and that is evident even though “We are just scratching the surface in understanding this process,” a researcher commented.

Factories of machines on the move:  The headline on a PhysOrg article reads, “Cell nuclei harbor factories that transcribe genes.”  This article focuses on nuclear pore complexes, gatekeepers or “customs agents” to the nucleus of the cell.  Nuclei have dozens of these elaborate portals composed of multiple proteins called nucleoporins.  A fascinating aspect of these gates recently came to light: “If the gene does not come to the pore … the pore comes to it.”  In other words, genes that need to be translated don’t have to find a way to the pore.  Machinery that activates those genes has the capability to locate the gene near a nuclear pore, so that after being translated, the messenger RNA can be exported quickly to the cytoplasm.  In addition, “various proteins [are] anchored to the  nucleoporins” to aid in the process.  “The nuclear pores thus create an environment conducive to the efficient production of gene copies,” the article said.  Though studied in yeast, it is believed similar processes take place in mammalian cells that are much larger.  The researchers from the University of Geneva believe that in mammalian cell nuclei, “it is the nucleoporins that move towards the activated genes and not vice versa.”

As usual, each of these articles had little or nothing to say about evolution, illustrating a law of nature: Darwinspeak is inversely proportional to the amount of detail provided about living systems.  The angel is in the details.  We think people should learn about the molecular machines at the foundation of life, not just because it’s fascinating, but because it hammers simplistic notions that these irreducibly complex, multi-part factories of moving parts could have arisen by mindless, aimless processes.  Machines that are “sensible” imply a sensible Designer.  Machines that produce “made to order” machines imply an orderly Maker.  Machines that make “faithful” copies imply a faithful Source.  Machines that create memories call us to “Remember now your Creator” (Ecclesiastes 12:1).



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