It Takes Work to Operate a Cell
Molecular machines are made of chemicals, but their actions are more mechanical than chemical. They do not just bounce into one another and share orbitals like the molecules we studied in basic chemistry. No; these biochemicals are true machines, performing work with moving parts. Like coin-operated robots, they spend energy in the form of ATP molecules to exert forces on other machines and molecules in a precise way, performing work (force x distance). Some recent scientific papers provide actual measurements of these physical forces.
GroEL, a machine illustrated in the Illustra film Unlocking the Mystery of Life, is a chaperone enzyme (so called because it helps other machines) that looks like a barrel with a lid. Newly translated proteins enter the chamber to fold. Recently, scientists at the University of Maryland, publishing in PNAS (open access paper), described their measurements of the mechanical work performed by the machine in kilojoules per mole. In “Measuring how much work the chaperone GroEL can do,” they said, “GroEL overcomes a load of 7.8 kJ/mol, demonstrating its ability to perform work on SP.” (Emphasis added.)
The DNA-transcribing molecule, RNA polymerase, has to work to get to a gene. It’s a harder job than illustrated in the simplified animation in the Illustra film, because much of DNA is “supercoiled” with coils upon coils, making access difficult. In a paper in Science, “Transcription Under Torsion,” researchers from Cornell and Penn State measured the torque that RNAP must put on these coils. RNAP can exert 11 picoNewton-nanometers before stalling.
The messenger-RNA translating robot, the ribosome (also featured in Unlocking the Mystery of Life), continues to yield its mechanical secrets. The two major domains of the ribosome appear to work in a ratcheting fashion as transfer RNAs proceed down the assembly line. In Science, “Translocation in Action,” Marina Rodnina of the Max Planck Institute summarized other recent papers that showed how the two domains “swivel” with respect to each other, while a protein named Elongation Factor G (EF-G) inserts itself like a clutch or pawl, blocking the ratchet from letting the chain slip through in the wrong direction (see details in Science). For a layman’s description of the process, see the article on PhysOrg.
One of the ID movement’s sentimental favorites among molecular machines, the bacterial flagellum (a star in Unlocking the Mystery of Life), was in the news recently. Researchers from the UK, Taiwan and Japan described in PNAS a flagellum that runs on sodium ions instead of protons. The paper, “Mechanism and kinetics of a sodium-driven bacterial flagellar motor,” uses the terms of physics:
The bacterial flagellar motor is a large rotary molecular machine that propels swimming bacteria, powered by a transmembrane electrochemical potential difference. It consists of an ∼50-nm rotor and up to ∼10 independent stators anchored to the cell wall. We measured torque-speed relationships of single-stator motors under 25 different combinations of electrical and chemical potential. All 25 torque-speed curves had the same concave-down shape as fully energized wild-type motors, and each stator passes at least 37 ± 2 ions per revolution. We used the results to explore the 25-dimensional parameter space of generalized kinetic models for the motor mechanism, finding 830 parameter sets consistent with the data. Analysis of these sets showed that the motor mechanism has a “powerstroke” in either ion binding or transit; ion transit is channel-like rather than carrier-like; and the rate-limiting step in the motor cycle is ion binding at low concentration, ion transit, or release at high concentration.
Ignoring Darwinian theory, the authors advertised their engineering model approach as broadly useful: “Our thorough search of the multidimensional parameter space of generalized motor models, guided by experimental data, is an approach that may be widely applicable,” they said.
Speaking of rotary motors running on sodium ions, a new variety of ATP synthase was announced in PLoS Biology -- a variation of the motor that runs on sodium ions instead of protons. Feel the power:
This enzyme catalyzes the phosphorylation of ADP by a rotary mechanism powered by a transmembrane electrochemical gradient, or ion-motive force, of either H+ or Na+ (proton-motive force [PMF] or sodium-motive force [SMF], respectively).
Found in a pathogenic bacterium, this version of the rotary engine that manufactures ATP for work in the cell appears to augment its force-generating torque without dislodging the hydrogen ions (protons) from the rotating c-subunits. The sodium-motive force runs the carousel-like c-ring, which generates torque on the “camshaft” domain, which in turn provides the force for the ATP-binding domain to perform work.
It’s amazing enough that scientists can study machinery at the scale of nanometers (billionths of a meter). Now that they routinely do it, providing unprecedented views of natural machines at work, the expectations of intelligent design are being made manifest. While Darwinian evolution would expect to find coddled parts minimally able to perform functions purely for survival, intelligent design would expect to see precision and order at hierarchical levels, with multiple independent parts and networks supporting complex, interacting functions. That’s exactly what we do see.
For the past few decades, accelerating advances in biochemistry have undermined Darwinism while amplifying intelligent design. That’s why “biochemistry” has really become “biophysics” and systems biology, seamlessly overlapping with advances in human nanotechnology. The future looks bright for design-theoretic science.