The electrochemical proton gradient across the inner mitochondrial membrane is used to drive ATP synthesis in the process of oxidative phosphorlyation. The molecular machine that makes this possible is a large membrane-bound enzyme called ATP synthase. This enzyme creates a hydrophilic pathway across the inner mitochondrial membrane that allows protons to flow down their electrochemical gradient. As these ions thread their way through the ATP synthase, they are used to drive an energetically unfavorable reaction to make ATP.

The machine has a large enzymatic portion, shaped like a mushroom called F1, projects on the matrix side of the inner mitochondrial membrane and is attached through a thinner multisubunit "stalk" to a transmembrane carrier for protons called F0. F1 is composed of five parts, and F0 is composed of three parts.

As defined by Dr. Behe, this system fits the definition of irreducible complexity. For F1 to work, all five parts, denoted by Greek letters alpha, beta, gamma,delta, and epsilon, are needed. For F0 to work all three parts a, b, and c are needed.

Here is a great illustration by Julie Thomas:

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To visualize how this enzyme works, try this very crude analogy. Make a fist with your right hand. Take your left hand and cover the fist. Your right wrist is the F0 components. It would be bathed in an oily layer that would be the membrane. Your first would be the gamma, delta, and epsilon components of the F1. Your left hand would be the alpha and beta components.

A few things about the alpha and beta components. The betas have a binding domain for ADP and P. When they bind to this protein in the active site, ATP is spontaneously formed (due to precise, maybe optimal, positioning). This type of domain is seen in other proteins. The problem for F1 is that once ATP is formed, it is bound so tightly it doesn't displace. That's where the rest of the machinery comes in. But before getting to this, it should be noted that there are three beta subunits in each ATPase. You can think of them as being 120 degrees apart from each other.

Here's the basic story about how this thing works. As I said, the F0 component (your wrist) is a proton channel. Biologists think of it is a "proton wire," allowing for a steady stream of proton flow. When the protons start flowing, they cause a conformational change in the FO near the gamma, delta, and epsilon subunits (your fist). In some strange way, this causes the "fist" to begin turning. As it turns, it contains an asymmetric feature that interacts with one of the beta subunits causing it to change shape. The result? ATP bound by the beta subunit is released.

Try it. Slightly extend one your knuckles on your fist and rotate your fist. As it turns in your left hand, imagine three spots on your left hand that would bind ATP. Everytime your right knuckle hit the palm of your left hand at one of these sites, a change would take place and ATP would be released.

Now, as the gamma/delta/epsilon component continues to turn, that beta subunit is no longer in contact with it and thus resumes its original shape to captures more ADP and P and "wait" for the next revolution. While it's turning, it causes the next beta subunit to change shape and release ATP. Around and around it goes, where each beta subunits is popping off ATP molecules in sequential circular order.

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Describing this device, Science News makes it clear that it is not like a machine, it is one.

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"With parts that resemble pistons and a drive shaft, the enzyme F1- ATPase looks suspiciously like a tiny engine. Indeed, a new study demonstrates that's exactly what it is. A movie of a single enzyme molecule in action shows that it spins like a motor to crank out ATP, the ubiquitous molecule that provides energy for biochemical processes in cells.......[The investigators] anchored molecules of F1-ATPase to a glass slide and - like putting a flag on top of a pole - attached a long, fluorescent filament of actin to the end of the drive shaft. By bathing the enzyme in ATP, the researchers made F1-ATPase break down the energy molecule and watched as it whirled the fluorescent filament around like a propeller. The enzyme puts out a very large torque, considering that the actin filament is more than 100 times the length of the enzyme itself, Yoshida [one of the investigators] says. "Can a man rotate a 150-meter rod?" The enzyme can spin such a long filament because it ratchets down the rotation rate when it carries a heavy load, he explains, suggesting that F1-ATPase can change gears - as a good motor should."
Noji et al., 1997, Nature 386,p. 299- 302 (summarized in Science News).

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