Finding wheels

        When I was a sophomore taking Biochemistry, one particular event stands out in my memory, perhaps because it was such an odd thing. Our Professor, Dr. X, knew his material very well. Our classroom had nine blackboards stacked in groups of three. As he wrote on one, Professor x would flip a switch and blackboard A would advance upward, then B, then C, following some pattern that only he knew, until at the end of class, having dragged us all through metabolism, he would neatly draw an arrow connecting blackboard I’s reaction with the one on the starting blackboard. He always left me staring at my notes in despair of connecting them.

            But that’s not what I remember about him the best. One day we were having a discussion about the marvelous things that were being found in biology. It was only a decade since the genetic code had been cracked, and the first DNA and the first protein had been sequenced. These were remarkable achievements. The development of the tools that made genetic engineering possible was happening at MIT there and then. I didn’t really realize how momentous it all was. But one thing Dr X said stuck in my brain. He said, “We will find marvelous things in biology because nature is very inventive. But one thing we will never find is a wheel.” Maybe he thought that the wheel was a man-made machine, smooth, round, and designed. Biology was made of bumpy lumpy proteins and was most emphatically not designed. But I speculate. He never gave his reasoning

Let us have a moment of silence to reflect on the dangers of hubris.

Now let me count the ways “unintelligent” nature has made circles, rotors, wheels and gears:

Porins : These proteins are pores in the membrane, holes to let compounds into or out of the cell. Not quite a wheel, they would be an uneven ride. The protein is shown here in three different ways: one showing every chemical bond (stick), one showing a cartoon of the protein’s secondary structure (the way the amino acids associate with one another), and one showing what the surface of the protein would look like to another protein, or a molecule trying to squeeze through its hole. Bacteria and mitochondria both have porins but not apparently of common origin.

ATP synthase : This molecular machine is 98% efficient at using a flow of protons across the inner mitochondrial membrane to change ADP back to ATP. Part of its essential inner structure is the c-ring rotor, shown in yellow. Its ring structure can best be seen in panel B. As protons pass through the inner channel, the ring begins to spin, acting as a rotor. The rotor contacts other proteins in blue on the “stator,” shown on the left in A. This causes a conformational change in the stator, which allows the ADP to ATP reaction to take place. (For a general description of the whole process see this DI video link here) The technical paper describing the structure, and from which this figure is borrowed is

Flagellum: Not just a wheel, but a water-cooled, acid-fueled, rotary motor, capable of up to 17,000 rpm that can reverse directions in one quarter turn. Very much analogous to human motors, it has parts that function as a drive shaft, stator, bushings, gaskets, and the motor itself.

Diatoms:  Well, maybe he didn’t mean whole organisms. But anyway:

A micrograph of the diatom Actinoptychus maculatus

Leaf hopper’s gears: My professor didn’t mention gears, which are even more stupendous. But see for yourself.

Truthfully, no one in the early 1970s had any idea the wonders there were still to discover in biology. And I think it’s safe to say, no one now should think we are ready to declare the riddle of life solved. We can’t even say that we are close to solving it, because we don’t know how much more there is to learn. Let’s let biology show us her wonders. Hubris has a bad name for a reason.

Adapted from a post originally published at Evolution News,


The Ultimate Recycler

a power grid reaches straight up to a blue sky. Demand for power is high how do we meet our own demand for power?
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When a city starts out with a major energy deficit, there are two changes that should be made: to be really, and I mean really efficient at recycling the critical resource, or to buy more energy.

What about in biology? Cells are like cities, right?

We already know from the previous post that the cell has an energy budget that is out of balance based solely on biosynthesis and use of AT.P It is in a predicament. It has an extreme shortfall in ATP in its balance sheet, needing six ATP just to make one. ATP is a high energy molecule. All that energy has to be loaded into the molecule during its synthesis by using up other ATP molecules.

The chemical structure of ATP shows three high energy phosphate bonds.

If chemical A is necessary for the synthesis of more chemical A, then A has the power of replication (such systems are known as autocatalytic systems). …We find that intermediary metabolism is invariably autocatalytic for ATP.

Kun et al., Genome Biology 2008, 9:R51

The cell needs to have ATP before it can make ATP, and it has to have more ATP than it can make. Can the cell rescue its metabolic state by bringing in ATP from outside? Sure, indirectly– if it eats biological material other cells have made, it can get ATP by breaking down glucose into pyruvate, and then pyruvate into citrate, and then ultimately, the energy is harvested and and a net gain in ATP is produced. The glucose to pyruvate digestion happens in the cytoplasm, but the citrate to final energy harvest all occurs in marvellous mysterious voyagers in our cells called mitochondria.

Mitochondria are the microscopic power plants of the cell whose purpose is to take citrate and convert it to ATP,

the cell’s energy currency. Resembling miniature blimps with corrugated double membranes, they carry out an interlocking series of chemical reactions that squeeze out every last possible ATP from the breakdown of glucose. It’s a highly efficient, environmentally friendly process.  Everything is recycled — one part of the process is called the citric acid cycle because it regenerates itself with each new round. In fact, everything cycles.

Most cells have many mitochondria, whose characteristic wrinkled stroma serve to increase the interior membrane surface area. Think of a bag with a much bigger bag neatly tucked in folds inside. Embedded in that folded inner membrane are all machinery of energy production that makes life possible. And that machinery is considerable. An ensemble of multiple proteins come together to make 5 protein complexes, shown in the picture below. In complexes 1-4, energy in the form of electrons is received by them and cycled through and, then using some of that energy to pump protons across the membrane. As citrate is gradually broken down, compounds like NADH or succinate are produced, and shunted off to the electron transport chain, and they also contribute to the process.

Even the last high-energy electrons from the breakdown process are not wasted: a chain of proteins in the inner membrane passes these electrons like little hot potatoes from one to another, using the energy of each transfer to pump hydrogen ions across the membrane, so that a molecular machine called ATP synthase can take advantage of the hydrogen gradient to create even more ATP.  

The protein structures of the electron transport chain of the mitochondrion. These complex structures harvest energy and pump protons so that AdP can be recycled back to ATP.
The protein complexes of the mitochondrial electron transport chain, showing the flow of molecules in and out of the mitochondrion at each stage. doi:

In the drawing you can see the direction of H+ flow out and then in again, and how many different proteins make up each protein complex. There are 5 complexes, whether in an animal, or a plant.

The fifth complex is ATP synthase. This is where the miracle happens that makes life possible. ATP synthase harvests the energy of the proton gradient to recycle ADP to ATP. Like a turbine in a hydroelectric plant, ATP synthase lets the hydrogen ions flow back across the membrane through itself, rotating as the ions pass through, and As it rotates it adds a phosphate to ADP at each crank, thus restoring ATP to use.

ATP synthase is the name of the protein complex that performs the ADP to ATP conversion. A video is listed that describes its action.

The engine ATP synthase is 98% efficient at what it does! Human machines can’t approach that. But this is what permits life. We burn through our body weight in ATP every day. Just breathing burns ATP.

Right now, within your bodies this little engine is cranking away. Without this machine, oxygen-dependent life could not exist. Strong statement, but I stand by it.

To put it all together, in all life’s glorious improbability and elegant design, will require another post. And I haven’t even gotten past the beginnings of biochemistry.

For a video: ATP Synthase: The power plant of the cell

Not A Simple Question

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I have come to a conclusion. Perhaps if I had thought about it more carefully at first I would not be surprised. But it has only recently occurred to me that a great deal of the disturbance about evolution—yes, no, theistic, atheistic, guided, unguided, young earth, old earth, Darwinist , near- neutralist, whatever! is about human origins. Where did WE come from? Are we descended from primates or not? And what did God have to do with it?

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