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Work of molecular ‘machines’ vital to sustaining life

Much of the “work” that keeps us alive is done with molecular “machines” made of protein. Proteins are also the structural material of which much of our bodies are made – the stuff of skin and hair and muscle, even, in part, of bones and teeth.

Proteins are long molecules – chains of smaller ones, amino acids – strung together like beads on a string. Crucial to the structure of every amino acid – and, thus, of every protein – are small clusters of atoms known as “amine groups.” Each amine group is essentially a molecule of ammonia (the gas that is dissolved in water to make the household cleaner).

At the center of every molecule of ammonia is an atom of nitrogen. Essential to making amine groups, amino acids and proteins, nitrogen is essential to life. Fortunately, nitrogen is plentiful, making up four-fifths of the air we breathe.



Unfortunately, the nitrogen atoms in air are joined in pairs, and the bond between them is so strong that under normal conditions it’s virtually unbreakable. How can life survive?

Bonds between nitrogen atoms are broken in the reaction vessels of fertilizer plants … at temperatures over 900 degrees Fahrenheit and at four-and-a-half tons per square inch pressure.




And the “Haber process” for making fertilizer was only invented a hundred or so years ago; nitrogen-dependent life has been on Earth close to four billion. Where did life get its nitrogen before there was artificial fertilizer?

Lightning heats the air to 50,000 or 60,000 degrees – hotter than the surface of the sun – and more than enough to break up nitrogen molecules. The nitrogen atoms can then combine with oxygen, the product dissolving in raindrops and falling to fertilize the Earth. But even with a hundred lightning strokes, each second, 24/7 (it’s always mid-afternoon – ideal thunderstorm time – over the tropics somewhere), the amount of nitrogen “fixed” in fertilizer is nowhere near enough to account for all the biomass that covers our planet.

Scotch broom is a member of the pea family, a pest we shouldn’t hesitate to pull up any chance we get. Gently pulling a plant up by the roots, one finds bumps (nodules) on the roots. The nodules have a pinkish tinge; the color is significant.

The broom’s roots are infected, but it’s an infection that’s good for the plant. And the nodules are tumors, but they, too, are good for the plant.

Triggered by chemicals released by the bacteria, the plant’s root cells have divided wildly, creating the nodules in which the bacteria have taken up lodging. Comfortably ensconced, the bacteria pull air from the soil around them. Using enzymes – molecular machines – rather than heat and pressure, the bacteria gently breaks apart nitrogen molecules and attaches their atoms to others, yielding molecules the host plant can use to make proteins.

But there’s a hitch. The bacteria must have access to air to get nitrogen, but the enzyme’s ability to convert nitrogen to plant food is destroyed by oxygen.

Somehow oxygen must be shuttled out of the nodules.

Within the root nodules, the bacteria construct a small molecule. The host plant simultaneously makes a small molecule of its own. The two small molecules then link, creating a larger molecule that is perfect for shuttling oxygen out of the nodule.

It is this larger, oxygen-shuttling molecule that colors the nodule pink. Manufactured in plants of the pea family (legumes), it is called leghemoglobin – very close cousin to the molecule that shuttles oxygen out of our lungs and gives our blood its color.

Alan Stahler trained as a biologist and is an amateur astronomer. He teaches enrichment classes for children and adults at Sierra Friends Center. His science programs can be heard at noon on alternate Tuesdays on KVMR-FM (89.5). He has been invited to debate “Evolution versus Creationism” on Monday, February 3, 6PM, at First Baptist Church, across from NUHS. The public is welcome.


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