Friday, February 06, 2009


There are twenty kinds of amino acids, modest little molecules. They seem to have been around almost since the beginning, stirred up and cobbled together by inanimate processes, in interstellar space, perhaps, or in deep-sea hydrothermal vents on Earth. One can stew them up in the laboratory by putting common chemicals in a jar and zapping them with energy.

String amino acids together, in their hundreds or thousands -- in a sequence prescribed by the DNA -- and you have a protein. The sequence determines the shape of the protein, as the various domains jostle and jockey into their lowest energy arrangement. Every protein is like a piece of a jigsaw puzzle, with knobs and pockets, in three dimensions. Proteins are the building blocks of life, just as the pieces of a jigsaw puzzle go together to make a picture.

Proteins are also the machinery of life. Proteins called enzymes catalyze chemical reactions. A molecule, glucose say, snuggles into an appropriately shaped pocket on an enzyme, like a key into a lock. Anther molecule, galactose say, snuggles into a nearby pocket, galactose-shaped. The disturbed enzyme shrugs in response, bringing the glucose and galactose close enough together to form a bond. The new united molecule pops out of the enzyme. The enzyme resumes its former shape and stands ready to do the job again. Snuggle, zip, pop. Snuggle, zip, pop.

"And that's basically all there is to biochemistry," says microbiologist Ursula Goodenough.

I was walking the beach yesterday and the sea was quiet and clear. Just beyond the tide line four big needle fish were herding a vast cloud of little silver fish, two needle fish at one end of the cloud, two at the other. Every now and then, in a splash of water, one of the needle fish extracted its dinner. I could not but feel a tad of sympathy for the little silver fish, dashing this way and that, confused and frightened. No other creature on Earth except ourselves would read sentimental significance into this little episode of eat-and-be-eaten. It's all a matter of passing around the molecules of life -- proteins, carbohydrates, lipids and nucleic acids.

And that's basically all there is to....