In biology textbooks , the way proteins work is often depicted by what looks like a set of puzzle pieces. A small piece, a regulator molecule, say, fits into a large piece, an enzyme, say. The enzyme’s shape then changes to one that fits snugly around a medium-sized piece, the enzyme’s substrate.
Those cartoons are meant to convey the exquisite specificity of biochemical reactions. Of the myriad reactions inside a cell, a given enzyme catalyzes just one. Not surprisingly, the picture doesn’t tell the whole story. What’s missing is the physical setting.
“In the world of a cell as small as a bacterium,” wrote Howard Berg and Edward Purcell in a classic 1977 paper, 1 “transport of molecules is effected by diffusion, rather than bulk flow; movement is resisted by viscosity, not inertia; the energy of thermal fluctuation, kT, is large enough to perturb the cell’s motion.”
Under those...
