In many molecular biology animations, a molecule just flies in and goes straight to the right spot. It's clearly a useful simplification, but I'm interested in learning more of the full story.
- I guess at short distances the electric polarizations of the molecules pull them into the right spot. But I have no idea what is "short" here, on the scale of these animations.
- This all is not happening in vacuum. There must be a lot of other molecules crowding around. (Water at least.) How does all that not clog up these mechanisms? I imagine an ATP synthase accidentally sucking in a stray RNA strand.
- I understand the animations are also slowed down a lot, foiling my intuition. Do the molecules just randomly bump into each other SO MUCH that hundreds of times per second an ADP randomly flies into the synthase?
Animation of an ATP synthase with ADP molecules flying in:
Animation of a DNA polymerase with green donuts (DNA primases?) flying in: