1) Compartmentalizing of biological functions. Its why a cell is a fundamental unit of life, and why organelles enable more complex life. Things are physically in closer proximity and in higher concentrations where needed.
2) Multienzyme complexes. Multiple reactions in a pathway have their catalysts physically colocated to allow efficient passing of intermediate compounds from one step to the next.
3) Random chance. Stuff jiggles around and bumps into other stuff. Up until a point, higher temperature mean more bumping around meaning these reactions happen faster, and the more opportunities you can have for these components fly together in the right orientation, the more life stuff can happen more quicky. There's a reason the bread dough that apparently everyone is making now will rise faster after yeast is added if the dough is left at room temp versus allowed to do a cold rinse in the fridge. There are just less opportunities for things to fly together the right way at a lower temperature.
3a) For the ultra complex protein binding to the DNA, how those often work in reality is that they bind sort of randomly and scan along the dna for a bit until they find what they're looking or fall off. Other proteins sometimes interact with other proteins that are bound to the DNA first which act as recruiters telling the protein where to land.
The common theme there is constrained proximity. To give random chance more of a chance.
My favorite illustration was a video of simulated icosahedral viral capsid assembly. The triangular panels were tethered together to keep them slamming into each other. Even then, the randomness and struggle was visceral. Lots of hopeless slamming; tragic almost but failing to catch; being smashed apart again; misassembling. It was clear that without the tethers forcing proximity, there'd be no chance of successful assembly.
Nice video... it's on someone's disk somewhere, but seemingly not on the web. The usual. :/
> yeast
Nice example. For a temperature/jiggle story, I usually pair refrigerating food to slow the bacterial jiggle of life, with heating food to jiggle apart their protein origami string machines of life. With video like https://www.youtube.com/watch?v=k4qVs9cNF24 .
> Compartmentalizing
I've been told the upcoming new edition of "Physical Biology of the Cell" will have better coverage of compartmentalization. So there's at least some hope for near-term increasing emphasis in introductory content.
Coincidentally I'm previewing PBotC just now. It looks really promising. Do you know roughly when the new edition is expected? Or if you have any favorite books on how things work at that scale, I'd be grateful for the pointer. (I've read a popular book by David Goodsell and am halfway through a somewhat deeper one.)
I've found the bionumbers database[1] very helpful. Google scholar and sci-hub for primary and secondary literature. But books... I'd welcome suggestions. I'm afraid I mostly look at related books to be inspired by things taught badly.
The bionumbers folks did a "Cell Biology by the Numbers" book... the draft is online[2].
Ha, they've done a Covid-19 by the numbers flyer[3].
If you ever encounter something nice -- paper, video, text, or whatever, or even discussion of what that might look like -- I'd love to hear of it. Sorry I can't be of more help.
1) Compartmentalizing of biological functions. Its why a cell is a fundamental unit of life, and why organelles enable more complex life. Things are physically in closer proximity and in higher concentrations where needed.
2) Multienzyme complexes. Multiple reactions in a pathway have their catalysts physically colocated to allow efficient passing of intermediate compounds from one step to the next.
https://www.tuscany-diet.net/2019/08/16/multienzyme-complexe...
3) Random chance. Stuff jiggles around and bumps into other stuff. Up until a point, higher temperature mean more bumping around meaning these reactions happen faster, and the more opportunities you can have for these components fly together in the right orientation, the more life stuff can happen more quicky. There's a reason the bread dough that apparently everyone is making now will rise faster after yeast is added if the dough is left at room temp versus allowed to do a cold rinse in the fridge. There are just less opportunities for things to fly together the right way at a lower temperature.
3a) For the ultra complex protein binding to the DNA, how those often work in reality is that they bind sort of randomly and scan along the dna for a bit until they find what they're looking or fall off. Other proteins sometimes interact with other proteins that are bound to the DNA first which act as recruiters telling the protein where to land.