3 ms·

Some other good ones: https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=B_zD3NxSsD8 http

Some other good ones: https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=B_zD3NxSsD8 https://www.youtube.com/watch?v=B_zD3NxSsD8 The GP is right in that our intuitions aren't cutting it down at the bottom. All these animations tend to edit out the water molecules so that the audience can understand better. The proteins aren't colored blobs at all. At these scales you'd clearly see individual atoms instead of blobs. But watching a bunch of really detailed atomic ball-stick models would be confusing. And not only are the H2Os battering everything like TIE fighters in the Hoth asteroid field [0], there are ions in there too (Na, K, Cl, etc) that really effect the cell. The membranes are also edited, as many cells are porcupined with receptors like an over crowded wave pool [1]. In addition to the water/saline being edited out, most of the other proteins, vesicles, and interior membranes are also gone for the sake of clarity. There is nearly no free 'space' in the cell, think of a really crammed subway car [2], with the air being like the water/saline. But only much much tighter. The cell is more like a frantically efficient liquidy crystaly thingy than a wonky wobbly blobby poofed-up juice box. And each one is utterly deeply profoundly fascinating. [0] https://www.youtube.com/watch?v=C_DnrceDEI8 https://www.youtube.com/watch?v=C_DnrceDEI8 [1] https://www.youtube.com/watch?v=Zg-GHmvtIeI https://www.youtube.com/watch?v=Zg-GHmvtIeI [2] https://www.youtube.com/watch?v=xG-meaGqg-M https://www.youtube.com/watch?v=xG-meaGqg-M

twic 7y ago
I think David Goodsell's beautiful paintings, in his book Machinery of Life, were the first serious attempt to depict how crammed a cell is (page down past the pictures of individual molecules to get the the cell cross-sections): https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedillustrations/ https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedi... Here's an interview with him, explaining and showing his process: https://www.youtube.com/watch?v=f0rPXTJzpLE https://www.youtube.com/watch?v=f0rPXTJzpLE Here's his recent painting of a coronavirus protease: https://pdb101.rcsb.org/motm/242 https://pdb101.rcsb.org/motm/242 The other thing missing from those videos is any indication of how random these processes are. At one point, an actin filament assembles by having monomers fly directly at the tip and stack neatly together. It's not like that. In reality, there are all sorts of molecules just randomly moshing around, and occasionally, an actin monomer will bump into the tip of the filament and stick, because it has a binding site. But sometimes one will bump into the tip and not stick! Sometimes, the tip of the filament will fall off! The growth is purely statistical: monomers are more likely to stick than to fall off, and more likely to stick than some random unrelated protein is to stick.

twic 7y ago

I think David Goodsell's beautiful paintings, in his book Machinery of Life, were the first serious attempt to depict how crammed a cell is (page down past the pictures of individual molecules to get the the cell cross-sections): https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedillustrations/ https://ccsb.scripps.edu/goodsell/machinery-of-life-reducedi... Here's an interview with him, explaining and showing his process: https://www.youtube.com/watch?v=f0rPXTJzpLE https://www.youtube.com/watch?v=f0rPXTJzpLE Here's his recent painting of a coronavirus protease: https://pdb101.rcsb.org/motm/242 https://pdb101.rcsb.org/motm/242 The other thing missing from those videos is any indication of how random these processes are. At one point, an actin filament assembles by having monomers fly directly at the tip and stack neatly together. It's not like that. In reality, there are all sorts of molecules just randomly moshing around, and occasionally, an actin monomer will bump into the tip of the filament and stick, because it has a binding site. But sometimes one will bump into the tip and not stick! Sometimes, the tip of the filament will fall off! The growth is purely statistical: monomers are more likely to stick than to fall off, and more likely to stick than some random unrelated protein is to stick.