5 ms·

Thanks for posting this. Looked further into atp synthase. Absolutely amazing. A little turbine, driven by the flow of protons, spinning in 120 degree discrete

by im3w1l 6y ago

Thanks for posting this. Looked further into atp synthase. Absolutely amazing. A little turbine, driven by the flow of protons, spinning in 120 degree discrete clicks, around catalyst pockets, where each click changes the shape of the pocket to a new one. And after the pocket has gone through a complete cycle, adp and phosphate have been fused. Never seen the chemical (proton concentration), converted into something mechanical (spinning), and back into chemical (adp + phosphate -> atp) in such a way before.

jcims 6y ago
ATP synthase is amazing. It uses the driving force from the potential gradient (aka voltage) built by the proton pump in the first video to spin at ~21,000 rpm and crank out ATP. I read that your body creates (and then consumes) about its own weight in ATP every day. This channel has a ton of great videos: https://www.youtube.com/user/WEHImovies/videos https://www.youtube.com/user/WEHImovies/videos Here's one on kinetichore and mitosis (which also shows kinesin and dynein which are comically odd) - https://www.youtube.com/watch?v=IvJrDsRuWxQ https://www.youtube.com/watch?v=IvJrDsRuWxQ There's a collection of their DNA ones here: https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=7Hk9jct2ozY Here's another view of the ATP synthesis process that shows the chaos a bit more: https://www.youtube.com/watch?v=OT5AXGS1aL8 https://www.youtube.com/watch?v=OT5AXGS1aL8 When I think of these systematically I just wonder what the intermediate steps were. The proton pump uses energy to create the potential gradient that ATP synthase runs on. You can't have a proton gradient without the proton pump, and without the proton gradient you don't have ATP. So these two exquisitely complex machines depend on each other and had to evolve together. It boggles my mind. Edit: Ah! Was looking for this one, sodium potassium pump - https://www.youtube.com/watch?v=ZKE8qK9UCrU https://www.youtube.com/watch?v=ZKE8qK9UCrU This is how our neurons propagate signals. They are driven by ATP.
- AstralStorm 6y ago
  Immediate step is a cell which is long and has a natural ion gradient. E.g. one with flagella on just one side. Then the better ones would evolve machinery to speed up the gradient, which happened to be using some energy but made said cell move and digest faster, thus also reproduce faster. At this point this could still be shut down during lack of food or activity, as there was a natural gradient when activity was nearby. The membrane is the later invention, dating to organelles which are suspected to be microcellular parasites that got integrated and then reduced. These membranes were much more efficient, however they were very hard to turn off for hibernation as the membrane is a static gradient and hard to disrupt temporarily.
  - im3w1l 6y ago
    So if you have a long cell with an ion-gradient along it, I guess you have to have the turbines attached to something right? Or else the protons will just push it around rather than spin it? And then there is still the issue of protons just flowing around the turbine rather than through it. It may be possible, but to my layman intuition it sounds way harder to get right than a membrane. I wonder if maybe an intermediate step could be just channels and turbine. But no pump. If the amount of protons surrounding membrane varies over time, the cell can open the channels when there are many protons outside, and close the channels when there are few (forcing equalization through turbines). Or maybe it can use acid protolysis to create protons?
    - jcims 6y ago
      This makes a lot of sense, thanks!
- im3w1l 6y ago
  I feel like learned nothing about how the pump works from that sodium - potassium video. They just handwaved it away with "conformational changes". Would be neat if they zoomed in on the moving parts. This one has a little more, even if a lot of questions still remain https://www.youtube.com/watch?v=LEefVREZ1Ao https://www.youtube.com/watch?v=LEefVREZ1Ao
  - jcims 6y ago
    Nice! Glad i'm not the only one decending into these worm holes.
DrAwdeOccarim 6y ago
It can also run backward when ATP concentrations are too high.
- jcims 6y ago
  Whoa.

by im3w1l 6y ago

jcims 6y ago

ATP synthase is amazing. It uses the driving force from the potential gradient (aka voltage) built by the proton pump in the first video to spin at ~21,000 rpm and crank out ATP. I read that your body creates (and then consumes) about its own weight in ATP every day. This channel has a ton of great videos: https://www.youtube.com/user/WEHImovies/videos https://www.youtube.com/user/WEHImovies/videos Here's one on kinetichore and mitosis (which also shows kinesin and dynein which are comically odd) - https://www.youtube.com/watch?v=IvJrDsRuWxQ https://www.youtube.com/watch?v=IvJrDsRuWxQ There's a collection of their DNA ones here: https://www.youtube.com/watch?v=7Hk9jct2ozY https://www.youtube.com/watch?v=7Hk9jct2ozY Here's another view of the ATP synthesis process that shows the chaos a bit more: https://www.youtube.com/watch?v=OT5AXGS1aL8 https://www.youtube.com/watch?v=OT5AXGS1aL8 When I think of these systematically I just wonder what the intermediate steps were. The proton pump uses energy to create the potential gradient that ATP synthase runs on. You can't have a proton gradient without the proton pump, and without the proton gradient you don't have ATP. So these two exquisitely complex machines depend on each other and had to evolve together. It boggles my mind. Edit: Ah! Was looking for this one, sodium potassium pump - https://www.youtube.com/watch?v=ZKE8qK9UCrU https://www.youtube.com/watch?v=ZKE8qK9UCrU This is how our neurons propagate signals. They are driven by ATP.

AstralStorm 6y ago
Immediate step is a cell which is long and has a natural ion gradient. E.g. one with flagella on just one side. Then the better ones would evolve machinery to speed up the gradient, which happened to be using some energy but made said cell move and digest faster, thus also reproduce faster. At this point this could still be shut down during lack of food or activity, as there was a natural gradient when activity was nearby. The membrane is the later invention, dating to organelles which are suspected to be microcellular parasites that got integrated and then reduced. These membranes were much more efficient, however they were very hard to turn off for hibernation as the membrane is a static gradient and hard to disrupt temporarily.
- im3w1l 6y ago
  So if you have a long cell with an ion-gradient along it, I guess you have to have the turbines attached to something right? Or else the protons will just push it around rather than spin it? And then there is still the issue of protons just flowing around the turbine rather than through it. It may be possible, but to my layman intuition it sounds way harder to get right than a membrane. I wonder if maybe an intermediate step could be just channels and turbine. But no pump. If the amount of protons surrounding membrane varies over time, the cell can open the channels when there are many protons outside, and close the channels when there are few (forcing equalization through turbines). Or maybe it can use acid protolysis to create protons?
  - jcims 6y ago
    This makes a lot of sense, thanks!
im3w1l 6y ago
I feel like learned nothing about how the pump works from that sodium - potassium video. They just handwaved it away with "conformational changes". Would be neat if they zoomed in on the moving parts. This one has a little more, even if a lot of questions still remain https://www.youtube.com/watch?v=LEefVREZ1Ao https://www.youtube.com/watch?v=LEefVREZ1Ao
- jcims 6y ago
  Nice! Glad i'm not the only one decending into these worm holes.

DrAwdeOccarim 6y ago

It can also run backward when ATP concentrations are too high.

jcims 6y ago
Whoa.