3 ms·

It always bothered me that in the standard explanations of how these processes work it always seemed that reaction ingredients would somehow magically seek each

It always bothered me that in the standard explanations of how these processes work it always seemed that reaction ingredients would somehow magically seek each other out, such as in videos like this where the amino acids arrive at the ribosome in order: https://www.youtube.com/watch?v=TfYf_rPWUdY https://www.youtube.com/watch?v=TfYf_rPWUdY The molecules really do move randomly, not magically, and it's just that they go so fast and are so numerous and collide so often that even random chance puts the right molecules in the right place many times per second. This article was a revelation when I first read it and I'm quite disappointed that this was never explained properly in my entire school life.

wombatmobile 6y ago
Don't be disappointed. Most of the things you were taught in school were simplifications of reality. The curriculum is taught this way to make it easier for you to incorporate a lot of axioms from different fields into your fledgling, inexperienced mind. Once you have a number of these axioms at your disposal, you are equipped to leave the nest and go out into the world and make sense of new things yourself, at whatever depth and speed suits your circumstances and interests.
- modeless 6y ago
  This isn't a simplification though. It's a complification. It's both more important and easier to understand than a lot of the biology stuff that I was taught. The curriculum should be rearranged to prioritize this higher.
  - sthnblllII 6y ago
    Correct. In most class-based education, biology is treated just like history and math and everything else. All subjects are just collections of disconnected factoids handed down from on high. Intuition requires initiative, and initiative means asking questions, and asking questions takes away class time from the unintuitive students learning more factoids. The point is: go to your professors' office hours!
mindfulplay 6y ago
This is fascinating and new to me. I thought it was designed by say the DNA or the rna to behave in that coordinated manner and to seek specific molecules. But if it's just a random walk and somehow this success at this scale and speed, it is even more simple yet incredible to think.
- jfarlow 6y ago
  Brownian motion dominates at the scale of a protein. In other words, the energy imparted by the ambient temperature is orders of magnitude greater than that that could be established through momentum of objects with that little mass. So everything bumps into everything, and the only distinguishing factor between various bumps is how long they stay stuck together. Most things just bounce right off. Sometimes they are repulsed, and in rare cases (when they've been selected for), multiple proteins can meet in just the right orientation that they stay stuck for a while (now scale this so that 3 or 4 objects must meet at the same time, and now you get into the 'regulation' of a cell at perception-relevant time-scales). This measurement of stickiness is called the "dissociation constant (Kd)" and is a measurement of what concentration of component A you need alongside component B such that half of component A is bound to component B. It is one of the primary drivers of most biochemical processes in a cell. https://en.wikipedia.org/wiki/Dissociation_constant https://en.wikipedia.org/wiki/Dissociation_constant
  - stillsut 6y ago
    Is there not some local disturbances in the circulation of cell contents that not all interactions are i.i.d? Some kind of repelling force on a large molecule that would keep similarly charged molecules at arms length. And in some cases act as a cell wide tidal force to diffusion? I'm thinking of the atari pong ball where you can ricochet the ball between the top of the court and bricks repeatedly; is there some locality in the cell which takes advantage of positioning to increase likelihood of collision?
    - jszymborski 6y ago
      tl;dr very much so, yes Cells are very subdivided, and the ease with which macromolecules traverse these spaces varies greatly. There are organelles and the nucleus that require only let certain proteins in and and out and at certain rates. There are also kinds of tar-pits that keep certain proteins around for longer. Stress granules and vesicles also gobble-up macromolecules into these fun party bags that burst in certain contexts. Sometimes you even have complexes of macromolecules like ribosomes whose entire job is to intercept other macromolecules so that they might interact (there is a subtle difference between enzymes/catalysis here if I understand correctly)
shpongled 6y ago
What's also fascinating is that the shapes and biochemical properties of proteins and other molecules in the cell are so finely tuned that they can be flying into each other, and still have such a high degree of specificity (e.g. proteins interacting with certain other protein domains, substrates, etc) that life actually works.

wombatmobile 6y ago

Don't be disappointed. Most of the things you were taught in school were simplifications of reality. The curriculum is taught this way to make it easier for you to incorporate a lot of axioms from different fields into your fledgling, inexperienced mind. Once you have a number of these axioms at your disposal, you are equipped to leave the nest and go out into the world and make sense of new things yourself, at whatever depth and speed suits your circumstances and interests.

modeless 6y ago
This isn't a simplification though. It's a complification. It's both more important and easier to understand than a lot of the biology stuff that I was taught. The curriculum should be rearranged to prioritize this higher.
- sthnblllII 6y ago
  Correct. In most class-based education, biology is treated just like history and math and everything else. All subjects are just collections of disconnected factoids handed down from on high. Intuition requires initiative, and initiative means asking questions, and asking questions takes away class time from the unintuitive students learning more factoids. The point is: go to your professors' office hours!

mindfulplay 6y ago

This is fascinating and new to me. I thought it was designed by say the DNA or the rna to behave in that coordinated manner and to seek specific molecules. But if it's just a random walk and somehow this success at this scale and speed, it is even more simple yet incredible to think.

jfarlow 6y ago
Brownian motion dominates at the scale of a protein. In other words, the energy imparted by the ambient temperature is orders of magnitude greater than that that could be established through momentum of objects with that little mass. So everything bumps into everything, and the only distinguishing factor between various bumps is how long they stay stuck together. Most things just bounce right off. Sometimes they are repulsed, and in rare cases (when they've been selected for), multiple proteins can meet in just the right orientation that they stay stuck for a while (now scale this so that 3 or 4 objects must meet at the same time, and now you get into the 'regulation' of a cell at perception-relevant time-scales). This measurement of stickiness is called the "dissociation constant (Kd)" and is a measurement of what concentration of component A you need alongside component B such that half of component A is bound to component B. It is one of the primary drivers of most biochemical processes in a cell. https://en.wikipedia.org/wiki/Dissociation_constant https://en.wikipedia.org/wiki/Dissociation_constant
- stillsut 6y ago
  Is there not some local disturbances in the circulation of cell contents that not all interactions are i.i.d? Some kind of repelling force on a large molecule that would keep similarly charged molecules at arms length. And in some cases act as a cell wide tidal force to diffusion? I'm thinking of the atari pong ball where you can ricochet the ball between the top of the court and bricks repeatedly; is there some locality in the cell which takes advantage of positioning to increase likelihood of collision?
  - jszymborski 6y ago
    tl;dr very much so, yes Cells are very subdivided, and the ease with which macromolecules traverse these spaces varies greatly. There are organelles and the nucleus that require only let certain proteins in and and out and at certain rates. There are also kinds of tar-pits that keep certain proteins around for longer. Stress granules and vesicles also gobble-up macromolecules into these fun party bags that burst in certain contexts. Sometimes you even have complexes of macromolecules like ribosomes whose entire job is to intercept other macromolecules so that they might interact (there is a subtle difference between enzymes/catalysis here if I understand correctly)

shpongled 6y ago

What's also fascinating is that the shapes and biochemical properties of proteins and other molecules in the cell are so finely tuned that they can be flying into each other, and still have such a high degree of specificity (e.g. proteins interacting with certain other protein domains, substrates, etc) that life actually works.