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Biology / Enzyme regulation
« on: March 18, 2005, 10:56:58 AM »
Working on metabolism, it occured to me that there is a big problem we face and we don't have means to address it. Imagine a metabolic chain:
A>B>C>D (releases energy)
and corresponding
A<B<C<D (consumes energy)
These need to be regulated somehow, otherwise they both run at the same time and just waste precious energy. How do cells do it?
One simple way is "mass action". PY (being a chemist) might explain it better. But basically it is like a gradient and diffusion. If you have a lot of A and little D, then reaction goes from left to right. If you have a lot of D and little A, it goes from right to left. The problem is that D and A are not compared in 1:1 ratio (this has something to do with free energy of reactions). So for a cell 1000 A may be less than 1 D and reaction will still go from right to left. And we will need to define these ratios of what is bigger than what and by how much. Or bots will need to. And these ratios are parts of cell's life strategy. They come up with a lot of crazy ways to adjust that.
For example, imagine that step B>C is actually B+X>C+Y. The cell can make huge amounts of X and throw away Y. Now because X is so much bigger than Y, the reaction will go from left to right, even if C is bigger than B.
This may sound complicated, but this is the meat and essense of any metabolism system. I don't see any way around this crazy thing at the moment. Especially if we have multistep reactions. If all reactions are one-step it is a bit easier. Bots can say
20
eatfat
and it would convirt fat to energy, or
20
makefat
and it would convert energy to fat.
But having multistep reactions requires control, so we'll need all these commands like
eatpyruvate
make AcCoA
etc
Which means that idea of having metabolism run behind the scene goes to hell.
Any ideas?
A>B>C>D (releases energy)
and corresponding
A<B<C<D (consumes energy)
These need to be regulated somehow, otherwise they both run at the same time and just waste precious energy. How do cells do it?
One simple way is "mass action". PY (being a chemist) might explain it better. But basically it is like a gradient and diffusion. If you have a lot of A and little D, then reaction goes from left to right. If you have a lot of D and little A, it goes from right to left. The problem is that D and A are not compared in 1:1 ratio (this has something to do with free energy of reactions). So for a cell 1000 A may be less than 1 D and reaction will still go from right to left. And we will need to define these ratios of what is bigger than what and by how much. Or bots will need to. And these ratios are parts of cell's life strategy. They come up with a lot of crazy ways to adjust that.
For example, imagine that step B>C is actually B+X>C+Y. The cell can make huge amounts of X and throw away Y. Now because X is so much bigger than Y, the reaction will go from left to right, even if C is bigger than B.
This may sound complicated, but this is the meat and essense of any metabolism system. I don't see any way around this crazy thing at the moment. Especially if we have multistep reactions. If all reactions are one-step it is a bit easier. Bots can say
20
eatfat
and it would convirt fat to energy, or
20
makefat
and it would convert energy to fat.
But having multistep reactions requires control, so we'll need all these commands like
eatpyruvate
make AcCoA
etc
Which means that idea of having metabolism run behind the scene goes to hell.
Any ideas?