Author Topic: Enzyme regulation  (Read 1776 times)

Offline shvarz

  • Moderator
  • Bot God
  • *****
  • Posts: 1341
    • View Profile
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?
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7718
    • View Profile
Enzyme regulation
« Reply #1 on: March 18, 2005, 11:06:54 AM »
The problem only really arises if we allow two way reactions.  Everything works somewhat in 2 directions, but some are negligable in reverse.

For those things that aren't, A->B is a different enzyme than B->A right?  So assuming that the reaction only occurs when an enzyme is present the bots need a way to control the number of each enzymes active.

If the reactions can occur spontaneously and enzymes only lower activation energy, it becomes much more complicated.

Offline shvarz

  • Moderator
  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Enzyme regulation
« Reply #2 on: March 18, 2005, 11:11:59 AM »
Well, say that A>B is energy to fat.  If you convert energy to fat, you better have an emzyme that conerts fat to energy.  Otherwise when you need energy, then you don't have time to wait until an enzyme is made.  But even if you can wait a cycle or two.  Then you have both enzymes (fat-making and fat-destroying) at the same time.  So your fat-destroying enzyme will make energy, but you don't have time to use it, because fat-making enzyme converts it back to fat on the next cycle.
Regulation is the key.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

  • Administrator
  • Bot God
  • *****
  • Posts: 7718
    • View Profile
Enzyme regulation
« Reply #3 on: March 18, 2005, 11:22:14 AM »
Then what we have is really two systems:

1. Digesting foreign materials.

2. Regulating internal costruction and destruction of stuff.

Complicated complicated...

Offline shvarz

  • Moderator
  • Bot God
  • *****
  • Posts: 1341
    • View Profile
Enzyme regulation
« Reply #4 on: March 18, 2005, 12:28:10 PM »
I think I came up with a way!

All different compounds have numbers assigned to them.  So bots can reference them directly if they want to.  But I'll use letters for now, it is easier.

Say we have a metabolic chain:

A>2B>2C>36D

where A is glucose, B is pyruvate, C is AcCoA and D is energy
I assume that we have enzyme system in place and our bot has all enzymes necessary for this chain (if there is no enzyme, then there is no chain, nothing works).

Say a bot needs energy ASAP.  The best way to do that is

cond
3000 nrg >
start
A
break
B
break
C
break
stop

break commands are applied sequencially, all in one cycle
This gene takes 1 glucose and in one cycle converts it to 36 energy points.  No B and C are found in the system at the end of the cycle.
This is a very smart bot.  

What if you don't want to bother and just want to make a stupid bot that is still able to use glucose?

you just say

cond 3000 nrg >
start
A
break
stop

The program breaks A into two B (in one cycle).  The rest happens behind the scenes.
Next cycle the program sees 2 B, it sends one up the chain (making 0.5 of A) and one down (making 1 of C).
Next cycle the program sees 1 C, it sends half of it up the chain (making 0.5 of B) and half down the chain (making 9 energy).

So stupid bot still can break glucose, but it takes 3 cycles instead of 1 and it gets only quarter of the energy.

This is just a general idea, the specifics can be worked out later.  But it should work!  And it will be backwords comaptible once the fat/carb/protein is set up.  And it is very open - we can introduce as many steps as we want and old bots would still function (just not as well).  

 :boing: I am a genious!  :boing:
 :clap:  :clap:  :clap:
« Last Edit: March 18, 2005, 12:29:27 PM by shvarz »
"Never underestimate the power of stupid things in big numbers" - Serious Sam