Ok so some more thoughts:
- I don’t think we should include water in our reactions – overall, biochemical reactions will generally not appreciably change the amount of water in the system, compared to the amount of water required for biochemistry as a solvent or for myriad other reasons.
- On that note, trying to balance water will only lead to tears.
- If we aren’t balancing water, then we really shouldn’t be trying to balance everything at all – we should just make sure that the change in free energy in each reaction makes sense, and that carbon, nitrogen, sulfur, etc (everything except oxygens lost/gained due to water, and hydrogen) are balanced, in most cases. Anything more and we risk creating reactions that don’t make biochemical sense.
- Hydrogen is another thing that we should not be trying to balance freely. Protons are important parts of a lot of biochemical reactions, yes, but their purpose depends greatly on a bunch of other factors – for example, what they are bound to (or whether they’re simply free), etc. I simply folded the protons involved in catabolism (eg, those bound to NAD+, or FAD+2) into their ATP-equivalent amounts of energy, for example.
- The exact amount of ATP involved in respiration, and Fatty Acid metabolism is subject to some tweaking – which I think is best done by having a range of possible ATP yields/efficiencies that can get better with evolution up to a certain point.
- I think, if we’re going to add Sulfur, and Phosphate, that it might make sense to add, say, iron, and nitrate, the first as another source of energy for chemosynthesizers and the second for a better nitrogen cycle. Luckily, as with the sulfur cycle, the CPA system still works even if those are not taken into account.
- As for sunlight, I’m not sure what the best way to calculate solar energy for photosynthesis would be, but I don’t think it would work to simply have a ‘sunlight’ reactant that scales the photosynthetic reaction. After all, if the CPA system works to maintain certain levels of every compound, then it won’t be easy to keep photosynthesis rate scale properly with sunlight.
Processes:
Photosynthesis: 6CO2 -> Glucose + 6O2
Glycolysis: 1 Glucose -> 2 Pyruvate + 2 ATP
Respiration: 1 Pyruvate + 3 Oxygen -> 3 CO2 + 18 ATP
Protein Synthesis: 1 Amino Acid + 4 ATP -> 1 protein
Protein Digestion: 1 Protein -> 1 Amino Acid
Amino Acid Synthesis: 1 Pyruvate + 3 ATP + 1 Ammonia -> 1 Amino Acid
Amino Acid Digestion: 1 Amino Acid -> 2 ATP + 1 Pyruvate + 1 Ammonia
Fatty Acid Synthesis: 9 Pyruvate + 56 ATP -> 1 Fatty Acid + 9 CO2
Fatty Acid Digestion: 1 Fatty Acid -> 6 Pyruvate + 45 ATP
Nucleic Acid Synthesis: 1 glucose + 8 ATP + 2 Amino Acid -> 1 Nucleotide
Nucleic Acid Digestion: 1 Nucleic Acid -> ???
Sulfur Respiration: 1 Pyruvate + 3 Sulfur -> 3 CO2 + 3 H2S + 8ATP
Nitrogen Fixation: 1 N2 + 16 ATP -> 2 NH3
If we don’t include nitrate:
Denitrification: 2 NH3 -> N2 + 10 ATP (some bacteria convert NH3 to NO3/NO2 aerobically, producing some energy, and others use NO2/NO3 as electron acceptors in anaerobic electron transport chains – adding them up we get about 8-10 ATP being recovered)
In the interest of keeping this discussion moving I’ve forked the colours discussion out so both can continue independently.