Let's figure our the colours first.
The list I had posted was:
Glucose - White
Amino Acids - Pinkish Red
Proteins - Darkish Red
Calcium - Cream / Beige (If included)
Hydrogen Sulfide - Light Yellow
Oxygen - Light Blue
Carbon Dioxide - Dark Blue
Ammonia - Light Grey
And the one from the GDD is:
Agents - Variable
Amino acids - Purple
Ammonia - Yellow
ATP - N/A
Calcium - White
Calcium carbonate - Cream
Carbon dioxide - Red
Glucose - Green
Hydrogen - Orange
Hydrogen cyanide - Brown
Lactic acid - Maroon
Nitrogen - Dark blue
Protein - Pink
Oxygen - Light blue
Water - N/A
I assume a lot of the colours on the GDD are so because that's how they currently appear in-game.
So I think from this we can agree that water and ATP aren't relevant, and agents are variable. This leaves the part of the list to decide.
Glucose - I suggest white, because glucose is sugar and sugar is white.
Amino Acids + Proteins - I suggest pinkish red and darkish red respectively, because muscle/meat is largely protein. Whatever colour we decide, I think it would be better if we made amino acids and proteins two different shades of the same colour, because amino acids are just the constituents of proteins.
Calcium / Calcium Carbonate - I suggest cream or beige. If we add both compounds, I suggest the same as above that both be different shades of the same colour (like light beige and medium beige, with different textures).
Hydrogen Sulfide - Yellow, because it has sulfur.
Oxygen + Carbon Dioxide - Carbon dioxide is listed as red in the GDD, but I think that doesn't make sense, and I much prefer TheCreator's idea of having oxygen and carbon dioxide exist in large and dilute clouds swirling through the environment, with oxygen being light blue and carbon dioxide being dark blue.
Ammonia - It says yellow in the GDD, but hydrogen sulfide makes much more sense as yellow, and ammonia is colourless, so we could make it light grey.
Hydrogen - Will this really need to exist in clouds?
Nitrogen - Will this really need to exist in clouds?
Hydrogen Cyanide - Although this is typically colourless, since Ammonia is light grey and Glucose is white we could make this light brown, light purple, or light orange?
Lactic Acid - White and cream and beige are taken, so we could make this light brown or light orange?