How do you know when to use subjunctive versus indicative?

You use indicative when your statement is concrete or facts. You use subjunctive when you're statement is not a fact, such as wishes or possibilities. For subjunctive, think of the "subject", it is used on how the subject feels or believes; it is not a hard fact.

mutagenesis of myoglobin, His(E7) to glycine, shows a reduction dissociation rate constant. His(E7) is a residue found in the active site and when myoglobin is exposed to carbon monooxide it creates a hydrogen bond to the Histidine residue. Would expect an increase or decrease in the glycine mutated myoglobin for the carbon monooxide reaction?

Glycine does not have a side chain that contains a hydroxide functional group. There would be no ability for carbon monooxide to hydrogen bond the glycine. An increase in the dissociation rate constant would be expected as dissociation would be more favorable without the electrostatic effect to hold carbon monooxide in the active site.

The lac operon, is a series of genes regulated by one promoter and a common repressor. It transcribes for lactose metabolizing proteins. Ligands can bind the repressor to activate its binding activity to the promoter in order to inhibit transcription of the genes. If the ligand is bound and there transcription of the genes. What sort of physiological signal (metabolite) is available to the model to activate this operon? What kind of mechanism to activate the lac operon would this be considered?

In order to activate the lac operon there has to be availability of lactose as a physiological signal to transduce into activation of the lac operon. The type of mechanism to activate the lac operon would be signal transduction.