Question

In genes that can splice alternatively, how does mRNA know which exons are necessary and which exons are optional?

Answer 1

The spliceosome not mRNA determines how the mRNA is spliced. The conformation and composition of the spliceosome is dynamic, giving it specificity during alternative splicing. As far as I know, the dynamic changes of the spliceosome is still being figured out as it will be different for every gene, cell type, situation, etc. I may be wrong, though. Look up spliceosome and snRNAs and you should get a better idea of what is going on during alternative splicing.