The hypothalamus - the brain's "command and control center" - converts thoughts and emotions into hundreds of different types of ligands, specifically neuropeptides. Emotions elicited for example by a perceived threat are POWERFUL, and initiate the release of specific chemicals in messenger molecules that, as I said earlier, adhere to certain parts of the cell receptor and affect cell function. What the hypothalamus "believes to be true" determines what the "manufactures" produces, and the chemical result is given. Neuropeptides affect our chemistry and our chemistry affects our biology.
In a nutshell:
EMOTIONS TRIGGER CELLULAR ACTIVITY.