A large number of second messenger molecules have been characterized, including cyclic nucleotides (nucleotide) (e.g., cyclic adenosine monophosphate, or cAMP, and cyclic guanosine monophosphate, or cGMP), ions (ion) (e.g., Ca²⁺), phospholipid-derived molecules (e.g., inositol triphosphate), and even a gas, nitric oxide (NO). The calcium ion Ca²⁺ has a critical role in the rapid responses of neurons (neuron) and muscle cells. At rest, cells maintain a low concentration of Ca²⁺ in the cytoplasm, expending energy to pump these ions out of the cell. When activated, neurons and muscle cells rapidly increase their cytoplasmic Ca²⁺ concentration by opening channels in the cell membrane (cell), which allow Ca²⁺ ions outside the cell to enter rapidly.

The cyclic nucleotide cAMP is synthesized by adenylyl cyclase enzymes (enzyme), which are downstream of heterotrimeric G-proteins ( guanine nucleotide binding proteins) and receptors. For example, when epinephrine (epinephrine and norepinephrine) binds to beta-adrenergic receptors in cell membranes, G-protein activation stimulates cAMP synthesis by adenylyl cyclase. The newly synthesized cAMP is then able to act as a second messenger, rapidly propagating the epinephrine signal to the appropriate molecules in the cell. This stimulatory signaling pathway leads to the production of effects such as increasing rate and force of contraction of the heart that are characteristic of epinephrine. caffeine also enhances the action of cAMP by inhibiting the enzyme phosphodiesterase, which degrades cAMP; the enhancement of cAMP activity contributes to the general stimulatory action of caffeine. As a gas, nitric oxide (NO) is distinct among second messengers in being able to diffuse across cell membranes, which allows signal information to cross into neighbouring cells.