Parts in the body that use or are affected by acetylcholine are referred to as cholinergic. Acetylcholine is the neurotransmitter used at the neuromuscular junction —in other words, it is the chemical that motor neurons of the nervous system release in order to activate muscles.This property means that drugs that affect cholinergic systems can have very dangerous effects ranging from paralysis to convulsions.cetylcholine has functions both in the peripheral nervous system (PNS) and in the central nervous system (CNS) as a neuromodulator. In the peripheral nervous system, acetylcholine activates muscles, and is a major neurotransmitter in the autonomic nervous system.