The physiological fight/flight response to an acute stimulus/stimuli is caused primarily by adrenaline (and noradrenaline), which is both a hormone acting on the body via the blood stream and a neurotransmitter.
In longer term stress adaptation and response (e.g. final weeks of semester, living in a violent/dangerous neighbourhood, military training) the primary agent is cortisol (a hormone). This hormone is also primarily responsible for the long term effects of stress (e.g. immune suppression).
Im confused the text im using doesnt go into much detail about how the body recognises a stressor activating the hpa axis ect..is there a particular neurotransmitter that causes a reaction from the hypothalmus to activate the hpa axis? i know that adrenaline is the end product ect...
As per LovesPhysics, there are believed to be multiple inputs that start the process, generally these are from higher cortical and midbrain areas - particularly primary sensory cortices, limbic and hippocampus. Without going into the details, its a combination of inhibitory and excitatory inputs to the hypothalamus that trigger it.
It has been observed in some cases that the pupils and blood vessels begin responding to threats even before conscious awareness of the threat - an amygdala-to-limbic associated response.