The real answer is that we (scientists) don't fully understand how this happens yet. But, the current thinking on it, and that is supported by the studies that have been done so far, is that those feelings you described are all psychological stressors. When someone experiences them, their body's stress response systems are activated. These include things like an increase in cortisol, a hormone produced by the adrenal gland, increased heart rate, etc. Basically, many of the same systems that would be activated for the classic "flight or fight" response. However, rather than the perceived danger coming, and quickly being taken care of, either by fighting an attacker or running away, with these other psychological stressors, "fight or flight" doesn't work and the stress sticks around chronically (long term). Some of the signals for stress remain, but the body doesn't respond in the same way when they stick around for a long time. The best example is that of cortisol. Even though the stress stays, cortisol concentrations decrease again in long-term stress and don't stay elevated. It just occurred to me that I don't know what happens to cortisol when a chronic stressor is finally removed (or goes away). [If anyone knows of a study where they've followed cortisol, or corticosterone (the rodent version of the hormone), concentrations in an animal after a chronic stressor was removed, please post a reference. I'd be curious to see it.]
Anyway, the main focus at this point has been on the interaction of cortisol, with components of the immune system. That's the point at which my knowledge ends on this. I know from the endocrinology perspective that such studies exist, but I'm not sure what detail they've reached on the immunology end of things yet.
The reason I'm curious about what happens to cortisol when the stressor is removed is that on the occassions when I've been under a lot of stress (important deadlines with a lot of work to get done for them), it seems I get sick right after the stress has passed, not while the stress is still present. Of course, that's on the immune side of things, and there are other health problems that can result from chronic stress, such as high blood pressure, heart attacks, stomach upset/aggravation of ulcers that happen during the stress. So, I guess it also depends on what you meant by sickness.
This is a growing field of research. Here is the website for the Psychoneuroimmunology Research Society, which includes links to their journal Brain, Behavior and Immunity that focuses on the type of research questions that are aimed at answering your question. http://www.pnirs.org/
I have been doing some research into the effects of cortisol and the links it has to smoking. In the reasearch I have completed it appears that not only is excessive cortisol released when stressed but it can also have the same flight or fight response to inflammation. When certain parts of the body such as the intestinal tract become inflamed it creates a response. The 'All Clear' hormone appears to be DHEA. When the stressor has gone or the adrenal gland supresses the release of cortisol and increases the flow of DHEA as a way of counteracted the long term effects of cortisol.
With regards to smoking, becuase excessive cortisol is produced due to the inflammation caused by inhaling large quanities of hot smoke. It triggers the fight or flight response. However there is no visible reason to go into survival mode. Like you said when you know the stressor has passed you can then start to calm down, However with smoking you do not know why you feel anxious. You coul run to the end of the earth and you would net get away from it. in contrast if you were afraid of dogs and saw a large one walking towards you you would feel the surge of adrenelin and cortisol pump into your bloodstream and prepare you to stand and fight or runa way. If you were to go behind a door, making a barrier between you and the dog the DHEA would be released as the all clear signal.
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