Pain is generally an unpleasant feeling in response to an event that either damages or can potentially damage the body's tissues. There are four main steps in the process of feeling pain: transduction , transmission, perception , and modulation .  The nerve cells that detect pain have cell bodies located in the dorsal root ganglia and fibers that transmit these signals to the spinal cord.  The process of pain sensation starts when the pain-causing event triggers the endings of appropriate sensory nerve cells . This type of cell converts the event into an electrical signal by transduction. Several different types of nerve fibers carry out the transmission of the electrical signal from the transducing cell to the posterior horn of spinal cord , from there to the brain stem , and then from the brain stem to the various parts of the brain such as the thalamus and the limbic system . In the brain, the pain signals are processed and given context in the process of pain perception . Through modulation, the brain can modify the sending of further nerve impulses by decreasing or increasing the release of neurotransmitters . 
This is a well known problem, and it is related to nausea (see above). It can be caused by a variety of factors. Your body is craving food and you have not eaten all night so your tummy feels queasy. Your body has way more hormones coursing through it than normal and this can cause nausea. You are sensitive to aromas and foods, so your morning coffee may not agree with you. The usual breakfast you typically have may not settle well in your stomach during this time. One woman usually had a scone along with a coffee late’ for breakfast, but found that during pregnancy it made her feel sick. She changed to tea and toast and that worked well for her. Each woman is different and will have different foods that may or may not contribute to morning sickness.