Medical Terminology

This post is taking a little bit away from the very serious talk about anatomy and physiology, but after everything I am an English person through and through. We must learn about the medical terminology and all the vocabulary that we learn really, really bothers me.
The first prefix that we learned was "a-" which means "not." This is used in words like asymmetrical, which means not symmetrical. My problem lies with the inconsistency in such prefixes. "A-" is a prefix for a lot of words:

• Amazing
• Abomination
• Align
• Attire

to name a few. My problem is that these words have absolutely nothing to do with the word "not." For example, amazing should mean not mazing, but it simply means terrific. Abomination should mean not a bomination, but what is an abomination. Ughhhhh. This drives the English side of me crazy! But now my English rant is over.