Yes, they are entirely different disorders. Although they have overlapping symptoms and can be pretty hard to distinguish in certain individuals. Borderline is a personality disorder. A personality disorder is (in sort of a simple way of looking at it), is a pattern of thoughts, emotions and behaviors that is considered to be 'abnormal'. So basically, the person's personality is considered to be the problem. Bipolar disorder is a mood disorder, it's primary problem is the mood of a person, and its very much a physical problem (i.e. chemicals in the brain arent behaving the way they're supposed to), and it really needs medication to stabilize it.
Borderline personality disorder is a personality disorder marked by a very disorganized personality. They generally have this love/hate relationship with people, their mood switches frequently, they can be very manipulative, they are known to engage in self harm and a lot of parasuicidal behavior (i.e. suicidal gestures where they had no intention of dying), they can be very dramatic, and have difficulty with impulse control. They tend to come off as a little crazy. That being said, they do feel these emotions and events that strongly. So they do feel like things are the end of the world. And so, it's not like they're acting in this way to be annoying. They really are in that much pain. It's a pretty severe diagnosis. Something you want more than one psychologist to confirm. You should look up the wikipedia page, it does a pretty good job. Also, if you could tell us what exactly you wanted to know about the disorder, it may help get a more specific answer? I am not entirely sure what the differential diagnosis between bipolar and borderline is (it's a very complicated thing because of the high degree of overlap), but I am guessing it would involve the prominence of the moods in the bipolar and not in the borderline.
Read through that and it'll tell you everything you want to know.