I had a similar problem, although from running, not cycling. My runs don't last very long; as soon as my left knee complains, the run is over. I only started running recently, and I seem to be going farther and farther, so I probably just have to ease into those long distance runs.
I did some research, and found that there are numerous reasons you might have knee discomfort. You can't treat the problem until you know the root cause, and if you try you may make things worse. I saw my family doctor, and I advise you to do the same -- there's no substitute for seeing a real doctor to get some advice. I also plan on visiting a nearby sports medicine clinic when I get a chance.