I just woke up, and the bottom of my throat is burning. What could it be?

GERD. One possibility is gastro-esophageal reflux.(gerd) this entity is extremely common and is the result of reflux of acid from the stomach up the esophagus to the throat and causes burning. There are many otc drugs that can reduce the symptoms. But the best advice is to consult a GI specialist for a specific diagnosis.