A capsule is a very small container that closes tightly. Many medicines come in capsules that can be easily swallowed.
Certain brands of laundry or dishwasher soap can be bought in capsule form, and you might hide a secret note or special mementos in a time capsule. A biologist probably thinks of a capsule as an anatomical structure that encloses an organ. This, in fact, is the word's earliest meaning — in French, it's a "membranous sac," from the Latin capsula, "small box or chest."