pene

The pen- words split into TWO Latin sources that happen to look alike. (1) paene = 'almost, nearly' gives peninsula ('almost an island'), penumbra ('almost a shadow'), and penultimate ('almost the last'). (2) penitus = 'deep within' and penetrare = 'to put or pass within' give penetrate, penetration, penetrating. The two meet at the idea of being 'on the edge of / inside' something, which is why they are taught together — but they are not the same Latin word.