You have 
apples left.
You have 5 whole apples, you took one whole apple out, which equals 4 whole apples left. Then with the whole apple you took out, you ate
of it.
Jack ate of an apple in 5 apples.
If you say that Jack ate of 3 apples, then he ate 
apples. So there isn't any difference when he ate of an apple.
You have 5 whole apples, you took one whole apple out, which equals 4 whole apples left. Then with the whole apple you took out, you ate
Jack ate
If you say that Jack ate