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.
 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.