Simple as it is :
Ich esse ja einen Apfel! ( normally it would be a suprised reaction but you would not use this because such a situation is really really rare)
Ich esse aber einen Apfel! ( if someone asks you why you don't eat something else and you answer " But i am eating an apple!" . For example : You should eat a banana, because it is more healthy! - > But i am eating an apple! (right now) )
Both cases are really rare in a conversation. You can make the sentence sound different if you put "ja" or "aber" in a specific sentence. You will learn that with time in conversations.