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I a new to the Chinese language and something that really confused me is that in some circumstances 呢 and 吗 could be used interchangeably, but in others they cannot. For example you cannot say 你吗？ but you could say 你呢？ You can say 你是同学吗？ and 你是同学呢?. Why are the two character interchangeable in one scenario but not the other? An explanation would be great, thank you!
(please tell me if I using the question feature wrong for the site and I will improve my question)
The usages of 吗 and 呢 are quite distinctive.
你吗？ VS 你呢？
你吗？ means "is that you?"
你呢？ means "how about you?"
Both 你是同学吗？ and 你是同学呢? are not quite natural. They could be: 你是我的同学吗？（are you my classmate?） and 你的同学呢？(how about your classmate?). If there isn't any context, 你的同学呢？ can mean 你的同学在哪？（where is your classmate?）.
Typically, the particle 吗 just forms a yes-or-no question, while 呢 requires you to reply with the actual content that has been inquired. See below examples:
A: 你去上学吗？(are you going to school?) B: 是的（yes）
A: 你干什么呢？(what are you doing?) B: 我玩游戏呢（I'm playing a game.）
吗 and 呢 are not interchangeable.
你是同学 means: "you are a classmate"
你是同学吗？ means: "are you a classmate? "
你同学 means: "your classmate"
你同学吗？ means: "is (he/she) your classmate?"
the final particle 吗 here denote 'interrogative' or 'inquisitive'. It short, it always turns a sentence into question form
~
你同学(呢)? depend on context, it can mean: 1. "(where) is your classmate?" or 2. "(how about) your classmate?"
the final particle 呢 here denote "alternative questions, affirmative negative questions (as stated in user60651's comment).
你是同学呢! is a different thing. The final particle 呢 in this sentence serve no interrogative function. Which mean it doesn't turn "你是同学" into a question. It serves to emphasize the sentence itself and/or the speaker's emotion (e.g. annoyed, determine) with the tone itself
When using the pause in a sentence, point out the topic.So "呢" and "吗"can be used interchangeably。 For example:“如今吗，可比往年强多了。”or“如今呢，可比往年强多了。”
