how does the constitution limit the power of the national government and protect the rights of the individual

Well, unfortunately, it kinda doesn't.

The answer your history teacher is looking for isn't the one I'm going to give you.

The national government can do many things via loopholes in the Constitution.

One example: A President can call a National Emergency, thereby placing us under Martial Law. We would have no rights, thus allowing them to take over, if they so wish. Congress isn't even really a factor. : /

So, yeah, sorry.