“Sir” in English is a form of personal address, more respectful than “hey, what’s-your-name”. Being knighted by a monarch also conveys it as an honorific (mistakenly called a “prefix” to a name) like Mister, Miss, Doctor… eg. “Sir James”
In the military, it’s also a form of address to a commissioned officer but when asked as a question “Sir?” it is a respectful way of expressing confusion about an order given by or statement made by a superior officer or it can be a subtle but nominally respectful way of disagreement with a superior officer through feigning confusion, sort of an implied “Sir, have you really thought this through?”