On page 26 of the DMG it describes knowledge checks as giving the players particular information, such as a history check to identify a region. But wouldn't a skill check be the same? Or does the skill check take place when needed and the knowledge check used at the start of an adventure to discover what encounters they might face?
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A knowledge check is a kind of skill check.
Skill checks involving answering the question "what do I know about X" or "do I know about X" are knowledge checks, and there are some specific rules governing knowledge checks that do not apply to other skill checks (such as using athletics to climb a wall)
One distinction I'd make comes to retrying the skill. If you're trying to climb up the side of a building, you can keep trying all day. With knowledge checks you either know something or you don't. You roll the die to see if your character has heard that trolls regenerate. If you fail the check, you don't get to try again (although I'd make an exception if the PC was in a library and wanted to treat knowledge as a research check). I don't believe there's a hard and fast rule for this in any book, but part of the GM's job is applying common sense so the game world makes sense.