MySQL's atomic and thread safe nature

I understood that MySQL is thread-safe, which means that even though two threads trying to access the DB, it will be safe since there is a lock mechanism. But I like to ask one question, which you might find as basic. Let's say we have some really bad SQL queries. It will take 15 seconds to run and finish. If some thread runs this query, does it means that other request should wait for 15 seconds no matter what? Is this is the main reason we always optimise our SQL query?