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System calls are an abstraction to simplify programming. For an example, lets assume that an application wants to save a file. It would be a terrible waste of effort to do it manually for each application, for each file system and each storage device, and it doesn't really care. The operating system knows how to do all that stuff, so the application generates a system call. It basically tells the operating system: "here's a bunch of data, save it to a file called myfile". The operating system hides all the messy details, and the application doesn't have to concern itself with them. There are all kinds of system calls, anywhere from getting the current time to playing noises on your speakers.
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