PHP comes standard with many functions and constructs. There are also functions that require specific PHP extensions compiled in otherwise you'll get fatal "undefined function" errors. For example, to use image functions such as imagecreatetruecolor(), you'll need your PHP compiled with GD support. Or, to use mysql_connect() you'll need your PHP compiled in with MySQL support. There are many core functions that are included in every version of PHP like the string and variable functions. A call to phpinfo() or get_loaded_extensions() will show you which extensions are loaded into your PHP. Also note that many extensions are enabled by default and that the PHP manual is split up by extension. See the configuration, installation, and individual extension chapters, for information on how to setup your PHP.
Reading and understanding a function's prototype is explained within the manual section titled how to read a function definition. It's important to realize what a function returns or if a function works directly on a passed in value. For example, str_replace() will return the modified string while usort() works on the actual passed in variable itself. Each manual page also has specific information for each function like information on function parameters, behavior changes, return values for both success and failure, and availability information. Knowing these important (yet often subtle) differences is crucial for writing correct PHP code.
See also function_exists(), the function reference, get_extension_funcs(), and dl().