The files themselves are not permissions. They
have permissions. The permissions associated with a file determine who can do what with that file. Without getting too detailed, there are three kinds of users (the owner of the file, other users in the same group as the owner, and everybody else) and three kinds of permissions (reading, writing and executing). For example, a script file that belongs to an administrative user might allow the owner to read, write and execute the file, and allow other administrative users to read it and execute it, but not write to it, and allow all other users to execute it but not read it or write to it. This means that only the person who wrote the script can change it. Other administrative users can use it, and they can read it to see how it works, but they can't change it; however, they can copy it and modify their own copy as they please. Other, non-administrative users are not even allowed to read the script, because it may contain information, such as passwords, that ordinary users should not be privy to.
If you don't like the term "permissions," POSIX calls them access control lists, or ACLs, and OS X is POSIX-compliant.
See
http://en.wikipedia.org/wiki/Filesystempermissions if you're interested in learning more about this.