Read permission for a
directory means that you can list files in it, write permission means that you can add or delete files, and execute permission means that you can search it
i.e., change directory to it or open any file inside it.
To change file permissions on a whole directory tree, use the -R (recursive) option to chmod. For example, to prevent anyone else from accessing anything in your home directory:
chmod -R go-rwx ~
(the "go-rwx" means to subtract read, write and execute permissions for group and others).