Protocol’s; What are they

I have taken TCP\IP as my MCSE elective, and read
the Sybex’s CCNA(Cisco Certified Network Associate), and researched many online RFC’s and followed links that have been provided by Tech Republic, and still would like to get my hand on a protocol!What are they really; C+ scripts, software drivers? As a Net. Admin., I really need a “visual” in order to lockdown a Domain. Thanks