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When one computer1 connects to computer2, the first thing it has to do is contact computer2 and tell it who it is and that it wants to connect. Computer2 then must decide to accept (or deny or ignore) the connection and then tell Computer1 that the connection is accepted.
The protocol is just the series of technical rules that this basic process must follow. For example, when a tcp connection is initiated by compter1 the protocol is to send a SYN packet to a specific port on Computer2. Computer2 then, if accepting the connection, sends an ACK packet back to Computer1. From that point on the tcp connection is considered open and all future packets will have both the SYN and ACK bits until the connection is closed.
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