A protocol engine (PE) for processing data within a protocol stack in a wireless transmit/receive unit (WTRU) is disclosed. The protocol stack executes decision and control operations. The data processing and re-formatting which was performed in a conventional protocol stack is removed from the protocol stack and performed by the PE. The protocol stack issues a control word for processing data and the PE processes the data based on the control word. Preferably, the WTRU includes a shared memory and a second memory. The shared memory is used as a data block place holder to transfer the data amongst processing entities. For transmit processing, the PE retrieves source data from the second memory and processes the data while moving the data to the shared memory based on the control word. For receive processing, the PE retrieves received data from the shared memory and processes it while moving the data to the second memory.