OK, my knowledge is a little rusty in this regard, as it's been about a decade since I dabbled in all this, but - what do you mean GENERATE timer interrupts? Inside your computer is a clock and an 8259A chip, which generates interrupts at a few million times a second, if memory serves me correctly (18.2 is the figure that keeps springing to my mind). When that happens, whatever is running at the moment stops and the CPU goes off to the handler for that interrupt. In a Linux system, I'd guess, that that interrupt is serviced by the scheduler inside the kernel, which handles multitasking, ie. when it gets it, it jumps off to do another task.
You can't ENTER Protected Mode in Linux, it already IS in Protected Mode - it switches to it when booting, it's one of the first things it does. That's why one process can't interfere with another *inside* the OS. You can't write a program to either enter or leave P-Mode INSIDE Linux, otherwise one errant program could crash the system.
If you're getting started learning Assembly Language programming and the lowest level of things, welcome!
Wish you the best of luck.