They were bred for obedience.
And they must obey the one that gave the order, Mr. Palpatine. So you see, they didn't actually switch sides.
In the event of Jedi officers acting against the interests of the Republic, and after receiving specific orders verified as coming directly from the Supreme Commander (Chancellor), GAR [Grand Army of the Republic] commanders will remove those officers by lethal force, and command of the GAR will revert to the Supreme Commander (Chancellor) until a new command structure is established.
It was his plan all along, make a fake war between the droid army and the clone army (in fact, create the clone army due to the fake threat from the droid army), to divert attention, make the Jedi busy, and eliminate them in that one swift blow.
See here for more detailed information
Utilizing the attack by Mace Windu as a pretext, Palpatine issues Order 66, a pre-arranged military command ordering all Clone Troopers to execute their Jedi commanders in the event that the Jedi "betray" the Republic. Darth Vader leads the raid on the Jedi Temple with the 501st Clone Trooper Legion and kills all the Jedi in the Temple, including Jedi younglings living in the Temple.
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