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Most calcium carbonate deposits are made up of the skeletal remains of marine plants and animals that have fallen to sediment on the bottom of shallow seas after their death. If the conditions are right, these sediments can build up over geological time to form extremely thick layers.
Part 1: Calcium carbonate does come from the shell, exoskeletons, and skeletons of dead animals, usually those that died, deposited in water, and settled at the bottom of an ocean or a basin. Water does amazing things with ionically bonded compounds, and over millions of years dissolves much of this calcium carbonate.