There's no absolute on-screen canon answer to this. Some fans think replicators can make matter out of pure energy, while others believe that replicators work with raw (or recycled) matter stocks.

I prefer the latter theory, primarily because of the dramatic storytelling limits of not having access to literal alchemy, but also because it is supported by the description of the replicator system from the TNG technical manual (pp. 90-91):

7.6 REPLICATOR SYSTEMS

Instead of using a molecular imaging scanner to determine the patterns of the raw stock, however, a quantum geometry transformational matrix field is used to modify the matter stream to conform to a digitally stored molecular pattern matrix. The matter stream is then routed through a network of waveguide conduits that direct the signal to a replicator terminal at which the desired article is materialized within another phase transition chamber.

In order to minimize replicator power requirements, raw stock for food replicators is stored in the form of a sterilized organic particulate suspension that has been formulated to statistically require the least quantum manipulation to replicate most finished foodstuffs (See: 13.5).