Yes they do. To understand transubstantiation you need to understand the philosophy behind it. Aristotle made a distinction between the substance of a thing, the core, essential properties that "form" it, and the accidental properties which will differ between any particular instance of the thing. Dogs can be quite different, but they share a fundamental dogness.

So using this way of thinking the body and bread are one in substance, but differ in accidental properties. The bread still looks and tastes like bread but an indiscernible change has occurred in its substance. Thomas says:

> I answer that, It is evident to sense that all the accidents of the bread and wine remain after the consecration. And this is reasonably done by Divine providence. First of all, because it is not customary, but horrible, for men to eat human flesh, and to drink blood. And therefore Christ's flesh and blood are set before us to be partaken of under the species of those things which are the more commonly used by men, namely, bread and wine. Secondly, lest this sacrament might be derided by unbelievers, if we were to eat our Lord under His own species. Thirdly, that while we receive our Lord's body and blood invisibly, this may redound to the merit of faith.

* caveat: I'm neither a philosopher nor a believer in transubstantiation