Scientific knowledge systems function as effective and specialized apparatus for formulating, analyzing and solving scientific problems. In science, problems become internal parts of the knowledge systems; thus they acquire new forms and properties in comparison with common-sense problems. Definite theoretical structures connected with problems and questions appear in the theory. Among them are erotetic expressions and languages, calculi and algebras of problems. On the basis of the structure-nominative reconstruction of a theory, the unified treatment of these structures is given. Methods of the theory of named sets are used in the logical analysis of problems and their systems. As a consequence a new formalized model of the problem part of theory is constructed.