  A universal feature of the biochemistry of any living system is that all the
molecules and catalysts that are required for reactions of the system can be
built up from an available food source by repeated application of reactions
from within that system. RAF (reflexively autocatalytic and food-generated)
theory provides a formal way to study such processes. Beginning with Kauffman's
notion of "collectively autocatalytic sets", this theory has been further
developed over the last decade with the discovery of efficient algorithms and
new mathematical analysis. In this paper, we study how the behaviour of a
simple binary polymer model can be extended to models where the pattern of
catalysis more precisely reflects the ligation and cleavage reactions involved.
We find that certain properties of these models are similar to, and can be
accurately predicted from, the simple binary polymer model; however, other
properties lead to slightly different estimates. We also establish a number of
new results concerning the structure of RAFs in these systems.
