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Finite state machine (FSM) theory has great potentialities in understanding key concepts and analyzing molecular biological systems, especially in the process of gene expression. Based on the previous research work, this paper extends the study on the control problems in metabolism and gene mutation with FSM. The goal is to interpret how to apply control technologies to process of metabolism, and how to eliminate the effects to secondary structures of protein caused by gene mutation. It is hoped that the proposed model-based analysis will provide an exploration of new interdisciplinary theories intersected by information science, control theory, and the Molecular Biology.