In this work we consider a molecular communication system based on free diffusion of molecules from transmitter to receiver. These molecules act as message carriers with information encoded in either the concentration or number of molecules. These molecules propagate through the medium to reach the receiver, where they react with a receiver molecular circuit which is a set of chemical reactions, to produce the output molecules. The number of these output molecules over time t is the output signal of the system. In this work we use reversible conversion (RC) type receiver molecular circuit which can be viewed as a linearized form of ligand-receptor binding. We realize the molecular communication system as an interconnection between the diffusion only (upstream) and reaction only (downstream) systems. In this work first we quantify the effect of reaction rate constants on the system performance. By using singular perturbation we find that the communication performance of the system changes with the variations in the association constant r (which depends on reaction rate constants) of the receiver circuit. We find that although the gain and capacity of the system is improved with the increase in r, the noise increases as well which results in lower signal to noise ratio (SNR). To overcome this problem and improve the system performance in terms of SNR and capacity we introduce an intermediate system of reactions between the upstream and downstream systems which is referred as phosphorylation cycle. By carefully choosing the parameter values of the intermediate system we can reduce the effect of the association constant r on behaviour of system.