Throughout our science education, as students we have always wondered how genes are regulated in a given organism.
To better understand biological processes in organisms we can take a look at a biological circuit, a term borrowed from electrical engineering that illustrates the interconnections among proteins or genes (1). Circuits can describe connections needed to regulate a single gene or an entire genome. Through a circuit we can visualize important components and reactions that are otherwise difficult to perceive. In this short study the organism of Neurospora crassa will be farther analyzed.
For the first time, it is now possible to place a particular biological circuit like those describing carbon metabolism, transcription, cell cycle, or the biological clock in simple eukaryotes in a larger context, and to examine the coupling of these circuits (12). In this report, we look at a network of reactions for the regulation of the qa cluster . As understood, the qa cluster is composed of five genes and two regulatory genes, as seen in the biological circuit Figure 1. 1.
Three of the genes, qa-2, qa-3, and qa-4, in the cluster encode enzymes involved in the catabolism of quinic acid. One gene, qa-y, encodes a permease allowing quinic acid into the cell, and another gene, qa-x, encodes an unknown function. All seven genes in the cluster are transcriptionally activated by the product of qa-1F, and the activator is repressed by the product of qa-1S. The cluster is glucose- and sucrose-repressed.
If this is true then when qa-1F^p is turned off then nothing should be produced and also if abundant portions of qa-1S^p are present then PCA should be present in limited quantities. These simple experiments will allow students such as myself to gain a better understand of what is going on visually and not only in text. Although these experiments may seem obvious, biological circuits are hard to grasp when first looked at, they can be very overwhelming. Methods/Procedures: Once the figure of the qa-cluster circuit was presented all of the equations and variables that take place in the circuit are entered into a template. The template is then uploaded into KINSOLVER workspace.
The uploaded template is shown in Figure 1. 2. According to this template there are 37 variables and 43 reactions that take place in this particular circuit. First random numbers were entered in the parameters for the qa-1F^p variable then random numbers were entered in the parameters for the qa-1S^p variable. Once certain parameters were chosen, each time a PCA vs. Time graph was illustrated.
TrialQuantity of qa-1F^pQuantity of qa-1S^p10 jfix=00210031000TrialQuantity of qa-1F^pQuantity of qa-1S^p40 0501060100Results: The results are graphed and attached. Trial 1: Figure 1. 3Trial 2: Figure 1. 4Trial 3: Figure 1.
5Trial 4: Figure 1. 6Trial 5: Figure 1. 7Trial 6: Figure 1. 8Conclusions: From the graphs in the figures attached, it can clearly be seen that the qa-1F^p gene is an activator gene. This means when it it is turned off, all the other genes are turned off causing no PCA to be produced.
Only when this gene is activated will PCA be produced. If the gene were turned on it would then activate the qa-1F^0, qa-1S^0, qa-y^0, qa-3^0, qa-4^0, qa-2^0, and then finally the qa-x^0 gene. Once all these are activated they each take on their own reactions to create their own products. In our next set of graphs we see as we increase the qa-1S^p product this decreases the amount of PCA produced, which means this is a repressor.