How cells represent their environment

This book was recommended to me: "An Introduction to Systems Biology" by Uri Alon. I have just started on it.

I like this idea from it: think of each transcription factor (TF) as a variable. The cell represents its environment (both external and internal) by means of these variables.

Background:

• A transcription factor is a protein that is either active or inactive. Some aspect of the environment will cause a molecule to be either active or inactive, e.g. a small molecule may bind to the TF, and cause the TF to undergo a conformational change. When active, it binds to a specific site on the DNA and causes transcription, which results in the production of a specific protein, which performs a function appropriate for the level of the environment variable.

The value of the variable that represents the environment is the proportion of TF in the active state.

Thus, the millions of real environment variables are projected onto a smaller parameter space: the number of distinct TFs.

E.Coli has 300 TFs, according to Alon. That's quite a small parameter space compared to the physical environment.

One comment: the kinetics of the TFs and the chemical species with which they interact is modulated by the physical environment, so the above view is simplified.