At the end of chapter 7 we said that although protein breakdown is a controllable process, it is probably less important than protein synthesis (gene expression) for regulating the internal state. We can now offer a plausible justification for this remark. Compared to transcription, protein breakdown is usually rapid. To inactivate a protein and to prepare it for disposal is usually the work of seconds rather than minutes. Therefore, while gene expression is best regarded as programming for the next internal state, protein breakdown is best regarded as an aspect of the current internal state.
Nevertheless there is a connection between gene expression and protein breakdown. The destruction and removal of a transcription factor or repressor (not to mention its messenger RNA) can contribute significantly to the pattern of gene expression. Faster breakdown means less of the protein. Every protein molecule has a finite lifespan, beginning with the initiation of transcription of the gene and ending with inactivation and dissolution, so its concentration in the cell can be altered by changing either the production rate or the removal rate. Protein breakdown receives little attention from present-day molecular biologists. Its true importance will only become clear after more research.
Some transcription factors have long lifespans but are only briefly active. Most of the time they are bound to immobile structures in the cytoplasm. In order to reach the nucleus and bind to their enhancer sequences, they have to be liberated from these restraints. Only certain particular internal-state conditions allow this to happen. So it is only when these conditions are met that the transcription factors function, switching on the genes to which they are related.
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