- Gene expression and internal state are mutually dependent and influence each other in a variety of ways. Once again, the familiar pattern of reciprocal dependence has appeared. Crucially, however, while gene expression is influenced by the current internal state, a change in gene expression alters a future internal state. This is because of the delay between the initiation of transcription and the appearance of the protein that the gene encodes.
- The interplay between internal state and gene expression is often the basis of cellular homeostasis. A perturbation of the internal state induces a change in gene expression that counters the perturbation.
- In this situation the perturbation tends to be "serially overcorrected". In cells that outwardly appear unchanging, the internal state parameters tend to oscillate about median values rather than remaining fixed.
- Transcription factors are themselves gene products, and one transcription factor might influence the rate of transcription of several different genes. Therefore, the interplay between gene expression and internal state means that a cell can undergo progressive change.
- One type of progressive change is the cell cycle. During a succession of internal states the DNA is duplicated and, later, the cell divides into two identical daughter cells, each of which returns to the initial internal state of the cycle. In principle, this cycling continues indefinitely, doubling and redoubling the cell population. This is how single-celled eukaryotes normally reproduce.
- Another type of progressive change is differentiation. This is a linear sequence of internal states. It occurs in cells of multicellular organisms. In the terminally differentiated state, most of the cell's resources are concentrated on very high expression rates of very few genes. The products of these genes equip the cell for its specialist role in the body. Most other genes are switched off. This means, among other things, that terminally differentiated cells can no longer divide.
- A third type of progressive change is apoptosis. Again, this is a linear sequence of internal states, but it leads to the death of the cell. The remnants of the dead cell are packaged in small vesicles; these are engulfed by other cells, digested by their lysosomes and recycled. Apoptosis is necessary for removing superfluous cells, for instance during development, and for destroying infected or otherwise damaged cells.
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