10.0: Introduction

In which we consider the signals, receptors, and molecular machinery that control how proteins come to be where they are needed within cells and organisms, and how cells interact with one another through various signaling systems.

As noted earlier, each cell is a bounded non-equilibrium system. The plasma membrane forms an unambiguous boundary between the rest of the universe and the cell. In prokaryotes, the cell is typically surrounded by a cell wall, a semi-rigid structure that protects the cell from osmotic effects among other things. As discussed, the cell’s metabolic activities occur primarily within the space defined by its cell membrane, the cytoplasm.^[385] A polypeptide synthesized within the cytoplasm has a number of places it might end up, and like other biological processes these outcomes are controlled by signals and receptors. In a prokaryote (←), a newly synthesized polypeptide can remain in the cytoplasm where it can interact with the organism’s genetic material, a circular DNA molecule also located in the cytoplasm. Alternatively, a newly synthesized polypeptide can end up embedded within the plasma membrane (an integral membrane protein) or it can pass through the membrane and be secreted. Secreted proteins (in a prokaryote) can remain within the periplasmic space, can become part of the cell wall, or can pass through the cell wall and into the external environment.
Eukaryotic cells (←) are more topologically complex and contain a distinctive double membrane structure, the nucleus. The cell’s genetic material, its DNA, is organized into linear chromosomes located within the nucleus. The synthesis of RNA molecules, occurs within the nucleus. The membranes of the nucleus are elaborated within the cytoplasm into a network known as the endoplasmic reticulum or ER. There are a number of other intracellular membranes, including the Golgi apparatus and various types of small vesicles, involved in moving molecules to and from the plasma membrane and between the ER and other intracellular membrane systems. Finally, there are the mitochondria and (in plants) chloroplasts; these are double-membrane structures with their own genomic (circular) DNAs, derived from apparent endosymbiotic events early in the history of eukaryotes (discussed earlier). Complex signal-receptor interaction mechanisms serve to maintain the topological details of cells as they give rise to new cells. Our focus here is on the general rules by which specific proteins are "targeted" to specific cellular locations and compartments.

---