Proteins confer upon each compartment its characteristic structural and functional properties. They catalyze the reactions that occur there and selectively transport small molecules into and out of the compartment. For membrane-enclosed organelles in the cytoplasm, proteins also serve as organelle-specific surface markers that direct new deliveries of proteins and lipids to the appropriate organelle.
An animal cell contains about 10 billion (1010) protein molecules of perhaps 10,000 kinds, and the synthesis of almost all of them begins in the cytosol, the space of the cytoplasm outside the membrane-enclosed organelles. Each newly synthesized protein is then delivered specifically to the organelle that requires it. The intracellular transport of proteins is the central theme of both this chapter and the next. By tracing the protein traffic from one compartment to another, one can begin to make sense of the otherwise bewildering maze of intracellular membranes.
The ComparTmenTalizaTion of Cells
In this brief overview of the compartments of the cell and the relationships between them, we organize the organelles conceptually into a small number of discrete families, discuss how proteins are directed to specific organelles, and explain how proteins cross organelle membranes.
all eukaryotic Cells have the same Basic set of membrane-enclosed organelles
Many vital biochemical processes take place in membranes or on their surfaces. Membrane-bound enzymes, for example, catalyze lipid metabolism; and oxidative phosphorylation and photosynthesis both require a membrane to couple the transport of H+ to the synthesis of ATP. In addition to providing increased membrane area to host biochemical reactions, intracellular membrane systems form enclosed compartments that are separate from the cytosol, thus creating functionally specialized aqueous spaces within the cell. In these spaces, subsets of molecules (proteins, reactants, ions) are concentrated to optimize the biochemical reactions in which they participate. Because the lipid bilayer of cell membranes is impermeable to most hydrophilic molecules, the membrane of an organelle must contain membrane transport proteins to import and export specific metabolites. Each organelle membrane must also have a mechanism for importing, and incorporating into the organelle, the specific proteins that make the organelle unique.
The ComparTmenTalizaTion  of Cells
The TransporT of moleCUles BeTWeen The nUCleUs anD The CYTosol
The TransporT of proTeins inTo miToChonDria anD ChloroplasTs
The enDoplasmiC reTiCUlUm 642 Chapter 12: intracellular Compartments and protein sorting endoplasmic reticulum with membrane-bound polyribosomes
Figure 12–1 illustrates the major intracellular compartments common to eukaryotic cells. The nucleus contains the genome (aside from mitochondrial and chloroplast DNA), and it is the principal site of DNA and RNA synthesis. The surrounding cytoplasm consists of the cytosol and the cytoplasmic organelles suspended in it. The cytosol constitutes a little more than half the total volume of the cell, and it is the main site of protein synthesis and degradation. It also performs most of the cell’s intermediary metabolism—that is, the many reactions that degrade some small molecules and synthesize others to provide the building blocks for macromolecules (discussed in Chapter 2).