Membrane and soluble secretory proteins synthesized on the rough ER undergo four principal modifications before they reach their final destinations: (1) covalent addition and processing of carbohydrates (glycosylation) in the ER and Golgi complex, (2) formation of disulfide bonds in the ER, (3) proper folding of polypeptide chains and assembly of multisubunit proteins in the ER, and (4) specific proteolytic cleavages in the ER, Golgi complex, and secretory vesicles. Generally speaking, these modifications promote the folding of secretory proteins into their native structures and add structural stability to proteins exposed to the extracellular environment. Modifications such as glycosylation also allow the cell to produce a vast array of chemically distinct molecules at the cell surface that are the basis of specific molecular interactions used in cell-to-cell adhesion and communication.

The majority of proteins that are synthesized on the rough ER and enter the lumen of the ER are modified by the addition of one or more carbohydrate chains. Proteins with attached carbohydrates are known as glycoproteins. Carbohydrate chains in glycoproteins attached to the hydroxyl (–OH) group in serine and threonine residues are referred to as O-linked oligosaccharides, and carbohydrate chains attached to the amide nitrogen of asparagine are referred to as N-linked oligosaccharides. The various types of O-linked oligosaccharides include the mucin-type O-linked chains (named after the abundant glycoproteins found in mucus) and the carbohydrate modifications on proteoglycans described in Chapter 20. O-linked chains typically consist of only one to four sugar residues in a linear chain, which are added to proteins by enzymes known as glycoslytransferases, located in the lumen of the Golgi complex. The more common N-linked oligosaccharides are larger and more complex, containing several branches. In this section, we focus on N-linked oligosaccharides, whose initial synthesis occurs in the ER. After the initial N-glycosylation of a protein in the ER, the oligosaccharide chain is modified in the ER and commonly in the Golgi complex as well.

Disulfide bond formation, protein folding, and assembly of multimeric proteins, which take place exclusively in the rough ER, are also discussed in this section. Only properly folded and assembled proteins are transported from the rough ER to the Golgi complex and ultimately to the cell surface or other final destination through the secretory pathway. Unfolded, misfolded, or partly folded and assembled proteins are selectively retained in the rough ER and marked for degradation. We consider several features of such “quality control” in the latter part of this section.

As discussed previously, N-terminal ER signal sequences are cleaved from soluble secretory proteins and type I membrane proteins in the ER. Some proteins also undergo other specific proteolytic cleavages in the Golgi complex or secretory vesicles. We cover these cleavages, as well as carbohydrate modifications that occur primarily or exclusively in the Golgi complex, in the next chapter.