The broad outlines of eukaryotic protein synthesis are the same as in prokaryotic protein synthesis. The genetic code is generally the same (some microorganisms and eukaryotic mitochondria use slightly different codons), rRNA and protein sequences are recognizably similar, and the same set of amino acids is used in all organisms. However, specific differences exist between the two types of protein synthesis at all steps of the process.
Both prokaryotes and eukaryotes initiate protein synthesis with a specialized methionyl‐tRNA in response to an AUG initiation codon. Eukaryotes, however, use an initiator met—tRNA met I—that is not formylated. Recognition of the initiator AUG is also different. Only one coding sequence exists per eukaryotic mRNA, and eukaryotic mRNAs are capped. Initiation, therefore, uses a specialized cap‐ binding initiation factor to position the mRNA on the small ribosomal subunit. Usually, the first AUG after the cap (that is, 3′ to it) is used for initiation.
Most differences in elongation result from the fact that the eukaryotic cell has different compartments, which are separated by membranes. Both prokaryotic and eukaryotic cells, of course, have an inside and outside; however, eukaryotic proteins can be targeted to, for example, the mitochondrion.
Translating ribosomes in eukaryotes are located in different places in the cell depending on the fate of their proteins. Free polysomes are in the cytoplasm and synthesize cytoplasmic proteins and those that are bound for most intracellular organelles, for example, the nucleus. Members of the second class of polysomes, membrane‐bound polysomes, are attached to the endoplasmic reticulum (forming the rough ER), and synthesize exported proteins. In cells that are actively secreting enzymes or hormones (for example, those in the pancreas), most of the protein synthesis occurs on the rough ER.
The messages encoding exported proteins must be recognized. For example, the digestive proteases are made in the pancreas. If they are released into the pancreas rather than the intestine, they will self‐digest the organ that makes them. Carrying out this export efficiently is obviously important. The signal hypothesis explains how proteins destined for export are discriminated. Proteins that are destined for export contain a short (less than 30 amino acids long) sequence made up of hydrophobic amino acids at their amino terminus. Because peptide synthesis occurs in the amino‐to‐carboxy direction, the signal peptide is the first part of the protein that is made. Signal peptides are not found in most mature secreted proteins because they are cleaved from the immature proteins during the secretion and maturation process. See Figure 1.
The process of protein export involves a small, cytoplasmic ribonucleoprotein particle (the Signal Recognition Particle or SRP) with the signal coding mRNA sequence and/or the signal peptide itself. This interaction stops translation of the protein. Then, the stalled or arrested ribosome moves to the endoplasmic reticulum (ER). A receptor on the ER binds the SRP.
Once the complex containing ribosome, mRNA, signal peptide, and SRP is “docked” onto the membrane, SRP leaves the complex and the ribosome resumes translation. The signal peptide inserts across the membrane; this insertion is dependent on the hydrophobic nature of the signal sequence. The rest of the protein follows the signal sequence across the membrane, like thread through the eye of a needle. The protein folds into its secondary and tertiary structure in the lumen (inside cavity) of the ER. The signal sequence is cut away from the protein either during translation (cotranslational processing) or, less often, after the protein is released from the ribosome (posttranslational processing). After the polypeptide chain is completed, the ribosome is released from the ER and is ready to initiate synthesis of a new protein. Secreted proteins are also made by prokaryotes by using a signal sequence mechanism, with the cell membrane taking the place of the ER membrane.
This scheme can also accommodate the synthesis of membrane‐bound proteins. In this case, the protein is not released into the lumen of the ER, but rather stays bound to the membrane. One or more anchor sequences (or “stop‐transfer sequences”) in the newly made protein keeps the partially folded region of the protein in the membrane.
Many eukaryotic membrane‐bound and secreted proteins contain a complex of sugar residues bound to the side chains of either asparagine to make N‐linked sugar residues or serine and threonine to make O‐linked sugar residues. The core of the glycosyl complex is assembled, not by adding sugars one after another to the protein chain, but by synthesizing the core oligosaccharide on a membrane lipid, dolichol phosphate.See Figure 2.
Dolichol is a long chain of up to twenty 5‐carbon isoprenoid units. The core oligosaccharide assembled on dolicol phosphate ultimately contains 14 saccharides that are transferred all at once to an asparagine residue on the protein. After the glycoprotein is assembled, the core oligosaccharide is trimmed by removal of the three glucose residues from the end, making a high‐mannose oligosaccharide on the protein. The high‐mannose oligosaccharide is moved from the ER for further modification in the Golgi complex, a structure composed of layered intracellular membranes. The completed glycoprotein moves to the plasma membrane in a membrane granule, which buds off from the Golgi. The granule fuses with the plasma membrane to release its contents. Binding to receptors in the plasma membrane brings some lysosomal enzymes back into the cell. The enzyme‐receptor complex is taken into the cell in a process that is essentially the reverse of secretion, although it involves different membrane proteins.