Protein Synthesis: Newly Synthesized Polypeptide Chains Undergo Folding and Processing
In the final stage of protein synthesis, the nascent polypeptide chain is folded and processed into its bio logically active form. During or after its synthesis, the polypeptide progressively assumes its native conformation, with the formation of appropriate hydrogen bonds and van der Waals, ionic, and hydrophobic interactions. In this way the linear, or one-dimensional, genetic message in the mRNA is converted into the three-dimensional structure of the protein. Some newly made proteins, both prokaryotic and eukaryotic, do not attain their final biologically active conformation until they have been altered by one or more processing reactions called posttranslational modifications.
Amino-Terminal and Carboxyl-Terminal Modifications The first residue inserted in all polypeptides is N-formylmethio nine (in bacteria) or methionine (in eukaryotes). How ever, the formyl group, the amino-terminal Met residue, and often additional amino-terminal (and, in some cases, carboxyl-terminal) residues may be removed enzymatically in formation of the final functional protein. In as many as 50% of eukaryotic proteins, the amino group of the amino-terminal residue is N-acetylated after translation. Carboxyl-terminal residues are also some times modified.
Loss of Signal Sequences As we shall see in Section 27.3, the 15 to 30 residues at the amino-terminal end of some proteins play a role in directing the protein to its ultimate destination in the cell. Such signal sequences are ultimately removed by specific peptidases.
Modification of Individual Amino Acids The hydroxyl groups of certain Ser, Thr, and Tyr residues of some proteins are enzymatically phosphorylated by ATP (Fi2a); the phosphate groups add negative charges to these polypeptides. The functional significance of this modification varies from one protein to the next. For example, the milk protein casein has many phospho serine groups that bind Ca2+. Calcium, phosphate, and amino acids are all valuable to suckling young, so casein efficiently provides three essential nutrients. And as we have seen in numerous instances, phosphorylation dephosphorylation cycles regulate the activity of many enzymes and regulatory proteins. Extra carboxyl groups may be added to Glu residues of some proteins. For example, the blood-clotting protein prothrombin contains a number of γ-carboxyglutamate residues (Fig. 2b) in its amino-terminal region, introduced by an enzyme that requires vitamin K. These carboxyl groups bind Ca2+, which is required to initiate the clotting mechanism.
FIGURE 1 Coupling of transcription and translation in bacteria. The mRNA is translated by ribosomes while it is still being tran scribed from DNA by RNA polymerase. This is possible because the mRNA in bacteria does not have to be transported from a nucleus to the cytoplasm before encountering ribosomes. In this schematic dia gram the ribosomes are depicted as smaller than the RNA polymerase. In reality the ribosomes (Mr 2.7x106) are an order of magnitude larger than the RNA polymerase (Mr 3.9 x105).
FIGURE 2 Some modified amino acid residues. (a)Phosphorylated amino acids. (b)A carboxylated amino acid. (c)Some methylated amino acids.
Monomethyl- and dimethyllysine residues (Fig. 27–29c) occur in some muscle proteins and in cytochrome c. The calmodulin of most species contains one trimethyllysine residue at a specific position. In other proteins, the carboxyl groups of some Glu residues undergo methylation, removing their negative charge. Attachment of Carbohydrate Side Chains The carbohydrate side chains of glycoproteins are attached covalently during or after synthesis of the polypeptide. In some glycoproteins, the carbohydrate side chain is attached enzymatically to Asn residues (N-linked oligosaccharides), in others to Ser or Thr residues (O-linked oligosaccha rides) . Many proteins that function extracellularly, as well as the lubricating proteoglycans that coat mucous membranes, contain oligosaccharide side chains (see Fig. 2).
Addition of Isoprenyl Groups A number of eukaryotic proteins are modified by the addition of groups derived from isoprene (isoprenyl groups). A thioether bond is formed between the isoprenyl group and a Cys residue of the protein . The isoprenyl groups are derived from pyrophosphorylated intermediates of the cholesterol biosynthetic pathway , such as farnesyl pyrophosphate (Fig. 3). Proteins modified in this way include the Ras proteins, products of the rasoncogenes and proto-oncogenes, and G proteins (both discussed in Chapter 12), and lamins, proteins found in the nuclear matrix. The isoprenyl group helps to anchor the protein in a membrane. The trans forming (carcinogenic) activity of the rasoncogene is lost when isoprenylation of the Ras protein is blocked, a finding that has stimulated interest in identifying inhibitors of this posttranslational modification pathway for use in cancer chemotherapy.
Addition of Prosthetic Groups Many prokaryotic and eu karyotic proteins require for their activity covalently bound prosthetic groups. Two examples are the biotin molecule of acetyl-CoA carboxylase and the heme group of hemoglobin or cytochrome c. Proteolytic Processing Many proteins are initially synthesized as large, inactive precursor polypeptides that are proteolytically trimmed to form their smaller, active forms. Examples include proinsulin, some viral proteins, and proteases such as chymotrypsinogen and trypsinogen. Formation of Disulfide Cross-Links After folding into their native conformations, some proteins form intrachain or interchain disulfide bridges between Cys residues. In eukaryotes, disulfide bonds are common in proteins to be exported from cells. The cross-links formed in this way help to protect the native conformation of the protein molecule from denaturation in the extracellular environment, which can differ greatly from intracellular conditions and is generally oxidizing.
FIGURE 3 Farnesylation of a Cys residue. The thioether linkage is shown in red. The Ras protein is the product of the rasoncogene.
