SUMMARY

• 40.1 Protein Synthesis Decodes the Information in Messenger RNA

  Protein synthesis takes place in three phases: initiation, elongation, and termination. In bacteria, mRNA, formylmethionyl-tRNA_f (the special initiator tRNA that recognizes AUG), and a 30S ribosomal subunit come together with the assistance of initiation factors to form a 30S initiation complex. A 50S ribosomal subunit then joins this complex to form a 70S initiation complex, in which fMet-tRNA_f occupies the P site of the ribosome.

  Elongation factor Tu delivers the appropriate aminoacyl-tRNA to the ribosome’s A (aminoacyl) site as an EF-Tu–aminoacyl-tRNA–GTP ternary complex. EF-Tu serves both to protect the aminoacyl-tRNA from premature cleavage and to increase the fidelity of protein synthesis by ensuring that the correct anticodon–codon pairing has taken place before hydrolyzing GTP and releasing aminoacyl-tRNA into the A site.

• 40.2 Peptidyl Transferase Catalyzes Peptide-Bond Synthesis

  A peptide bond is formed when the amino group of the aminoacyl-tRNA attacks the ester linkage of the peptidyl-tRNA. The ribosome catalyzes the formation of the peptide bond by using proximity and orientation catalysis as well as by stabilizing the transition state.

  On peptide-bond formation, the tRNAs and mRNA must be translocated for the next cycle to begin. The deacylated tRNA moves to the E site and then leaves the ribosome, and the peptidyl-tRNA moves from the A site into the P site. Elongation factor G uses the free energy of GTP hydrolysis to drive translocation. Protein synthesis is terminated by release factors, which recognize the termination codons UAA, UGA, and UAG and cause the hydrolysis of the ester bond between the polypeptide and tRNA.

• 40.3 Bacteria and Eukaryotes Differ in the Initiation of Protein Synthesis

  The basic plan of protein synthesis in eukaryotes is similar to that of bacteria, but there are some significant differences. Eukaryotic ribosomes (80S) consist of a 40S small subunit and a 60S large subunit. The initiating amino acid is again methionine, but it is not formylated. The initiation of protein synthesis is more complex in eukaryotes than in bacteria. The AUG codon closest to the 5′ end of mRNA is nearly always the start site. The 40S ribosome finds this site by binding to the 5′ cap and then scanning the RNA until AUG is reached. Eukaryotic mRNA is circularized by interaction between eukaryotic initiation factor 4 and the poly(A)-binding protein.

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• 40.4 A Variety of Biomolecules Can Inhibit Protein Synthesis

  Protein synthesis is the site of action of an array of antibiotics. Virtually all aspects of protein synthesis are sensitive to one antibiotic or another. The fact that many antibiotics target protein synthesis in bacteria but not eukaryotes makes them clinically useful. Toxins such as diphtheria toxin and ricin are lethal because they inhibit protein synthesis. Diphtheria toxin modifies and inactivates a protein factor, and ricin removes a base from 28S rRNA, eliminating its catalytic activity.

• 40.5 Ribosomes Bound to the Endoplasmic Reticulum Manufacture Secretory and Membrane Proteins

  Proteins contain signals that determine their ultimate destination. In eukaryotes, some proteins are transported into organelles, such as mitochondria and nuclei, posttranslationally. Other proteins, following the secretory pathway, are inserted into the endoplasmic reticulum cotranslationally. Protein synthesis continues in the cytoplasm unless the nascent chain contains a signal sequence that directs the ribosome to the endoplasmic reticulum. Amino-terminal signal sequences consist of 9 to 12 hydrophobic amino acids. A signal-recognition particle (SRP) recognizes signal sequences and brings ribosomes bearing them to the ER. A GTP–GDP cycle releases the signal sequence from the SRP and then detaches the SRP from its receptor. The nascent chain is then translocated across the ER membrane.

• 40.6 Protein Synthesis Is Regulated by a Number of Mechanisms

  In eukaryotes, genes encoding proteins that transport and store iron are regulated at the translational level. Iron-response elements (IREs), structures that are present in certain mRNAs, are bound by an IRE-binding protein when this protein is not binding iron. Whether the expression of a gene is stimulated or inhibited in response to changes in the iron status of a cell depends on the location of the IRE within the mRNA. Recently discovered microRNAs also can regulate protein synthesis either by causing RNA degradation or by inhibiting the translation of mRNA.