The document summarizes key aspects of protein synthesis, including the roles of initiation, elongation, and termination factors. Many factors involved are GTP-binding proteins whose conformations change depending on whether GTP or GDP is bound. Guanine nucleotide exchange factors (GEFs) stimulate the release of GDP and binding of GTP to reactivate GTP-binding proteins. Initiation requires initiation factors IF-1, IF-2, and IF-3. Elongation involves elongation factors EF-Tu, EF-Ts, and EF-G, which are GTP-binding proteins that deliver aminoacyl-tRNAs and catalyze translocation.

5. The active site for GTP hydrolysis is on the GTP-binding protein, although a GAP may contribute an essential active site residue. GEFs & GAPs may be separately regulated . Unique GEFs and GAPs interact with different GTP-binding proteins A GTPase activating protein ( GAP ) causes a GTP-binding protein to hydrolyze its bound GTP to GDP + P i .

6. Members of the family of small GTP-binding proteins have diverse functions . In some cases, the difference in conformation, with substitution of GDP for GTP allows a GTP-binding protein to serve as a " switch ". In other cases the conformational change may serve a mechanical role or alter the ability of the protein to bind to membranes.

13. The change in ribosomal conformational associated with formation of a correct codon-anticodon complex leads to altered positions of active site residues in the bound EF-Tu, with activation of EF-Tu GTPase activity. The ribosome thus functions as GAP for EF-Tu.

14. When EF-Tu delivers an aminoacyl-tRNA to the ribosome, the tRNA initially has a distorted conformation. As GTP on EF-Tu is hydrolyzed to GDP + P i , EF-Tu undergoes a large conformational change & dissociates from the complex. The tRNA conformation relaxes, & the acceptor stem is repositioned to promote peptide bond formation. This process is called accommodation . EF-Tu colored red

15. It includes rotation of the single-stranded 3 ' end of the acceptor stem of the A-site tRNA around an axis that bisects the peptidyl transferase center of the ribosomal large subunit. This positions the 3 ' end with its attached amino acid in the active site , near the 3 ' end of the P-site tRNA, & adjacent to the mouth of the tunnel through which nascent poly-peptides exit the ribosome. For images depicting the proposed rotational movement, see Fig. 5B in website of A. E. Yonath.

16. Interaction with EF-Ts causes EF-Tu to release GDP . Upon dissociation of EF-Ts, EF-Tu binds GTP , which is present in the cytosol at higher concentration than GDP. EF-Ts functions as GEF to reactivate EF-Tu.

20. The 23S rRNA may be considered a " ribozyme ." As part of the reaction a proton ( H + ) is extracted from the attacking amino N.

21. This H + is then donated to the hydroxyl of the tRNA in the P site, as the ester linkage is cleaved.

23. The nascent polypeptide, one residue longer, is now linked to the A-site tRNA.

24. However, translocation has already partly occurred, because peptide bond formation is associated with rotation of the single-stranded 3' end of the A-site tRNA toward the P-site, positioning the aminoacyl moiety for catalysis. This rotary movement also positions the nascent polypeptide to feed into the entrance to the protein exit tunnel , which is located midway between A & P sites.