Site Of Protein Synthesis In The Cytoplasm – Home » Student Resources » Online Chemistry Textbooks » CH450 and CH451: Biochemistry – Defining Life at the Molecular Level » Chapter 11: Translation

Figure 11.31 One cycle of elongation. (Left) During one round of amino acid elongation in the nascent peptide, the EF-Tu protein binds to the cognate aa-tRNA molecule and delivers it to the A-site of the ribosome. Hydrolysis of GTP by EF-Tu leads to hybridization of the anticodon of tRNA with the codon of mRNA and dissociation of EF-Tu (bound to GDP) from the ribosome. (Center) After dissociation of EF-Tu, a peptide bond is formed, which causes the resulting peptide to transfer from the P-site tRNA to the A-site tRNA. (Right) Peptide bond formation causes a conformational change that allows EF-G (GTP Bound) to bind near the A-site of the ribosome. Rapid hydrolysis of GTP by EF-G causes a large conformational shift in the protein, which twists the large subunit of the ribosome and moves bound tRNAs from the A to the P site; P to E-site; or from the E-site to exit from the ribosome.

Site Of Protein Synthesis In The Cytoplasm

Site Of Protein Synthesis In The Cytoplasm

EF-G is a GTP hydrolase protein bound to the A-site of the ribosome. The EF-G protein has a high degree of flexibility that allows it to function as a hinge. EF-G folding is dependent on GTP hydrolysis. Thus, upon binding to the ribosome, the rapid hydrolysis of GTP induces a conformational shift in the ribosome that forces the EF-G protein to fold, enabling the translocation of mRNA with tRNA residues. Translocation of tRNA is accompanied by large-scale collective movements of the ribosome: relative rotation of ribosomal subunits and L1-stalk movement (Fig. 11.32). The L1 stem, the flexible part of the large particle, contacts and moves from the RNA to the E site together with the tRNA. Once in the EF-G-GDP form, the factor rapidly dissociates from the ribosome, opening the A-site to recruit the next aa-tRNA molecule. The elongation cycle continues until a stop codon is reached.

Junctional Localization Of Septin 2 Is Required For Organization Of Junctional Proteins In Static Endothelial Monolayers

Figure 11 .32 Large-scale movement of the large subunit of the ribosome during translocation. (a) Structure of the ribosome before translocation with tRNAs at the A and P sites (green, brown). The L1 stem of the large subunit is shown in purple. (b) Movements accompanying tRNA translocation.

The elongation phase in eukaryotic translation is very similar to prokaryotic elongation. Essentially, mRNA is decoded by the ribosome, requiring the selection of each aminoacyl-transfer RNA (aa-tRNA), which is determined by the mRNA codon in the acceptor (A) region of the ribosome, the formation of the peptide bond, and the movement of both. tRNAs and mRNA via the ribosome (Figure 11.33) A new amino acid is incorporated into a nascent peptide in about one-sixth of a second. The first step in this process requires guanosine triphosphate (GTP)-bound eukaryotic elongation factor 1A (eEF1α) to recruit aa-tRNA to an aminoacyl (A) site that is cognate to the codon sequence of the mRNA. This sampling prevents the anticodon of the tRNA from first base-pairing with the A-site codon. Instead, the tRNA dynamically remodels, generating a codon-anticodon helix that stabilizes the binding of the tRNA-eEF1α-GTP complex to the A site of the ribosome. This helix structure is energetically favorable for cognate or proper pairing, thus distinguishing between noncognate or mismatched and single mismatched or closely related species. This is important for decoding accuracy as it provides a mechanism to reject non-cognate tRNA carrying the wrong amino acid. Codon pairing with tRNA induces GTP hydrolysis by eEF1α, which is then released from the A site. Parallel to this process, the ribosome undergoes a conformational change that stimulates the binding between the 3′ end of the aa-tRNA in the A region and the tRNA carrying the polypeptide chain in the peptidyl (P) region. A positional shift of the two tRNAs [to the P site of A and to the exit (E) site of P] results in ribosome-catalyzed peptide bond formation and transfer of the polypeptide to the aa-tRNA, thus co-elongating the polypeptide. amino acid. The second step of the elongation cycle requires a GTPase, eukaryotic elongation factor 2 (eEF2), which enters the A-site and induces a conformational change of the ribosome by hydrolysis of GTP. This stimulates translocation of the ribosome to allow the next aa-tRNA to enter the A-site, thus initiating a new cycle of elongation.

Figure 11.33 Elongation phase of eukaryotic translation. This scheme represents the four main steps of eukaryotic translation elongation. The ribosome contains three tRNA binding sites: aminoacyl (A), peptidyl (P), and exit (E) sites. In the first step of peptide elongation, tRNA complexed with eIF1 and GTP and containing an anticodon cognate to the mRNA coding sequence enters the A site. Recognition of tRNA leads to hydrolysis of GTP and release of eEF1 from the A site. In parallel, the deacylated tRNA at the E site is released. The tRNAs in the A site and the P site interact, allowing ribosome-catalyzed peptide bonds to form. This involves transferring the polypeptide to aa-tRNA, thus extending the nascent polypeptide by one amino acid. eIF5A allosterically facilitates the formation of certain peptide bonds, e.g. proline-proline. eEF2 then enters the A site and induces a change in ribosome conformation by hydrolysis of GTP and stimulates translocation. The ribosome is then in the correct conformation to accept the next aa-tRNA and initiate another cycle of elongation.

Termination of bacterial protein synthesis occurs when a stop codon occurs at the ribosomal A-site and is recognized by a class I release factor, RF1 or RF2. These release factors (RFs) have different but overlapping features, with RF1 reading UAA and UAG and RF2 reading UAA and UGA, strongly discriminating against sense codons. RFs are multidomain proteins in which binding and termination of codon recognition by domain 2 at the decoding site results in the insertion of the universally conserved GGQ motif of domain 3 into the A-site of the PTC, 80 Å away from the decoding site. This event triggers the hydrolysis of the peptidyl-tRNA bond at the P-site of the PTC, and the resulting peptide chain can then be released through the ribosomal exit tunnel (Fig. 11.34). After releasing the peptide, RF1 and RF2 dissociate from the post-termination complex. Dissociation is accelerated by a class II release factor called RF3, which acts as a translational GTPase that binds and hydrolyzes GTP during termination.

Essential Amino Acids: Chart, Abbreviations And Structure

RF3 increases the efficiency of peptide hydrolysis, but is not an essential protein for the process. In gene knockout studies, RF3 is essential for Escherichia coli growth and its expression is not conserved across bacterial lineages. For example, RF3 is absent in thermophilic model organisms of the genera Thermus and Thermatoga and in the infectious Chlamydiales and Spirochaetae. This suggests that both RF1 and RF2 are capable of performing a complete round of termination independently of RF3, or that other GTPases of the translation elongation or initiation phases can compensate for RF3’s action.

Release factors RF1 and RF2 have an open conformation on the 70S ribosome (Figure 11.34), which is distinctly different from the closed conformation observed in crystal structures of free RF. Conformational equilibria of free RF in solution show that this open conformation is approximately 80% dominant.

Figure 11.34. Bacterial 70S ribosome termination complex with RF2. (A) View of the ribosome termination complex with E- and P-site tRNAs (brown), mRNA (green), and RF2 (dark blue). (B) Close-up of the RF2 hinge region between domains 1 and 4 used for virtual screening, where the putative binding region is indicated by the docking ligand (red).

Site Of Protein Synthesis In The Cytoplasm

During peptide hydrolysis, RF factors induce rotation and conformational changes within the ribosome that bind to ribosome recycling factor (RRF) and EF-G GTPase, leading to dissociation and release of the large subunit from the small subunit. of mRNA (Figure 11.35).

Ribosomes And Protein Synthesis

Figure 11.35 Termination of translation. When the stop codon enters the A-site of the ribosome, RF1 or RF2 enters the A-site and binds to the mRNA. This causes the protein to be hydrolyzed and released through the exit tunnel. Binding of RF3 and GTP hydrolysis causes dissociation of RF factors and conformational changes in ribosome structure. Subsequent binding to the ribosome recycling factor, RRF, and EF-G results in dissociation of the large and small ribosomal subunits and mRNA release.

In eukaryotes and archaea, on the other hand, the unipotent RF reads all three stop codons. Although the mechanism of translation termination is largely identical, apart from the universally conserved GGQ motif required for peptide hydrolysis from tRNA, there is neither sequence nor structural homology between bacterial RF and eukaryotic eRF1. eRF3

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