This Process Of Protein Synthesis Is Also Called – 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 on a nascent peptide, the EF-Tu protein binds with the cognate aa-tRNA molecule and shuttles it to the A-site of the ribosome. GTP hydrolysis by EF-Tu leads to the hybridization of the anticodon of the tRNA with the codon of the mRNA and causes the dissociation of the EF-Tu (GDP-bound) from the ribosome. (Center) After the dissociation of EF-Tu, the peptide bond is formed leading to the transfer of the nascent peptide from the tRNA in the P site, to the tRNA in the A site. (Right) Peptide bond formation leads to a conformational change in the ribosome that allows the binding of EF-G (GTP Bound) near the A site of the ribosome. Rapid hydrolysis of GTP by EF-G causes a large conformational shift in the protein that twists the large subunit of the ribosome and shifts the bound tRNAs from the A- to the P-site; from the P- to the E-site; or from the E site to exit the ribosome.

This Process Of Protein Synthesis Is Also Called

EF-G is a GTP hydrolase protein that binds to the A site of the ribosome. The EF-G protein has a high flexibility that allows it to act as a hinge. Folding of EF-G is dependent on GTP hydrolysis. Thus, when binding to the ribosome, the rapid hydrolysis of GTP acts as a power move folding the EF-G protein and causing a conformational shift in the ribosome that enables the translocation of the tRNA residues and the mRNA. Translocation of tRNAs is accompanied by large-scale collective movements of the ribosome: relative rotation of ribosomal subunits and L1-stalk movement (Fig. 11.32). The L1 stalk, which is a flexible part of the large subunit, is in contact and moves along with the tRNA from the P to the E site. Once in the EF-G-GDP form, the factor quickly dissociates from the ribosome, opening up the A site for the recruitment of the next aa-tRNA molecule. The elongation cycle will continue to be repeated until a termination codon is reached.

Protein Production: A Simple Summary Of Transcription And Translation

Figure 11.32 Large-scale movement of the large subunit of the ribosome during translocation. (a) Pre-translocation structure of the ribosome with tRNAs in A and P sites (green, brown). The L1 stalk of the large subunit is shown in purple. (b) Motions accompanying tRNA translocation.

The elongation phase in eukaryotic translation is very similar to prokaryotic elongation. Essentially, the mRNA is decoded by the ribosome in a process that requires selection of each aminoacyl-transfer RNA (aa-tRNA), which is dictated by the mRNA codon in the ribosome acceptor (A) site, peptide bond formation and movement from both tRNAs and the mRNA by the ribosome (Fig. 11.33) A new amino acid is incorporated into a nascent peptide at a rate of approximately one every sixth of a second. The first step of this process requires guanosine triphosphate (GTP)-bound eukaryotic elongation factor 1A (eEF1α) to recruit an aa-tRNA to the aminoacyl (A) site, which has an anticodon loop cognate to the codon sequence of the mRNA. The anticodon of the sampling tRNA does not initially base pair with the A-site codon. Instead, the tRNA dynamically remodels to generate a codon-anticodon helix, which stabilizes the binding of the tRNA-eEF1α-GTP complex to the ribosome A site. This helical structure is energetically favorable for cognate or correct pairing, and thus discriminates between the non-cognate or unpaired and single mismatched or near-cognate species. This is important for decoding accuracy since it provides a mechanism to reject a non-cognate tRNA that carries an inappropriate amino acid. The pairing of the tRNA and codon induces GTP hydrolysis by eEF1α, which is then evicted from the A site. In parallel with this process, the ribosome undergoes a conformational change that stimulates contact between the 3′ end of the AA-tRNA in the A site and the tRNA carrying the polypeptide chain in the peptidyl (P) site. The shift in position of the two tRNAs [A to the P site and P to the exit (E) site] results in ribosome-catalyzed peptide bond formation and the transfer of the polypeptide to the aa-tRNA, thus extending the polypeptide with one amino acid. The second stage of ​​the elongation cycle requires a GTPase, eukaryotic elongation factor 2 (eEF2), which enters the A-site and, through the hydrolysis of GTP, induces a change in the ribosome conformation. This stimulates ribosome translocation to allow the next aa-tRNA to enter the A site, thus starting a new elongation cycle.

Figure 11.33 Eukaryotic translation elongation phase. This schematic represents the four basic steps of eukaryotic translation elongation. The ribosome contains three tRNA-binding sites: the aminoacyl (A), peptidyl (P) and exit (E) sites. In the first step of peptide elongation, the tRNA, which is in a complex with eIF1 and GTP and contains the cognate anticodon to the mRNA coding sequence, enters the A site. Recognition of the tRNA leads to the hydrolysis of GTP and eviction of eEF1 from the A site. In parallel, the deacylated tRNA in the E site is ejected. The A site and the P site tRNAs interact, allowing the formation of ribosome-catalyzed peptide bonds. This involves the transfer of the polypeptide to the aa-tRNA, thus extending the nascent polypeptide by one amino acid. eIF5A allosterically assists in the formation of certain peptide bonds, e.g. Proline-proline. eEF2 then enters the A site and, through the hydrolysis of GTP, induces a change in the ribosome conformation and stimulates translocation. The ribosome is then in a correct conformation to accept the next aa-tRNA and start another cycle of elongation.

Termination of bacterial protein synthesis occurs when a stop codon is presented in the ribosomal A site and is recognized by a class I release factor, RF1 or RF2. The release factors (RFs) have different but overlapping specificities, where RF1 reads UAA and UAG and RF2 reads UAA and UGA, with strong discrimination against sense codons. The RFs are multi-domain proteins, where binding and stop codon recognition by domain 2 at the decoding site causes the universally conserved GGQ motif of domain 3 to insert into the A site of the PTC, some 80 Å away from the decoding site. This event triggers hydrolysis of the peptidyl-tRNA bond in the P-site of the PTC, and the nascent peptide chain can be released through the ribosomal exit tunnel (Fig. 11.34). After peptide release, RF1 and RF2 dissociate from the post-termination complex. This dissociation is accelerated by a class II release factor called RF3, which functions as a translational GTPase that binds and hydrolyzes GTP in the course of termination.

Mechanisms And Regulation Of Protein Synthesis In Mitochondria

While RF3 increases the efficiency of peptide hydrolysis, it is not an essential protein for this process. In gene knockout studies, RF3 is dispensable for growth of Escherichia coli, and its expression is not conserved in all bacterial lines. For example, RF3 is not present in the thermophilic model organisms of the genera Thermus and Thermatoga and in infectious Chlamydiales and Spirochaetae. This means that both RF1 and RF2 are able to perform a complete termination cycle independently of RF3 or that other GTPases from the elongation or initiation phases of translation can compensate for the action of RF3.

The release factors RF1 and RF2 acquire an open conformation (Fig. 11.34) on the 70S ribosome, which is distinctly different from the closed conformation observed in crystal structures of free RFs. The conformational equilibrium of free RFs in solution shows that the open conformation dominates about 80%.

Figure 11.34. The 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 view of the hinge region of RF2 between domains 1 and 4 used for virtual screening, where the putative binding region is indicated by a duct ligand (red).

During peptide hydrolysis, the RF factors cause rotational and conformational changes in the ribosome that allow the binding of a ribosome recycling factor (RRF) and the EF-G GTPase, which leads to the dissociation of the large subunit from the small subunit and the release . of the mRNA (Fig. 11.35).

Chapter 13.2 (pgs ): Ribosomes And Protein Synthesis

Figure 11.35 Termination of translation. When a stop codon enters the A-site of the ribosome RF1 or RF2 enter the A-site and bind with the mRNA. This leads to the hydrolysis of the protein and release through the exit tunnel. Binding of RF3 and GTP hydrolysis causes the dissociation of the RF factors and conformational change of the ribosome structure. Subsequent binding of the ribosome recycling factor, RRF, and EF-G causes the dissociation of the large and small ribosomal subunits and the release of the mRNA.

In eukaryotes and archaea, on the other hand, a single omnipotent RF reads all three stop codons. Although the mechanism of translation termination is essentially the same, there is neither sequence nor structural homology between the bacterial RFs and the eukaryotic eRF1, except for the universally conserved GGQ motif that is required for peptide hydrolysis of the tRNA. The eRF3

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