Textbook - BIOLOGICAL CHEMISTRY - Gubsky Yu.I. - 2000

Chapter IV. MOLECULAR MECHANISMS OF HEREDITY AND REALIZATION OF GENETIC INFORMATION

CHAPTER 21. PROTEIN BIOSYNTHESIS IN RIBOSOMES

21.3. STAGES AND MECHANISMS OF TRANSLATION

The MOLECULAR MECHANISMS OF ribosomal Translation in PROKARYOTES AND EUKARYOTES share common features and, similarly to the Synthesis of Other Biopolymers, are divided into the stages of initiation, elongation, and termination.

Class="center">The process of translation in Eukaryotic Cells

1. Translation initiation.

The prerequisite for the functioning of the ribosomal protein-synthesizing system is The formation of the initiation complex, which includes:

- 40S and 60S subunits combined into an 80S ribosome; the intact ribosome has two structural sites for binding aminoacyl-tRNA molecules during translation: the aminoacyl (A) site (A-site) and the peptidyl (P) site (P-site), the former of which is linked to aminoacyl-tRNA during translation, and the latter to peptidyl-tRNA;

- mRNA, which necessarily possesses a 7-methylguanosine "cap" at the 5' end; mRNA binds to the ribosome in such a way that the initiation codon, AUG, is positioned opposite its P-site, which according to METABOLISM/28.html">The Genetic Code table corresponds to The amino acid Methionine—The initiating amino acid (and interacts with the anticodon of Met-tRNA);

- Met-tRNA_i, a specialized type of tRNA that accepts and delivers the first, initiating amino acid—methionine—to the ribosome (initially to the P-site) (incorporation of methionine into the interior of the peptide chain requires the presence of another tRNA—a special tRNA_met); the binding of Met-tRNA_i to the 40S ribosomal subunit requires the participation of the initiation factor eIF-2.

Thus, methionine becomes the N-terminal amino acid for most eukaryotic Proteins; its Cleavage from the N terminus is possible at the stage of post-translational peptide modification. In prokaryotes, the first, initiating amino acid is modified methionine—formylmethionine, which enters the ribosome as formylmethionyl-tRNA;

- protein initiation factors (eIF-1, eIF-2, eIF-3, etc.—up to ten initiation factors are currently known); in particular, the Formation of the intact 80S ribosome from subunits and its stabilization require the presence of initiation factors eIF-3, eIF-4C, and eIF-6;

- GTP and ATP Coenzymes, which provide energy for the various stages of initiation.

The structural diagram of the initiation complex is presented in Fig. 21.4.

Fig. 21.4. Initiation complex consisting of two ribosomal subunits, mRNA, Met-tRNA_i, and protein initiation factors.

G^mTP — 7-methylguanosine triphosphate (cap); (A)_n — mRNA polyadenylate tail.

2. Elongation of the polypeptide chain.

Strictly speaking, elongation consists in the formation of peptide bonds between amino acid residues linked via respective tRNAs to the A- and P-sites of the translating ribosome. The steps of elongation are schematically shown in Fig. 21.5.

Fig. 21.5. The process of Polypeptide chain elongation.

The prerequisite for the onset of elongation is the binding to the A-site of the ribosome (which is free at this stage) of the 2nd amino acid (generally the (n + 1)-th amino acid, counting from the N terminus of the synthesized peptide) bound to tRNA (Fig. 21.5a). This (n + 1)-th amino acid corresponds (According to the genetic code) to the mRNA codon that immediately follows the initiation (i.e., AUG) codon.

Peptidyl transferase reaction

The formation of a peptide bond between the 1st (initiating—methionine) and 2nd Amino Acids, linked via their tRNAs to the P- and A-sites of the ribosome, respectively, is catalyzed by the enzyme peptidyl transferase. Peptidyl transferase activity is associated with the 50S subunit in prokaryotes and the 60S subunit in eukaryotes.

This same peptidyl transferase reaction also drives the subsequent stages of elongation, in which the P- and A-sites of the ribosome are occupied, respectively, by peptidyl-tRNA (containing "n" amino acid residues) and the specific incoming ("n + 1") amino acid.

During the peptidyl transferase reaction, the peptide fragment (linked via its respective tRNA to the P-site) is transferred to the amino acid (linked via tRNA to the A-site) in such a way that the newly formed peptide becomes attached to the ribosomal A-site. The tRNA initially bound to the P-site is released (Fig. 21.5b).

Translocation Reaction

Following peptide bond formation, the elongated peptide attached to the tRNA (peptidyl-tRNA) shifts from the A-site to the P-site—a process known as translocation.

Simultaneously, the ribosome moves to the right along the mRNA strand. As a result, the next, (n + 2)-th mRNA codon positions itself opposite the ribosomal A-site, corresponding to the subsequent (n + 2)-th amino acid, which can bind to the ribosome as a tRNA complex (Fig. 21.5c).

Translocation is mediated by the elongation factor eEF-2. The energy required for translocation is provided by the GTPase-driven cleavage of GTP to GDP.

3. Translation termination.

Translation termination occurs when the translating ribosome, while moving along the mRNA strand, reaches one of the termination codons—UAA, UAG, or UGA.

The appearance of a termination codon in the A-site is recognized by protein release factors, which induce the Hydrolysis of the bond between the peptide and the tRNA molecule occupying the ribosomal P-site. This process results in the release of the newly synthesized peptide and the dissociation of the 80S ribosome into 40S and 60S subunits.

Post-Translational Modification of Peptide Chains

The polypeptide chain resulting from ribosomal translation acquires its biological properties after folding into its characteristic, unique spatial conformation—a process that in many cases is preceded by post-translational modification (Processing).

Reactions of post-translational peptide modification include:

a) Modification of the N- and C-termini—removal of N-terminal formylmethionine (in prokaryotes) and methionine (in eukaryotes); Acetylation of the N- and C-termini;

b) modification of hydroxyl, amino, and carboxyl groups in the side chains of Peptides via phosphorylation, carboxylation, methylation, acetylation, etc.;

c) attachment of prosthetic groups to peptides—CARBOHYDRATES (glycosylation), heme, coenzymes (flavin NUCLEOTIDES, biotin, Porphyrins, etc.);

d) chemical modification of the covalent framework of amino acid residues; for example, The conversion of a Histidine residue within the eukaryotic initiation factor eEF-2 into the Structure/68.html">Unusual amino acid residue diphthamide.