BIOCHEMISTRY - Textbook - Ostapchenko L. I. - 2012

Chapter 6. AMINO ACID METABOLISM AND FUNCTIONS. PROTEIN BIOSYNTHESIS

6.10. Protein biosynthesis

6.10.4. Ribosomes: structure and functions

Ribosomes are the smallest non-membranous cellular Organelles of a ribonucleoprotein nature involved in the synthesis of protein molecules in both prokaryotes (represented mainly by Bacteria) and eukaryotes (animals, plants, Fungi). In prokaryotes, ribosomes are dispersed throughout the protoplasm, accounting for up to 30-40 % of the dry mass of bacteria, with their number varying from (1-7) · 10⁴ per Cell; in eukaryotes, the ribosome content does not exceed 5 % by mass. Two main Translation sites are distinguished in the Cytoplasm: free ribosomes and ribosomes bound to The Endoplasmic reticulum. The latter primarily synthesize secretory and Membrane Proteins, whereas free ribosomes synthesize proteins for intracellular needs. Eukaryotes are also characterized by ribosomes associated with the Cytoskeleton and specialized ribosomes located in Mitochondria and METABOLISM/14.html">Chloroplasts.

Ribosomes are compact particles of specific shape lacking internal and external Symmetry; they resemble a sphere with a diameter of 18 nm and a Molecular Weight of 2.7 · 10⁶ in prokaryotes, and a diameter of 23 nm with a molecular weight of 4.2 · 10⁶ in eukaryotes. Based on the sedimentation coefficient, which depends on particle size, shape, and density, ribosomes are divided into 70S prokaryotic and 80S eukaryotic types. Chloroplast ribosomes of higher plants belong to the 70S type. Fungal mitochondrial ribosomes have a sedimentation coefficient of 75S, whereas mammalian mitochondria contain mini-ribosomes (55S), although they are functionally similar to prokaryotic 70S ribosomes.

Ribosomes are ribonucleoprotein particles whose stability is maintained at certain concentrations of Mg²⁺ ions (1 · 10^-3 mol/L) and other cations, such as Polyamines. Prokaryotic 70S ribosomes contain on average 65 % rRNA and 35 % protein, whereas in eukaryotic 80S ribosomes this ratio is nearly 1 : 1. Data on the composition of ribosomes are shown in Fig. 6.36.

Prokaryotic 70S ribosomes consist of a large 50S subunit and a small 30S subunit. The small subunit contains high-polymer 16S rRNA and 21 proteins, and is designated as S (from Small). The large 50S subunit consists of high-polymer 23S rRNA, 5S rRNA, and 36 proteins, and is designated as L (from Large). The Introduction/19.html">Primary Structure of almost all E. coli proteins has been established and proven to be unique. All proteins vary in Size and Structure, with their molecular weights ranging from 6 · 10³ to 7.5 · 10⁴.

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Eukaryotic 80S cytoplasmic ribosomes are characterized by a larger size and more complex structure. The 40S small ribosomal subunit contains 18S rRNA and approximately 33 proteins. The large 60S subunit contains high-polymer 28S rRNA, 5S rRNA, 5.8S rRNA, and nearly 50 proteins (Fig. 6.36).

Eukaryotic and prokaryotic ribosomal proteins are predominantly asymmetric, globular, compact molecules containing α-helices and β-sheets, as well as extended irregular regions. The bonds between rRNA and proteins in the ribosome are considered to be primarily electrostatic. Due to the high content of positively charged amino acid residues (Lysine - 12 %, Arginine - 11 %, Histidine - 3 %) in protein molecules, interaction with negatively charged phosphates within the rRNA is ensured, which structurally organizes the ribosome. Thus, rRNAs form the core of ribosomal subunits and execute A number of ribosomal activities, while protein clusters stabilize their local structures, thereby facilitating the attainment of the active conformation of rRNA.

Fig. 6.36. Structural characteristics of prokaryotic and eukaryotic ribosomes

Data on the localization of the centers where the MAIN STAGES OF polypeptide chain Biosynthesis take place are of fundamental importance for explaining the functioning of the cellular ribosomal apparatus. X-ray crystallographic studies with a resolution of up to 5.5 Å have revealed that Protein Synthesis occurs in the interface between the ribosomal subunits. The ribosome contains centers associated with the substrates of the transpeptidation reaction. The aminoacyl site (A-site) is where the anticodon of the aminoacyl-tRNA binds to the mRNA codon located in that center. The peptidyl site (P-site) is where peptidyl-tRNA binds—that is, the tRNA that carries the already synthesized peptide. Deacylated tRNA exits from the E-site (exit site); the ribosome also features a peptidyl transferase center as well as centers for the localization of mRNA and protein translation factors. All this indicates that, structurally and functionally, the ribosome is a complex molecular machine that sequentially scans the mRNA chain and accordingly selects from the cytoplasm those aminoacyl-tRNAs whose anticodons are complementary to the triplet combinations (codons) of the mRNA currently residing in the ribosome. Codon-anticodon interactions between mRNA and aminoacyl-tRNA are stabilized via standard Watson-Crick base pairing. The movement of the ribosome along the mRNA dictates a strict temporal order for The entry of specific aminoacyl-tRNAs into the ribosome. The amino acid residue is covalently attached to the polypeptide chain, and the deacylated tRNA is released from the ribosome.