Ribosome Structure and Functional Centers
Ribosomes are molecular «factories» consisting of ribonucleoprotein complexes (ribosomal RNA and specific proteins). Each ribosome is divided into small and large subunits.
- In prokaryotes (bacteria): the total size is 70S (about 20 nm). The small 30S subunit contains 16S rRNA and 21 proteins. The large 50S subunit consists of 23S and 5S rRNA, as well as 31 proteins. Their number in a cell can reach tens of thousands.
- In eukaryotes (mammals): the complex size is 80S (about 24 nm). The small 40S subunit contains 18S rRNA and 33 proteins, while the large 60S subunit is formed by 28S, 5.8S, and 5S rRNAs along with 49 proteins. The subunits are synthesized in the nucleoli and function in the cytoplasm (often on the membranes of the rough endoplasmic reticulum). Mitochondria, however, possess their own 70S-type ribosomes.
The ribosome structure features operational zones (functional centers):
- M-center (on the small subunit) is the mRNA-binding site.
- A-site (aminoacyl) is where the incoming aminoacyl-tRNA binds.
- P-site (peptidyl) holds the tRNA attached to the growing polypeptide chain.
- E-site (exit) is the egress zone where the deacylated tRNA leaves the complex.
Mechanism and Stages of Translation
Before synthesis begins, the enzyme aminoacyl-tRNA synthetase (codase) performs recognition—identifying and attaching the appropriate amino acid to a specific transfer RNA. The translation process itself proceeds in three stages:
1. Initiation The process begins with the assembly of mRNA, the small ribosomal subunit, and the initiator tRNA (carrying methionine in eukaryotes, formylmethionine in prokaryotes). Prokaryotes locate the start codon (AUG) by binding the purine-rich Shine-Dalgarno sequence on the mRNA to the complementary rRNA region of the small subunit. Eukaryotes rely on a universal signal—the 5' cap structure. Once positioned at the start codon, the large ribosomal subunit joins the complex. The process requires magnesium ions and protein initiation factors.
2. Elongation This is the polypeptide chain extension cycle, consisting of three steps:
- Codon recognition: an incoming aminoacyl-tRNA enters the vacant A-site, its anticodon complementary to the mRNA codon.
- Peptide bond formation: the enzyme peptidyl transferase (a ribosomal component) catalyzes peptide bond formation between amino acids.
- Translocation: the ribosome moves precisely by three nucleotides (one triplet) in the 3' direction of the mRNA. The deacylated tRNA shifts to the E-site and dissociates, freeing the A-site for a new molecule.
3. Termination Movement along the template stops when one of the three stop codons enters the A-site: UAA, UAG, or UGA. Release factors (RF) bind to the complex instead of a tRNA. The completed polypeptide is released, and the ribosome dissociates into its two initial subunits.
Post-Translational Protein Modifications
The newly synthesized polypeptide chain typically lacks functional activity and requires modifications for «maturation»:
- Proteolysis: cleavage of extra fragments (e.g., terminal amino acids) by exopeptidases.
- Folding: spatial conformation of the molecule to form secondary and tertiary structures.
- Quaternary structure formation: assembly of multiple polypeptide chains into a single complex.
- Complexation: conjugation with carbohydrates (glycoproteins) or lipids (lipoproteins).
A classic clinical example is insulin synthesis in pancreatic cells. Initially, a long inactive preproinsulin is translated. Subsequently, during maturation, the N-terminal segment and the central portion (C-peptide) are cleaved off, yielding the active hormone insulin.
Differences in Translation Between Prokaryotes and Eukaryotes
The mechanisms of gene expression depend on cellular organization.
| Characteristic | Prokaryotes | Eukaryotes |
|---|---|---|
| Gene structure | Strict colinearity, no introns | Interrupted genes (introns and exons) |
| Spatial separation | Absent | Nuclear envelope separates the processes |
| Coupling with transcription | Occur simultaneously (coupled) | Strictly separated (processing precedes) |
| Primary transcript | Directly serves as mature mRNA | Requires splicing, capping, poly-A tail |
Briefly: answers to topical questions
What protein factors are required for the translation elongation stage?
Protein elongation factors are required for the translation elongation stage. Prokaryotic elongation factors include EF-Tu, EF-Ts, and EF-G (translocation factor). Elongation factor EF2 (EF-2) is also indicated for translocation: translocation is the movement of the ribosome along the mRNA by one codon in the 5'- to 3'-direction; it requires GTP energy. Phosphorylation of EF2 leads to the inhibition of protein synthesis, and inactivation of EF-2 leads to complete cessation of protein synthesis.
Which helper proteins ensure the correct folding of the polypeptide chain after translation?
Correct folding of the polypeptide chain and maintenance of the native conformation of proteins are ensured by chaperones. Heat shock proteins (HSP) normally perform the function of chaperones. A distinction is made between constitutive chaperones, which are synthesized constantly (Hsp 70, Hsp 60), and inducible chaperones (heat shock proteins), which are synthesized under stress. According to molecular weight, chaperones are classified into Hsp 100, Hsp 90, Hsp 70, Hsp 60 (chaperonins), and small ones. In mammals, HSP20, HSP40, HSP60, HSP70, and HSP90 are specified.
Class and exam questions
What does the letter S mean in the designation of ribosomal subunits (e.g., 70S)?
This is the sedimentation coefficient measured in Svedberg units. It indicates the rate of particle sedimentation during ultracentrifugation, which depends on the molecular weight and shape of the object.
How does an amino acid bind to its cognate tRNA prior to translation?
A special enzyme, aminoacyl-tRNA synthetase (codase), is responsible for this process. It performs recognition: it recognizes a specific tRNA and attaches a strictly defined amino acid to it in the cytoplasm.
What is the difference between start codon recognition in bacteria and mammals?
In bacteria, the small subunit binds to the purine-rich Shine-Dalgarno sequence on the mRNA. In mammals, initiation factors recognize the universal cap structure and scan the chain to the first AUG codon.
What else to study on this topic
- Functions of prokaryotic translation protein factors (IF, EF, RF)
- Stages of pre-mRNA processing in eukaryotes: splicing, capping, polyadenylation
- Spatial topography and mechanism of action of the peptidyl transferase center
- Protein folding mechanisms and quaternary structure formation
- Energy supply for elongation processes and the role of GTP hydrolysis
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