Genetic Code and Translation in Prokaryotes

Study Notes

The genetic code is a triplet code, meaning that each codon consists of three nucleotides.
The code is specific, meaning that each codon codes for only one amino acid.
The code is degenerate, meaning that more than one codon can code for the same amino acid.
The initiation codon is AUG, which codes for methionine (Met). This codon sets the reading frame for the translation process.
The code is non-overlapping, meaning that each nucleotide is part of only one codon.
Termination codons (UAA, UAG, UGA) indicate the end of the coding sequence.
The code is universal, meaning that the same codons code for the same amino acids in all organisms.

Expressome: The complex of transcription and translation machinery.
Ribosome Binding Site: The Shine-Dalgarno sequence on mRNA allows the ribosome to bind.

Initiation:
- 30S Preinitiation Complex (30S PIC): Formation of the complex involves the 30S ribosomal subunit, initiation factors (IF1, IF2, IF3), GTP, and fMet-tRNAfMet.
- 30S Initiation Complex (30S IC): mRNA is recruited to the 30S PIC, bringing the ribosome to the start codon.
- 70S Initiation Complex (70S IC): The 50S ribosomal subunit joins the 30S IC. This step releases the initiation factors and positions fMet-tRNAfMet in the P site of the ribosome.
Elongation:
- Decoding: Recognition of the correct tRNA by the ribosome based on the codon on mRNA.
- Peptide Bond Formation: The amino acid attached to tRNA in the A site forms a peptide bond with the amino acid in the P site.
- Translocation: The ribosome moves one codon down the mRNA. The tRNA in the P site moves to the E site and exits the ribosome. The tRNA in the A site moves to the P site.
Termination:
- Release Factors (RF1/2): Recognize stop codons and hydrolyze the bond between the polypeptide chain and the tRNA in the P site.
- RF3: Helps to dissociate RF1/2 from the ribosome.
- Ribosome Recycling Factor (RRF): Works with EF-G to separate the 30S and 50S ribosomal subunits.
- **IF3 participates in tRNA dissociation, preparing the ribosomal subunits for another round of translation.

Post-translational modifications are covalent modifications to amino acids within a polypeptide.
These modifications can change the structure and chemical properties of the peptide.
Common post-translational modifications include:
- Trimming: Removal of amino acids from the ends of a polypeptide.
- Phosphorylation: Addition of a phosphate group to an amino acid.
- Glycosylation: Addition of sugar molecules to an amino acid.
- Acetylation: Addition of an acetyl group to an amino acid.
- Methylation: Addition of a methyl group to an amino acid.
Post-translational modifications can be reversible or irreversible.

tRNA molecules have a cloverleaf structure with four arms: acceptor stem, D arm, TΨC arm, and variable arm.
The acceptor stem is where the amino acid attaches.
The anticodon arm contains the anticodon, which binds to the mRNA codon during translation.

Chaperonins are protein complexes that help other proteins fold properly.
They provide a favorable environment for protein folding and prevent aggregation.