StudyKit: Translation and Protein Synthesis

Key Molecules for Translation

• Ribosome
• mRNA code
• tRNA adapter
• Amino acids
• Proteins (other helpful molecules)

General Information on Translation (tln)

• Protein synthesis is slower in eukaryotes than in bacteria (5 vs 20 amino acids/sec).
• Translation has a higher error rate compared to DNA replication, as mutations in protein are not passed on.

Vocabulary

• Aminoacyl tRNA synthetases perform "charging" by attaching amino acids to tRNAs.
• Elongation factors bring aminoacyl-tRNAs to ribosomes.

tRNA Adapter

• Needed for chemical adaptation (bridging language gap between mRNA and amino acids).
• Needed for spatial adaptation (linking mRNA and amino acid chain in 3D ribosome space).

tRNA Structure

• Approximately 75 nucleotides with a cloverleaf 2D structure.
• CCA tail at 3' end (site of amino acid attachment).
• Anticodon arm pairs with mRNA.
• Conserved D-arm and TPseudoC arm.

tRNA Tertiary Structure

• Constant distance between anticodon arm and CCA tail for ribosome matching.
• Exhibits base pair triples in 3D structure.

tRNA Specificity and Conformity

• Use of modifications to transcend genetic code, with post-transcriptional modifications.
• 13 modifications on average per tRNA.
• Modifications impact gene expression, protein stability, and stress response.

Impact of tRNA Modifications

1. Encourage correct secondary/tertiary structure.
2. Impart thermodynamic stability.
3. Increase biological stability (prevent degradation).
4. Encourage translation efficiency/fidelity.

Specific Modifications

• PseudoU: Allows new hydrogen bonds, increasing stability.
• Dihydrouridine: Adds flexibility by breaking double bonds.
• m1A (1-methyladenosine): Structural impact on folding.

Anticodon Crowding and Wobble Pairing

• Anticodon crowding: Spatial issues preventing perfect base pairing.
• Wobble pairing: Deviation allowed in the 3rd codon position, enabling flexibility.

Codon and Amino Acid Activation

• Codon: Triplet of nucleotides specifying an amino acid or a stop signal.
• Amino acid activation: Involves 20 activating enzymes and aminoacyl-tRNA synthetases (aaRS).
• Aminoacylation: Two-step process involving AMP attachment and transfer to tRNA.

Ribosome Structure and Function

• Catalyzes peptide bond formation.
• Composed of large and small subunits.
• Subunit interface and periphery are vital for function.

Ribosomal Binding Sites

1. Aminoacyl (A) site
2. Peptidyl (P) site
3. Exit (E) site

Translation Process Overview

1. Initiation
2. Elongation
3. Termination
4. Ribosome recycling

Translation Initiation

• Initiated at AUG codon by initiation factors (IFs) and special initiator tRNA.
• Different in eukaryotes and bacteria.

Translation Elongation

1. Loading of charged tRNA into A site by elongation factors.
2. Peptide bond formation.
3. Translocation of mRNA/tRNA through ribosome.
4. tRNA exits from E site.

Translation Termination and Recycling

• Stop codons recognized by release factors (RFs).
• Promotes release of polypeptide and ribosome dissociation.

Eukaryotic vs. Bacterial Initiation

• Eukaryotes: Initiation typically at first AUG, involves ribosome scanning.
• Bacteria: Initiation at start codon guided by Shine-Dalgarno sequence.

Additional Notes

• Polysomes: Multiple ribosomes on a single mRNA.
• Hybrid states model describes tRNA movement through ribosome subunits.
• Translation factors mimic tRNA structure to access the ribosome efficiently.