mRNA to Protein (Translation)

mRNA to Protein Translation

Overview

  • Translation is the process of synthesizing proteins from messenger RNA (mRNA).

Key Components of Translation

  • tRNA (transfer RNA): Bridges mRNA and amino acids; contains a specific nucleotide triplet codon that corresponds to an amino acid.

    • Amino Acid Binding: Each amino acid is bound to the 3’ end of a tRNA molecule.

Wobble Codon

  • The third base of each codon plays a lesser role in specifying an amino acid. This is referred to as the wobble codon where tRNA recognizes multiple codons for a single amino acid.

    • The codon-anticodon interaction is less stringent at the third position, allowing one tRNA to pair with several codons.

  • Codon/Amino Acid Codiversity: 4 bases of tRNA allow for coding of 20 amino acids.

Table 27-4: Codon Recognition by tRNA

  • Anticodon Recognition: Different anticodons can pair with codons giving rise to varying recognition capabilities.

    1. One codon recognized:

      • Anticodon (3') X-Y-C (5') corresponds to Codon (5') Y-X-G (3').

      • Anticodon (3') X-Y-A (5') corresponds to Codon (5') Y-X-U (3').

    2. Two codons recognized:

      • Anticodon (3') X-Y-U (5') corresponds to Codon (5') Y-X-(3') and (5') Y-X-C (3').

    3. Three codons recognized:

      • Anticodon (3') X-Y-I (5') corresponding includes Codon variation.

Open Reading Frame (ORF)

  • Nonoverlapping Code: Clarifies how sequences are read without sharing nucleotides.

  • Overlapping Code: Shows how some nucleotides may be included in more than one reading frame.

  • Reading Frames: E.g.: AUACGAGUC has three reading frames based on starting position within the sequence.

tRNA Structure

  • The end of the anticodon arm has seven unpaired nucleotides:

    • Modified nucleotides include: mG (methylguanosine), dimethylguanosine T, ribothymidine I, inosine Psi, pseudouridine D, 5,6-dihydrouridine, and mI (methylinosine).

  • nucleotide variations: Extra nucleotides can appear in the extra arm or D arm of tRNA.

Structural Variants of tRNA

  • Key Loops:

    • D loop

    • Anticodon loop

    • Variable loop

    • Accepting stem

  • tRNA arms: Example structures visualized on specific diagrams. CCA at 3' end is crucial for amino acid attachment.

Amino Acid Activation

  • Ester Bond Formation: An ester bond forms between an amino acid and the 3' end OH of tRNA:

    • This process consumes 1 ATP and is catalyzed by aminoacyl-tRNA synthetase.

  • Aminoacyl-tRNA Synthetase: Ensures the correct amino acid is bound to its corresponding tRNA.

Editing Mechanism in Synthetases

  • Hydrolytic Editing: There is a proofreading mechanism via hydrolytic editing in AA-tRNA synthetase that removes incorrectly bound amino acid after synthesis occurs.

    • This is crucial for ensuring fidelity in protein synthesis.

Ribosome Composition and Function

  • Ribosome Structure: Ribosomes are large complex machines that catalyze protein synthesis, made of RNA and protein.

    • Bacterial Ribosome: Consists of a 70S unit formed by a large 50S subunit and a small 30S subunit, with equal parts RNA and protein.

  • Heavier in Eukaryotes: Eukaryotic ribosomes are larger and more complex than prokaryotic ones.

Components of the Bacterial Ribosome

  • Large Subunit (50S):

    • Contains rRNAs: 5S (120 nt), 23S (2900 nt), and approximately 34 proteins.

  • Small Subunit (30S):

    • Contains 16S rRNA (1540 nt) and approximately 21 proteins.

Comparison of Prokaryotic and Eukaryotic Ribosomes

  • Bacterial: Total Weight: 70S (2.5 MDa), large unit: 50S, small unit: 30S.

  • Eukaryotic: Total Weight: 80S (4.2 MDa), large unit: 60S (2.8 MDa) with more extensive rRNA varieties (5S, 5.8S, 28S) and corresponding proteins.

The Shine-Dalgarno Sequence

  • Translation Initiation: The Shine-Dalgarno sequence is essential for ribosome alignment with the mRNA.

    • Requires initiation factor proteins (IFs) and GTP hydrolysis for effective binding.

    • Each Open Reading Frame (ORF) includes its own Ribosome Binding Site (RBS).

Peptide Bond Formation**

  • E,P,A Sites: The ribosome contains E (exit), P (peptidyl), and A (aminoacyl) sites facilitating amino acid addition and peptide bond formation during translation.

    • fMet-tRNA brings the start codon (AUG) into the ribosome's P site.

  • Peptide bonds are formed between amino acids at the A site creating a growing peptide chain.

Directionality during Translation

  • Peptide Chain Growth: The direction of ribosome movement is described in relation to codon positioning on the mRNA strand; crucial towards understanding peptide synthesis.

Ribosome Movement and Dynamics**

  • Translocation: Mediated by elongation factors with energy input from GTP. The growing peptide chain continues to attach at the A-site tRNA and subsequently moves to the P site.

  • Visualization: Diagrams illustrate ribosome structure, alignment with mRNA and detailed sites for E, P, and A interactions during translation.