Protein Translation

Overview of Translation

  • Translation = decoding of messenger RNA (mRNA) from nucleic-acid language into amino-acid language (protein).
  • Central Dogma flow referenced:
    • DNA (double-stranded; coding strand 5' \rightarrow 3', template strand 3' \rightarrow 5').
    • During transcription, RNA polymerase copies the template strand → complementary pre-mRNA produced 5' \rightarrow 3'; sequence identical to coding strand except U replaces T.
  • Protein synthesis direction: polypeptide grows from amino (N-) terminus → carboxyl (C-) terminus while ribosome reads mRNA 5' \rightarrow 3'.

Genetic Code Fundamentals

  • Triplet (codon) system → 4^3 = 64 possible triplets.
  • Start/Initiation codon: AUG → methionine (Met, one-letter M).
    • Sets the reading frame for subsequent codons.
  • Stop/Termination codons: UAA, UAG, UGA → signal end of translation; no amino acids specified.
  • Codon catalogue:
    • Every amino acid has ≥1 codon; frequently used residues (Arg, Gly, Leu, Pro, Ser) have multiple.
    • Example one-letter & three-letter abbreviations provided (e.g.
    • Met = M = MET).

Reading Frame & Its Importance

  • Any mRNA region can be read in three potential frames; wrong frame → entirely different protein.
  • Example sequence (simplified from slide):
    1. Frame 1 (starts CUC): Leu – Ser – Val – Thr.
    2. Frame 2 (starts UCA): totally different amino-acid composition.
    3. Frame 3 (starts ???): again different output.
  • Therefore AUG’s first appearance establishes the correct frame, preventing frameshift errors.

Codon Table Usage

  • One typical layout:
    • 1st base on left, 2nd across top, 3rd on right.
  • Lookup example: AUG
    1. Row A (1st base) → restricts to block.
    2. Column U (2nd base).
    3. Third base G within block → identifies Met/start.
  • Students must practice decoding any triplet and reverse-translating amino-acid strings.

Properties of the Genetic Code

  • Composed of non-overlapping triplets (no gaps/commas).
  • Degenerate (redundant): multiple codons per amino acid.
    • Silent mutation example: original CCC (Pro) → CCG via 3rd-base C→G still codes Pro.
  • Ordered: AUG (start) & three dedicated stops clearly demarcated.
  • Nearly universal among all living organisms.

Translation Machinery & Molecular Players

  • Ribosome
    • Two subunits (large + small) composed of ribosomal RNA (rRNA) & proteins.
    • Contains 3 functional sites:
    1. A site (Aminoacyl/Arrival) – incoming aa-tRNA.
    2. P site (Peptidyl) – holds tRNA with growing chain; peptidyl-transferase activity.
    3. E site (Exit) – deacylated tRNA leaves.
  • Transfer RNAs (tRNAs)
    • Cloverleaf adapters; each carries a specific amino acid to the ribosome.
    • Anticodon (3 bases) pairs antiparallel & complementary to mRNA codon (e.g. start tRNA anticodon = UAC).
  • Amino-acyl tRNA synthetases ("amino-acid activating enzymes")
    • 20 highly specific enzymes; attach correct amino acid to its cognate tRNA (require ATP).
  • Soluble initiation, elongation, and termination factors
    • Proteins that facilitate assembly, translocation, GTP usage, and polypeptide release.
  • Release factors (RFs)
    • Recognize stop codons; trigger hydrolysis of peptide-tRNA bond → release nascent protein.

Mechanism of Translation

Initiation

  • Small ribosomal subunit + initiator Met-tRNA form a pre-initiation complex.
  • Complex scans mRNA 5' \rightarrow 3' until first AUG encountered → anticodon UAC pairs.
  • Large subunit joins → completed 80S (eukaryotic) or 70S (prokaryotic) initiation complex.
  • Met-tRNA located in P site; A & E sites empty.

Elongation (cyclic process)

  1. aa-tRNA delivery: Next codon exposed in A site; corresponding charged tRNA enters.
  2. Peptide bond formation: Peptidyl-transferase (rRNA catalytic) moves growing chain from P-site tRNA to amino acid on A-site tRNA.
  3. Translocation: Ribosome shifts one codon toward 3' end of mRNA.
    • Former A-site tRNA (now bearing chain) → P site.
    • Deacylated P-site tRNA → E site → exits.
  4. Repeat until stop codon appears.

Termination

  • When UAA/UAG/UGA enters A site:
    • No matching tRNA; instead release factor binds.
    • Hydrolyzes ester bond, freeing polypeptide into cytoplasm.
    • Ribosomal subunits, mRNA, and RF dissociate; components recycled.

Summary & Key Takeaways

  • Translation integrates three RNA types (mRNA, rRNA, tRNA) + numerous proteins/enzymes.
  • Directionality: mRNA read 5' \rightarrow 3'; protein synthesized N → C terminus.
  • Start: AUG (Met); Stop: UAA, UAG, UGA.
  • Genetic code: 64 triplets → 61 sense (encode 20 amino acids) + 3 stop.
  • Code is non-overlapping, degenerate, ordered, nearly universal.
  • Accurate amino-acid incorporation depends on:
    • Correct amino-acylation of tRNA.
    • Proper reading frame initiation.
    • Cyclic interplay of A, P, E sites during elongation.
  • Silent mutations often occur in 3rd position due to degeneracy; more deleterious frameshifts avoided by strict AUG frame setting.
  • Post-translationally, initial Met can be removed or modified.