Chapter 9

The Molecular Biology of Translation

Overview of Genetic Information Flow

Translation is the process by which the genetic code carried by mRNA is decoded to produce a specific polypeptide, or protein. This process is a key component of the central dogma of molecular biology, which describes the flow of genetic information from DNA to RNA to protein.

• Transcription: DNA is transcribed into messenger RNA (mRNA).

• Translation: mRNA is translated into a polypeptide chain at the ribosome.

• Polypeptide directionality: The N-terminus (amino end) corresponds to the start codon, and the C-terminus (carboxyl end) corresponds to the stop codon.

mRNA Structure and Codons

Messenger RNA (mRNA) contains both coding and non-coding regions that are essential for translation.

• 5' and 3' Untranslated Regions (UTRs): Segments outside the translated region; contain regulatory sequences such as the Shine-Dalgarno (bacteria) or Kozak (eukaryotes) sequences.

• Codons: Triplets of nucleotides (A, U, C, G) that specify amino acids. There are 64 possible codons for 20 standard amino acids, making the code redundant but not ambiguous.

• Start Codon: AUG (codes for methionine).

• Stop Codons: UAA, UAG, UGA (do not code for any amino acid).

tRNA and Ribosome Structure

Transfer RNA (tRNA) and ribosomes are essential for decoding mRNA and synthesizing proteins.

• tRNA: Adaptor molecules with an anticodon region that base-pairs with mRNA codons and an acceptor stem for amino acid attachment.

• Charging: Aminoacyl-tRNA synthetases attach the correct amino acid to each tRNA using ATP.

• Wobble Hypothesis: Flexible base pairing at the third codon position allows fewer tRNA types to recognize multiple codons.

• Ribosome: Composed of large and small subunits, with three key sites: A (aminoacyl), P (peptidyl), and E (exit).

Stages of Translation

Translation occurs in three main stages: initiation, elongation, and termination.

Initiation

• Bacteria: The small ribosomal subunit binds the Shine-Dalgarno sequence on mRNA, and the initiator tRNA (fMet-tRNAfMet) pairs with the start codon.

• Eukaryotes: The small subunit, initiation factors, and initiator tRNA scan the mRNA for the Kozak sequence and start codon.

• Large ribosomal subunit joins, forming the complete initiation complex.

Elongation

• Charged tRNAs are recruited to the A site.

• Peptidyl transferase catalyzes peptide bond formation between amino acids at the P and A sites.

• The ribosome translocates along the mRNA, moving the tRNA from the A site to the P site, and the uncharged tRNA exits via the E site.

Termination

• When a stop codon enters the A site, release factors bind and trigger the release of the polypeptide chain.

• The ribosome dissociates, and the mRNA is released.

Comparing Bacterial and Eukaryotic Translation

There are key differences between translation in prokaryotes and eukaryotes:

• Ribosome Size: Prokaryotes have 70S ribosomes (50S + 30S), eukaryotes have 80S ribosomes (60S + 40S).

• Initiation Sequences: Shine-Dalgarno in bacteria, Kozak in eukaryotes.

• Simultaneity: In bacteria, transcription and translation can occur simultaneously; in eukaryotes, they are separated by the nuclear envelope.

Protein Structure and Function

The sequence of amino acids in a polypeptide determines its three-dimensional structure and function. The side chains (R groups) of amino acids confer specific chemical properties, influencing protein folding and activity.

• Primary Structure: Linear sequence of amino acids.

• Secondary, Tertiary, and Quaternary Structures: Higher-order folding and assembly of polypeptide chains.

• Mutations: Single nucleotide changes can have significant or negligible effects on protein function, depending on their location and nature.