Genetic Code and Translation

The Genetic Code

The Genetic Code Overview

  • Definition: The genetic code consists of codons, which are sequences of three nitrogenous bases (nucleotides) in DNA or mRNA that code for amino acids.

  • Presentation: Codons are represented in mRNAs in the 5' to 3' orientation.

  • Key Codons:
      - Start Codon: AUG, which codes for methionine.
      - Stop Codons: UAA, UAG, UGA (do not code for any amino acids).

Reading Frame

  • Definition: A linear sequence of codons in a nucleic acid defined by a start codon and ending with a stop codon, establishing how the sequence is read by the ribosome.

Codon Table

Codon to Amino Acid Mapping

  • Start Codon: AUG (Methionine - Met)

  • Stop Codons: UAA, UAG, UGA.

  • Codon List:
      - UUU - Phenylalanine (Phe)
      - UUC - Phenylalanine (Phe)
      - UUA - Leucine (Leu)
      - UUG - Leucine (Leu)
      - CUU - Leucine (Leu)
      - …
      - GUA - Valine (Val)
      - GUC - Valine (Val)
      - AUG - Methionine (Met)

Characteristics of the Genetic Code

  • Unambiguous: Each of the 61 triplets codes for only one of the 20 amino acids.

  • Degenerate: Most amino acids are encoded by more than one codon.

  • Universal: Most living organisms use the same code, though exceptions exist (e.g., some mitochondrial codes).

  • Commaless: Codons are read continuously without breaks in the reading frame.

  • Non-overlapping: Codons in a reading frame do not overlap; they are read in sequence.

Flow of Genetic Information

Components

  • DNA: Template strand transcribed into mRNA.

  • mRNA: Carries codons for translation.

  • Proteins: Resulting polypeptide chains formed through translation.

Mutations

Substitution Mutations

  • Definition: A mutation where a base is replaced by a different base in DNA resulting in a permanent single-codon change in a protein-coding gene.

  • Types:
      - Silent Mutation: The new codon codes for the same amino acid as the original codon.
      - Missense Mutation: The new codon codes for a different amino acid.
      - Nonsense Mutation: The new codon is a stop codon, resulting in a shorter polypeptide.

  • Causes: Spontaneous mutations or errors in DNA replication.

Examples of Substitution Mutations

  • Wild-type: AUG ACA CGG AGU AGA UAU UAA (Met Thr Arg Ser Arg Tyr Stop)

  • Silent: AUG ACA CGG AGC AGA UAU UAA (Met Thr Arg Ser Arg Tyr Stop)

  • Missense: AUG ACA CGG AAU AGA UAU UAA (Met Thr Arg Asn Arg Tyr Stop)

  • Nonsense: AUG ACA CGG AGU UGA UAU UAA (Met Thr Arg Ser Stop)

Insertion and Deletion Mutations

  • Insertion: A mutation where a single base is added, resulting in a frameshift mutation.

  • Deletion: A single base is removed, also resulting in a frameshift mutation.

  • Impact: All codons from the insertion or deletion site onward are altered, potentially leading to nonfunctional proteins.

Translation Process

Requirements

  • mRNA

  • Charged tRNA (transfer RNAs with attached amino acids)

  • Ribosome

  • Other Requirements: Initiation factors, elongation factors, and energy sources (GTP); no primers needed.

Transfer RNA (tRNA)

Structure

  • Cloverleaf Model: tRNA is a single RNA molecule with intramolecular base pairings.

  • Function: The anticodon loop base-pairs with a codon in mRNA, and an amino acid is attached to the 3' end of the tRNA.

Unusual Bases

  • Inosine: A modified adenine found in tRNAs formed through post-transcriptional modifications.

Wobble Hypothesis

  • Concept: The interaction between the third position of mRNA codons and the first position of tRNA anticodons is less strict; this 'wobble' allows some tRNA bases to pair with multiple mRNA bases, reducing the need for all possible tRNA types.

  • Example: Inosine can pair with multiple bases in the wobble position of tRNA.

Anticodon-Codon Base Pairing Rules

  • tRNA Base Pairing:
      - 5’ base: A pairs with U or G; C pairs with G; G pairs with C or U; U pairs with A or G; Inosine can pair with A, U, or C.

Charging of tRNA

Process

  • Step 1: Amino Acid Activation: Amino acid is converted to aminoacyladenylic acid (AA-AMP). This step requires ATP.
      - Energy-consuming: This step is crucial for forming peptide bonds later.

  • Step 2: Charging: AA-AMP loses AMP; the carboxyl group of the amino acid attaches to the 3' end of tRNA resulting in charged tRNA.

Ribosomes

Prokaryotic Ribosome Structure

  • Definition: A complex of ribosomal RNA (rRNA) and proteins where translation occurs.

  • Subunits:
      - Small Subunit: 30S
      - Large Subunit: 50S
      - Complete Ribosome: 70S

  • Svedberg Unit: Measures the rate particles sediment in a centrifugal field, which provides insights on size, shape, and molecular weight.

Initiation of Translation Steps

  1. Binding: mRNA binds to the small ribosomal subunit positioned with the AUG codon at the P site.

  2. tRNA Binding: f-Met-tRNA binds to the AUG codon.

  3. Joining of Large Subunit: The large subunit joins the complex. This requires GTP and initiation factors (IF proteins).

Ribosome Sites

  • P Site: Peptidyl site

  • A Site: Aminoacyl site

  • E Site: Exit site

Elongation of the Polypeptide Chain

  • Aminoacyl-tRNA: The second tRNA enters the A site facilitated by elongation factor EF-Tu and GTP.

  • Peptide Bond Formation: The amino acid on the first tRNA forms a peptide bond with the amino acid on the second tRNA.

  • Ribosome Movement: The ribosome shifts to accommodate the next codon.

Summary of Translation Process

Initiation

  • The initiation complex is formed with mRNA and initiator tRNA.

Elongation

  • New tRNAs sequentially bind to the A site, resulting in di- to tripeptide formation as the ribosome progresses along the mRNA.

Termination of Translation

  • A stop codon moves to the A site.

  • Release Factors: RF1 binds to stop codons, signaling the termination of protein synthesis.

  • Disassembly: The GTP-dependent RF3 releases the polypeptide from the last tRNA, dissociating the complex.

  • No tRNAs bind to stop codons, concluding the translation process.

Polyribosomes

  • Definition: Structures where multiple ribosomes translate the same mRNA simultaneously, allowing rapid protein synthesis.