ch13

Introduction to Translation

  • Process by which messenger RNA (mRNA) is translated into protein.

  • Involves the ribosome, transfer RNA (tRNA), and various factors.

  • Ribosomes are composed of large (50S) and small (30S) subunits:

    • 50S subunit: Contains the peptidyl (P) & exit (E) sites.

    • 30S subunit: Contains the aminoacyl (A) site.

Topics Covered

  1. Codons: Sense and nonsense codons explained.

  2. Characteristics of the Genetic Code: Features that define the genetic code.

  3. Amino Acids: Their role in protein synthesis; tRNA and ribosome structure discussed.

  4. Translation in Bacteria: Process specifics.

  5. Translation in Eukaryotes: Comparison to bacterial translation.

  6. Nonsense Suppressor Mutations: Impact and mechanisms.

  7. Nonsense-mediated Decay: Mechanism of mRNA surveillance.

  8. Posttranslational Modifications: Changes occurring after protein synthesis.

Translation and the Genetic Code
13.2 The Relationship between the Genetic Code and Protein Synthesis

  • In 1958, Francis Crick formulated the central dogma of molecular genetics:

    • Information flow: DNA → RNA → Protein.

    • Transcription: DNA is transcribed into RNA.

    • Translation: RNA is translated into proteins.

  • Major types of RNA involved:

    • Messenger RNA (mRNA): Codes for amino acids.

    • Ribosomal RNA (rRNA): Combines with proteins to form ribosomes.

    • Transfer RNA (tRNA): Carries amino acids to the ribosome during protein synthesis.

    • Micro RNA (miRNA): Regulates gene expression.

    • Small interfering RNA (siRNA): Regulates mRNA stability.

    • Telomerase RNA: Maintains telomere length in eukaryotes.

Functions of Major RNA Molecules

  • Messenger RNA (mRNA): Encodes amino acids in polypeptides; may be polycistronic in prokaryotes (multiple proteins) or monocistronic in eukaryotes (single protein).

  • Ribosomal RNA (rRNA): Forms the structure of ribosomes; crucial for ribosomal function.

  • Transfer RNA (tRNA):

    • Has an anticodon that pairs with the codon on mRNA.

    • Essential for assembling amino acids into a polypeptide chain.

  • Small Nuclear RNA (snRNA): Plays a role in splicing precursor mRNA.

  • MicroRNA (miRNA): Regulates mRNA stability and translation efficiency.

The Genetic Code

  • Consists of nucleotide triplets called codons; each codon specifies an amino acid or a stop signal.

  • Types of Codons:

    • Sense codon: Codes for an amino acid (e.g., AUG).

    • Start codon for translation: AUG (codes for methionine in eukaryotes and fMet in bacteria).

    • Nonsense codon: Does not code for any amino acid (e.g., UAA, UAG, UGA).

  • Codon structure and implications:

    • A codon is defined as a sequence of three RNA nucleotides that corresponds to a specific amino acid or stop signal.

Characteristics of the Genetic Code

  1. Universal: The genetic code is nearly the same in all organisms.

  2. Degenerate: More than one codon can code for the same amino acid.

  3. Redundant: Some amino acids are coded by multiple codons, with variations in third base (wobble).

  4. Non-overlapping: Each nucleotide is part of only one codon.

  5. Contiguous: Coding regions are composed of a continuous string of codons (open reading frame - ORF), excluding UTRs.

  6. Wobble: The third nucleotide in codons can vary; flexibility in base pairing allows for tRNA to recognize multiple codons.

Peptide Bond Formation

  • Proteins (polypeptides) are chains of amino acids linked by peptide bonds.

  • Sequence determines 3D shape and functionality of proteins.

Structure and Function of tRNA (13.4)

  • tRNA is charged with a specific amino acid by aminoacyl-tRNA synthetases; there are 20 different synthetases (one for each amino acid).

Ribosome Structure (13.5)

  • Composed primarily of rRNA (~67% of the ribosome mass) and proteins.

  • Ribosomal sites:

    • A site: Accepts incoming tRNA.

    • P site: Holds the tRNA carrying the growing polypeptide chain.

    • E site: Contains uncharged tRNA ready to exit the ribosome.

Stages of Translation (13.6)
1. Initiation (in Bacteria)

  • 30S binds to mRNA at the Shine-Dalgarno sequence.

  • Initiator tRNA carrying fMet binds to the start codon (AUG).

  • 50S joins 30S with initiator tRNA in the P site.

2. Elongation

  • Steps include:

    1. tRNA corresponding to the next codon binds in the A site.

    2. Peptidyl transferase catalyzes the formation of a peptide bond.

    3. Ribosome translocates, moving tRNA from A to P site, and nonsense tRNA to E site.

  • Polyribosomes: Multiple ribosomes can translate the same mRNA simultaneously.

3. Termination

  • When a stop codon is reached, a release factor binds to the A site, leading to the release of the newly synthesized polypeptide and dissociation of ribosomal components.

Comparison of Bacterial and Eukaryotic Translation

  • Eukaryotes:

    • Ribosomes are larger (80S) compared to bacteria (70S).

    • Use of the 7-methylguanosine cap for initiation.

    • More initiation factors required for the assembly of the initiation complex.

    • Kozak's rules for identifying the start codon during scanning.

Nonsense Suppressor Mutations

  • Allow insertion of an amino acid where a stop codon would normally halt translation.

  • Example of Transcription and Translation outcomes with normal versus mutant tRNA.

Nonsense-Mediated Decay (NMD)

  • Detrimental response to mRNA containing premature termination codons (PTCs).

  • Exon Junction Complexes (EJCs) play a role in marking splicing completion.

  • PTCs prevent downstream EJCs from being displaced, triggering degradation of the mRNA.

  • Clinical relevance with diseases like cystic fibrosis and Duchenne muscular dystrophy.

Posttranslational Modifications

  • Protein Folding: Assisted by chaperon proteins.

  • Terminal Modifications: For example, removal of the formyl group from fMet in bacteria.

  • Modification of Individual Amino Acids:

    • Phosphorylation, acetylation, methylation, glycosylation, carboxylation, etc.

  • Proteolytic Processing: Conversion of inactive precursors to active forms (example: insulin).

  • Addition of Prosthetic Groups: Need for co-factors such as vitamins and metal ions.

  • Protein Trafficking: Directs proteins to specific cellular compartments based on signal sequences.

Ubiquitination: Targets proteins for degradation in the 26S proteasome if deemed nonfunctional or damaged.