Translation of mRNA

Translation of mRNA

Introduction

• Overview of mRNA Translation
    - Process converts mRNA codons into amino acid sequences, leading to protein synthesis.
    - Involves various cellular components: proteins, RNAs, and small molecules.
    - Discusses molecular features of mRNA translation.

13.1 The Genetic Basis for Protein Synthesis

• Role of Proteins:
    - Central to cell structure and function.
• Transcription of Genes:
    - Genes encoding polypeptides are termed protein-encoding or structural genes.
    - Transcription process creates messenger RNA (mRNA).
• Function of Genetic Material:
    - Encodes production of cellular proteins at the right time and amount.

13.2 The Relationship Between the Genetic Code and Protein Synthesis

• Translation:
    - Interprets nucleotide language of mRNA into the amino acid language of proteins.
    - Relies on the genetic code.
    - mRNA: encoded in groups of three nucleotides called codons.
• Genetic Code Characteristics:
    - Codon Table Reference (Table 13.1): Outlines codon sequences and corresponding amino acids.

Table 13.1: The Genetic Code

• Special Codons:
    - AUG: Start codon (specifies methionine).
    - UAA, UAG, UGA: Stop codons; terminate translation.
    - Degeneracy: More than one codon can specify the same amino acid.
    - E.g., GGU, GGC, GGA, GGG all code for glycine.
    - The third base is often variable.
    - Universality: The code is nearly universal with few exceptions (see Table 13.2).

13.3 Other Exceptions to the Genetic Code

• Special Amino Acids:
    - Selenocysteine and Pyrrolysine: Considered 21st and 22nd amino acids, found in specialized enzymes.
    - Encoded by UGA and UAG codons, respectively.
    - Require specific tRNAs that transport them to the ribosome and need downstream sequences in mRNA for incorporation.

Overview of Gene Expression

• Transcription and Translation: (Figure 13.3)
    - Coding strand of DNA to mRNA message, then to polypeptide.
• Directionality in Polypeptide Chain:
    - Peptide bond forms between carboxyl group of last amino acid and amino group of the incoming amino acid.
    - Result is N-terminal (amino terminal) and C-terminal (carboxyl terminal) ends in polypeptide.

Amino Acids and Protein Structure

• Types of Amino Acids:
    - Nonpolar, Aliphatic: Hydrophobic, typically found in interior of folded proteins.
    - Aromatic: Contains cyclic structures with conjugated double bonds.
    - Polar, Neutral: Often found on protein surfaces.
    - Polar, Acidic: Have side chains that can donate protons.
    - Polar, Basic: Have side chains that can accept protons.
    - Nonstandard Amino Acids: Occur infrequently in proteins, with specific functions.

Levels of Structure in Proteins

• Four Levels:
    1. Primary Structure: Amino acid sequence (Figure 13.6).
    2. Secondary Structure: Regular structures, such as alpha helices and beta sheets. Stabilized by hydrogen bonds.
    3. Tertiary Structure: Three-dimensional shape from folding and interactions.
    4. Quaternary Structure: Assembly of two or more polypeptides into functional proteins.

Functions of Proteins

• Roles:
    - Key cell characteristics depend on protein types made.
    - Enzymatic functions in speeding up chemical reactions: chemical modifications, cleavage, synthesis.

13.4 Structure and Function of tRNA

• Adaptor Hypothesis by Francis Crick:
    - tRNA recognizes mRNA codons and carries corresponding amino acids.
• tRNA Structure:
    - Cloverleaf pattern with stem-loop structures, and an acceptor stem (3’ single strand region). Includes modified nucleotides.

tRNA Charging Process

• Aminoacyl-tRNA Synthetases: Enzymes attaching amino acids to tRNAs, one for each amino acid.
    - Catalyze two-step process using amino acid, tRNA, ATP.
    - Results in charged tRNA.

tRNAs and the Wobble Rule

• Degeneracy in Genetic Code: The third position in codons can wobble, accommodating mismatches.
• Isoacceptor tRNAs: Different tRNAs that can recognize the same codon.

13.5 Ribosome Structure and Assembly

• Ribosome Types:
    - Bacteria: Single type of ribosome in cytoplasm.
    - Eukaryotes: Two types in cytoplasm and organelles.
• Ribosome Composition:
    - Large and small subunits formed from proteins and rRNA.
    - Different sedimentation coefficients for bacterial (70S) and eukaryotic (80S) ribosomes.

Functional Sites of Ribosomes

• Ribosomes have three sites:
    - Peptidyl (P) Site: Holds the tRNA carrying the growing polypeptide chain.
    - Aminoacyl (A) Site: Accommodates the incoming charged tRNA.
    - Exit (E) Site: Where uncharged tRNAs exit the ribosome.

13.6 Stages of Translation

• Overview: Takes place in three stages: initiation, elongation, and termination (Figure 13.14).

Initiation Stage

• mRNA, initiator tRNA, and ribosomal subunits form an initiation complex.
• In bacteria, initiator tRNA recognizes the start codon AUG, GUG, or UUG.
    - Utilizes initiation factors (IF1, IF2, IF3) and the Shine-Dalgarno sequence for effective binding.

Elongation Stage

• Amino acids added one by one through a coordinated series of steps (Figure 13.17).
    - Bacterial elongation rate: 15-20 amino acids/second.
    - Eukaryotic elongation rate: 2-6 amino acids/second.

Termination Stage

• Stop codons (UAG, UAA, UGA) trigger termination process.
    - Release factors recognize stop codons and dissociate components (Figure 13.18).

13.7 Comparison of Bacterial and Eukaryotic Translation

• Differences in processes due to structural variations in ribosomes, mRNA, and initiation factors (Table 13.7).

13.8 Antibiotics Affecting Translation

• Certain antibiotics inhibit translation in bacteria by targeting bacterial components without affecting eukaryotic translation (Table 13.8).
• Examples include:
    - Chloramphenicol: Blocks elongation as a competitive inhibitor of peptidyl transferase.
    - Erythromycin: Interferes with translocation by binding to 23S rRNA.
    - Puromycin: Causes premature release of polypeptide.
    - Tetracycline: Inhibits binding of aminoacyl-tRNAs.
    - Streptomycin: Misreads codons, producing abnormal proteins.