Notes on Protein Synthesis

Chapter 30: Protein Synthesis

Essential Question

  • How is the nucleotide sequence of an mRNA molecule translated into the amino acid sequence of a protein molecule?

Outline

  • What is the genetic code?

  • How is an amino acid matched with its proper tRNA?

  • What are the rules in codon-anticodon pairing?

  • What is the structure of ribosomes, and how are they assembled?

  • What are the mechanics of mRNA translation?

  • How are proteins synthesized in eukaryotic cells?

30.1 What Is the Genetic Code?

  • The Genetic Code:

    • The genetic code is a triplet code, read from a fixed starting point in each mRNA.

    • A group of 3 bases (a codon) codes for one amino acid.

    • The code is not overlapping; each nucleotide is part of one codon.

    • All the codons have meaning and are necessary for translation.

    • The genetic code is degenerate; in most cases, each amino acid can be coded for by any of several triplet codons.

    • The base sequence is read from a fixed starting point without punctuation.

    • The genetic code is “universal”; it is consistent across almost all known organisms.

Figure 30.1 - Generalized secondary structure of tRNA molecules. Circles represent nucleotides in the tRNA sequence.

Figure 30.2 - (a) An overlapping versus a non-overlapping code. (b) A continuous versus a punctuated code.

30.2 What is the Genetic Code?

TABLE 30.1 The Genetic Code

  • Breakdown of variations of codons and their amino acid assignments is outlined.

    • First Position (3'-end), Second Position (5'-end), Third Position:

    • U: F (2) | U, C, A, G: Y (1), L (6), S (2), Stop (2)

    • C: L (2, 14), A (1), Q (1), …

    • A: I (3, L), T (5), L (9), S (1)

  • Three-out-of-four Rule:

    • The third base is often irrelevant due to codon degeneracy.

  • Unique Definitions: Certain codons have unique functions (e.g., AUG for Methionine, UGG for Tryptophan).

30.3 How Is an Amino Acid Matched with Its Proper tRNA?

  • Codon Recognition:

    • Achieved by aminoacyl-tRNAs; the appropriate aminoacyl-tRNA must match the mRNA codon through base pairing.

    • The code by which each aminoacyl-tRNA synthetase matches up its amino acid with tRNAs is referred to as a second genetic code.

  • Aminoacyl-tRNA Synthetases:

    • These enzymes interpret the second genetic code and select the correct tRNA and amino acid. They ensure fidelity during protein synthesis.

Evolution of Aminoacyl-tRNA Synthetases

  • Two classes of aminoacyl-tRNA synthetases:

    • Class I: Adds the amino acid to the 2'-OH of tRNA before moving to 3'-OH.

    • Class II: Directly adds the amino acid to the 3'-OH of tRNA.

TABLE 30.2 The Two Classes of Aminoacyl-tRNA Synthetases

  • Overview of different amino acids and their associated aminoacyl-tRNA synthetases based on classification (Class I or Class II).

The Aminoacyl-tRNA Synthetase Reaction

  • Two-Step Process:

    1. Formation of aminoacyl-adenylate.

    2. Transfer of the activated amino acid to the tRNA.

tRNA Molecules

  • tRNA has two key regions:

    • Acceptor stem at one end where the amino acid attaches.

    • Anticodon at the other end, which base-pairs with the mRNA codon.

30.4 What Is the Structure of Ribosomes, and How Are They Assembled?

  • Ribosomes:

    • Compact ribonucleoprotein particles vital for protein biosynthesis, located in the cytosol.

    • E. coli Ribosome Characteristics:

    • Diameter: 25 nm, Mass: 2520 kD.

    • Composed of two subunits:

      • 30S subunit: 930 kD with 21 proteins and 16S rRNA.

      • 50S subunit: 1590 kD with 31 proteins and two rRNAs (23S rRNA and 5S rRNA).

TABLE 30.5 Structural Organization of E. coli Ribosomes

  • Breakdown of ribosomal mass, RNA, and protein composition detailed for both subunits.

Ribosomal Features

  • Ribosomes play a major role in translation and consist of approximately 2/3 RNA by mass.

  • Presence of roughly 20,000 ribosomes in a cell, making up 20% of the cell's total mass.

30.5 What Are the Mechanics of mRNA Translation?

  • Phases of Translation:

    • Initiation: mRNA and initiator aminoacyl-tRNA bind to the small subunit; the large subunit then attaches.

    • Elongation: The ribosome moves along mRNA and synthesizes peptide bonds; tRNAs occupy the A (acceptor) and P (peptidyl) sites.

    • Termination: Occurs when a stop codon is encountered.

Ribosomal Binding Sites

  • Distinct Binding Sites for tRNA:

    • A (Acceptor) site, P (Peptidyl) site, and E (Exit) site are crucial during translation processes.

Peptide Chain Initiation in Prokaryotes

  • Required components include mRNA, both ribosomal subunits, set of initiation factors, GTP, and f-Met-tRNAifMet.

  • Initiation Factors (IF): Facilitate the formation and stability of the initiation complex.

  • Transformylation Process: The formyl group is added to Methionyl-tRNAifMet by formyl transferase.

    • N-formyl methionine is the starting amino acid for E. coli proteins, often removed post-translationally.

Shine-Dalgarno Sequence

  • The essential sequence of bases that allows for alignment of mRNA with ribosomal binding site, crucial for translation initiation.

Properties of E. coli Initiation Factors

  • Detailed breakdown of the mass, number of molecules, and functions of E. coli initiation factors.

Events of Initiation

  • Evolution of the initiation complex involves multiple molecular interactions and the binding of initiation factors and ribosomal subunits.

Peptide Chain Elongation in Prokaryotes

  • Various elongation factors and their roles are outlined; this includes steps of amino-acid tRNA binding, peptide bond formation, and translocation of tRNA within the ribosome.

    • Significant percentages of total protein components in E. coli dedicated to synthesis efficiency.

Peptidyl Transfer

  • This central reaction involves no energy input and is catalyzed by the peptidyl transferase activity associated with 23S rRNA in the 50S subunit.

Peptide Chain Termination

  • Release factors identify stop codons, facilitating the release of newly synthesized polypeptides from the ribosome.

30.6 How Are Proteins Synthesized in Eukaryotic Cells?

  • Post-Transcriptional Modifications:

    • Eukaryotic mRNAs feature a 5'-terminal 7-methyl-GTP cap and a 3'-terminal poly(A) tail.

  • Translation Initiation:

    • More elaborate than the prokaryotic process; involves additional initiation factors and the scanning of mRNA to locate the start codon, AUG.

TABLE 30.9 Properties of Eukaryotic Translation Initiation Factors

  • Overview of various factors, their functions, sizes, and roles in the eukaryotic translation process.

Diphtheria Toxin Mechanism

  • Affects eEF2, inactivating it by ADP-ribosylation, which can lead to cell death at low concentrations.

Inhibitors of Protein Synthesis

  • Overview of various antibiotics and their mechanisms of action in inhibiting prokaryotic and eukaryotic protein synthesis, including their clinical applications.

Summary

  • Protein synthesis is a complex process essential for cell function and regulation, featuring distinct mechanisms in prokaryotic versus eukaryotic cells, underscored by various factors and sequences crucial to the initiation, elongation, and termination phases.