15.5 Ribosomes and Protein Synthesis

Ribosomes and Protein Synthesis

Ribosomes read the genetic code from mRNA and build proteins by linking amino acids together in the correct order. This process, called translation (or protein synthesis), is how genetic information becomes functional molecules. Since proteins carry out most cellular functions, understanding translation is central to understanding how cells work and respond to their environment.

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

Steps of Protein Synthesis

1. Initiation

This is the assembly phase, where the ribosome finds the right starting point on the mRNA.

• The small ribosomal subunit binds to the mRNA and locates the start codon (AUG), which marks the beginning of the protein-coding sequence.
• An initiator tRNA carrying the amino acid methionine base-pairs with the start codon in the ribosome's P site.
• The large ribosomal subunit joins, forming a complete ribosome ready to build the polypeptide.

Every protein begins with methionine because AUG is always the start codon. (Sometimes the methionine is removed later.)

2. Elongation

This is where the protein actually gets built, one amino acid at a time.

1. A tRNA with an anticodon complementary to the next mRNA codon enters the A site.
2. Peptidyl transferase (part of the ribosome itself) catalyzes a peptide bond between the amino acid in the A site and the growing chain in the P site.
3. The ribosome translocates (shifts) one codon down the mRNA. The tRNA that was in the A site moves to the P site, the spent tRNA in the P site moves to the E site and exits, and the A site is now open for the next tRNA.
4. This cycle repeats, adding amino acids according to the mRNA sequence.

3. Termination

Translation ends when the ribosome hits a stop codon (UAA, UAG, or UGA). No tRNA recognizes these codons. Instead:

1. Release factors bind to the stop codon in the A site.
2. The release factors trigger hydrolysis of the bond between the polypeptide and the tRNA in the P site.
3. The completed polypeptide is released.
4. The ribosome dissociates into its two subunits, which can be recycled for another round of translation.

Key Players During Translation

Ribosomes

Ribosomes consist of a small and large subunit that come together on the mRNA. They have three tRNA binding sites:

• A site (aminoacyl): where new charged tRNAs enter
• P site (peptidyl): where the tRNA holding the growing polypeptide chain sits
• E site (exit): where uncharged tRNAs leave the ribosome

A helpful way to remember: A = Arrival, P = Polypeptide, E = Exit.

The ribosome also has enzymatic activity. Peptidyl transferase, which forms peptide bonds, is actually catalyzed by the rRNA in the large subunit (making it a ribozyme, not a traditional protein enzyme).

tRNAs

tRNAs are adapter molecules that physically connect the mRNA code to the correct amino acid. Each tRNA has:

• An anticodon (a three-nucleotide sequence) that base-pairs with a complementary mRNA codon
• An amino acid attachment site at its 3' end

Before translation, aminoacyl-tRNA synthetases attach the correct amino acid to each tRNA. There's a different synthetase for each amino acid, and this matching step is critical for accuracy. If the wrong amino acid gets loaded, the wrong protein gets made.

Amino Acids

These are the building blocks of proteins. The sequence in which amino acids are joined determines the protein's shape and function. They're linked by peptide bonds during elongation, forming a polypeptide chain.

The Genetic Code and Protein Structure

The genetic code is the set of rules that maps three-nucleotide sequences in mRNA to specific amino acids.

• Codons are three-nucleotide sequences on mRNA. Each codon specifies one amino acid (or a stop signal). With four possible bases at each of three positions, there are $4^3 = 64$ possible codons coding for just 20 amino acids, which means the code is redundant (multiple codons can code for the same amino acid).
• A polypeptide is a chain of amino acids linked by peptide bonds. This chain forms the primary structure of a protein, which then folds into higher-order structures that determine function.
• Nucleotides are the basic units of nucleic acids (DNA and RNA), each consisting of a sugar, a phosphate group, and a nitrogenous base.

Prokaryotic vs. Eukaryotic Protein Synthesis

Translation follows the same basic logic in all cells, but there are notable differences between prokaryotes and eukaryotes.