28.5 Translation of RNA: Protein Biosynthesis

The Genetic Code and tRNA

The genetic code is the set of rules cells use to translate an mRNA sequence into a chain of amino acids. Understanding this code is central to seeing how nucleic acid structure connects to protein function.

Decoding of mRNA Codons

mRNA is read in the 5' → 3' direction, three nucleotides at a time. Each group of three is called a codon, and each codon specifies either an amino acid or a signal to stop building the protein.

Since there are 4 different nucleotides, the number of possible three-letter combinations is $4^3 = 64$. That gives 64 codons total:

• 61 codons code for the 20 standard amino acids
• 3 codons (UAA, UAG, UGA) are stop codons that signal the end of the polypeptide chain

Because 61 codons map to only 20 amino acids, the code is degenerate (also called redundant). Multiple codons can specify the same amino acid. For example, both UUU and UUC code for phenylalanine. Degeneracy most often shows up in the third position of the codon, sometimes called the "wobble" position.

The genetic code is nearly universal across all living organisms. A codon means the same thing in bacteria, plants, and humans, with only minor exceptions in mitochondria and a few microorganisms.

Function of tRNA in Translation

tRNA molecules act as adapters that physically connect a codon on mRNA to the correct amino acid. Each tRNA has two critical regions:

• Anticodon (at one end): a sequence of three nucleotides complementary to a specific mRNA codon. During translation, the anticodon base-pairs with its matching codon.
• Amino acid attachment site (at the 3' end): where the corresponding amino acid is covalently bonded.

The enzyme aminoacyl-tRNA synthetase is responsible for loading the correct amino acid onto its matching tRNA. This "charging" step is crucial for accuracy because the ribosome itself doesn't verify whether the right amino acid is attached. A tRNA carrying its amino acid is called aminoacyl-tRNA (or "charged tRNA"). Once charged, the aminoacyl-tRNA delivers its amino acid to the ribosome for incorporation into the growing polypeptide.

Protein Biosynthesis

Translation is the process of reading an mRNA sequence and assembling a polypeptide chain from amino acids. It takes place in the cytoplasm on ribosomes, which are composed of ribosomal RNA (rRNA) and proteins organized into a large subunit and a small subunit. The ribosome has three internal binding sites for tRNA: the A site (aminoacyl), the P site (peptidyl), and the E site (exit).

Process of Protein Biosynthesis

Translation proceeds in three stages: initiation, elongation, and termination.

Initiation:

1. The small ribosomal subunit binds to the 5' end of the mRNA and scans until it reaches the start codon (AUG), which codes for methionine.
2. A special initiator tRNA carrying methionine base-pairs with the AUG codon in the P site.
3. The large ribosomal subunit joins, forming the complete, functional ribosome.

Elongation:

1. The next aminoacyl-tRNA enters the A site, with its anticodon base-pairing to the next mRNA codon.
2. A peptide bond forms between the amino acid in the P site and the amino acid in the A site. This reaction is catalyzed by the ribosome itself (specifically its peptidyl transferase activity, which resides in the rRNA of the large subunit, making the ribosome a ribozyme).
3. The ribosome translocates one codon along the mRNA. The tRNA that was in the A site shifts to the P site (carrying the growing chain), and the now-empty tRNA moves from the P site to the E site, where it dissociates.
4. Steps 1–3 repeat for each new codon until a stop codon is reached.

Termination:

1. When a stop codon (UAA, UAG, or UGA) enters the A site, no aminoacyl-tRNA recognizes it. Instead, a release factor protein binds to the A site.
2. The release factor triggers hydrolysis of the bond between the polypeptide and the tRNA in the P site.
3. The completed polypeptide chain is released.
4. The ribosomal subunits dissociate from the mRNA and can be recycled for another round of translation.

Protein Synthesis Overview

Protein synthesis spans two major stages. Transcription (covered in earlier sections) copies DNA into mRNA in the nucleus. Translation, described above, then reads that mRNA to build a polypeptide in the cytoplasm. The polypeptide chain subsequently folds into its functional three-dimensional shape, sometimes with the help of chaperone proteins, to become an active protein.