14.1 Genetic code and tRNA

Genetic Code

Codons and Degeneracy

The genetic code maps nucleotide sequences in mRNA to amino acids. It's read in codons, which are triplets of nucleotides. Each codon specifies either a particular amino acid or a signal to stop translation.

Because there are four possible nucleotides (A, U, C, G) and each codon is three nucleotides long, there are $4^3 = 64$ possible codons. But only 20 standard amino acids need to be encoded, so many amino acids are specified by more than one codon. This property is called degeneracy.

• Both UUU and UUC code for phenylalanine, for instance
• Leucine has six different codons (UUA, UUG, CUU, CUC, CUA, CUG)
• Degeneracy tends to occur at the third position of the codon, which matters for the wobble hypothesis (covered below)

This redundancy acts as a buffer against point mutations. A single nucleotide change, especially at the third codon position, often still produces the same amino acid. That's why degeneracy is sometimes called a built-in error tolerance.

Of the 64 codons, 61 code for amino acids and 3 are stop codons.

Start and Stop Codons

• AUG is the start codon. It initiates translation and codes for methionine. In bacteria, the initiator methionine is formylated (fMet), while in eukaryotes the initial methionine is often removed post-translationally.
• UAA, UAG, and UGA are the three stop codons. They don't code for any amino acid. Instead, when a stop codon enters the ribosomal A site, release factors bind and trigger hydrolysis of the polypeptide from the tRNA, followed by ribosome dissociation from the mRNA.

The genetic code is nearly universal across all domains of life. A few exceptions exist, most notably in mitochondrial genomes, where certain codons have been reassigned (for example, UGA codes for tryptophan in human mitochondria rather than acting as a stop codon).

tRNA Structure and Function

Transfer RNA (tRNA) and Anticodons

Transfer RNA (tRNA) is the adaptor molecule that physically connects a codon to its corresponding amino acid during translation. Without tRNA, there would be no way to convert nucleotide information into amino acid sequence.

tRNA has a distinctive cloverleaf secondary structure with four key regions:

• Acceptor stem: The 3' end where the amino acid is covalently attached. All tRNAs end with the sequence CCA at this stem.
• Anticodon loop: Contains the three-nucleotide anticodon that base-pairs with the mRNA codon in an antiparallel orientation.
• D loop (dihydrouridine loop): Contains modified uridine bases and helps with tRNA folding.
• TψC loop: Involved in ribosome binding.

In three dimensions, the cloverleaf folds into an L-shaped tertiary structure. The anticodon sits at one end of the L, and the amino acid attachment site sits at the other. This shape is critical because it positions the anticodon in the ribosome's decoding center while the amino acid end reaches into the peptidyl transferase center.

An example: a tRNA with the anticodon 3'-UAC-5' will base-pair with the mRNA codon 5'-AUG-3' (the start codon), and it carries methionine.

Aminoacyl-tRNA Synthetases and the Wobble Hypothesis

Aminoacyl-tRNA synthetases are the enzymes responsible for "charging" each tRNA with its correct amino acid. This is where translation fidelity really begins, because if the wrong amino acid gets attached, the ribosome has no way to catch the error.

The charging reaction occurs in two steps:

1. The synthetase activates the amino acid by reacting it with ATP to form an aminoacyl-AMP intermediate (releasing pyrophosphate, $PP_i$).
2. The activated amino acid is then transferred to the 3' end of the appropriate tRNA, forming an aminoacyl-tRNA (also called a "charged" tRNA).

There are typically 20 aminoacyl-tRNA synthetases per cell, one for each amino acid. Each synthetase must recognize all the tRNA molecules that correspond to its amino acid. Some synthetases also have a proofreading (editing) site that hydrolyzes incorrectly attached amino acids, further increasing accuracy.

The Wobble Hypothesis

Francis Crick proposed the wobble hypothesis to explain why fewer than 61 different tRNAs are needed to read all 61 sense codons. The key idea:

• The first two positions of the codon (read 5' to 3') form strict Watson-Crick base pairs with positions 3 and 2 of the anticodon.
• The third codon position (the "wobble position") allows non-standard base pairing with the first position of the anticodon.

Common wobble pairs include:

• G in the anticodon can pair with either C or U in the codon
• U in the anticodon can pair with either A or G in the codon
• Inosine (I) in the anticodon can pair with U, C, or A in the codon. Inosine is a modified base (deaminated adenosine) found frequently at the wobble position of tRNA anticodons.

For example, a tRNA with anticodon 3'-GAI-5' (where I = inosine) can recognize codons 5'-CUU-3', 5'-CUC-3', and 5'-CUA-3', all of which code for leucine. This means a single tRNA species can service multiple codons for the same amino acid, which is why organisms get by with fewer than 61 tRNA types.