Final answer:
Preferred codons are associated with the most abundant tRNA molecules in a cell, and reflect codon bias - a feature that can influence the efficiency of protein synthesis, with GC-rich codons often encoding charged amino acids and codons containing a middle U encoding uncharged ones.
Step-by-step explanation:
Preferred codons are represented by the most abundant tRNA molecules that correspond to them within the cell. The genetic code is a universal code of three-base codons that encodes genetic instructions for the amino acid sequences of proteins. In the context of codon bias, some organisms show preference for certain codons which is often reflected in a genome's nucleotide composition. For example, charged (polar) amino acids are encoded by triplet codons with more G (guanine) bases, indicating a GC-rich codon bias. Conversely, codons for uncharged amino acids more often contain a middle U (uracil) than any other base, which may indicate a relative abundance of such tRNAs in the cell.
The triplet codons have patterns of redundancy known as degeneracy. This means that several codons can code for the same amino acid, with the third nucleotide being the least important for determining the amino acid, often called the 'wobble position'. Of the 64 possible mRNA codons, three are stop codons, and one is the start codon AUG, which is also the codon for methionine. The second position of a codon is the most crucial for amino acid specificity.
Different organisms may have different levels of certain tRNAs, which can lead to a bias towards using certain codons that correspond to the most abundant tRNA, optimizing the efficiency of protein synthesis. This codon bias can be influenced by the overall nucleotide bias in the organism's genome, which in turn can affect genetic code expression.