Human Biochemistry, Volume 2 - Murray R. 1993

Structure, Function, and Replication of Informational Macromolecules
Protein Synthesis and the Genetic Code
Codons and Protein Synthesis

The nucleotide sequence of an mRNA molecule contains codons for every amino acid. Transfer RNA (tRNA) molecules act as adapters that translate the codon sequence into the Amino Acid Sequence of a protein. The intracellular component where all elements of the protein Translation machinery converge and interact is called the ribosome. Multiple Ribosomes can simultaneously translate a single mRNA strand, forming structures known as polyribosomes (Polysomes). The rough Endoplasmic reticulum is a cellular compartment where membrane-bound polysomes produce both Membrane Proteins and proteins destined for excretion and transport. Polyribosome structures also exist freely in the Cytoplasm, where they synthesize intracellular proteins.

The synthesis of cellular proteins requires 20 Amino Acids. Consequently, there must be at least 20 different codons comprising METABOLISM/28.html">The Genetic Code. Since mRNA consists of only four types of NUCLEOTIDES, each codon must be composed of more than one nucleotide. Two-nucleotide codons could provide only 16 (4²) different codon variants, whereas three-nucleotide codons yield 64 (4³) variants.

From a series of studies initiated by Matthaei and Nirenberg, we know that each codon consists of three nucleotides; in other words, the code is triplet-based. The cracking of the genetic code was accomplished largely in Nirenberg's laboratory. The success of this work was profoundly driven by the research of Khorana, who synthesized nucleotide polymers, including those with a triplet Structure.

Three of the 64 codons do not code for any Amino Acids and are termed nonsense codons. At least two of these function as termination signals, dictating where the Synthesis of the polypeptide chain must stop. The functional role of the remaining triplets is to code for the 20 amino acids. A crucial property of the genetic code is its degeneracy, meaning that multiple codons encode the same amino acid. An Analysis of the genetic code table (Table 40.1) reveals that all 64 codons can be divided into 16 families. A single family groups together codons that share identical nucleotide bases at the First and Second positions. In the table, each family occupies a vertical Column between the horizontal lines. For example, the codon CCN, where N can be U, C, A, or G, defines the family In the second column located between the first and second horizontal dividing lines. In some families, all four codons encode the same amino acid, as in the aforementioned CC family. Such families are called non-mixed; eight out of the 16 families are non-mixed.

Class="center">Table 40.1. The genetic code (functional meaning of codons in Messenger RNA)¹⁾

¹⁾ The terms first, second, and third refer to THE POSITION OF the given nucleotide in the triplet codon: U denotes uridine nucleotide; C, cytidine nucleotide; A, adenosine nucleotide; G, guanosine nucleotide. The Methionine codon AUG acts as the initiation codon; Term represents the termination codon (three-letter amino acid Abbreviations are explained in Chapter 3).

²⁾ In mammalian Cell/35.html">Mitochondria, AUA codes for Met, UGA codes for Trp, and AGA and AGG function as terminators.

Families that encode more than one amino acid are called mixed families. In six mixed families, codons with a pyrimidine nucleotide at the third position encode one amino acid, whereas codons with a purine at the end encode another amino acid or a termination signal (Table 40.1). The remaining two families—the UG and AU families—do not belong to either of the aforementioned types and are unique in this sense. Thus, in terms of the Specificity of incorporating a particular amino acid, the third nucleotide in codons is generally less critical than the first two. This is precisely how the aforementioned degeneracy of the code is manifested. At the same time, each given codon corresponds to one and only one specific amino acid. In this sense, the genetic code is strictly unambiguous. It is important to clearly understand the fundamental difference between these two vital properties—degeneracy and unambiguity—which are simultaneously inherent in the genetic code.

Unambiguity alongside code degeneracy can be easily explained at THE MOLECULAR LEVEL. The recognition of a specific codon within mRNA by a tRNA molecule is determined by The ability to form complementary Base Pairs between the codon and the anticodon. Each tRNA molecule contains a region complementary to the codon, known as the anticodon. For a given codon, there is only one type of tRNA molecule carrying the corresponding anticodon. Since each tRNA molecule can carry only one strictly defined amino acid, each codon corresponds to only one specific amino acid. However, some types of tRNA can use the same anticodon to recognize more than one fixed codon. As follows from the analysis of codon families given above, the anticodon may be insensitive to the third (3'-) nucleotide of the codon—either partially (in mixed families) or even completely (in non-mixed families). This relaxed stringency in recognizing the third nucleotide of a codon is referred to as "wobble". Consequently, directed by a given codon, only one specific amino acid is incorporated into the protein chain, although each amino acid may be encoded by more than one specific codon.

As will be shown below, The process of reading the genetic code during Protein Synthesis does not allow for codon overlapping. Therefore, the genetic code is non-overlapping. Starting at a specific codon, the reading of directly adjacent nucleotide triplets proceeds sequentially without any gaps until a nonsense codon is reached. In this sense, the genetic code is said to be punctuation-free. Until recently, the genetic code was considered entirely universal. It is now known that the tRNA set in the mitochondria of both lower and higher Eukaryotic Cells reads four codons differently than the cytoplasmic tRNA molecules of the same or any other cells. As seen in Table 40.1, in mammalian mitochondria, the codon AUA is read as Met, while UGA codes for Trp. These two codons belong to the UG and AU families, which were noted above as unique. Perhaps in order to minimize the number of tRNA molecules required for translation, the UG and AU families underwent conversion in mitochondria into simple mixed-type families. Furthermore, the codons AGA and AGG are used not as Arginine codons, but as stop codons—that is, as Translation termination signals. As a result, mitochondria require only 22 types of tRNA, whereas cytoplasmic protein synthesis utilizes the full set of 31 tRNA molecule types. Nevertheless, with the aforementioned exception, the genetic code is universal. The frequency of codon usage varies from species to species and even among Tissues within the same species. Codon usage tables are constantly being refined as The nucleotide sequences of an increasing number of genes are determined. This is critical because researchers frequently need to predict an mRNA sequence from an available protein or peptide fragment sequence in order to synthesize an oligonucleotide probe for Gene cloning.