Triplet codons

The terms first, second, and third nucleotide refer to the individual nucleotides of a triplet codon. U, uridine nucleotide C, cytosine nucleotide A, adenine nucleotide G, guanine nucleotide Term, chain terminator codon. AUG, which codes for Met, serves as the initiator codon in mammalian cells and encodes for internal methionines in a protein. (Abbreviations of amino acids are explained in Chapter 3.)... 

The 64 triplet codons are listed in the 5 —>3 direction in which they are read. The three termination (term) ... 

Genetic code Sequence of nucleotides along the DNA and coded in triplets (codons) along the mRNA that determines the sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRNA sequence, and subsequently to predict the amino acid sequence. 

The triplet codon genetic codes of mRNA are translated into amino acids as shown below. 

DNA shuffling A method to exchange portions of DNA among similar genes, in order to select for a certain trait, genetic code The set of rules that decodes nucleotide triplets (codons) into amino acids, which is identical in nearly every organism. 

Now that we have specifically attached each amino acid to its cognate tRNA, we need to make the interface between each aminoacyl-tRNA and the correct triplet codon on mRNA. The aminoacyl moiety has nothing to do with this it is simply a matter of codon-anticodon recognition, which is shown schematically in figure 13.3. 

Transfer RNA molecules are adaptors they adapt each amino acid to its triplet codon on messenger RNA. 

There are 64 possible triplet codons (64 = 43 there are four choices of base at each of the three positions in a codon). However, only 61 codons are used to designate amino acids three codons are used to signal the end of the amino acid sequence for a protein, and these three codons are called termination or stop codons. With 20 amino acids used in most proteins and 61 codons to specify amino acids, some amino acids are coded for by more than one codon, i.e., there are synonymous... 

A standard version of the genetic code for the triplet codons on a messenger RNA is given in Table 2.2. 

On each of the tRNA molecules, one of the single-stranded loops contains a trinucleotide sequence that is complementary to the triplet codon sequence used in the genetic code to specify a particular amino acid. This loop on the tRNA is known as the anticodon loop, and it is used to match the tRNA with a complementary codon on the mRNA. In this way the amino acids carried by the tRNA molecules can be aligned in the proper sequence for polymerization into a functional protein. 

The triplets of nucleotide units in DNA determine the amino acids in a protein through the intermediary mRNA. One of the DNA strands serves as a template for synthesis of mRNA, which has nucleotide triplets (codons) complementary to those of the DNA. In some bacterial and many eukaryotic genes, coding sequences are interrupted at intervals by regions of noncoding sequences (called introns). 

FIGURE 27-2 Crick s adaptor hypothesis. Today we know that the amino acid is covalently bound at the 3 end of a tRNA molecule and that a specific nucleotide triplet elsewhere in the tRNA interacts with a particular triplet codon in mRNA through hydrogen bonding of complementary bases. 

Consolidation of the results from many experiments permitted the assignment of 61 of the 64 possible codons. The other three were identified as termination codons, in part because they disrupted amino acid coding patterns when they occurred in a synthetic RNA polymer (Fig. 27-6). Meanings for all the triplet codons (tabulated in Fig. 27-7) were established by 1966 and have been verified in many different ways. The cracking of the genetic code is regarded as one of the most important scientific discoveries of the twentieth century. 

The general nature of the genetic code was suggested by the structure of DNA. Both DNA and proteins are linear polymers. Thus, it was logical to suppose that the sequence of the bases in DNA codes for the sequence of amino acids. There are only four bases in DNA but 20 different amino acids in proteins at the time of their synthesis. It is obvious that each amino acid must be specified by some combination of more than one base. While 16 pairs of bases are possible, this is still too few to specify 20 different amino acids. Therefore, it appeared that at least a triplet group of three nucleotides would be required to code for one amino acid.371 Sixty-four (43) such triplet codons exist, as is indicated in Tables 5-5 and 5-6. 

The genetic code is the sequence relationship between nucleotides in the messenger RNA and amino acids in the proteins they encode. Triplet codons are arranged on the messenger in a nonoverlapping manner without spacers. 

The genetic code invariance persuaded evolutionists to throw the first shy proponents of polyphyletic models into the dungeons.17, 18 The contention that chance would not have provided even for two origins with an identical triplet codon for protein synthesis was then and still is absolutely correct and certainly relevant, but the conclusion reached because of it by nearly everyone was not. Multiple origins were declared impossible whereas chance should have been disqualified as an inappropriate term in this equation (which it is), and this was the error that has dominated thinking for more than 150 years and is still defended with vehemence. 

The synthetic genetic system has even been coupled to unnatural protein synthesis. Adding extra letters to the genetic alphabet has been shown to increase the number of triplet codons that are accessible to a messenger RNA. In 1993, Bain et al. showed that additional triplet codons made possible by extra nucleobases and delivered by synthetic biological efforts could encode extra amino acids.14 That result was obtained with the terran ribosome. 

RNA base triplets (codons) exist for the 20 amino acids used in protein synthesis (Chap. 17). The ability of an organism to live and grow is dependent on protein synthesis and hence on a supply of all 20 amino acids. Higher plants are able to synthesize all 20, but many microorganisms and higher animals make considerably fewer. Humans make 10 of the 20 amino acids the remainder must be supplied in the diet, usually in the form of plant or animal protein. The amino acids that humans cannot synthesize de novo but are essential for life are termed the essential amino acids. Those that we can synthesize are called the nonessential amino acids. The essential and nonessential amino acids are listed in Table 15.1. 

The ribosome is the enzyme that catalyzes peptide bond formation. The bacterial ribosome is a large 2500 kDa ribonucleic acid/protein complex comprised of a large subunit (LSU or SOS subunit) and a small subunit (SSU or 30S subunit) (Fig. 4.1). The small ribosomal subunit binds to messenger RNA (mRNA) and reads the genetic code by aligning its base triplet codons with anticodons of transfer RNA molecules (tRNA). The large ribosomal subunit binds to opposite ends of tRNA molecules and catalyzes peptide bond formation. 

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