Triplet of bases

We know fhat the anticodon is a triplet of bases occupying the anticodon loop in the tRNA structure. By Watson-Crick base-pairing, this anticodon can recognize the... 

Codon a triplet of bases in DNA or mRNA that specifies a specific amino acid in proteins or a termination signal. 

Cenetic code the relationship between triplets of bases in mRNA and the corresponding amino acids in proteins (or a termination signal) for which the triplet codes. 

An overview of protein synthesis is shown in Fig. S.A12. The linear sequence in mRNA that is translated to protein contains four bases, adenine, uracil, guanine and cytosine. The four letters A,U,G and C constitute the mRNA alphabet . This basic alphabet is used in triplets of bases called codons. The codons on mRNA pair up with anticodon or complementary triplets on the tRNA, thus matching the mRNA code to an amino-acid sequence. 

Codons that specify the same amino acid are called synonyms. Most synonyms differ only in the third base of the codon for example GUU, GUC, GUA and GUG all code for valine. During protein synthesis, each codon is recognized by a triplet of bases, called an anticodon, in a specific tRNA molecule (see Topics G10 and H2). Each base in the codon base pairs with its complementary base in the anticodon. However, the pairing of the third base of a codon is less stringent than for the first two bases (i.e. there is some wobble base-pairing ) so that in some cases a single tRNA may base-pair with more than one codon. For example, phenylalanine tRNA, which has the anticodon GAA, recognizes both of the codons UUU and UUC. The third position of the codon is therefore also called the wobble position. 

The genetic code refers to specific sequences of RNA bases (or DNA bases) that encode specific amino acids. Kach of these sequences is composed of a triplet of bases (three bases in a row). Hence, any mRNA molecule can be considered a continuous polymer of successive triplets. For example, the triplet UUU codes for phenylalanine, CAU encodes histidine, GAG encodes glutamate, AAA encodes lysine, and AUG codes for methionine. DNA is used for information storage, while mRNA is used for information transfer. 

The above task, once accomplished, allows the researcher to view the sequence of DNA bases (read from the polyacrylamide gel) in terms of a series of consecutive codons (triplets of bases that code for amino acids). The next task is to search for the translation start site and the translation stop site. Once the entire sequence of the polypeptide has been acquired from the DNA sequence, the researcher may compare the amino acid sequence with those of all known proteins. This task, which is performed on the computer, can reveal whether or not the polypeptide being studied is closely related to another, better characterized polypeptide. If a close match is found, the researcher may gain insight into the functions of the gene being sequenced. 

Selenium is incorporated into Se-requiring enzymes by the modification of serine. This serine is not modified when it is in the free state or when it occurs in a polypeptide chain. The serine residue in question is modified when it occurs boimd to transfer RNA, that is, eis the aminoacyl-tRNA derivative. Seryl-tRNA is converted to selenocysteinyl-tRNAby the action of selenocysteine synthase (Stur-chler et al, 1993). The codon for selenocysteine is UGA (TGA in DNA UGA in mRNA). The fact that this particular triplet of bases codes for an amino acid is very imusual, as UGA normally is a stop codon. Stop codons occur in mRNA and signal the termination of synthesis of the protein however, in the case of the UGA codons that code for selenocysteine residues, regions of the mRNA that lie beyond the coding sequence somehow convert the UGA from a codon that halts translation to one that codes for selenocysteine (Figure 10.55). The structure of selenocysteine is shown in Figure 10.56. 

There are 20 different amino acids but only four RNA bases. Thus, a single base cannot specify a single amino acid. In fact, a group of three, or a triplet of bases in RNA indicates a particular amino acid. For example, the sequence of bases GUC causes valine to be added to a growing polypeptide. The complete genetic code lists the RNA triplets and their corresponding amino acids. You can use Skills Toolkit 1 to decode RNA sequences to their corresponding amino acid sequences, as shown below. 

The Ames test allows one to test the ability of a substance to interfere with DNA, which has the information necessary for expression of specific proteins. This information is encoded by the sequence of base pairs in the DNA molecule, with triplets of base pairs (mRNA codons) encoding for a specific amino acid in the sequence of a protein. Ames system focuses on the fact that mutations in oncogenes and tumor suppressor genes of somatic cells can be involved in tumor formation. 

Ames developed strains of bacteria that had carefully selected lethal mutations. In a test system the bacteria could survive only when its mutation had been corrected by experiencing another mutation caused by the tested material. This correction could be accomplished by causing a point mutation or frameshift mutations . Point mutations are base-pair substitutions, that is, a base change in DNA of at least one DNA base pair. In a reverse mutation test, this change in base pairs may occur at the site of the original mutation, or at a secondary site in the bacterial genome. Frameshift mutations are the addition or deletion of one or more base pairs in the DNA. Since amino acids are encoded by triplets of base pairs in sequence, any addition or deletion of 1 or 2 base pairs will dramatically alter the expressed protein from that point on. The Ames system employs strains of Salmonella typhimurium and Escherichia coli that require amino acids (histidine or tryptophan, respectively) to detect such reverse point and frameshift mutations. The reverse mutation allows the S. typhimurium or E. coli strains to restore the functional capability of the bacteria to be able to synthesize the specific amino acid on their own, independent of amino acid content in the medium. 

Production of proteins from mRNA requires translation of the base sequence into an amino acid sequence. The collection of base sequences (codons) that correspond to each amino acid and to signals for termination of translation is the genetic code. The code consists of 64 triplets of bases (Table 25-2). The codons are written with the 5 terminus... 

The precise sequence of bases along the DNA carries the genetic information. An individual amino acid is coded by a triplet of bases. The genetic code for all the amino acids is shown in table 3.3. 

DNA encodes the information needed to make proteins in the form of triplets of bases (codons), for example thymine-adenine-cytosine (TAG) in the diagram below. As RNA is synthesized from DNA, these are turned into complementary codons (in the example below, AUG) by pairing up the bases as shown on p. 1138. This RNA forms the instructions for protein synthesis by the ribosome—perhaps the most elaborate molecular structure in the known universe. Each codon of the RNA chain tells the ribosome to add a specific amino acid to the growing protein. For example, the codon AUG indicates methionine, which we met as a component of SAM. Methionine is a typical amino acid of the kind present in proteins, but is also the starter unit of all proteins. 

After the discovery of three-letter codons, researchers were anxious to answer the next question Which triplets of bases (codons) code for which amino acids In 1961, Marshall Nirenberg and his coworkers at the National Institutes of Health (NIH) in Bethesda, Maryland, attempted to break the code in a very ingenious way. They made a synthetic molecule of mRNA consisting of uracil bases only. Thus, this mRNA contained only one codon, the triplet UUU. They incubated this synthetic mRNA with ribosomes, amino acids, tRNAs, and the appropriate enzymes for protein synthesis. The exciting result of this experiment was that a polypeptide that consisted only of phenylalanine was synthesized. Thus, the first word of the genetic code had been deciphered UUU phenylalanine. 

Selection of the specific aminoacyl-tRNA to be bound at the ribosomal A site is by base-pairing between the relevant mRNA codon and the tRNA anticodon. Because this interaction involves only a triplet of bases and hence a maximum of nine hydrogen bonds (see Fig. IB), it is intrinsically unstable at physiological temperatures and is probably stabilized by components of the ribosome to allow sufficient time for peptide bond synthesis to occur. Also, the codon-anticodon pairing must be monitored for fidelity in order to minimize errors in translation. In E. coli there is genetic and biochemical evidence that one of the proteins of the small ribosomal subunit, S12, is involved in ensuring the fidelity of normal translation and in causing the mistranslation which occurs in the presence of the antibiotic streptomycin due to incorrect codon-anticodon interactions. 

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