Amino acid base triplets

Initiation of the polypeptide chain. mRNA bearing the code for the polypeptide is bound to the small sub-unit of RNA, followed by the initiating amino-acid, and is attached to its tRNA to form an initiation complex. The tRNA of the initiating amino-acid-base pairs with a specific nucleotide triplet or codon on the mRNA that signals the beginning of the polypeptide chain. This process requires GTP (ATP equivalent), plus three proteins called initiation factors. 

The genetic code is degenerate. Most amino acids are encoded by more than one codon. There are 64 possible base triplets and only 20 amino acids, and in fact 61 of the 64 possible triplets specify particular amino acids. Three triplets (called stop codons) designate the termination of translation. "Thus,/or most amino acids, there is more than one code word. 

The desired a-amino acid sequence in the peptide chain is achieved by the triplet code each set of three nucleotide residues contains all the information required to identify the a amino acid. The triplet code is simultaneously the simplest way of identifying a total of 20 different kinds of cx-amino acids by the four different kinds of base in RNA or DNA. There are, of course, 4 = 64 possibilities with a triplet code of four bases, whereas there are only 4 = 16 possibilities with a doublet code. Thus, a doublet code has fewer possibilities than the number of common a-amino acids available. But a triplet code has 64 — 20 = 44 more possible incorporation possibilities than there are different a-amino acids available. Thus, more than one triplet or codon must be able to code for the incorporation of a given amino acid. (Table 30-5). 

At the loop of still another arm is a specific sequence of bases, called the anticodon. The anticodon is highly important because it allows the tRNA to bind with a specific site—called the codon—of mRNA. The order in which amino acids are brought by their tRNA units to the mRNA strand is determined by the sequence of codons. This sequence, therefore, constitutes a genetic message. Individual units of that message (the individual words, each corresponding to an amino acid) are triplets of nucleotides. 

Genetic code the rules for translation of base sequences in nucleic acids into amino acid sequences in polypeptides (see Protein synthesis). The nucleic acid bases are read off as triplets. There are four bases, and thus 64 (43) different permutations ( words ). As there are only 20 amino acids specified by the code, many triplets can be, and are, redundant. The table lists the amino acids by triplet, or codon. 

As shown in Figure 45.1, the bases appear in complementary pairs, A with T and G with C in this particular example, the sequence for one strand of DNA is A-T-C-G-T- while the other strand is -T-A-G-C-A-. The sequences of the bases attached to the sugar-phosphate backbone direct the production of proteins from amino acids. Along each strand, groups of three bases, called codons, correspond to individual amino acids. For example, in Figure 45.1, the triplet CGT, acting as a codon, would correspond to the amino acid serine. One codon, TAG, indicates where synthesis should begin in the DNA strand, and other codons, such as ATT, indicate where synthesis should stop. 

The genetic code (Table 28.3) is the message caiiied by mRNA. It is made up of triplets of adjacent nucleotide bases called codons. Because mRNA has only four different bases and 20 amino acids must be coded for, codes using either one or two nucleotides per amino acid are inadequate. If nucleotides are read in sets of three, however, the four mRNA bases generate 64 possible words, more than sufficent to code for 20 amino acids. 

The specific ribonucleotide sequence in mRNA forms a message that determines the order in which amino acid residues are to be joined. Each "word," or codon, along the mRNA chain consists of a sequence of three ribonucleotides that is specific for a given amino add. For example, the series UUC on mRNA is a codon directing incorporation of the amino acid phenylalanine into the growing protein. Of the 43 = 64 possible triplets of the four bases in RNA, 61 code for specific amino acids and 3 code for chain termination, fable 28.1 shows the meaning of each codon. 

An opening frame contains a series of codons (base triplets) coding for amino acids without any termination codons. There are six potential reading frames of an unidentified sequence. 

In 1994, a conference with the title Aminoacyl-tRNA Synthetases and the Evolution of the Genetic Code was held in Berkeley, California its patron was the Institute of Advanced Studies in Biology. The conference dealt with the development of the synthetases and that of the genetic code (see Sect. 8.2), i.e., the assignment of the various amino acids to the corresponding base triplets of the nucleic acids. 

The genetic code is composed of four letters —two pyrimidine nitrogenous bases, thymine and cytosine, and two purine bases, guanine and adenine—which can be regarded functionally as arranged in codons (or triplets). Each codon consists of a combination of three letters therefore, 43 (64) different codons are possible. Sixty-one codons code for specific amino acids (three produce stop signals), and as only 20 different amino acids are used to make proteins, one amino acid can be specified by more than one codon. 

The many (possibly more than 30) types of collagens found in human connective tissues have substantially the same chemical structure consisting mainly of glycine with smaller amounts of proline and some lysine and alanine. In addition, there are two unusual amino acids, hydroxyproline and hydroxylysine, neither of which has a corresponding base-triplet or codon within the genetic code. There is therefore, extensive post-translational modification of the protein by hydroxylation and also by glycosylation reactions. 

To transcribe information from DNA to mRNA, one strand of the DNA is used as a template. This is called the anticoding, or template, strand and the sequence of mRNA is complementary to that of the template DNA strand (Fig. A2.8) (i.e., C->G, G->C, T->A, and A U note that T is replaced by U in mRNA). The other DNA strand, which has the same base sequence as the mRNA, is called the coding, or sense, strand. There are 64 (4 x 4 x 4) possible triplet codes of the four bases 61 are used for coding amino acids and three for termination signals. As there are 20 amino acids for the 61 codes, some triplets code for the same amino acid. A table of the genetic code is presented in Exhibit A2.2. 

Figure 12.5 The structures for four tRNA molecules of yeast, (a) Alanyl-tRNA (b) phenylalanyl-tRNA (c) seryl-tRNA (d) tyrosyl-tRNA. The single letter designations identify the sequence of bases along the single chain. Note that several of these are unusual bases, most of which are methylated (Me). Note also the ACC sequence at the 3 terminus of each tRNA. This is the site to which amino acids are attached in the process of protein synthesis, as indicated. These tRNA molecules have a substantial amount of secondary structure created by formation of Watson-Crick base pairs. Finally, note that the anticoding triplet in the bottom loop is shown.

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. 

Both molecules are folded in such a way that the 3 end and the 5 end are close together. As in DNA, most of the bases are located in the inside of the structures, while the much more polar backbone is turned outwards. An exception to this is seen in the three bases of the anticodon of the tRNA (pink), which have to interact with mRNA and therefore lie on the surface of the molecule. The bases of the conserved CCA triplet at the 3 end (red) also jut outward. During amino acid activation (see p.248), they are recognized and bound by the ligases. 

The actual information transfer is based on the interaction between the mRNA codons and another type of RNA, transfer RNA (tRNA see p. 82). tRNAs, of which there are numerous types, always provide the correct amino acid to the ribosome according to the sequence information in the mRNA. tRNAs are loaded with an amino acid residue at the 3 end. Approximately in the middle, they present the triplet that is complementary to each mRNA codon, known as the anticodon (GAA in the example shown). If the codon UUC appears on the mRNA, the anticodon binds a molecule of Phe-t-RNA to the mRNA (5) and thus brings the phenylalanine residue at the other end of the molecule into a position in which it can take over the growing polypeptide chain from the neighboring tRNA (6). 

As there are 20 proteinogenic amino acids (see p. 60), the nucleic acid language has to contain at least as many words (codons). However, there are only four letters in the nucleic acid alphabet (A, G, C, and U or T). To obtain 20 different words from these, each word has to be at least three letters long (with two letters, there would only be 4 = 16 possibilities). And in fact the codons do consist of three sequential bases (triplets). 

A set of coding rules are in action as in the translation process. First, a set of three adjacent nucleotides compose the code for each amino acid. A single amino acid can have several triplet codes or codons. Since there are four different nucleotides (or four different bases) in DNA and RNA, there exist 4 = 64 trinucleotide combinations. For instance, using U as a symbol for uracil, which is present in RNA, the triplet or code or codon UUU is specific for phenylalanine. 

The specific ribonucleotide sequence in the mRNA forms a code that determines the order in which the different amino acid residues have to be joined. The four bases, i.e.. A, C, G and U have been shown to act in the form of triplets. Since a particular amino acid codes a specific amino acid, therefore, these triplets are called codons. Since there are four bases, therefore, 4 = 64 triplets or codons are possible. 

Three base-pairs code for one amino acid, and two more triplets are required to start and stop signals, or 3 X 129 + 3 + 2 = 393 base pairs. 

The sequence of bases in the polynucleotide chain is also important because it determines the exact sequence of amino acids used in the synthesis of a protein. Twenty amino acids are commonly found in proteins, while only four bases are used in the DNA molecule. Thus, more than one base must specify each amino acid. The genetic code is in fact read as triplets and there are 64 possible triplet combinations using 4 nucleotides. Each triplet of nucleotides is termed a codon, and given the redundancy, some amino acids are specified by more than one codon. 

ITABLE V.1. Degenerative base triplet on ribonucleotides that codes for specific amino acids... 

The way in which the coding strand of DNA specifies the sequence of amino acids in a protein is known as the genetic code. The code is made up of triplets of nucleic acid bases, known as codons. A given series of three bases in the coding strand DNA of a gene will unambiguously specify a particular amino acid and no other. 

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... 

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