Amino acids in the genetic code

Aminoacylation is a two-step process, catalyzed by a set of enzymes known as aminoacyl-tRNA synthetases. Twenty aminoacyl-tRNA synthetases reside in each cell, one per amino acid in the genetic code. In the first step of aminoacyl-tRNA synthesis, ATP and the appropriate amino acid form an aminoacyl adenylate intermediate. Inorganic pyrophosphate is released and subsequently broken down to free phosphate by the enzyme inorganic pyrophosphatase. The aminoacyl adenylate is a high-energy intermediate, and in the second step, the transfer of amino acids to the acceptor end of tRNA occurs without any further input of ATP, as shown in Figure 11-2. 

Proteins are composed of chains of amino acids. In the genetic code of deoxyribonucleic acid (DNA), a codon or three-base sequence codes for the placement of each amino acid for example, the codon UUU places phenylalanine at that location in the protein and replacement of the third base with adenine results in the placement of leucine instead of phenylalanine. If a portion of the original code read. . . UUUACG. . . , deleting one of the uridine bases would cause that portion of the code to read. . . UUACG. .. the sequence UUA would then specify leucine. A point mutation changing one base might result in the formation of a different protein. 

The answer is e. (Murray, pp 452-467. Schver, pp 3-45. Sack, pp 245-257. Wilson, pp 151—180.) Chain termination is determined by three codons UAA, UAG, and UGA. Aside from chain termination codons, each group of three bases in a sequence codes for an amino acid. The next three bases specify another amino acid. Thus, the genetic code is nonoverlap-... 

According to the central dogma, when one strand of DNA is transcribed into RNA and translated to make proteins, three consecutive nucleotides form a codon. Each codon specifies an amino acid or amino acid chain termination. For example, the nucleotide sequence, or codon, GGA specifies the amino acid glycine. The genetic code has substantial redundancy, in that two or more codons code for the same amino acid. For example, both GGA and GGC code for glycine. Amino acids are the basic constituents of proteins, which mediate all cellular functions. Only 20 different amino acids, in various arrangements, form the basic units of all the proteins in the human body. 

The addition of a non-canonical amino acid to the genetic code requires - in the first case - additional components of the protein producing system a noncanonical amino acid, an exogenous tRNA/aminoacyl-tRNA synthetase pair, and an unique codon that specifies the amino acid of interest. Orthogonality between the exogenous translational components (Scheme 1-30) and their endogenous opposite numbers is the key feature of this approach. With the effect... 

The genetic code, regardless of whether it is a product of a "frozen accident" [1] or a deterministic interaction between the nucleotides and the amino acids [2], displays an apparent correlation between the nucleotides found at particular codon positions and the physico-chemical properties of the protein amino acid residues encoded by the nucleotides [2-10]. A variety of analytical methods have been employed to quantitatively examine these relationships. SjdstrOm and Wold [5], for example, have used Principal Component Analysis (PCA) to relate twenty physical properties of the amino acids to the genetic code. They find that 58% of the variance in the data can be accounted for by considering just three factors. In order of importance, the predominant contributions are 1) hydrophobicity, 2) molar volume, and 3) electronic descriptors (e.g. pKgS and NMR chemical shifts). Fig. 1 presents a concise display of... 

This double helix was identified by Crick and Watson in 1954 the rungs of the twisted ladder correspond to the pair of bases. DNA is always formed by replication/duplication upon separation of the double strands the intermediate single strands are the matrices for the generation of new DNA chains. After replication, each double helix includes one old strand and a new one. Three successive nucleotides of DNA provide the code for one amino acid, and the genetic code is determined by the sequence of these triplets. 

Despite the differences in nuclear structures between prokaryotes and eukaryotes, the genetic code, i.e. the combination of bases which does for a particular amino acid in the process of protein synthesis, is the same as it is in all living organisms. 

Twenty amino acids are constituents of the peptide chains found in nature. These are generally referred to as the common amino acids (Table 6.1). Less-common amino acids are listed in Table 6.2, including selenocysteine, often called the 21st natural amino acid . Although of little relevance here, we note that the 22nd amino acid , pyrrolysine, was discovered in 2002 in the genetic code of certain Archea and eubacteria [1],... 

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. 

In the genetic code of human nuclear DNA, one of the codons specifying the amino acid tyrosine is UAC. Another codon specifying this same amino acid is ... 

The significance of Sanger s work is immense. It proved for the first time that the structure of a protein is unique that is, aU molecules of bovine insulin, for example, possess the same sequence of amino acids along the polypeptide chains. This sequence has no obvious order, but it is unique. This singular finding requires that there is a genetic code information encoded in a molecule which specifies the sequence of amino acids in the insulin molecule and, for that matter, in all protein molecules. 

The amino acids that are included in the genetic code (see p.248) are described as proteinogenic. With a few exceptions (see p. 58), only these amino acids can be incorporated into proteins through translation. Only the side chains of the 20 proteinogenic amino acids are shown here. Their classification is based on the chemical structure of the side chains, on the one hand, and on their polarity on the other (see p. 6). The literature includes several slightly different systems for classifying amino acids, and details may differ from those in the system used here. 

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. 

FIGURE 27-5 Reading frames in the genetic code. In a triplet, nonoverlapping code, all mRNAs have three potential reading frames, shaded here in different colors. The triplets, and hence the amino acids specified, are different in each reading frame. 

One would expect little room for variation in the genetic code. Even a single amino acid substitution can have profoundly deleterious effects on the structure of a protein. Nevertheless, variations in the code do occur in some organisms, and they are both interesting and instructive. The types of variation and their rarity provide powerful evidence for a common evolutionary origin of all living things. 

In the next step, translation, the sequence of nucleotides in the newly synthesized mRNA strand is used to determine the sequence of amino acids in the protein to be synthesized. This is done by way of a genetic code, which was fully deciphered by 1966 and is shown in Figure 13.34. According to the genetic code, it takes three mRNA nucleotides—each three-nucleotide unit is called a codon—to code for a single amino acid. The mRNA nucleotide sequence AGU, for example, codes for the amino acid serine, and AAG codes for lysine. (Note from Figure 13.34 that more than one codon can call for the same amino acid.) A few codons, such as AUG and UGA, are the signals for protein synthesis to either start or stop. 

The sequences of the amino acids in the chains from which proteins are constructed are encoded in the nucleotide sequences of DNA (deoxyribonucleic acid). The coding sequence for a protein in the DNA is found in the structural gene for that protein. The RNA enzymes are also encoded by DNA genes. A fourth major theme of the book deals with the nature of the genetic code used in DNA and with the processes by which cells read and interpret the code. It also includes study of the methods by which thousands of genes have been mapped to specific positions in chromosomes, isolated, cloned, and sequenced. 

Some amino acids utilize only one codon of the 64 in the genetic code. Other amino acids use as many as six codons (Tables 5-5,5-6). What advantages to a cell is provided by utilization of several codons for a single amino acid ... 

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. 

TRANSLATION The process by which a particular messenger RNA (mRNA) nucleotide sequence determines a specific amino acid sequence of a polypeptide chain occurs as the polypeptide is synthesized and is therefore the second step in the readout of the information in the genetic code (the first is transcription). 

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