Amino acid three letter code

Amino acid Three- letter code One- letter code Mass of residue in. b proteins Accessible surface area, 2 nm Hydrophobicity index ionizable side chain Occurrence in n/ proteins, /o Relative mutabihty... 

One-letter code of amino acids, three-letter code and codons (5 -3 ) coding for the amino acid... 

Table 1 lists various a-aminoboronic acids and peptides that have been synthesized. Within this section, a-aminoboronic acids are denoted from the relevant amino acid three-letter code preceded by boro, e.g. boroPhe is H2NCH(Bzl)B(OH)2. 

Amino acid Three-letter code One-letter code Side-chain... 

Amino acid Three- letter code Single- letter code Nominal mass Monoisotopic mass Average mass... 

Amino acid Single- letter code Three- letter code Amino acid Single- letter code Three- letter code... 

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

The sequence of amino acids in a peptide can be written using the three-letter code shown in Figure 45.3 or a one-letter code, both in common use. For example, the tripeptide, ala.ala.phe, could be abbreviated further to AAF Although peptides and proteins have chain-like structures, they seldom produce a simple linear system rather, the chains fold and wrap around each other to give complex shapes. The chemical nature of the various amino acid side groups dictates the way in which the chains fold to arrive at a thermodynamically most-favored state. 

Also shown are the one-letter and three-letter codes used to denote amino acids. For each amino acid, the ball-and-stick (left) and space-filling (right) models show only the side chain. (Irving GSs)... 

Table 8.1 The genetic code as a three-letter code, with the normal abbreviations for the 20 pro-teinogenic amino acids. The first base corresponds to the 5 end, the third to the 3 end of the nucleotide chain... 

Although only a few types of amino acids were available during the first few million years of the development of the code, it is likely that three-letter codes were used from the beginning. F. Crick also believes in a three-letter code, because of the continuity principle . It is possible that the third base had no function in the early days but was only necessary for steric reasons for example, because with a two-letter code (only two bases) in the mRNA strand, there would not have been enough room for two amino acid-bearing tRNA molecules. 

Another model is based on the fact that the genetic code shows a number of regularities, some of which have already been mentioned above. It is suspected that codons beginning with C, A or U code for amino acids which were formed from a-ketoacids (or a-ketoglutarate, 1-KG), oxalacetate (OAA) and pyruvate. This new model, which is quite different from the previous models, assumes that a covalent complex formed from two nucleotides acted as a catalyst for chemical reactions such as the reductive amination of a-ketoacids, pyruvate and OAA. More recent analyses suggest that the rTCA cycle (see Sect. 7.3) could have served as a source of simple a-ketoacids, including glyoxylate, pyruvate, OAA and a-KG. a-Ketoacids could, however, also have been formed via a reductive acetyl-CoA reaction pathway. The bases of the two nucleotides specify the amino acid synthesized and were retained until the modern three-letter codes were established (Copley et al., 2005). 

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. 

FIGURE 6.3 Twenty standard amino acids used for cluster analysis of chemical structures. For the three-letter codes, see Table 6.1. 

The single-letter code is helpful to describe longer amino acid sequences. It is derived from the three-letter code of amino acids (aa). 

Throughout this article, the heteroring will be referred to as either piperazine-2,5-dione or occasionally as cyclodipeptide. The earlier practice of referring to the ring as diketopiperazine has been avoided. The numbering of the piperazinedione ring is as shown in (1). In the cyclodipeptide nomenclature, the common three-letter code for the two amino acids, with the necessary prefix to indicate absolute configuration, will be used. 

By the 1960s it had long been apparent that at least three nucleotide residues of DNA are necessary to encode each amino acid. The four code letters of DNA (A, T, G, and C) in groups of two can yield only 42 = 16 different combinations, insufficient to encode 20 amino acids. Groups of three, however, yield 43 = 64 different combinations. 

The nomenclature of the peptoid monomers that have the same side chain as a corresponding amino acids, consist of an N prefix followed by the three-letter code of the amino acid in small letters. Thus, for example, the peptoid isomer of His is Nhis. 

The large amount of work devoted to the synthesis of oligo-p-peptides has created a need for some standardization in nomenclature. The proposals of Seebach 5 will be used throughout this section, i.e. the P-peptides will be named according to their substitution pattern with the superscript representing the position of the substituent on the peptide backbone (Scheme 1) the prefix H to the three-letter code for amino acids has been used throughout to denote a homoamino acid, e.g. HLeu is homoleucine, HVal is homovaline, etc. 

Natural amino acids are designated by the standard three-letter code. Nva, norvaline Nle, norleucine Chg, cyclohexylglycine tBu, fert-butyl Trt, trityl Pmc, 2,2,5,7,8-pentamethylchroman-6-sulfonyl. 

The three-letter code used for all amino acids refers always to the corresponding L-amino acids. D-Enantiomers are abbreviated by d- followed by the corresponding three-letter code, such as D-Ser for D-serine. 

Figure 14.1. Construction of query saccharide structure for energy minimization with SWEET. Three-letter codes (IUBMB) for monosaccharides and amino acids are employed to construct oligosaccharide or oligopeptide chains. For monosaccharides, a- and p-anomers are prefixed with a and b, respectively. Pyranose and furanose rings are denoted as p and f, respectively.

The common three letter codes for amino acids are used throughout. 

Amino Acid Chemical Formula Isotopic Molar Mass(Da) Chemical Molar Mass (Da) Isoelectric Point (pH) Three- Letter Code Single- Letter Code Residue Mass (Aaa/amu (or Daltons)... 

C-termlnus means the end of the peptide that carries the terminal G02H group. The other end, carrying die NH2 group, isthefV-- terminus. By convention, we write the W-terminus on the left and the O-terminus on the right. The structure of oxytocin is represented here in terms of the three-letter codes for amino acids—there is a full list in Chapter 49. 

All of the amino acids are represented by both a three-letter code and a one-letter code. 

Peptide structure is described by using three-letter codes, or one-letter codes, for the individual amino acids, starting with the N-terminal amino acid. 

Note Nonprotein amino acids are marked. Three-letter codes in brackets are not recommended. ... 

The order, or sequence, of amino acids in the protein chain is called the primary structure, conveniently indicated by using three-letter codes for the amino acids (see Fig. 22.18), where it is understood that the terminal carboxyl group is on the right and the terminal amino group is on the left. For example, one possible sequence for a tripeptide containing the amino acids lysine, alanine, and leucine is... 

One kind of RNA—called, fittingly, messenger RNA—carries a message to the ribosome, where protein synthesis actually takes place. At the ribosome, messenger RNA calls up a series of transport RNA molecules, each of which is loaded with a particular amino acid. The order in which the transport RNA molecules are called up—the sequence in which the amino acids are built into the protein chain—depends upon the sequence of bases along the messenger RNA chain. Thus, GAU is the code for aspartic acid UUU, phenylalanine GUG, valine. There are 64 three-letter code words codons) and only 20-odd amino acids, so that more than one codon can call up the same amino acids CUU and CUC, leucine GXA and GAG, glutamic acid. 

Using the three-letter code names for amino acids, write the structures of all possible peptides containing the following amino acids ... 

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