Amino acid classification according

In biochemistry, the most common and perhaps most practical classification of proteinogenic amino acids is according to the side chain polarity and its ionic forms occurring in neutral solutions, which is related to non-bonding interactions in proteins (see Section 7.6.2.2). The following groups of amino acids are recognised ... 

Amino acids are classified as acidic or basic according to their R groups because in proteins, these are the only groups that can dissociate. The a-amino and a-carboxyl groups are in peptide bonds and lose their acid-base character. This system of classification can be confusing since the words add and base are used in a way slightly different than discussed in the section above. 

In this section, enzymes in the EC 2.4. class are presented that catalyze valuable and interesting reactions in the field of polymer chemistry. The Enzyme Commission (EC) classification scheme organizes enzymes according to their biochemical function in living systems. Enzymes can, however, also catalyze the reverse reaction, which is very often used in biocatalytic synthesis. Therefore, newer classification systems were developed based on the three-dimensional structure and function of the enzyme, the property of the enzyme, the biotransformation the enzyme catalyzes etc. [88-93]. The Carbohydrate-Active enZYmes Database (CAZy), which is currently the best database/classification system for carbohydrate-active enzymes uses an amino-acid-sequence-based classification and would classify some of the enzymes presented in the following as hydrolases rather than transferases (e.g. branching enzyme, sucrases, and amylomaltase) [91]. Nevertheless, we present these enzymes here because they are transferases according to the EC classification. 

Classification of the twenty amino acids found in proteins, according to the charge and polarity of their side chains is shown here and continues in Figure 1.3. Each amino acid is shown in its fully protonated form, with dissociable hydrogen ions represented in red print. The pK values for the a-carboxyl and a-amino groups of the nonpolar amino acids are similar to those shown for glycine. (Continued on Figure 1.3.)... 

Classification of the twenty amino acids found in proteins, according to the charge and polarity of their side chains (continued from Figure 1.2). 

Literature data on the carbon skeleton elongation may be classified according to the number of carbon atoms added. Such a classification, although far from being ideal, is useful from the synthetic viewpoint. Scheme 2 illustrates the usefulness of a-amino acids (in particular a-amino-(3-hydroxy acids e.g., serine, threonine, and their homologues) in the synthesis of amino sugars. 

According to a long-used classification amino acids are ketogenic if (like leucine) they are converted to acetyl-CoA (or acetyl-CoA and acetoacetate). When fed to a starved animal, ketogenic amino acids cause an increased concentration of acetoacetate and other ketone bodies in the blood and urine. On the other hand, glucogenic amino acids such as valine, when... 

Classification In accordance with the structure of the R-group. the amino adds of primary importance can be classified into eight groups. Additional amino acids composing protein are not included in this classification, because they occur infrequently. See Table 4. 

Among the various free amino acids reported in citrus juices (32), arginine is the only semi-indispensable amino acid that occurs in moderate amounts. The majority of amino acids in citrus are considered to be nonessential according to the classification... 

The number of known enzymes has risen significantly, from 712 in the first edition of Enzyme Nomenclature of 1961 through 2477 in 1984 to 3196 in 1992, the year of the third edition. It is important to note that this classification scheme does not organize enzymes according to amino acid sequence or type of three-dimensional structure, and in principle not even according to chemical mechanism. 

TABLE 11.1. Classification of Amino Acids According to their Biochemical Properties... 

The side chains of the amino acids do not form a natural series, and thus, there is no easy way to learn their structures. It is useful to classify them according to whether they are polar or nonpolar, aromatic or aliphatic, or acidic or basic, although these classifications are not mutually exclusive. Tyrosine, for example, can be considered to be both aromatic and polar, although the polarity introduced by a single hydroxyl group in this aromatic compound is somewhat feeble. 

Proteases are classified according to their catalytic mechanism. There are serine, cysteine, aspartic, and metalloproteases. This classification is determined through reactivity toward inhibitors that act on particular amino acid residues in the active site region of the enzyme. The serine proteases are widely distributed among microbes. The enzymes have a reactive serine residue in the active site and are generally inhibited by DFP or PMSF. They... 

Metallothioneins are evolutionarily conserved in that they contain a high cysteine content and lack of aromatic amino acids. However, few invertebrate MTs have been characterized, and these can exhibit wide variation in noncysteine amino acid residues. Initially, MTs were classified according to their structural characteristics. Class I MTs consist of polypeptides with highly conserved cysteine residue sequences and closely resemble the equine renal MT. Mammalian MTs consist of 61-68 amino acids residues and the sequence is highly conserved with respect to the position of the cysteine residues (e.g., cys-x-cys, cys-x-y-cys, and cys-cys sequences, where x and y are noncysteine, non-aromatic amino acids). Class II MTs have less conserved cysteine residues and are distantly related to mammalian MTs. Class III MTs are defined as atypical and consist of enzymatically synthesized peptides such as phy-tochelatins and cadystins. This former classification scheme has been replaced by a more complex system to include the increasing number of identified isoforms. 

During natural evolution, a broad variety of enzymes has been developed, which are classified according to the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). Thus, for each type of characterized enzyme an EC (Enzyme Commission) number has been provided (see http // www.expasy.ch/enzyme/). For instance, all hydrolases have EC number 3 and further subdivisions are provided by three additional digits, e.g. all lipases (official name triacylglycerol lipases) have the EC number 3.1.1.3 and are thus distinguished from esterases (official name carboxyl esterases) having the EC number 3.1.1.1. This classification is based on the substrate (and cofactor) specificity of an enzyme only, however often very similar amino acid sequences and also related three-dimensional structures can be observed. 

Phylogenetic analysis of amino acid sequences of c-type egg-white lysozymes from a variety of birds is generally in accord with taxonomic classification. However, there are some differences For example, the chachalaca is classified normally in the order Galliformes, but its lysozyme differs more in sequence from those of pheasandike birds than do the c-type lysozymes of ducks (for a discussion of this and other examples, see Jolles and Jolles, 1984). 

The protein amino acids are classified according to the chemical nature of their R groups as aliphatic, aromatic, heterocyclic and sulphur containing amino acids. More meaningful classification of amino acids is based on the polarity of the R groups. The polarity of the R groups varies widely from totally non-polar to highly polar. The 20 amino acids are classified into four main classes. 

The amino acids can be classified according to whether they are glucogenic or ketogenic. This classification is based on the pathways of catabolism followed by... 

The Sizes of Some Atoms Structure and Chemical Properties of Side Chain Groups of Amino Acids Approximate Torsion Angles for Some Regular Peptide Structures Classification of Protein Residues According to Their Tendencies to Form a Helix, P Structure, and P Turns... 

Brazzein, the smallest of sweet proteins, was discovered only in 1994 (Ming and Hellekant, 1994) in Pentadiplandra brazzeana B. This protein, whose sequence contains 54-amino acid residues, is 2000 times sweeter than sucrose when compared to a 2% sucrose aqueous solution. Its taste was described as more similar to sucrose than that of thaumatin (Ming and Hellekant, 1994). As can be seen in Figure 5C, the 3D structure of brazzein, determined by NMR spectroscopy in solution at pH 5.2 (Caldwell et al., 1998), is very simple. It contains one a-helix and three strands of antiparallel )3-sheet. The structure is stabilized by four disulfide bonds, three connecting the helix to the jS-sheet. It does not resemble either that of monellin or that of thaumatin instead, it resembles those of plant y-thionins and defensins and arthropod toxins. According to the SCOP classification (Murzin et al., 1995), brazzein belongs to the Scorpion toxin-like superfamily. 

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