Amino acids not in proteins

See also D-Amino Acids, Amino Acids Not In Proteins, Bacterial Cell Walls... 

See also Amino Acids Not In Proteins, Metabolism of Serine, Glycine, and Threonine, Metabolism of Valine, Leucine, Isoleucine, and Lysine, Metabolism of Sulfur-Containing Amino Acids... 

See also Amino Acids Not In Proteins, Vitamin B12, Metabolism of Sulfur-Containing Amino Acids... 

The addition of ammonia to the variety of acids derivable from either the breakdown of glucose, glycolysis, or of the pentose shunt reaction products, ribose and NADPH, and from the citrate cycle, gives the amino acids (see Table 4.7 and Figure 4.4) Polymerisation of amino acids in cells gives proteins. In some of the amino acids sulfur and selenium can be incorporated easily. We assume NH3 was present. (Note that Se is in a coded amino acid not in Table 4.7.) Some selective metal-binding properties can be seen in Table 4.7, but amino acid carboxylates can bind all. 

Until the introduction of capillary columns, it was not possible to separate all the amino acids found in proteins on one column. The choice of stationary phase will depend upon the types of derivatives that have been prepared and in some situations it still may be preferable to use two different columns simultaneously. 

Small ACTH fragments related to ACTH-(4-10) have also been investigated for the presence of ordered structure. CD of ACTH--(5-10) in TFE showed a random structure (50) as was found with H-NMR for fragment 4-10 (51). The addition of anionic or cationic surfactants to an aqueous solution of ACTH-(4-11) dit not promote any a-helix or 3-form in this peptide (CD experiments S2). When ACTH-(1-14) and 1-10 were measured by CD and NMR respectively, indications for a helical or ordered structure were found (90, ). Thus it seems that the addition of the non-helix "prone" fragment 1-3 or 1-4 can promote the formation of a helical structure in the adjacent sequence. Arguments in favour of this come from the theoretical work of Argos and Palau (53) on amino acid distribution in protein secondary structures. They found that Ser and Thr frequently occur at the N-terminal helical position (cf. Ser in ACTH) to provide stability the position adjacent to the helical C-terminus is often occupied by Gly or Pro (adjacent toTrp in ACTH we have Gly ) acidic amino acid residues are frequently found at the helix N-terminus (cf. Glu in ACTH) and/or basic residues at the C-terminus (cf. Arg ). 

FIGURE 3-8 Uncommon amino acids, (a) Some uncommon amino acids found in proteins. All are derived from common amino acids. Extra functional groups added by modification reactions are shown in red. Desmosine is formed from four Lys residues (the four carbon backbones are shaded in yellow). Note the use of either numbers or Creek letters to identify the carbon atoms in these structures, (b) Ornithine and citrulline, which are not found in proteins, are intermediates in the biosynthesis of arginine and in the urea cycle. 

It may also be surprising how easily this racemization may occur. Friedman and Liardon (126) studied the racemization kinetics for various amino acid residues in alkali-treated soybean proteins. They report that the racemization of serine, when exposed to 0.1M NaOH at 75°C, is nearly complete after just 60 minutes. However, caution must be used when examining apparent racemization rates for protein-bound amino acids. Liardon et al. (127) have also reported that the classic acid hydrolysis, employed to liberate constituent amino acids, causes amino acids to racemize to various degrees. This will necessarily result in D-isomer determinations that are biased high. Widely applicable correction factors are not possible since the racemization behavior of free amino acids is different from that of amino acid residues in proteins (which can be further affected by sequence). Of course, this is not a problem for free amino acid isomer determinations since the acid hydrolysis is unnecessary. Liardon et al. also describe an isotopic labeling/mass spectrometric method for determining true racemization rates unbiased by the acid hydrolysis. For an extensive and excellent review of the nutritional implications of the racemization of amino acids in foods, the reader is directed to a review article written by Man and Bada (128). 

Certain amino acid residues in proteins are particularly important ligands, notably cysteine and histidine which provide SH and imidazole groups respectively. These are shown in Figure 2, which also lists other important residues. The y-carboxyglutamate residue found in the, gla proteins is noteworthy as an important binding group for Ca2+, while other high affinity sites for calcium contain the j8-hydroxyaspartate residue, one not found previously in proteins. 

INTRON A region of a gene (i.e., ENA) that is transcribed in the synthesis of RNA, but enzymatically removed (by "splicing") from the final mRNA before its translation into an amino acid sequence in protein introns are characteristic of gene structure in eukaryotic, but not prokaryotic, cells. (See also EXON and CODING SEQUENCE)... 

Fife as we know it builds its proteins primarily from the same 20 amino acids, although there are many other amino acids that might have been utilized. While it is important that the collection of amino acids used in proteins includes a sufficient number of small, large, hydrophilic, hydrophobic, and charged amino acids, the exact identities of the amino acids in each of these classes may not be critical. Moreover, the amino acids utilized for protein synthesis by familiar life are all F-amino acids, and there is no reason to think that D-amino acids could not have been utilized instead. 

Mirror-Image Proteins As noted in Chapter 3, The amino acid residues in protein molecules are exclusively L stereoisomers. It is not clear whether this selectivity is necessary for proper protein function or is an accident of evolution. To explore this question, Milton and colleagues (1992) published a study of an enzyme made entirely of D stereoisomers. The enzyme they chose was HIV protease, a proteolytic enzyme made by HIV that converts inactive viral pre-proteins to their active forms. 

The pyrophosphate thus produced is often degraded by a ubiquitous enzyme, pyrophosphatase, to inorganic phosphate, thus pushing the reaction ever further toward completion. Another process that requires energy input is the formation of peptide bonds, which hold amino acids together in proteins. Peptide bonds cannot form spontaneously, and their biosynthesis requires at least four ATP equivalents, amounting to some 33,600 cal. The whole point of ATP hydrolysis in biologic systems is thus to drive forward those reactions that would otherwise not occur because of unfavorable AG. ... 

Which amino acid found in proteins does not show optical activity ... 

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