Species specific amino acids

To explain the species-specific amino acid pattern one can assume that each organism secretes one particular calcifying protein which to a limited extent is controlled by the environment. Alternately, a series of different proteins can yield the observed pattern, however, we have to postulate that each one is secreted at a constant rate. Changes in rate of secretion, perhaps environmentally induced, will effect the ratio of the individual proteins and thus account for slight variation in the amino acid distribution in the hydrolyzed matrix. 

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

Transfer RNAs (tRNAs), the smallest of the three major species of RNA molecules (4S), have between 74 and 95 nucleotide residues. There is at least one specific type of tRNA molecule for each of the twenty amino acids commonly found in proteins. Together, tRNAs make up about fifteen percent of the total RNA in the cell. The tRNA molecules contain unusual bases (for example, pseudouracil, see Figure 22.2, p. 290) and have extensive intrachain base-pairing (Figure 30.3). Each tRNA serves as an "adaptor molecule that carries its specific amino acid—covalently attached to its 3-end—to the site of protein synthesis. There it recognizes the genetic code word on an mRNA, which specifies the addition of its amino acid to the growing peptide chain (see p. 429). 

During silica deposition in diatoms a marked increase in protein concentration in cell walls is observed543 however, incorporation of carbohydrates increases only after Si-deposition. In addition, we have seen that there are consistent trends among specific amino acids in all analyzed species, while the sugars exhibit great variability. These two observations suggest that silicification is protein mediated548. ... 

Minimally, each module requires three domains - an adenylation domain (A), which activates a specific amino acid for incorporation a thiolation domain (T), also known as a peptidyl carrier protein (PCP), which transfers the growing peptide from one module to another, and the condensation (C) domain, which carries out the condensation of two residues. Analysis and comparison of the primary sequences of numerous adenylation domains has led to the establishment of a code that can be used to predict the amino acid activated by a particular adenylation domain. Genetic analysis of these sequences has shown that they clade together based on the amino acid encoded, rather than by species of origin. ... 

Although glycine conjugates are the most commonly found metabolites, the specific amino acid acceptor depends on both the animal species and the chemical structure of the xenobiotic. Little is known about this conjugation pathway in parasites. A. suum,... 

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