Amino Acid Information

See also Amino Acid Information, Table 5.2, Stereochemistry... 

In addition to protein-building amino acids, nonprotein amino acids occur in vegetables as well as in other plants. Tables 17.5 and 17.6 present data on the occurrence and stmcture of these amino acids. Information about their biosynthetic pathways is given below. 

The protein folding problem is the task of understanding and predicting how the information coded in the amino acid sequence of proteins at the time of their formation translates into the 3-dimensional structure of the biologically active protein. A thorough recent survey of the problems involved from a mathematical point of view is given by Neumaier [22]. 

The sequence of each different peptide or protein is important for understanding the activity of peptides and proteins and for enabling their independent synthesis, since the natural ones may be difficult to obtain in small quantities. To obtain the sequence, the numbers of each type of amino acid are determined by breaking down the protein into its individual amino acids using concentrated acid (hydrolysis). For example, hydrolysis of the tetrapeptide shown in Figure 45.3 would give one unit of glycine, two units of alanine, and one unit of phenylalanine. Of course, information as to which amino acid was linked to which others is lost. 

For example, a polypeptide is synthesized as a linear polymer derived from the 20 natural amino acids by translation of a nucleotide sequence present in a messenger RNA (mRNA). The mature protein exists as a weU-defined three-dimensional stmcture. The information necessary to specify the final (tertiary) stmcture of the protein is present in the molecule itself, in the form of the specific sequence of amino acids that form the protein (57). This information is used in the form of myriad noncovalent interactions (such as those in Table 1) that first form relatively simple local stmctural motifs (helix... 

Legume forages, such as alfalfa or clover, are considered high quaHty, readily available protein sources. Animal sources of supplemental protein include meat and bone meal blood meal, 80% CP fish meal other marine products and hydroly2ed feathermeal, 85—90% CP. Additionally, synthetic amino acids are available commercially. Several sources (3,9,19) provide information about the protein or amino acid composition of feedstuffs. 

Although FeMo-cofactor is clearly knpHcated in substrate reduction cataly2ed by the Mo-nitrogenase, efforts to reduce substrates using the isolated FeMo-cofactor have been mosdy equivocal. Thus the FeMo-cofactor s polypeptide environment must play a critical role in substrate binding and reduction. Also, the different spectroscopic features of protein-bound vs isolated FeMo-cofactor clearly indicate a role for the polypeptide in electronically fine-tuning the substrate-reduction site. Site-directed amino acid substitution studies have been used to probe the possible effects of FeMo-cofactor s polypeptide environment on substrate reduction (163—169). Catalytic and spectroscopic consequences of such substitutions should provide information concerning the specific functions of individual amino acids located within the FeMo-cofactor environment (95,122,149). 

Gas Chromatography (gc). A principal advantage of gas chromatography has been the faciUty with which it can be combined with mass spectrometry for amino acid identification and confirmation of purity. The gc-mass spectrometry combination offers the advantage of obtaining stmctural information rather than the identification by retention time in hplc. 

Spectrometric Analysis. Remarkable developments ia mass spectrometry (ms) and nuclear magnetic resonance methods (nmr), eg, secondary ion mass spectrometry (sims), plasma desorption (pd), thermospray (tsp), two or three dimensional nmr, high resolution nmr of soHds, give useful stmcture analysis information (131). Because nmr analysis of or N-labeled amino acids enables determiaation of amino acids without isolation from organic samples, and without destroyiag the sample, amino acid metaboHsm can be dynamically analy2ed (132). Proteia metaboHsm and biosynthesis of many important metaboUtes have been studied by this method. Preparative methods for labeled compounds have been reviewed (133). 

Cellular Protein Biosynthesis. The process of cellular protein biosynthesis is virtually the same in all organisms. The information which defines the amino acid sequence of a protein is encoded by its corresponding sequence of DNA (the gene). The DNA is composed of two strands of polynucleotides, each comprising some arrangement (sequence) of the four nucleotide building blocks of the nucleic acids adenine (A), thymine (T),... 

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