Amino acids processed proteins

FIGURE 1.9 (a) Amino acids build proteins by connecting the n-carboxyl C atom of one amino acid to the n-amino N atom of the next amino acid in line, (b) Polysaccharides are built by combining the C-1 of one sugar to the C-4 O of the next sugar in the polymer, (c) Nucleic acids are polymers of nucleotides linked by bonds between the 3 -OH of the ribose ring of one nucleotide to the 5 -P04 of its neighboring nucleotide. All three of these polymerization processes involve bond formations accompanied by the elimination of water (dehydration synthesis reactions). 

Transfer RNA (tRNA) serves as a carrier of amino acid residues for protein synthesis. Transfer RNA molecules also fold into a characteristic secondary structure (marginal figure). The amino acid is attached as an aminoacyl ester to the 3 -terminus of the tRNA. Aminoacyl-tRNAs are the substrates for protein biosynthesis. The tRNAs are the smallest RNAs (size range—23 to 30 kD) and contain 73 to 94 residues, a substantial number of which are methylated or otherwise unusually modified. Transfer RNA derives its name from its role as the carrier of amino acids during the process of protein synthesis (see Chapters 32 and 33). Each of the 20 amino acids of proteins has at least one unique tRNA species dedicated to chauffeuring its delivery to ribosomes for insertion into growing polypeptide chains, and some amino acids are served by several tRNAs. For example, five different tRNAs act in the transfer of leucine into... 

Proteases (proteinases, peptidases, or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. The process is called peptide cleavage, a common mechanism of activation or inactivation of enzymes. They use a molecule of water for this, and are thus classified as hydrolases. 

Glutamates can be produced by fermentation of starches or sugars, but also by breaking the bonds between amino acids in proteins, leaving free amino acids. This process is done by heat or by enzymes it is called hydrolyzing, because the bonds are broken by adding water. 

If the environmental temperature is constant, the racemization process takes place at a uniform rate, which is determined, at any time during the process, by the relative amounts of / and d forms of the amino acid can be measured. As the racemization proceeds and the concentration of the / form amino acid decreases, the rate of racemization gradually slows down. When there is a mixture of 50% of each of the d and / forms, the racemization process stops altogether. The half-life of the racemization of aspartic acid, for example, a common amino acid in proteins, at 20°C is about 20,000 years. This half-life makes it possible to date proteins as old as about 100,000 years. So far, however, the dates obtained with the technique have proved somewhat inconsistent, probably because of the difficulty in verifying whether the temperature of the amino acids has been constant. 

In 1963, Armin Weiss (then at the University of Heidelberg, Germany) reported the intercalation of amino acids and proteins in mica sheet silicates (Weiss, 1963). Some years later, U. Hoffmann, also from Heidelberg, published an article titled Die Chemie der Tonmineralien (The Chemistry of Clay Minerals), in which he mentioned possible catalytic activity of clays in processes which could have led to the emergence of life (Hoffmann, 1968). 

Growth can be defined as the production of organic matter by increase in size or volume. This process involves the uptake of water, carbon dioxide and minerals. In plants, growth is made possible by the process of photosynthesis, which produces the sugars (as primary components) from which compounds such as starch, cellulose, amino acids and proteins are derived. 

The modification of amino acids in proteins and peptides by oxidative processes plays a major role in the development of disease and in aging (Halliwell and Gutteridge, 1989, 1990 Kim et al., 1985 Tabor and Richardson, 1987 Stadtman, 1992). Tissue damage through free radical oxidation is known to cause various cancers, neurological degenerative conditions, pulmonary problems, inflammation, cardiovascular disease, and a host of other problems. Oxidation of protein structures can alter activity, inhibit normal protein interactions, modify amino acid side chains, cleave peptide bonds, and even cause crosslinks to form between proteins. 

The two forms of mirror images are called enantiomers, or stereoisomers. All amino acids in proteins are left-handed, and all sugars in DNA and RNA are right-handed. Drug molecules with chiral centers when synthesized without special separation steps in the reaction process result in 50/50 mixtures of both the left- and right-handed forms. The mixture is often referred to as a racemic mixture. 

Neurotransmitter Production. Neurotransmitters are relatively simple chemicals, and our bodies make most of the ones that we use. The nerve cell receives precursor substances such as amino acids from proteins in the diet and chemically processes these precursors to form neurotransmitter chemicals. The neurotransmitter is then stored in small sacs inside the neuron called storage vesicles. These storage vesicles reside inside the axon terminals. 

Small methyl groups are important in the stractnre of some small compounds, nucleotides, some bases in DNA mole-cnles and in postranslational modification of amino acids in proteins. The transfer of a single carbon atom is important in the synthesis of purine nncleotides. The componnds involved in the whole process of methyl gronp transfer, and are carbon metolism, are methionine, homocysteine, serine and the vitamins, folic acid and B12. 

In theory, if the net charge, q, on a molecule is known, it should be possible to measure / and obtain information about the hydrodynamic size and shape of that molecule by investigating its mobility in an electric field. Attempts to define /by electrophoresis have not been successful, primarily because Equation 4.3 does not adequately describe the electrophoretic process. Important factors that are not accounted for in the equation are interaction of migrating molecules with the support medium and shielding of the molecules by buffer ions. This means that electrophoresis is not useful for describing specific details about the shape of a molecule. Instead, it has been applied to the analysis of purity and size of macromolecules. Each molecule in a mixture is expected to have a unique charge and size, and its mobility in an electric field will therefore be unique. This expectation forms the basis for analysis and separation by all electrophoretic methods. The technique is especially useful for the analysis of amino acids, peptides, proteins, nucleotides, nucleic acids, and other charged molecules. 

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