Acids in-, proteins

Neural networks have been applied to IR spectrum interpreting systems in many variations and applications. Anand [108] introduced a neural network approach to analyze the presence of amino acids in protein molecules with a reliability of nearly 90%. Robb and Munk [109] used a linear neural network model for interpreting IR spectra for routine analysis purposes, with a similar performance. Ehrentreich et al. [110] used a counterpropagation network based on a strategy of Novic and Zupan [111] to model the correlation of structures and IR spectra. Penchev and co-workers [112] compared three types of spectral features derived from IR peak tables for their ability to be used in automatic classification of IR spectra. 

The deterruination of amino acids in proteins requires pretreatment by either acid or alkaline hydrolysis. However, L-tryptophan is decomposed by acid, and the racemi2ation of several amino acids takes place during alkaline hydrolysis. Moreover, it is very difficult to confirm the presence of cysteine in either case. The use of methanesulfonic acid (18) and mercaptoethanesulfonic acid (19) as the protein hydroly2ing reagent to prevent decomposition of L-tryptophan and L-cysteine is recommended. En2ymatic hydrolysis of proteins has been studied (20). 

One of the historically most significant examples of aromatie nueleophilie substitution is the reaetion of amines with 2,4-dinitrofluorobenzene. This reaetion was used by Sanger to develop a method for identifieation of the N-terminal amino acid in proteins and the proeess opened the way for struetural eharacterization of proteins and other biopolymers. 

The macromolecules of cells are built of units—amino acids in proteins, nucleotides in nucleic acids, and carbohydrates in polysaccharides—that have structural polarity. That is, these molecules are not symmetrical, and so they can be thought of as having a head and a tail. Polymerization of these units to form macromolecules occurs by head-to-tail linear connections. Because of this, the polymer also has a head and a tail, and hence, the macromolecule has a sense or direction to its structure (Figure 1.9). 

Table 26.1 The 20 Common Amino Acids in Proteins (continued) Name Abbreviations MW Stricture...

Humans are able to synthesize only 11 of the 20 amino acids in proteins, called nonessential amino acids. The other 9, called essential amino acids, are biosynthesized only in plants and microorganisms and must be obtained in our diet. The division between essential and nonessential amino acids is not clearcut, however tyrosine, for instance, is sometimes considered nonessential because humans can produce it from phenylalanine, but phenylalanine itself is essential and must be obtained in the diet. Arginine can be synthesized by humans, but much of the arginine we need also comes from our diet. 

The importance of Heinrich Ritthausen s fundamental studies, 1862 to 1899, on analytical procedures for the determination of amino acids in proteins has been emphasized in the biographical sketches which have been presented by Osborne (210), Vickery (289), and Chibnall (47). It is of particular interest to note here the prediction made by Ritt-hausen about 1870 that the amino acid composition would prove to be the most adequate basis for the characterization of proteins. Ritthausen and Kreusler (230) were the first, in 1871, to determine amino acids derived from proteins, and some of the values which they found for aspartic and glutamic acids are given in Table III (cited by Chibnall, 47, and Vickery, 286). 

Block, R. J., and Bolling, D., Determination of Amino Acids in Proteins and Foods, Spring-... 

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. 

Two amino acids—cysteine and tyrosine—can be synthesized in the body, but only from essential amino acid ptecutsots (cysteine from methionine and tyrosine from phenylalanine). The dietary intakes of cysteine and tytosine thus affect the requirements for methionine and phenylalanine. The remaining 11 amino acids in proteins are considered to be nonessential or dispensable, since they can be synthesized as long as there is enough total protein in the diet—ie, if one of these amino acids is omitted from the diet, nitrogen balance can stiU be maintained. Howevet, only three amino acids—alanine, aspartate, and glutamate—can be considered to be truly dispensable they ate synthesized from common metabolic intetmediates (pyruvate, ox-... 

As the name implies, an amino acid is a bifunctional molecule with a carboxylic acid group at one end and an amine group at the other. All proteins are polyamides made from condensation reactions of amino acids. Every amino acid in proteins has a central carbon atom bonded to one hydrogen atom and to a second group, symbolized in Figure 13-31 as R. 

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. 

Dinitrofluorobenzene (86, X = F) is, because of its reactivity, much used for tagging the NH2 group of terminal amino-acids in protein end group analysis. Once it has reacted with the NH2 it is very difficult to remove again and will thus withstand the subsequent hydrolysis of the protein to its constituent amino-acids. 

As already mentioned, a continual inflow of energy is necessary to maintain the stationary state of a living system. It is mostly chemical energy which is injected into the system, for example by activated amino acids in protein biosynthesis (see Sect. 5.3) or by nucleoside triphosphates in nucleic acid synthesis. Energy flow is always accompanied by entropy production (dS/dt), which is composed of two contributions ... 

Genetic code Sequence of nucleotides along the DNA and coded in triplets (codons) along the mRNA that determines the sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRNA sequence, and subsequently to predict the amino acid sequence. 

Amino acids are the building blocks of protein. Except for glycine, all amino acids come into two different chiral forms, laevorotatory (L) and dextrorotatory (D) these forms are called enantiomers. In living organisms, the amino acids in protein are almost exclusively... 

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. 

Proteins are highly complex, folded polypeptide chains consisting of at least 20 different amino acids that are strung together in unique sequences, which relate to structure and function. Particular amino acids in proteins may be further modified post-translationally to contain a wide variety of covalent modifications normally found in native proteins. The way in which a peptide chain is wrapped and folded governs each amino acid s relative exposure to the outside environment, but post-translational modifications also can obscure the protein surface from easy access to the solvent environment. 

Figure 1.21 Comparison of the solvent exposed surface area of amino acids in proteins. Data are plotted as a percentage of each amino acid in a protein having greater than a 30 A2 exposure to the aqueous environment. Charged and polar amino acids are seen to have the most solvent exposure, while uncharged, aromatic, or aliphatic amino acids have the least exposure.

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