The Amino Acids in Proteins

The general structure of the amino acids occurring in proteins is H2N - CHR -COOH (except for the amino acids proline and 4-hydroxyproline see Table 13.1). They are all a-amino acids. The asterisk at the a-C-atom indicates the asymmetry 

Cyclic structures the R-group folds back to the N-atom 

TABLE 13.1 (continued) Amino Acids Occurring in Proteins  

Asparagine Asn N CONH, 1 CH, NHj—CH—COjH Polar side groups converted into Asp and Glu at extreme pH values 

Lysine Lys K (CH2)4 -NH2 NHj—CH—COjH Side group contains polar and apolar parts, and is cationic 

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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... 

Now that we have the monomers, which are pretty complex in this case, it remains to define how they are joined together to create the polymer. The amino acids in proteins are linked by peptide bonds. The nucleotides in nucleic acids are linked by phosphodiester bonds, as is shown in figure 12.2. These DNA phosphodiester bonds are very stable. Indeed, samples of largely intact DNA can be recovered from organisms that have been extinct for thousands of years. This remarkable stability should not come as a surprise the central importance of DNA in all forms of life requires that it be stable to various sorts of insults. 

The ( y / diagram (also known as a Rama-chandran plot) was developed from modeling studies of small peptides. However, the conformations of most of the amino acids in proteins are also located in the permitted areas. The corresponding data for the small protein, insulin (see p. 76), are represented by black dots in 1. 

A variety of methods are available to detect proteins separated by electrophoresis or to measure the concentration of total protein in a solution. These methods are normally based on the binding of a dye to one of the amino acids in protein, or a color reaction with an amino acid side chain. The most commonly used stains for protein detection on gels are Coomassie Brilliant Blue (98) and silver stain (99,100). These methods detect any protein residues, either in solution or on an electrophoresis gel. Their main requirement is sensitivity, not specificity. New, more sensitive dyes are being developed for the proteomic analysis of protein structure and sequence, for example Ruby Red (101). 

In living organisms, chiral molecules are usually present in only one of their chiral forms. For example, the amino acids in proteins occur only as their l isomers glucose occurs only as its D isomer. (The conventions for naming stereoisomers of the amino acids are described in Chapter 3 those for sugars, in Chapter 7 the RS system, described above, is the most useful for some biomolecules.) In contrast, when a compound with an asymmetric carbon atom is chemically synthesized in the laboratory, the reaction usually pro-... 

Attention has been drawn to the fact that the reduction potentials of the amino acids in proteins may differ by -0.2 and +0.3 V from the above values, and this may also influence the repair capability of proteins surrounding the DNA. ET in DNA and proteins over a longer distance have been discussed above. 

Amino acyl 5 -adenylates have been known as products in the first stage of activation for the amino acids in protein biosynthesis before they are coupled to t-RNA. The... 

Amino acids in proteins are joined together in a specific way. These bonds constitute the peptide linkage. The formation of peptide linkages is a condensation process involving the loss of water. For example, consider the condensation of alanine, leucine, and tyrosine shown in Figure 3.3. When these three amino acids join together, two water molecules are eliminated. The product is a /n peptide since there are three amino acids involved. The amino acids in proteins are linked as shown for this tripeptide, except that many more monomeric amino acid groups are involved. 

During baking there is an evaporation of water from the loaf, this is particularly marked near the surface of the loaf, and this evaporation plus the occurrence of the Maillard reaction cause a characteristic dark brown crust to be formed on the exterior of the loaf. The Maillard reaction is a complex set of chemical reactions in which the amino acids in proteins react with reducing sugars such as glucose and fructose, and which are very important to our perception of flavour in baked bread. 

Extra attention was devoted to proteins and en7ymes, as they have been the traditional "bread and butter" of the nutritional biochemist. The amino acids that form proteins can be classified in several ways (1) relatively hydrophilic or lipophilic, (2) dispensable or indispensable (noncssentiai or essential), (3) glycogenic or ketogenic, and, hnally, (4) classical or modified. Only a minority of the amino acids in proteins are modified after incorporation into the polypeptide chain. 

Let us consider the protein structure shown in Figure 2. Here R represents a group ranging from an H atom (in the amino acid glycine) to moderately complex structures. The amino acids in proteins are joined zt peptide linkages outlined by dashed lines. 

Rideal and Roberts also discuss the additivity of absorption of the amino acids in proteins and conclude that quantitative agreement between the observed and calculated absorption curves of proteins is poor, even at wavelengths longer than 2600 A. where peptide linkage absorption is absent. They suggest that longwave shifts and changes in the extinction coefficients of the aromatic amino acid residues, both due to peptide combination, may be responsible for such discrepancies. 

Dye-sensitized photooxygenation of the amino acids In proteins or the bases In nucleic acids is believed to be the basis for most of the phenomena classified under "photodynamic action" (see Figure 3). 1-02 Is probably Intermediate In some but not... 

The least abundant of the main types of RNA is mRNA. In most cells, it constitutes no more than 5%-10% of the total cellular RNA. The sequences of bases in mRNA specify the order of the amino acids in proteins. In rapidly growing cells, many different proteins are needed within a short time interval. Fast turnover in protein synthesis becomes essential. Consequently, it is logical that mRNA is formed when it is needed, directs the synthesis of proteins, and then is degraded so that the nucleotides can be recycled. Of the main types of RNA, mRNA is the one that usually turns over most rapidly in the cell. Both tRNA and rRNA (as well as ribosomes themselves) can be recycled intact for many rounds of protein synthesis. 

The amino acids in proteins or peptides are usually listed with their three-letter or one-letter code. 

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