Carboxylate groups sites

ACID DYES Commercial acid dyes contain one or more sulfonate groups, thereby providing solubility in aqueous media. These dyes are apphed in the presence of organic or mineral acids (pH 2—6). Such acids protonate any available cationic sites on the fiber, thereby making possible bonding between the fiber and the anionic dye molecule. Wool, an animal fiber, is an amphoteric coUoid, possessing both basic and acidic properties because of the amino and carboxylic groups of the protein stmcture. In order to dye such a system, coulombic interactions between the dye molecule and the fiber must take place ie, H2N" -wool-COO + H2N" -wool-COOH. The term acid dye is appHed to those that are capable of such interactions. Acid dyes... 

The alkanoic acids, with the exception of formic acid, undergo typical reactions of the carboxyl group. Formic acid has reducing properties and does not form an acid chloride or an anhydride. The hydrocarbon chain of alkanoic acids undergoes the usual reactions of hydrocarbons except that the carboxyl group exerts considerable influence on the site and ease of reaction. The alkenoic acids in which the double bond is not conjugated with the carboxyl group show typical reactions of internal olefins. All three types of reactions are industrially important. 

Weakly acidic cation-exchange resins have carboxylic groups (COOH) as the exchange sites. When operated on the hydrogen cycle, the weakly acidic resins are capable of removing only those cations equivalent to the amount of alkalinity present in the water, and most efficiently the hardness (calcium and magnesium) associated with alkalinity, according to these reactions ... 

The first hint that two active-site carboxyl groups—one proto-nated and one ionized—might be involved in the catalytic activity of the aspartic proteases came from studies of the pH dependence of enzymatic activity. If an ionizable group in an enzyme active site is essential for activity, a plot of enzyme activity versus pH may look like one of the plots at right. 

FIGURE 18.32 Biotin is covalently linked to a protein via the e-amino group of a lysine residue. The biotin ring is thus tethered to the protein by a 10-atom chain. It functions by carrying carboxyl groups between distant sites on biotin-dependent enzymes. 

Results from an array of methods, including X-ray absorption, EXAFS, esr and magnetic circular dichroism, suggest that in all ureases the active sites are a pair of Ni" atoms. In at least one urease,these are 350 pm apart and are bridged by a carboxylate group. One nickel is attached to 2 N atoms with a fourth site probably used for binding to urea. The second nickel has a trigonal bipyramidal coordination sphere. 

The HIV-1 protease, like other retroviral proteases, is a homodimeric aspartyl protease (see Fig. 1). The active site is formed at the dimer interface, with the two aspartic acids located at the base of the active site. The enzymatic mechanism is thought to be a classic acid-base catalysis involving a water molecule and what is called a push-pull mechanism. The water molecule is thought to transfer a proton to the dyad of the carboxyl groups of the aspartic acids, and then a proton from the dyad is transferred to the peptide bond that is being cleaved. In this mechanism, a tetrahedral intermediate transiently exists, which is nonconvalent and which is mimicked in most of the currently used FDA approved inhibitors. 

However, when the X-ray crystal structure of the MoFe protein was examined, it was clear that homocitrate could not directly hydrogen bond to the histidine, since the carboxylate group and imidazole are stacked parallel to each other in the crystal. Nevertheless, as noted in the previous section, studies on model complexes have suggested that homocitrate can become monodentate during nitrogenase turnover, with the molybdenum carboxylate bond breaking to open up a vacant site at molybdenum suitable for binding N2. 

In the case of prothrombin and related clotting factors, interruption of the vitamin K cycle leads to the production of nonfunctional, undercarboxylated proteins, which are duly exported from hepatocytes into blood (Thijssen 1995). They are nonfunctional because there is a requirement for the additional carboxyl residues in the clotting process. Ionized carboxyl groups can establish links with negatively charged sites on neighboring phospholipid molecules of cell surfaces via calcium bridges. 

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