Amino acid residues, basic functional groups

Figure 8.49 Mechanisms of three enzymes that utilise general acid-base catalysis as part of their mechanistic paths to successful bio-catalysis, (a) triose phosphate isomerase (TIM), (b) lysozyme, (c) RNAse A. In all cases substrates are shown in red. Lone pair donor amino acid residues are general bases, lone pair acceptor amino acid residues are general acids. Note that pK (a commonly used term) is the equivalent of p/f/ or pK (as written in this text book) as appropriate for an acidic or basic functional group.

At the time the hormone is introduced into the LBD (Fig. 1.4), a conformational change is produced in the three-dimensional structure of the receptor, a change that is key to the subsequent steps in hormonal action. This change is produced by a few contacts (between 6 or 7 and 15) of the receptor s amino acids with related groups from the hormone s structure. Some basic amino acid residues, particularly from arginine, which are preserved virtually intact among receptors, are critical in the execution of this function (Quingley et al. 1995). 

In view of the fact that the number of basic amino acid residues in pepsinogen exceeds that present in pepsin, and these residues may function as conformational determinants, the dependence of the specific optical rotation, [a ]366, on the pH of the solution had to be considered. If the pH of the solution is altered from 6.5 to 11.5, the levorotation increases markedly in the pH range of 9.2 to 10.8 with the mid-point at pH 10.0. This value approximates the apparent pK of the -amino group of the lysyl residues if present in peptide linkage. 

Coenzymes have very little activity in the absence of the enzyme and very little specificity. The enzyme provides specificity, proximity, and orientation in the substrate recognition site, as well as other functional groups for stabilization of the transition state, acid-base catalysis, etc. For example, thiamine is made into a better nucleophilic attacking group by a basic amino acid residue in the enzyme that removes the dissociable proton (EnzB in Fig. 8.11), thereby generating a negatively charged thiamine carbon anion. Later in the reaction, the enzyme returns the proton. 

Because of the complexity of biological polymers, their IR spectra are generally more difficult to analyze than the IR spectra of synthetic polymers. At present, IR spectra have been used basically as an analytic tool to identify certain functional groups of biological polymers. For proteins, the amide I and II bands appear in the region 1700-1500 cm and are localized in the —CO—NH— group. The frequencies of these bands are not dependent on the neighboring amino acid residue side... 

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