Binding, geometry primary

Au(OH) c. Additionally, silica does not stabilize goldNPs against agglomeration. It appears that, on silica, one of the primary roles of Pt is to help stabilize small particles. Pt may also add additional functionality to the catalyst by binding O2 and locating bound or activated O2 near active Au sites. Alternately, the presence of Pt may affect the surface structure of Au, helping it to adopt a more active geometry. 

Why did nature use an Fe-S cluster to catalyze this reaction, when an enzyme such as fumarase can catalyze the same type of chemistry in the absence of any metals or other cofactors One speculation would be that since aconitase must catalyze both hydrations and dehydrations, and bind substrate in two orientations, Fe in the comer of a cubane cluster may provide the proper coordination geometry and electronics to do all of these reactions. Another possibility is that the cluster interconversion is utilized in vivo to regulate enzyme activity, and thus, help control cellular levels of citrate. A third, but less likely, explanation is that during evolution an ancestral Fe-S protein, whose primary function was electron transfer, gained the ability to catalyze the aconitase reaction through random mutation. 

Distinguish between the primary, secondary and tertiary structure of proteins. Which is usually responsible for the geometry and properties of the substrate binding site How are the properties of the binding site reflected by the induced fit model ... 

Dooley et al. first proposed an inner-sphere electron transfer mechanism where O2 binds directly to copper(I) 55 this was based upon precedence that suggested very rapid reactions between O2 and synthetic copper(I) compounds used as spectroscopic models for enzyme active sites. A three-coordinate copper(I) geometry in the CAOs had been demonstrated upon reduction with dithionite under anaerobic conditions.56 The reduction of the enzyme anaerobically with primary amine substrates actually produces two states, a copper(I)/semiquinone and a copper (II)/aminoquinol (Figure 9.11). In plant-derived and bacterial CAOs, these states have been demonstrated to exist in rapid equilibrium, due to intraprotein electron... 

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