Special sites

It now seems clear tliat, under certain conditions, massive enhancements of what is nonnally a very weak process can be achieved. The ability to obtain vibrational spectra would be a great advance in tlie characterization of single molecules if metliods could be found to reproducibly observe all molecules in a sample, not only tliose tliat happen to bind to special sites on tlie colloid. 

Allan, V.J., Vale, R.D.(1994). Movement of membrane tubules along microtubules in vitro Evidence for specialized sites of motor attachment. J. Cell Sci. (in press). 

There is no doubt that all the special sites listed above might have adsorptive and other properties differing from those of normal surface atoms. For this reason the rate of an electrochemical reaction could be higher or lower at such sites. The sign and magnitude of the overall effect depends on the relative numbers of special points and normal surface atoms. 

Clathrin-mediated (or clathrin-dependent) endocytosis normally occurs at specialized sites, where complex structures called coated pits are assembled in order to concentrate surface proteins for internalization. The coat consists of many different proteins that are needed for stabilization of both the pit and the forming of the clathrin-coated vesicle. The two most abundant proteins found within these structures are clathrin and the adaptor protein AP-2 (9). 

The amount of aluminium introduced into the framework reached ceiling level with increase of reaction time and partial pressure of aluminium trichloride, and showed a gently-sloping peak at around 940 K reaction temperature. Moreover, they did not correspond to the amount of silicone removed from the silicalite during the reaction [8,11]. From these results, it is suggested that by the atom-planting, aluminium atoms occupy special sites in the zeolite framework, and do not substitute silicon atoms in the framework. 

Re combinational DNA repair of a circular bacterial chromosome, while essential, sometimes generates deleterious byproducts. The resolution of a Holliday junction at a replication fork by a nuclease such as RuvC, followed by completion of replication, can give rise to one of two products the usual two monomeric chromosomes or a contiguous dimeric chromosome (Fig. 25-41). In the latter case, the covalently linked chromosomes cannot be segregated to daughter cells at cell division and the dividing cells become stuck. A specialized site-specific recombination system in E. coli, the XerCD system, converts the dimeric chromosomes to monomeric chromosomes so that cell division can proceed. The reaction is a site-specific deletion reaction (Fig. 25-39b). This is another example of the close coordination between DNA recombination processes and other aspects of DNA metabolism. 

FIGURE 25-41 DNA deletion to undo a deleterious effect of re-combinational DNA repair. The resolution of a Holliday intermediate during recombinational DNA repair (if cut at the points indicated by red arrows) can generate a contiguous dimeric chromosome. A specialized site-specific recombinase in E. coli, XerCD, converts the dimer to monomers, allowing chromosome segregation and cell division to proceed. 

Figure 5-13 Electron micrograph of a DNA molecule (from a bacterial virus bacteriophage T7) undergoing replication. The viral DNA is a long ( 14 pm) duplex rod containing about 40,000 base pairs. In this view of a replicating molecule an internal "eye" in which DNA has been duplicated is present. The DNA synthesis was initiated at a special site (origin) about 17% of the total length from one end of the duplex. The DNA was stained with uranyl acetate and viewed by dark field electron microscopy. Micrograph courtesy J. Wolfson and D. Dressier.

Many specific parts of ribosomal RNA molecules and specific proteins within the intact ribosome were located prior to the determination of high resolution crystal structures. One major approach was the use of immunoelectron microscopy. Antibodies to specific ribosomal proteins or to special sites in the RNA were prepared, and electron microscopy was used to map the binding sites of the antibodies on the ribosomal... 

Nucleation often begins at the surface, where the product is not totally surrounded by reactant molecules. It may, however, occur at special sites either on the surface or in the bulk of the solid. The method of compound preparation and handling influences both surface area and the number and type of defects. Consequently, the rates of solid-phase reactions can depend on the history of the solid. 

Equations (5) and (10) imply that the velocity of an uncatalyzed reaction increases indefinitely with an increase in the concentration of the reactants. With enzyme-catalyzed reactions, something very different is observed. The rate usually increases linearly with substrate concentration at low concentrations, but then levels off and becomes independent of the concentration at high concentrations (fig. 7.6). The explanation for this hyperbolic dependence on substrate concentration is straightforward. For an enzyme to affect AG, the substrate must bind to a special site on the protein, the active site (fig. 7.7). At very low concentrations of substrate, the active sites of most of the enzyme molecules in the solution are unoccupied. Increasing the substrate concentration brings more enzyme molecules into play, and the reaction speeds up. At high concentrations, on the other hand, most of the enzyme molecules have their active sites occupied, and the observed rate depends only on the rate at which the bound reactants are converted into products. Further increases in the substrate concentration then have little effect. 

The best understood chemical neurotransmission occurs at synapses, specialized sites that connect two neurons. Neurons are organized so that they can both send synaptic... 

Relative energy of a nucleus at special sites as a function of the equilibrium wetting angle. Adapted from J. W. Cahn, Acta Met. 4 (1956) 456. 

These are the tools of a chemist, and to use these tools effectively, we must organize them in a sensible manner and look for patterns of reactivity that permit us make plausible predictions. Most of these reactions occur at special sites of reactivity known as functional groups, and these constitute one organizational scheme that helps us catalog and remember reactions. This is best accomplished by perceiving the reaction pathway or mechanism of a reaction. 

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