Substrate (chemistry)

About: Substrate (chemistry) is a research topic. Over the lifetime, 35902 publications have been published within this topic receiving 740722 citations. The topic is also known as: enzyme substrate.

Transition State Analog Inhibitors and Enzyme Catalysis

Abstract: Enzymes, like midwives, ease the difficult passage of substances from one metastable situation to another. Catalysis appears to depend on the development of strong forces of attraction between the enzyme and activated forms of the substrate, which subside as the product is formed and the enzyme returns to its free state. It can be shown, on the basis of any rate theory that assumes the existence of an equilibrium of activation, that the substrate in its passage to product acquires a fleeting, but greatly elevated, affinity for the enzyme. So great is this affinity that a stable substance that "looks" to the enzyme like a substrate in the midst of its conversion to product is expected to be an unusually effective inhibitor ( 1-3). General reviews of some experimental and theoretical aspects of transition state affinity, and of early efforts to design potential "transition state analogs," have appeared (4-7). As of early 1975, almost 60 possible examples had been described. In addition to their possible use as anti metabolites, inhibitors of this kind can provide a useful indication of the particular mechanism by which a substrate is transformed by the enzyme that it inhibits. The structure of an effective inhibitor should reflect and confirm the mechanism on which its design was based. In certain cases it may be difficult to isolate reaction intermediates, and inhibitors can sometimes provide mechanistic information that is not easily accessible by other methods. In the case of adenosine deaminase, for example, inhibitors provided the initial indication that the substrate adenosine is attacked directly by the second substrate, water. A double displacement mechanism, so common among hydrolytic enzymes, seemed improbable in the case of this particular enzyme, and subsequent work appears to support this conclusion. Structural features of strong inhibitors may also provide an indication of binding determinants at the active site, which are important for catalysis. The binding of analogs of activated intermediates in substrate transformation, in conjunction with cxact structural studies, may help to provide a dynamic picture of the succession of events that occur during the catalytic process, and may be useful for examining

An improved and accurate method for determining the dehydrogenase activity of soils with iodonitrotetrazolium chloride.

Abstract: Conditions for a rapid, precise [100 μg iodonitrotetrazolium chloride (INT)-formazan ml-1 assay mixture], and easily reproducible assay of potential soil dehydrogenase activity are described, using 2(p-iodophenyl)-3-(p-nitrophenyl)-5-phenyl tetrazolium chloride (iodonitrotetrazolium chloride, INT) as the substrate. Reduced iodonitrotetrazolium formazan (INTF) was measured by spectrophotometry (464 nm) after extraction with N,N-dimethylformamide and ethanol. With this method, the coloured complex formed is highly stable. The effects of pH, buffer concentration, temperature, substrate concentration, amount of soil weight, and reaction time on dehydrogenase activity were investigated. The rate of substrate hydrolysis was proportional to soil weight; the optimal INT reduction was achieved with 1 M TRIS buffer (pH 7.0) at 40 °C. It was possible to determine the biotic and abiotic substrate reduction by comparing assays of autoclaved and unsterile soil samples. Different investigations have confirmed that the intracellular enzyme is highly correlated with the microbial biomass, and indicate that this activity is suitable as an indirect parameter of microbial biomass, measurement.

Biodegradation kinetics of benzene, toluene, and phenol as single and mixed substrates for Pseudomonas putida F1

Abstract: Although microbial growth on substrate mixtures is commonly encountered in bioremediation, wastewater treatment, and fermentation, mathematical modeling of mixed substrate kinetics has been limited. We report the kinetics of Pseudomonas putida F1 growing on benzene, toluene, phenol, and their mixtures, and compare mathematical models to describe these results. The three aromatics are each able to act as carbon and energy sources for this strain. Biodegradation rates were measured in batch cultivations following a protocol that eliminated mass transfer limitations for the volatile substrates and considered the culture history of the inoculum and the initial substrate to inoculum mass ratio. Toluene and benzene were better growth substrates than phenol, resulting in faster growth and higher yield coefficients. In the concentration ranges tested, toluene and benzene biodegradation kinetics were well described by the Monod model. The Monod model was also used to characterize phenol biodegradation by P. putida F1, although a small degree of substrate inhibition was noted. In mixture experiments, the rate of consumption of one substrate was found to be affected by the presence of the others, although the degree of influence varied widely. The substrates are catabolized by the same enzymatic pathway, but purely competitive enzyme kinetics did not capture the substrate interactions well. Toluene significantly inhibited the biodegradation rate of both of the other substrates, and benzene slowed the consumption of phenol (but not of toluene). Phenol had little effect on the biodegradation of either toluene or benzene. Of the models tested, a sum kinetics with interaction parameters (SKIP) model provided the best description of the paired substrate results. This model, with parameters determined from one- and two-substrate experiments, provided an excellent prediction of the biodegradation kinetics for the three-component mixture.