Explore chapters and articles related to this topic
Introduction to constraint-based modelling
Published in Karthik Raman, An Introduction to Computational Systems Biology, 2021
The directionality of reactions within the cell is governed by thermodynamics. Some reactions in the cell are reversible, while others are irreversible and proceed only in one direction. Enzymes can only convert a limited number of substrate molecules to product per unit time (“turnover number”, kcat). The maximum rate, vmax, of an enzyme-catalysed reaction is kcat[E0] (see §5.3.1), which gives rise to capacity constraints. A recent study has also shown the existence of other constraints such as cellular Gibbs energy dissipation rate [10]. Other constraints include those arising from the kinetics of reactions within cells and osmotic pressure [8].
Principles of Chemistry
Published in Arthur T. Johnson, Biology for Engineers, 2019
A substrate is any substance on which an enzyme can act to form a product. Rates of simple enzyme–substrate reactions are often described by the Michaelis–Menten construction. It has been found that the rate of product formation depends directly on the substrate concentration, but that the dependence is small for low substrate concentrations and for high substrate concentrations, and the dependence is highest somewhere between. The curve of rate of product formation plotted against substrate concentration forms an “S” shape (Figure 3.5.1). The steeper the “S,” the higher is the affinity of the enzyme for the substrate. A typical enzyme-substrate system has a rate of product formation equal to half the maximum (saturation) rate at about 5 mM at room temperature. Changing the concentration of an enzyme will affect the position of the curve.
Biodegradation of Phenol
Published in Donald L. Wise, Debra J. Trantolo, Remediation of Hazardous Waste Contaminated Soils, 2018
C. Vipulanandan, S. Wang, S. Krishnan
The inhibition of bacterial growth is often due to the inhibition of enzyme systems. An enzyme inhibitor reduces the rate of an enzymatically catalyzed reaction by binding either with the free enzyme and/or with the enzyme-substrate complex. Three types of models are frequently used to explain cell growth inhibition: competitive, noncompetitive, and uncompetitive. Competitive inhibition occurs when a substrate competes with another substrate for a site on either the cell or the enzyme. Noncompetitive inhibition occurs when the inhibitor can combine with both the free cell or enzyme and the cell/enzyme–substrate complex. An uncompetitive inhibitor binds with the cell/enzyme-substrate complex, which cannot undergo further reaction to yield product. Uncompetitive inhibition is believed to be the most frequently responsible mechanism for cell growth inhibition.
Intracellular-to-extracellular localization switch of acidic lipase in Enterobacter cloacae: evaluation of production kinetics and enantioselective esterification potential for pharmaceutical applications
Published in Preparative Biochemistry & Biotechnology, 2023
Atim Asitok, Maurice Ekpenyong, Nkpa Ogarekpe, Richard Antigha, Iquo Takon, Anitha Rao, Juliet Iheanacho, Sylvester Antai
Substrate specificity is a function of enzyme conformation or structure, especially at the active site, substrate structure and prevailing factors that influence enzyme-substrate binding.[43]p-NP-laurate (C12) was selected as best substrate for E. cloacae lipase with a relative activity of 162.48% (Figure 2B). This was followed by p-NP-myristate (C14) with 133.47%. Dunnet’s test of multiple comparison showed that mean differences between all p-nitrophenol-ester were significantly different from the control except that between control and p-NP-stearate. Similar results have earlier been reported for acidic lipase from Candida viswanathii.[13] However, selection of an optimum fatty acyl substrate may be strain-specific, in addition to the inherent structural differences among lipases, no matter how small.
Textile azo dyes discolouration using spent mushroom substrate: enzymatic degradation and adsorption mechanisms
Published in Environmental Technology, 2023
Juliana Barden Schallemberger, Nelson Libardi, Beatriz Lima Santos Klienchen Dalari, Mariane Bonatti Chaves, Maria Eliza Nagel Hassemer
In contrast, in the Linewaever-Burk linearisation (Figure 2B), the lines referring to NaCl concentrations and the absence of inhibitor intersect in the same area of the graph’s abscissa, however they intersect different areas of the ordinate, inferring a non-competitive inhibition. In this type of inhibition, the inhibitor binds to the enzyme at a different site from the active site, allowing normal binding of the substrate with the enzyme, however, complete inactivation of the enzyme occurs which prevents the conversion of the substrate into product. With the decrease in the amount of active enzymes in the medium as the inhibitor binds to the enzyme, the Vmax is reduced, while the Km is not affected as the inhibitor does not block the active enzyme site [70]. However, it was found that Km increased in the presence of NaCl. In contrast, Enaud et al. [71] found a competitive inhibition between ABTS and NaCl by representing Lineweaver–Burk, albeit a mixed inhibition according to the Cornish-Bowden model.
Relationship between denitrification and anammox rates and N2 production with substrate consumption and pH in a riparian zone
Published in Environmental Technology, 2023
Shuangjian Li, Xuefei Xie, Hu Li, Dongmei Xue
Environmental factors and substrates display significant effects on denitrification and anammox processes. The optimum reaction temperature is 20–37°C for anammox [14–16] and 20–35°C for denitrification [17,18]. Too high or too low a temperature will physiochemically change the lipid or protein in the cell membrane to decrease the reaction rates [19,20]. The denitrification and anammox processes are also greatly affected by pH, as the electrolyte balance in cells, the activity and survival status of microorganisms are associated with pH [21]. The optimum pH for anammox is 6.7–8.3 [14,22], and 6–9 for denitrification [19]. Denitrification rates demonstrated linear relations with the substrate of NO3−, higher NO3− contents corresponding to higher denitrification rates [23,24]. As heterotrophic bacteria, denitrifying bacteria require organic carbon for stimulating denitrification and accelerating N turnover, and low organic carbon contents will decrease denitrification rates [25] . There is a certain threshold value of NH4+ in the anammox reaction. Within the threshold range, the reaction rate increases with the increase in substrate concentration. After exceeding the threshold value, NH4+ contents produce more free ammonia (NH3) that influences the activity of anammox bacteria and then show a certain inhibition effect on the anaerobic ammonia oxidation reaction [26–28] .