Metabolism, stoichiometry

The respiratory quotient (RQ) is often used to estimate metabolic stoichiometry. Using quasi-steady-state and by definition of RQ, develop a system of two linear equations with two unknowns by solving a matrix under the following conditions the coefficient of the matrix with yeast growth (y = 4.14), ammonia (yN = 0) and glucose (ys = 4.0), where the evolution of C02 and biosynthesis are very small (o- = 0.095). Calculate the stoichiometric coefficient for RQ =1.0 for the above biological processes ... 

The stoichiometry of growth and metabolism can also be described by elemental material balances. This approach can provide an insight into the potential of the organism for biomass or product production, and thus the scope for process improvement. 

A considerable improvement over purely graph-based approaches is the analysis of metabolic networks in terms of their stoichiometric matrix. Stoichiometric analysis has a long history in chemical and biochemical sciences [59 62], considerably pre-dating the recent interest in the topology of large-scale cellular networks. In particular, the stoichiometry of a metabolic network is often available, even when detailed information about kinetic parameters or rate equations is lacking. Exploiting the flux balance equation, stoichiometric analysis makes explicit use of the specific structural properties of metabolic networks and allows us to put constraints on the functional capabilities of metabolic networks [61,63 69]. 

This section mainly builds upon classic biochemistry to define the essential building blocks of metabolic networks and to describe their interactions in terms of enzyme-kinetic rate equations. Following the rationale described in the previous section, the construction of a model is the organization of the individual rate equations into a coherent whole the dynamic system that describes the time-dependent behavior of each metabolite. We proceed according to the scheme suggested by Wiechert and Takors [97], namely, (i) to define the elementary units of the system (Section III. A) (ii) to characterize the connectivity and interactions between the units, as given by the stoichiometry and regulatory interactions (Sections in.B and II1.C) and (iii) to express each interaction quantitatively by... 

Note that Eq. (6) includes thermodynamic equilibrium (v° = 0) as a special case. However, usually the steady-state condition refers to a stationary nonequilibrium state, with nonzero net flux and positive entropy production. We emphasize the distinction between network stoichiometry and reaction kinetics that is implicit in Eqs. (5) and (6). While kinetic rate functions and the associated parameter values are often not accessible, the stoichiometric matrix is usually (and excluding evolutionary time scales) an invariant property of metabolic reaction networks, that is, its entries are independent of temperature, pH values, and other physiological conditions. 

In principle, once the stoichiometry and rate constants of all elementary steps are specified, the dynamic behavior of the entire metabolic network can be evaluated using the dynamic mass-balance Eq. (5). However, such an approach is only rarely employed in practice. The numerical simulation of enzymatic... 

The elements of the matrix A are fully specified by the stoichiometry matrix N and the metabolic state of the system. Usually, though not necessarily, the metabolic state corresponds to an experimentally observed state of the system and is characterized by steady-state concentrations S° and flux values v(S°). 

The dependence (1 TP of v, on ATP is modeled as in the previous section, using an interval C [—00,1] that reflects the dual role of the cofactor ATP as substrate and as inhibitor of the reaction. All other reactions are assumed to follow Michaelis Menten kinetics with ()rs E [0, 1], No further assumption about the detailed functional form of the rate equations is necessary. Given the stoichiometry, the metabolic state and the matrix of saturation parameter, the structural kinetic model is fully defined. An explicit implementation of the model is provided in Ref. [84],... 

The most common anaerobic heterotrophic metabolisms found in the water column are denitrification and sulfete reduction. Their stoichiometries are given in Eqs. 8.11... 

Biological nitrogen fixation is energetically costly, so this metabolism is found only in environments where Nr concentrations are low. As shown by the following stoichiometry, 8 electrons and 16 molecules of ATP are required to reduce one molecule of N2. ... 

Empath is a Cabinet database of metabolic pathways that models a metabolic pathway chart. It initially models the Boehringer Mannheim wall chart [35] but other pathway layouts are possible. It currently includes 1462 steps (metabolic reactions). The Empath database consists of more than 8000 live objects. Every object has an exact geometric location, that is, x, y coordinate, which is optionally indicated by visible hotspots. The chart is clickable everywhere and the image recenters itself around the selected point. The current object is the one closest to the center of the image and is identified by a bull s eye. A summary of the object is given (e.g., its structure, EC number, SMILES, reaction stoichiometry, etc.). Empath provides navigational features such as zoom in/out, wider, thinner, taller and shorter. 

In our example, EC book and Empath find an exact match to HMG-CoA reductase. The Empath link shows the metabolic step that the enzyme catalyzes (Figure 10.5 [50]). The reaction is between S-3-hydroxy-3-methylglutaryl-CoA and Mevalonate. The step summary on the right side of the chart image shows activation and regulation of the enzyme, its biological scope, direction, reversibility and stoichiometry. A pathway search... 

Variations in ferritin protein coats coincide with variations in iron metabolism and gene expression, suggesting an Interdependence. Iron core formation from protein coats requires Fe(Il), at least experimentally, which follows a complex path of oxidation and hydrolytic polymerization the roles of the protein and the electron acceptor are only partly understood. It is known that mononuclear and small polynuclear Fe clusters bind to the protein early in core formation. However, variability in the stoichiometry of Fe/oxidant and the apparent sequestration and stabilization of Fe(II) in the protein for long periods of time indicate a complex microenvironment maintained by the protein coats. Full understanding of the relation of the protein to core formation, particularly at intermediate stages, requires a systematic analysis using defined or engineered protein coats. 

Biosynthesis of Digalloylglucose. Besides the above mentioned acyltransferase, oak leaves also contained a completely different type of acyltransferase that catalyzed the formation of digalloylglucose (41). It became evident that this ester was synthesized by a new reaction mechanism in which / -glucogallin was utilized as both acyl donor and acceptor this conclusion was supported by the isolation of analogous acyltransferases related to other metabolic pathways (cf. Table III). Recent studies (54) have shown, in accordance with previous proposals (5,7,8), that 1,6-O-digalloylglucose was produced by the enzyme, and that the stoichiometry of the reaction... 

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