Abstract
This chapter summarizes the fundamentals of metabolic flux balancing as a computational tool of metabolic engineering and systems biology. It also presents examples from the literature for its applications in medicine. These examples involve mainly liver metabolism and antibiotic production. Metabolic flux balancing is a computational method for the determination of metabolic pathway fluxes through a stoichiometric model of the cellular pathways, using mass balances for intracellular metabolites. It is a powerful tool to study metabolism under normal and abnormal conditions with a view to engineer the metabolism. Its extended potential in medicine is emphasized in the future trends.
TopMetabolism converts substrates into metabolic energy, redox potential and metabolic end products that are essential for cellular function. Several independent reactions that govern the synthesis and organisation of the macromolecules into a functioning cell can be classified as fueling reactions, biosynthetic reactions, polymerisation reactions and assembly reactions.
Characteristics of metabolic pathways can be summarized as follows:
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Almost all metabolic reactions are reversible.
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Metabolic pathways however, are irreversible.
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Every metabolic pathway has a first committed step.
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All metabolic pathways are regulated.
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Metabolic pathways in eukaryotic cells occur in specific cellular locations.
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Different metabolic pathways are connected by metabolites that participate in more than one pathway by pathway branching. These metabolites, therefore, connect one reaction sequence with another.
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Co-factors like ATP, NADH and NADPH also take part in pathway integration because of their central roles in biosynthetic reactions. Biosynthetic reactions continuously form and utilise these co-factors and hence connect individual reactions both within the same pathway and between different pathways.
While cell composition may vary with cell-type and physiological and environmental conditions, a typical cell can be assumed to contain: protein, RNA, DNA, lipids, lipopolysaccharides, peptidoglycan, glycogen and free amino acids. The 12 precursor metabolites formed in the biosynthetic pathways are used to synthesize about 75-100 building blocks, coenzymes and prosthetic groups needed for cellular synthesis. The major biosynthetic pathways involved in cell growth include the biosynthesis of amino acids, nucleotides, sugars, amino sugars and lipids. The building blocks produced in biosynthetic reactions are sequentially linked into long branched or unbranched polymeric chains during polymerisation reactions. These long polymeric chains are called the macromolecules of cellular biomass and can be grouped into ribonucleic acid (RNA), deoxyribonucleic acid (DNA), proteins, carbohydrates, free amino acids and lipids.
Metabolic flux balancing is a computational method for the determination of metabolic pathway fluxes (specific rates of reactions) through a stoichiometric model of the cellular pathways, using mass balances for intracellular metabolites.
Key Terms in this Chapter
Volumetric reaction rate: It is defined as:
Biomass: In this context, it means cells, tissues, organs. It is often measured and expressed as the concentration of dry biomass (dry weight).
Matrix: In mathematics, a matrix is a table of elements. These elements, members or entries, may be numbers of any abstract quantities that can be added and multiplied. Matrices are useful in describing the linear equations in a short format. They are also used to keep track of the coefficients of linear algebraic operations.
Metabolic Pathways: A metabolic pathway is any sequence of feasible and observable biochemical reaction steps catalysed by enzymes and connecting a specified set of input and output metabolites.
Transpose of a Matrix: In linear algebra, the transpose of a matrix A is another matrix A T obtained by writing the rows of A as the columns of A T and the columns of A as the rows of A T .
Flux: In this context, the metabolic flux is identical to the specific metabolic reaction rates. The most frequently used units are: (mmol metabolite) (g dry wt biomass) -1 (h) -1 .
Specific Reaction Rate: The specific rate of a microbial activity is equal to the volumetric rate for that activity divided by the cell concentration performing that activity. Substituting the definition of volumetric rate in to this equation, the specific reation rate becomes:
Metabolic Product: A metabolic product is a compound produced by the cells and is excreted to the extracellular medium. It could be produced in the primary metabolism, e.g. carbon dioxide, ethanol, acetate, or lactate, or a more complex one, e.g. a secondary metabolite or a heterologous protein secreted to the extracellular medium.
Substrate: A substrate is a compound that is present in a sterile culture medium and can either be further metabolized by, or directly incorporated into, the cell. The substrate could therefore, range from carbon, nitrogen, and energy sources to various minerals, vitamins essential for cell function.