PDFTable of Contents
Metabolism can be defined as the sum of all the enzyme-catalysed reactions occurring in a cell. There are relatively few metabolic pathways, but each of these can be broken down into many individual, enzyme-specific, catalysed steps. Metabolism is a highly integrated process. Individual metabolic pathways are linked into complex networks through common, shared substrates. A series of nested and cascaded feedback loops are employed to allow flexibility and adaptation to changing environmental conditions and demands. Negative feedback (usually by end-product inhibition) prevents the over-accumulation of intermediate metabolites and it contributes to maintaining homeostasis.
Understanding the mechanism involved in metabolic regulation has important implications in both biotechnology and in medicine. For example, it is estimated that at least a third of all serious health problems such as coronary heart disease, diabetes and strokes are caused by metabolic disorders. Due to the integrated nature of metabolism, it is often difficult to predict how changing the activity of a single enzyme will affect the entire reaction pathway.
Mathematical kinetic models have been applied to help elucidate the behaviour of biochemical networks. Many of these kinetic models have been published, but presented here are the raw CellML descriptions of metabolic models which have been based on textbook defined pathways. We have assumed that all enzyme-catalysed reactions have Michaelis-Menten kinetics, and that all non-catalysed reactions have mass action kinetics. All metabolites and enzymes have a default concentration of one micromolar, and km, vmax and reaction rate constants also have a default value of one.
Metabolism has two principal functions: it provides the energy required to maintain the internal composition of the cell and support its functions, and it also provides the metabolites the cell requires to synthesise its constituents and products. As emphasised above, metabolism is an integrated process, but in order to facilitate its analysis, it can be divided into several artificial subdivisions. Classically these are:
Carbohydrate Metabolism — glycolysis, gluconeogenesis, the pentose phosphate pathway, the electron transport chain and the TCA cycle.
Lipid Metabolism — fatty acid activation and oxidation, fatty acid synthesis, cholesterol biosynthesis, phospholipid synthesis, glycolipid synthesis and triacylglycerol synthesis.
Nitrogen Metabolism — transamination, purine and pyrimidine synthesis and degradation, amino acid catabolism, non-essential amino acid synthesis and the urea cycle.
glycolysis_model.xml — the raw XML.
glycolysis_model.html — an HTML version for browsing online.
glycolysis_model.pdf — a PDF version suitable for printing.
glycolysis_model.tar.gz — a gzipped tarball with the XML and this documentation.
glycolysis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
glycolysis_model_with_encapsulation.xml — the raw XML.
glycolysis_model_with_encapsulation.html — an HTML version for browsing online.
glycolysis_model_with_encapsulation.pdf — a PDF version suitable for printing.
glycolysis_model_with_encapsulation.tar.gz — a gzipped tarball with the XML and this documentation.
glycolysis_model_with_encapsulation_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
gluconeogenesis_model.xml — the raw XML.
gluconeogenesis_model.html — an HTML version for browsing online.
gluconeogenesis_model.pdf — a PDF version suitable for printing.
gluconeogenesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
gluconeogenesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
the_pentose_phosphate_pathway_model.xml — the raw XML.
the_pentose_phosphate_pathway_model.html — an HTML version for browsing online.
the_pentose_phosphate_pathway_model.pdf — a PDF version suitable for printing.
the_pentose_phosphate_pathway_model.tar.gz — a gzipped tarball with the XML and this documentation.
the_pentose_phosphate_pathway_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
the_electron_transport_chain_model.xml — the raw XML.
the_electron_transport_chain_model.html — an HTML version for browsing online.
the_electron_transport_chain_model.pdf — a PDF version suitable for printing.
the_electron_transport_chain_model.tar.gz — a gzipped tarball with the XML and this documentation.
the_electron_transport_chain_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
the_TCA_cycle_model.xml — the raw XML.
the_TCA_cycle_model.html — an HTML version for browsing online.
the_TCA_cycle_model.pdf — a PDF version suitable for printing.
the_TCA_cycle_model.tar.gz — a gzipped tarball with the XML and this documentation.
the_TCA_cycle_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
fatty_acid_activation_and_oxidation_model.xml — the raw XML.
fatty_acid_activation_and_oxidation_model.html — an HTML version for browsing online.
fatty_acid_activation_and_oxidation_model.pdf — a PDF version suitable for printing.
fatty_acid_activation_and_oxidation_model.tar.gz — a gzipped tarball with the XML and this documentation.
fatty_acid_activation_and_oxidation_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
oxidation_of_odd_chain_fatty_acids_model.xml — the raw XML.
oxidation_of_odd_chain_fatty_acids_model.html — an HTML version for browsing online.
oxidation_of_odd_chain_fatty_acids_model.pdf — a PDF version suitable for printing.
oxidation_of_odd_chain_fatty_acids_model.tar.gz — a gzipped tarball with the XML and this documentation.
oxidation_of_odd_chain_fatty_acids_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
fatty_acid_synthesis_model.xml — the raw XML.
fatty_acid_synthesis_model.html — an HTML version for browsing online.
fatty_acid_synthesis_model.pdf — a PDF version suitable for printing.
fatty_acid_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
fatty_acid_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
cholesterol_biosynthesis_model.xml — the raw XML.
cholesterol_biosynthesis_model.html — an HTML version for browsing online.
cholesterol_biosynthesis_model.pdf — a PDF version suitable for printing.
cholesterol_biosynthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
cholesterol_biosynthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
phospholipid_synthesis_model.xml — the raw XML.
phospholipid_synthesis_model.html — an HTML version for browsing online.
phospholipid_synthesis_model.pdf — a PDF version suitable for printing.
phospholipid_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
phospholipid_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
glycolipid_synthesis_model.xml — the raw XML.
glycolipid_synthesis_model.html — an HTML version for browsing online.
glycolipid_synthesis_model.pdf — a PDF version suitable for printing.
glycolipid_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
glycolipid_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
triacylglycerol_synthesis_model.xml — the raw XML.
triacylglycerol_synthesis_model.html — an HTML version for browsing online.
triacylglycerol_synthesis_model.pdf — a PDF version suitable for printing.
triacylglycerol_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
triacylglycerol_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
transamination_model.xml — the raw XML.
transamination_model.html — an HTML version for browsing online.
transamination_model.pdf — a PDF version suitable for printing.
transamination_model.tar.gz — a gzipped tarball with the XML and this documentation.
transamination_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
pyrimidine_nucleotide_synthesis_model.xml — the raw XML.
pyrimidine_nucleotide_synthesis_model.html — an HTML version for browsing online.
pyrimidine_nucleotide_synthesis_model.pdf — a PDF version suitable for printing.
pyrimidine_nucleotide_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
pyrimidine_nucleotide_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
purine_nucleotide_synthesis_model.xml — the raw XML.
purine_nucleotide_synthesis_model.html — an HTML version for browsing online.
purine_nucleotide_synthesis_model.pdf — a PDF version suitable for printing.
purine_nucleotide_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
purine_nucleotide_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
purine_nucleotide_degradation_model.xml — the raw XML.
purine_nucleotide_degradation_model.html — an HTML version for browsing online.
purine_nucleotide_degradation_model.pdf — a PDF version suitable for printing.
purine_nucleotide_degradation_model.tar.gz — a gzipped tarball with the XML and this documentation.
purine_nucleotide_degradation_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
pyrimidine_nucleotide_degradation_UMP_and_CMP_model.xml — the raw XML.
pyrimidine_nucleotide_degradation_UMP_and_CMP_model.html — an HTML version for browsing online.
pyrimidine_nucleotide_degradation_UMP_and_CMP_model.pdf — a PDF version suitable for printing.
pyrimidine_nucleotide_degradation_UMP_and_CMP_model.tar.gz — a gzipped tarball with the XML and this documentation.
pyrimidine_nucleotide_degradation_UMP_and_CMP_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
pyrimidine_nucleotide_degradation_dTMP_model.xml — the raw XML.
pyrimidine_nucleotide_degradation_dTMP_model.html — an HTML version for browsing online.
pyrimidine_nucleotide_degradation_dTMP_model.pdf — a PDF version suitable for printing.
pyrimidine_nucleotide_degradation_dTMP_model.tar.gz — a gzipped tarball with the XML and this documentation.
pyrimidine_nucleotide_degradation_dTMP_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
amino_acid_catabolism_model.xml — the raw XML.
amino_acid_catabolism_model.html — an HTML version for browsing online.
amino_acid_catabolism_model.pdf — a PDF version suitable for printing.
amino_acid_catabolism_model.tar.gz — a gzipped tarball with the XML and this documentation.
amino_acid_catabolism_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
the_urea_cycle_model.xml — the raw XML.
the_urea_cycle_model.html — an HTML version for browsing online.
the_urea_cycle_model.pdf — a PDF version suitable for printing.
the_urea_cycle_model.tar.gz — a gzipped tarball with the XML and this documentation.
the_urea_cycle_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
non_essential_amino_acid_synthesis_model.xml — the raw XML.
non_essential_amino_acid_synthesis_model.html — an HTML version for browsing online.
non_essential_amino_acid_synthesis_model.pdf — a PDF version suitable for printing.
non_essential_amino_acid_synthesis_model.tar.gz — a gzipped tarball with the XML and this documentation.
non_essential_amino_acid_synthesis_model_maths.pdf — a PDF of the equations described in the model generated directly from the CellML description using the MathML Renderer.
