10-01 - BIO 5099 Molecular Biology for Computer...

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BIO 5099: Molecular Biology for Computer Scientists (et al) Lecture 11: Metabolic Pathways http://compbio.uchsc.edu/hunter/bio5099 [email protected] Metabolism Metabolism is the chemical change of compounds by organisms Evolutionarily created to improve fitness Catalyzed by enzymes Various classes Matter (anabolism of amino acids, nucleotides, lipids, etc.) Detoxification (catabolism of dangerous compounds) Substrates and products are “metabolites.” All but input and output are “intermediates” Metabolic pathways A series of chemical reactions involved in the metabolism of a compound (or compounds). Each step is a single enzymatic reaction Fluxes of metabolites can be Linear (series of transformations mapping single substrate to a single product) Branching (single substrate, multiple products) Cyclic (multiple substrates, multiple products) Pathways are regulated in various ways to control the fluxes of metabolites.
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interconnected graph Intermediates in one pathway are often inputs to another. Intermediates in energy metabolism are inputs to synthesis of most amino acids Nucleotides (esp. adenosine) are inputs in energy metabolism (e.g. to make ATP, NAD, etc.) Universality of pathways Much intermediary metabolism is widely shared throughout life. Broad functional categories are nearly universal: Protein translation, modification, transport and degradation Cell motility, secretion and signal transduction Carbohydrates Amino Acids Inorganic ions Lipids Nucleotides Coenzymes Diversity of pathways Most organisms exhibit some diversity from the “universal” intermediary metabolism Sometimes the differences are major: E.g. some Archaea run the oxidative Krebs cycle (more shortly) backwards to create ATP in highly reducing environments Usually the differences are in the presence or absence of particular enzymes, making alternative pathways through the network. Different niches require different metabolisms.
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10-01 - BIO 5099 Molecular Biology for Computer...

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