Metabolic Engineering

  1. Fundamentals of Cellular Metabolism
    1. Core Metabolic Pathways
      1. Glycolysis
        1. Embden-Meyerhof-Parnas Pathway
          1. Key Enzymes and Regulation
            1. Energy Yield and Intermediates
              1. Metabolic Branch Points
              2. Pentose Phosphate Pathway
                1. Oxidative Phase
                  1. Non-Oxidative Phase
                    1. NADPH Generation
                      1. Ribose-5-Phosphate Production
                      2. Entner-Doudoroff Pathway
                        1. Pathway Steps
                          1. Organism Distribution
                            1. Comparison to Glycolysis
                            2. Tricarboxylic Acid Cycle
                              1. Cycle Steps and Intermediates
                                1. Energy Generation
                                  1. Reducing Power Generation
                                    1. Anaplerotic Reactions
                                    2. Glyoxylate Shunt
                                      1. Role in Carbon Conservation
                                        1. Isocitrate Lyase
                                          1. Malate Synthase
                                        2. Anabolism and Catabolism
                                          1. Definitions and Differences
                                            1. Anabolic Pathway Examples
                                              1. Catabolic Pathway Examples
                                                1. Metabolic Coupling
                                                2. Stoichiometry of Metabolic Reactions
                                                  1. Balancing Metabolic Equations
                                                    1. Yield Calculations
                                                      1. Cofactor Balances
                                                        1. Atom Economy
                                                        2. Thermodynamics of Metabolic Reactions
                                                          1. Gibbs Free Energy in Metabolism
                                                            1. Reaction Coupling
                                                              1. Thermodynamic Constraints
                                                                1. Driving Force Analysis
                                                                2. Enzyme Kinetics
                                                                  1. Michaelis-Menten Kinetics
                                                                    1. Derivation and Assumptions
                                                                      1. Kinetic Parameters
                                                                        1. Substrate Inhibition
                                                                        2. Allosteric Regulation
                                                                          1. Allosteric Sites and Effectors
                                                                            1. Cooperative Binding
                                                                              1. Hill Equation
                                                                                1. Examples in Central Metabolism
                                                                                2. Enzyme Inhibition
                                                                                  1. Competitive Inhibition
                                                                                    1. Non-Competitive Inhibition
                                                                                      1. Uncompetitive Inhibition
                                                                                    2. Regulation of Metabolic Flux
                                                                                      1. Transcriptional Regulation
                                                                                        1. Operons and Regulons
                                                                                          1. Transcription Factors
                                                                                            1. Global Regulatory Networks
                                                                                            2. Post-Translational Modification
                                                                                              1. Phosphorylation
                                                                                                1. Acetylation
                                                                                                  1. Other Covalent Modifications
                                                                                                  2. Allosteric Control
                                                                                                    1. Feedback Inhibition
                                                                                                      1. Feedforward Activation
                                                                                                        1. Metabolite Sensing
                                                                                                        2. Substrate Availability
                                                                                                          1. Transporter Regulation
                                                                                                            1. Nutrient Sensing Mechanisms
                                                                                                              1. Metabolite Channeling

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                                                                                                          1. Introduction to Metabolic Engineering

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                                                                                                          3. Tools for Genetic Modification