Biochemistry

  1. Bioenergetics and Metabolism
    1. Introduction to Metabolism
      1. Metabolic Pathways
        1. Linear Pathways
          1. Cyclic Pathways
            1. Branched Pathways
              1. Metabolic Networks
              2. Catabolism and Anabolism
                1. Energy-Yielding Pathways
                  1. Energy-Requiring Pathways
                    1. Amphibolic Pathways
                    2. Regulation of Metabolism
                      1. Allosteric Regulation
                        1. Covalent Modification
                          1. Compartmentalization
                            1. Substrate Availability
                              1. Hormonal Control
                              2. Metabolic Control
                                1. Flux Control
                                  1. Rate-Limiting Steps
                                    1. Feedback Inhibition
                                      1. Feedforward Activation
                                    2. Glycolysis and Gluconeogenesis
                                      1. Glycolysis
                                        1. Overview and Significance
                                          1. Preparatory Phase
                                            1. Glucose Phosphorylation
                                              1. Isomerization Reactions
                                                1. Second Phosphorylation
                                                2. Payoff Phase
                                                  1. Aldolase Reaction
                                                    1. Oxidation and Phosphorylation
                                                      1. ATP Generation
                                                      2. Key Enzymes
                                                        1. Hexokinase
                                                          1. Phosphofructokinase-1
                                                            1. Pyruvate Kinase
                                                            2. Energetics
                                                              1. ATP Yield
                                                                1. NADH Production
                                                                  1. Overall Stoichiometry
                                                                  2. Regulation
                                                                    1. Allosteric Control
                                                                      1. Hormonal Regulation
                                                                        1. Tissue Differences
                                                                      2. Fates of Pyruvate
                                                                        1. Aerobic Conditions
                                                                          1. Pyruvate Dehydrogenase Complex
                                                                            1. Acetyl-CoA Formation
                                                                            2. Anaerobic Conditions
                                                                              1. Lactic Acid Fermentation
                                                                                1. Ethanol Fermentation
                                                                                  1. Other Fermentation Pathways
                                                                                2. Gluconeogenesis
                                                                                  1. Biological Significance
                                                                                    1. Substrates
                                                                                      1. Lactate
                                                                                        1. Glycerol
                                                                                          1. Amino Acids
                                                                                            1. Propionate
                                                                                            2. Bypass Reactions
                                                                                              1. Pyruvate Carboxylase
                                                                                                1. PEPCK
                                                                                                  1. Fructose-1,6-bisphosphatase
                                                                                                    1. Glucose-6-phosphatase
                                                                                                    2. Energetics
                                                                                                      1. ATP Cost
                                                                                                        1. Reducing Equivalents
                                                                                                        2. Regulation
                                                                                                          1. Reciprocal Control with Glycolysis
                                                                                                            1. Hormonal Control
                                                                                                          2. Pentose Phosphate Pathway
                                                                                                            1. Oxidative Phase
                                                                                                              1. Glucose-6-phosphate Dehydrogenase
                                                                                                                1. 6-Phosphogluconolactonase
                                                                                                                  1. 6-Phosphogluconate Dehydrogenase
                                                                                                                    1. NADPH Generation
                                                                                                                    2. Non-oxidative Phase
                                                                                                                      1. Transketolase Reactions
                                                                                                                        1. Transaldolase Reactions
                                                                                                                          1. Ribose-5-phosphate Formation
                                                                                                                          2. Biological Functions
                                                                                                                            1. NADPH for Biosynthesis
                                                                                                                              1. Ribose for Nucleotides
                                                                                                                                1. Antioxidant Defense
                                                                                                                                2. Regulation
                                                                                                                                  1. NADP+/NADPH Ratio
                                                                                                                                    1. Glucose-6-phosphate Availability
                                                                                                                                3. Citric Acid Cycle
                                                                                                                                  1. Overview and Significance
                                                                                                                                    1. Central Role in Metabolism
                                                                                                                                      1. Amphibolic Nature
                                                                                                                                      2. Entry of Acetyl-CoA
                                                                                                                                        1. Sources of Acetyl-CoA
                                                                                                                                          1. Pyruvate Dehydrogenase Complex
                                                                                                                                            1. Transport Mechanisms
                                                                                                                                            2. Reactions of the Cycle
                                                                                                                                              1. Citrate Synthase
                                                                                                                                                1. Aconitase
                                                                                                                                                  1. Isocitrate Dehydrogenase
                                                                                                                                                    1. Alpha-Ketoglutarate Dehydrogenase
                                                                                                                                                      1. Succinyl-CoA Synthetase
                                                                                                                                                        1. Succinate Dehydrogenase
                                                                                                                                                          1. Fumarase
                                                                                                                                                            1. Malate Dehydrogenase
                                                                                                                                                            2. Energetics
                                                                                                                                                              1. NADH Production
                                                                                                                                                                1. FADH2 Production
                                                                                                                                                                  1. GTP/ATP Production
                                                                                                                                                                    1. Overall Stoichiometry
                                                                                                                                                                    2. Regulation
                                                                                                                                                                      1. Allosteric Control
                                                                                                                                                                        1. Product Inhibition
                                                                                                                                                                          1. Substrate Availability
                                                                                                                                                                            1. Energy Charge
                                                                                                                                                                            2. Anaplerotic Reactions
                                                                                                                                                                              1. Pyruvate Carboxylase
                                                                                                                                                                                1. PEP Carboxykinase
                                                                                                                                                                                  1. Replenishing Intermediates
                                                                                                                                                                                2. Oxidative Phosphorylation
                                                                                                                                                                                  1. Electron Transport Chain
                                                                                                                                                                                    1. Complex I (NADH Dehydrogenase)
                                                                                                                                                                                      1. Structure and Function
                                                                                                                                                                                        1. Proton Pumping
                                                                                                                                                                                        2. Complex II (Succinate Dehydrogenase)
                                                                                                                                                                                          1. Structure and Function
                                                                                                                                                                                            1. No Proton Pumping
                                                                                                                                                                                            2. Complex III (Cytochrome bc1)
                                                                                                                                                                                              1. Q Cycle
                                                                                                                                                                                                1. Proton Pumping
                                                                                                                                                                                                2. Complex IV (Cytochrome Oxidase)
                                                                                                                                                                                                  1. Oxygen Reduction
                                                                                                                                                                                                    1. Proton Pumping
                                                                                                                                                                                                    2. Mobile Electron Carriers
                                                                                                                                                                                                      1. Coenzyme Q
                                                                                                                                                                                                        1. Cytochrome c
                                                                                                                                                                                                      2. Chemiosmotic Theory
                                                                                                                                                                                                        1. Proton Gradient
                                                                                                                                                                                                          1. Electrochemical Gradient
                                                                                                                                                                                                            1. Proton-Motive Force
                                                                                                                                                                                                              1. Mitchell's Hypothesis
                                                                                                                                                                                                              2. ATP Synthase
                                                                                                                                                                                                                1. Structure
                                                                                                                                                                                                                  1. F1 Subunit
                                                                                                                                                                                                                    1. F0 Subunit
                                                                                                                                                                                                                    2. Mechanism
                                                                                                                                                                                                                      1. Binding Change Mechanism
                                                                                                                                                                                                                        1. Rotational Catalysis
                                                                                                                                                                                                                      2. Energetics
                                                                                                                                                                                                                        1. P/O Ratios
                                                                                                                                                                                                                          1. ATP Yield from NADH
                                                                                                                                                                                                                            1. ATP Yield from FADH2
                                                                                                                                                                                                                            2. Regulation
                                                                                                                                                                                                                              1. Respiratory Control
                                                                                                                                                                                                                                1. ADP Availability
                                                                                                                                                                                                                                  1. Oxygen Availability
                                                                                                                                                                                                                                  2. Inhibitors and Uncouplers
                                                                                                                                                                                                                                    1. ETC Inhibitors
                                                                                                                                                                                                                                      1. ATP Synthase Inhibitors
                                                                                                                                                                                                                                        1. Uncoupling Agents
                                                                                                                                                                                                                                        2. Shuttle Systems
                                                                                                                                                                                                                                          1. Malate-Aspartate Shuttle
                                                                                                                                                                                                                                            1. Glycerol-3-phosphate Shuttle
                                                                                                                                                                                                                                              1. NADH Transport
                                                                                                                                                                                                                                            2. Lipid Metabolism
                                                                                                                                                                                                                                              1. Lipid Digestion and Absorption
                                                                                                                                                                                                                                                1. Pancreatic Lipases
                                                                                                                                                                                                                                                  1. Bile Salts
                                                                                                                                                                                                                                                    1. Micelle Formation
                                                                                                                                                                                                                                                      1. Chylomicron Formation
                                                                                                                                                                                                                                                      2. Fatty Acid Oxidation
                                                                                                                                                                                                                                                        1. Fatty Acid Activation
                                                                                                                                                                                                                                                          1. Acyl-CoA Synthetase
                                                                                                                                                                                                                                                            1. ATP Cost
                                                                                                                                                                                                                                                            2. Transport into Mitochondria
                                                                                                                                                                                                                                                              1. Carnitine Shuttle
                                                                                                                                                                                                                                                                1. CPT-1 and CPT-2
                                                                                                                                                                                                                                                                2. Beta-Oxidation
                                                                                                                                                                                                                                                                  1. Four-Step Cycle
                                                                                                                                                                                                                                                                    1. Acyl-CoA Dehydrogenase
                                                                                                                                                                                                                                                                      1. Enoyl-CoA Hydratase
                                                                                                                                                                                                                                                                        1. 3-Hydroxyacyl-CoA Dehydrogenase
                                                                                                                                                                                                                                                                          1. Thiolase
                                                                                                                                                                                                                                                                          2. Energetics
                                                                                                                                                                                                                                                                            1. ATP Yield Calculation
                                                                                                                                                                                                                                                                              1. Acetyl-CoA Production
                                                                                                                                                                                                                                                                              2. Oxidation of Unsaturated Fatty Acids
                                                                                                                                                                                                                                                                                1. Additional Enzymes
                                                                                                                                                                                                                                                                                  1. Isomerase and Reductase
                                                                                                                                                                                                                                                                                  2. Oxidation of Odd-Chain Fatty Acids
                                                                                                                                                                                                                                                                                    1. Propionyl-CoA Formation
                                                                                                                                                                                                                                                                                      1. Conversion to Succinyl-CoA
                                                                                                                                                                                                                                                                                    2. Ketone Body Metabolism
                                                                                                                                                                                                                                                                                      1. Ketogenesis
                                                                                                                                                                                                                                                                                        1. Acetoacetyl-CoA Formation
                                                                                                                                                                                                                                                                                          1. HMG-CoA Synthesis
                                                                                                                                                                                                                                                                                            1. Acetoacetate Formation
                                                                                                                                                                                                                                                                                              1. Beta-hydroxybutyrate Formation
                                                                                                                                                                                                                                                                                              2. Ketolysis
                                                                                                                                                                                                                                                                                                1. Tissue Utilization
                                                                                                                                                                                                                                                                                                  1. Conversion to Acetyl-CoA
                                                                                                                                                                                                                                                                                                  2. Regulation
                                                                                                                                                                                                                                                                                                    1. Hormonal Control
                                                                                                                                                                                                                                                                                                      1. Metabolic Conditions
                                                                                                                                                                                                                                                                                                    2. Fatty Acid Biosynthesis
                                                                                                                                                                                                                                                                                                      1. Acetyl-CoA Transport
                                                                                                                                                                                                                                                                                                        1. Citrate-Pyruvate Cycle
                                                                                                                                                                                                                                                                                                        2. Acetyl-CoA Carboxylase
                                                                                                                                                                                                                                                                                                          1. Biotin Requirement
                                                                                                                                                                                                                                                                                                            1. Regulation
                                                                                                                                                                                                                                                                                                            2. Fatty Acid Synthase
                                                                                                                                                                                                                                                                                                              1. Multifunctional Enzyme
                                                                                                                                                                                                                                                                                                                1. Reaction Sequence
                                                                                                                                                                                                                                                                                                                2. Elongation and Desaturation
                                                                                                                                                                                                                                                                                                                  1. Chain Elongation
                                                                                                                                                                                                                                                                                                                    1. Desaturase Enzymes
                                                                                                                                                                                                                                                                                                                    2. Regulation
                                                                                                                                                                                                                                                                                                                      1. Allosteric Control
                                                                                                                                                                                                                                                                                                                        1. Hormonal Control
                                                                                                                                                                                                                                                                                                                          1. Nutritional Status
                                                                                                                                                                                                                                                                                                                        2. Cholesterol Metabolism
                                                                                                                                                                                                                                                                                                                          1. Cholesterol Biosynthesis
                                                                                                                                                                                                                                                                                                                            1. HMG-CoA Reductase
                                                                                                                                                                                                                                                                                                                              1. Mevalonate Pathway
                                                                                                                                                                                                                                                                                                                              2. Cholesterol Transport
                                                                                                                                                                                                                                                                                                                                1. Lipoproteins
                                                                                                                                                                                                                                                                                                                                  1. LDL and HDL
                                                                                                                                                                                                                                                                                                                                  2. Regulation
                                                                                                                                                                                                                                                                                                                                    1. Feedback Inhibition
                                                                                                                                                                                                                                                                                                                                      1. SREBP Pathway
                                                                                                                                                                                                                                                                                                                                  3. Amino Acid Metabolism
                                                                                                                                                                                                                                                                                                                                    1. Amino Acid Catabolism
                                                                                                                                                                                                                                                                                                                                      1. Deamination
                                                                                                                                                                                                                                                                                                                                        1. Oxidative Deamination
                                                                                                                                                                                                                                                                                                                                          1. Glutamate Dehydrogenase
                                                                                                                                                                                                                                                                                                                                          2. Transamination
                                                                                                                                                                                                                                                                                                                                            1. Aminotransferases
                                                                                                                                                                                                                                                                                                                                              1. Pyridoxal Phosphate
                                                                                                                                                                                                                                                                                                                                              2. Carbon Skeleton Fates
                                                                                                                                                                                                                                                                                                                                                1. Glucogenic Amino Acids
                                                                                                                                                                                                                                                                                                                                                  1. Ketogenic Amino Acids
                                                                                                                                                                                                                                                                                                                                                    1. Mixed Amino Acids
                                                                                                                                                                                                                                                                                                                                                  2. Nitrogen Disposal
                                                                                                                                                                                                                                                                                                                                                    1. Ammonia Toxicity
                                                                                                                                                                                                                                                                                                                                                      1. Urea Cycle
                                                                                                                                                                                                                                                                                                                                                        1. Carbamoyl Phosphate Synthetase I
                                                                                                                                                                                                                                                                                                                                                          1. Ornithine Transcarbamylase
                                                                                                                                                                                                                                                                                                                                                            1. Argininosuccinate Synthetase
                                                                                                                                                                                                                                                                                                                                                              1. Argininosuccinate Lyase
                                                                                                                                                                                                                                                                                                                                                                1. Arginase
                                                                                                                                                                                                                                                                                                                                                                2. Regulation of Urea Cycle
                                                                                                                                                                                                                                                                                                                                                                  1. Allosteric Control
                                                                                                                                                                                                                                                                                                                                                                    1. Enzyme Induction
                                                                                                                                                                                                                                                                                                                                                                    2. Alternative Nitrogen Disposal
                                                                                                                                                                                                                                                                                                                                                                      1. Glutamine Formation
                                                                                                                                                                                                                                                                                                                                                                        1. Alanine Transport
                                                                                                                                                                                                                                                                                                                                                                      2. Amino Acid Biosynthesis
                                                                                                                                                                                                                                                                                                                                                                        1. Essential vs Nonessential Amino Acids
                                                                                                                                                                                                                                                                                                                                                                          1. Biosynthetic Families
                                                                                                                                                                                                                                                                                                                                                                            1. Glutamate Family
                                                                                                                                                                                                                                                                                                                                                                              1. Serine Family
                                                                                                                                                                                                                                                                                                                                                                                1. Aspartate Family
                                                                                                                                                                                                                                                                                                                                                                                  1. Pyruvate Family
                                                                                                                                                                                                                                                                                                                                                                                    1. Aromatic Family
                                                                                                                                                                                                                                                                                                                                                                                    2. Regulation
                                                                                                                                                                                                                                                                                                                                                                                      1. Feedback Inhibition
                                                                                                                                                                                                                                                                                                                                                                                        1. Enzyme Repression
                                                                                                                                                                                                                                                                                                                                                                                      2. Specialized Amino Acid Metabolism
                                                                                                                                                                                                                                                                                                                                                                                        1. One-Carbon Metabolism
                                                                                                                                                                                                                                                                                                                                                                                          1. Folate Coenzymes
                                                                                                                                                                                                                                                                                                                                                                                            1. Methionine Cycle
                                                                                                                                                                                                                                                                                                                                                                                            2. Sulfur Amino Acid Metabolism
                                                                                                                                                                                                                                                                                                                                                                                              1. Methionine and Cysteine
                                                                                                                                                                                                                                                                                                                                                                                              2. Aromatic Amino Acid Metabolism
                                                                                                                                                                                                                                                                                                                                                                                                1. Phenylalanine and Tyrosine
                                                                                                                                                                                                                                                                                                                                                                                                  1. Tryptophan

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                                                                                                                                                                                                                                                                                                                                                                                            Go to top

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