Biochemistry

  1. Enzymes
    1. Introduction to Enzymes
      1. Enzymes as Biological Catalysts
        1. Catalytic Efficiency
          1. Specificity
            1. Regulation
            2. Cofactors and Coenzymes
              1. Metal Ion Cofactors
                1. Organic Coenzymes
                  1. Prosthetic Groups
                    1. Holoenzymes and Apoenzymes
                    2. Activation Energy and Catalysis
                      1. Energy Profile of Reactions
                        1. Transition State Theory
                          1. Lowering Activation Energy
                          2. Enzyme-Substrate Interactions
                            1. Lock-and-Key Model
                              1. Induced Fit Model
                                1. Enzyme-Substrate Complex
                                2. The Active Site
                                  1. Structure
                                    1. Microenvironment
                                      1. Substrate Binding
                                        1. Catalytic Residues
                                      2. Enzyme Kinetics
                                        1. Reaction Rates
                                          1. Initial Velocity
                                            1. Rate Laws
                                              1. Factors Affecting Rate
                                                1. Enzyme Concentration
                                                  1. Substrate Concentration
                                                    1. Temperature
                                                      1. pH
                                                    2. Michaelis-Menten Kinetics
                                                      1. Derivation of Equation
                                                        1. Michaelis-Menten Equation
                                                          1. Kinetic Parameters
                                                            1. Vmax
                                                              1. KM
                                                                1. Interpretation of Parameters
                                                              2. Graphical Analysis
                                                                1. Michaelis-Menten Plot
                                                                  1. Lineweaver-Burk Plot
                                                                    1. Hanes Plot
                                                                      1. Eadie-Hofstee Plot
                                                                      2. Catalytic Efficiency
                                                                        1. Turnover Number (kcat)
                                                                          1. Specificity Constant (kcat/KM)
                                                                            1. Diffusion-Limited Reactions
                                                                            2. Multi-Substrate Reactions
                                                                              1. Sequential Mechanisms
                                                                                1. Ordered Sequential
                                                                                  1. Random Sequential
                                                                                  2. Ping-Pong Mechanisms
                                                                                    1. Kinetic Analysis
                                                                                  3. Enzyme Inhibition
                                                                                    1. Reversible Inhibition
                                                                                      1. Competitive Inhibition
                                                                                        1. Mechanism
                                                                                          1. Kinetic Effects
                                                                                            1. Ki Determination
                                                                                            2. Uncompetitive Inhibition
                                                                                              1. Mechanism
                                                                                                1. Kinetic Effects
                                                                                                2. Mixed Inhibition
                                                                                                  1. Mechanism
                                                                                                    1. Kinetic Effects
                                                                                                    2. Noncompetitive Inhibition
                                                                                                      1. Special Case of Mixed Inhibition
                                                                                                    3. Irreversible Inhibition
                                                                                                      1. Covalent Modification
                                                                                                        1. Mechanism-Based Inhibitors
                                                                                                          1. Suicide Inhibitors
                                                                                                            1. Time-Dependent Inhibition
                                                                                                          2. Catalytic Mechanisms
                                                                                                            1. General Catalytic Strategies
                                                                                                              1. Proximity and Orientation Effects
                                                                                                                1. Preferential Binding of Transition State
                                                                                                                  1. Strain and Conformational Changes
                                                                                                                  2. Chemical Mechanisms
                                                                                                                    1. General Acid-Base Catalysis
                                                                                                                      1. Covalent Catalysis
                                                                                                                        1. Metal Ion Catalysis
                                                                                                                          1. Electrostatic Stabilization
                                                                                                                          2. Case Studies
                                                                                                                            1. Chymotrypsin
                                                                                                                              1. Serine Protease Mechanism
                                                                                                                                1. Catalytic Triad
                                                                                                                                  1. Oxyanion Hole
                                                                                                                                  2. Lysozyme
                                                                                                                                    1. Mechanism of Action
                                                                                                                                      1. Substrate Binding
                                                                                                                                      2. Ribonuclease A
                                                                                                                                        1. RNA Cleavage Mechanism
                                                                                                                                    2. Regulation of Enzyme Activity
                                                                                                                                      1. Allosteric Regulation
                                                                                                                                        1. Allosteric Sites
                                                                                                                                          1. Homotropic Effects
                                                                                                                                            1. Heterotropic Effects
                                                                                                                                              1. Sigmoidal Kinetics
                                                                                                                                                1. Concerted Model
                                                                                                                                                  1. Sequential Model
                                                                                                                                                  2. Covalent Modification
                                                                                                                                                    1. Phosphorylation
                                                                                                                                                      1. Protein Kinases
                                                                                                                                                        1. Protein Phosphatases
                                                                                                                                                        2. Other Modifications
                                                                                                                                                          1. Methylation
                                                                                                                                                            1. Acetylation
                                                                                                                                                              1. Ubiquitination
                                                                                                                                                            2. Proteolytic Activation
                                                                                                                                                              1. Zymogens
                                                                                                                                                                1. Activation Cascades
                                                                                                                                                                  1. Digestive Enzymes
                                                                                                                                                                    1. Blood Clotting
                                                                                                                                                                    2. Compartmentalization
                                                                                                                                                                      1. Spatial Organization
                                                                                                                                                                        1. Metabolic Channeling
                                                                                                                                                                        2. Enzyme Induction and Repression
                                                                                                                                                                          1. Transcriptional Control
                                                                                                                                                                            1. Post-transcriptional Control
                                                                                                                                                                            2. Isozymes
                                                                                                                                                                              1. Tissue-Specific Isoforms
                                                                                                                                                                                1. Developmental Regulation
                                                                                                                                                                                  1. Functional Differences

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                                                                                                                                                                              4. Bioenergetics and Metabolism