Enzymology

  1. Enzyme Structure and Composition
    1. The Protein Nature of Enzymes
      1. Amino Acids as Building Blocks
        1. Structure of Amino Acids
          1. Classification of Amino Acids
            1. Peptide Bond Formation
            2. Levels of Protein Structure
              1. Primary Structure
                1. Amino Acid Sequence
                  1. Peptide Backbone
                    1. Sequence Determinants of Function
                    2. Secondary Structure
                      1. Alpha Helices
                        1. Beta Sheets
                          1. Turns and Loops
                            1. Hydrogen Bonding Patterns
                              1. Structural Motifs
                              2. Tertiary Structure
                                1. Three-Dimensional Fold
                                  1. Domains and Folds
                                    1. Stabilizing Interactions
                                      1. Hydrophobic Interactions
                                        1. Ionic Bonds
                                          1. Disulfide Bonds
                                            1. Hydrogen Bonds
                                          2. Quaternary Structure
                                            1. Subunit Assembly
                                              1. Oligomeric Enzymes
                                                1. Functional Implications of Subunit Interactions
                                            2. The Active Site
                                              1. Definition and Properties
                                                1. Microenvironment
                                                  1. Three-Dimensional Arrangement
                                                    1. Size and Shape Complementarity
                                                    2. Substrate Binding Site
                                                      1. Recognition of Substrate
                                                        1. Binding Interactions
                                                          1. Hydrogen Bonds
                                                            1. Hydrophobic Interactions
                                                              1. Ionic Interactions
                                                                1. Van der Waals Forces
                                                              2. Catalytic Site
                                                                1. Residues Involved in Catalysis
                                                                  1. Mechanistic Roles
                                                                  2. Role of Specific Amino Acid Residues
                                                                    1. Catalytic Triads and Dyads
                                                                      1. Acidic Residues
                                                                        1. Basic Residues
                                                                          1. Nucleophilic Residues
                                                                        2. Cofactors, Coenzymes, and Prosthetic Groups
                                                                          1. Distinction and Roles
                                                                            1. Definitions
                                                                              1. Functional Importance
                                                                                1. Holoenzyme vs Apoenzyme
                                                                                2. Metal Ions as Cofactors
                                                                                  1. Common Metal Ions
                                                                                    1. Zinc
                                                                                      1. Magnesium
                                                                                        1. Iron
                                                                                          1. Copper
                                                                                            1. Manganese
                                                                                            2. Structural Roles
                                                                                              1. Catalytic Roles
                                                                                              2. Organic Coenzymes
                                                                                                1. Cosubstrates
                                                                                                  1. NAD+/NADH
                                                                                                    1. NADP+/NADPH
                                                                                                      1. FAD/FADH2
                                                                                                        1. Coenzyme A
                                                                                                          1. ATP/ADP
                                                                                                          2. Prosthetic Groups
                                                                                                            1. Heme
                                                                                                              1. Biotin
                                                                                                                1. Flavin
                                                                                                                  1. Pyridoxal Phosphate
                                                                                                                2. Vitamins as Coenzyme Precursors
                                                                                                                  1. Water-Soluble Vitamins
                                                                                                                    1. Fat-Soluble Vitamins
                                                                                                                      1. Deficiency Diseases
                                                                                                                    2. Isozymes and Allozymes
                                                                                                                      1. Definitions and Biological Significance
                                                                                                                        1. Genetic Variants
                                                                                                                          1. Tissue-Specific Expression
                                                                                                                            1. Functional Diversity
                                                                                                                            2. Examples of Isozymes
                                                                                                                              1. Clinical Significance

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                                                                                                                            1. Introduction to Enzymes

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                                                                                                                            3. Principles of Enzyme Catalysis