Proteins and Proteomics

  1. Protein Function and Diversity
    1. Catalysis: Enzymes
      1. Enzyme Structure and Function
        1. Active Site Architecture
          1. Substrate Specificity
            1. Induced Fit Model
              1. Lock and Key Model
              2. Enzyme Classification
                1. EC Number System
                  1. Six Major Classes
                  2. Enzyme Kinetics
                    1. Michaelis-Menten Kinetics
                      1. Derivation and Assumptions
                        1. Km and Vmax Parameters
                          1. Lineweaver-Burk Plot
                          2. Enzyme Inhibition
                            1. Competitive Inhibition
                              1. Non-competitive Inhibition
                                1. Uncompetitive Inhibition
                                  1. Mixed Inhibition
                                  2. Allosteric Regulation
                                    1. Positive and Negative Effectors
                                      1. Sigmoidal Kinetics
                                        1. Monod-Wyman-Changeux Model
                                      2. Mechanisms of Catalysis
                                        1. Transition State Stabilization
                                          1. Acid-Base Catalysis
                                            1. Covalent Catalysis
                                              1. Metal Ion Catalysis
                                                1. Proximity and Orientation Effects
                                                  1. Electrostatic Stabilization
                                                  2. Cofactors and Coenzymes
                                                    1. Metal Cofactors
                                                      1. Organic Coenzymes
                                                        1. Prosthetic Groups
                                                          1. Coenzyme Regeneration
                                                          2. Enzyme Regulation
                                                            1. Covalent Modification
                                                              1. Compartmentalization
                                                                1. Enzyme Induction and Repression
                                                              2. Structural Roles
                                                                1. Cytoskeletal Proteins
                                                                  1. Actin
                                                                    1. G-Actin and F-Actin
                                                                      1. Polymerization Dynamics
                                                                        1. Actin-Binding Proteins
                                                                        2. Tubulin
                                                                          1. Alpha and Beta Tubulin
                                                                            1. Microtubule Assembly
                                                                              1. Dynamic Instability
                                                                              2. Intermediate Filaments
                                                                                1. Keratin Family
                                                                                  1. Vimentin
                                                                                    1. Neurofilaments
                                                                                      1. Lamins
                                                                                    2. Extracellular Matrix Proteins
                                                                                      1. Collagen
                                                                                        1. Triple Helix Structure
                                                                                          1. Collagen Types
                                                                                            1. Biosynthesis and Modification
                                                                                            2. Elastin
                                                                                              1. Cross-linking and Elasticity
                                                                                                1. Tropoelastin Precursor
                                                                                                2. Fibronectin
                                                                                                  1. Domain Structure
                                                                                                    1. Cell Adhesion Functions
                                                                                                    2. Laminin
                                                                                                      1. Basement Membrane Component
                                                                                                    3. Membrane Structural Proteins
                                                                                                      1. Integral Membrane Proteins
                                                                                                        1. Peripheral Membrane Proteins
                                                                                                          1. Membrane Protein Topology
                                                                                                        2. Transport and Storage
                                                                                                          1. Oxygen Transport
                                                                                                            1. Hemoglobin
                                                                                                              1. Quaternary Structure
                                                                                                                1. Cooperative Oxygen Binding
                                                                                                                  1. Bohr Effect
                                                                                                                    1. 2,3-BPG Regulation
                                                                                                                    2. Myoglobin
                                                                                                                      1. Structure and Function
                                                                                                                        1. Oxygen Storage
                                                                                                                          1. Comparison with Hemoglobin
                                                                                                                        2. Membrane Transport Proteins
                                                                                                                          1. Channels
                                                                                                                            1. Ion Channels
                                                                                                                              1. Aquaporins
                                                                                                                                1. Gating Mechanisms
                                                                                                                                2. Pumps
                                                                                                                                  1. ATP-Powered Pumps
                                                                                                                                    1. Light-Driven Pumps
                                                                                                                                      1. Electrochemical Gradients
                                                                                                                                      2. Carriers
                                                                                                                                        1. Facilitated Diffusion
                                                                                                                                          1. Active Transport
                                                                                                                                            1. Symporters and Antiporters
                                                                                                                                          2. Storage Proteins
                                                                                                                                            1. Ferritin
                                                                                                                                              1. Iron Storage Mechanism
                                                                                                                                                1. Ferroxidase Activity
                                                                                                                                                2. Casein
                                                                                                                                                  1. Milk Protein Complex
                                                                                                                                                    1. Calcium Binding
                                                                                                                                                    2. Ovalbumin
                                                                                                                                                      1. Egg White Protein
                                                                                                                                                  2. Movement and Motility
                                                                                                                                                    1. Motor Proteins
                                                                                                                                                      1. Myosin
                                                                                                                                                        1. Myosin II in Muscle Contraction
                                                                                                                                                          1. Unconventional Myosins
                                                                                                                                                            1. ATP Hydrolysis Cycle
                                                                                                                                                            2. Kinesin
                                                                                                                                                              1. Plus-End Directed Movement
                                                                                                                                                                1. Cargo Transport
                                                                                                                                                                  1. Processivity
                                                                                                                                                                  2. Dynein
                                                                                                                                                                    1. Minus-End Directed Movement
                                                                                                                                                                      1. Ciliary and Flagellar Motion
                                                                                                                                                                        1. Cytoplasmic Dynein
                                                                                                                                                                      2. Mechanisms of Molecular Motors
                                                                                                                                                                        1. Power Stroke Mechanism
                                                                                                                                                                          1. Conformational Changes
                                                                                                                                                                            1. Directionality Determination
                                                                                                                                                                              1. Regulation of Motor Activity
                                                                                                                                                                              2. Muscle Contraction
                                                                                                                                                                                1. Sliding Filament Model
                                                                                                                                                                                  1. Calcium Regulation
                                                                                                                                                                                    1. Troponin and Tropomyosin
                                                                                                                                                                                  2. Signaling and Regulation
                                                                                                                                                                                    1. Receptors
                                                                                                                                                                                      1. G-protein Coupled Receptors
                                                                                                                                                                                        1. Seven-Transmembrane Structure
                                                                                                                                                                                          1. G-Protein Activation
                                                                                                                                                                                            1. Second Messenger Systems
                                                                                                                                                                                            2. Receptor Tyrosine Kinases
                                                                                                                                                                                              1. Dimerization and Autophosphorylation
                                                                                                                                                                                                1. Downstream Signaling Cascades
                                                                                                                                                                                                2. Ion Channel Receptors
                                                                                                                                                                                                  1. Ligand-Gated Channels
                                                                                                                                                                                                    1. Neurotransmitter Receptors
                                                                                                                                                                                                    2. Nuclear Receptors
                                                                                                                                                                                                      1. Hormone-Activated Transcription Factors
                                                                                                                                                                                                    3. Signaling Molecules
                                                                                                                                                                                                      1. Hormones
                                                                                                                                                                                                        1. Peptide Hormones
                                                                                                                                                                                                          1. Steroid Hormones
                                                                                                                                                                                                            1. Thyroid Hormones
                                                                                                                                                                                                            2. Cytokines
                                                                                                                                                                                                              1. Interleukins
                                                                                                                                                                                                                1. Interferons
                                                                                                                                                                                                                  1. Tumor Necrosis Factors
                                                                                                                                                                                                                  2. Growth Factors
                                                                                                                                                                                                                    1. EGF Family
                                                                                                                                                                                                                      1. FGF Family
                                                                                                                                                                                                                        1. TGF-Beta Family
                                                                                                                                                                                                                        2. Neurotransmitters
                                                                                                                                                                                                                          1. Amino Acid Neurotransmitters
                                                                                                                                                                                                                            1. Biogenic Amines
                                                                                                                                                                                                                              1. Neuropeptides
                                                                                                                                                                                                                            2. Intracellular Signal Transduction
                                                                                                                                                                                                                              1. Kinases
                                                                                                                                                                                                                                1. Serine/Threonine Kinases
                                                                                                                                                                                                                                  1. Tyrosine Kinases
                                                                                                                                                                                                                                    1. Dual-Specificity Kinases
                                                                                                                                                                                                                                    2. Phosphatases
                                                                                                                                                                                                                                      1. Protein Phosphatases
                                                                                                                                                                                                                                        1. Lipid Phosphatases
                                                                                                                                                                                                                                        2. Second Messengers
                                                                                                                                                                                                                                          1. cAMP and cGMP
                                                                                                                                                                                                                                            1. Calcium Signaling
                                                                                                                                                                                                                                              1. Inositol Phosphates
                                                                                                                                                                                                                                                1. Diacylglycerol
                                                                                                                                                                                                                                            2. Immune Defense
                                                                                                                                                                                                                                              1. Antibodies (Immunoglobulins)
                                                                                                                                                                                                                                                1. Structure and Classes
                                                                                                                                                                                                                                                  1. IgG, IgM, IgA, IgD, IgE
                                                                                                                                                                                                                                                    1. Heavy and Light Chains
                                                                                                                                                                                                                                                      1. Variable and Constant Regions
                                                                                                                                                                                                                                                      2. Antigen Recognition
                                                                                                                                                                                                                                                        1. Complementarity Determining Regions
                                                                                                                                                                                                                                                          1. Antigen-Antibody Interactions
                                                                                                                                                                                                                                                          2. Effector Functions
                                                                                                                                                                                                                                                            1. Complement Activation
                                                                                                                                                                                                                                                              1. Fc Receptor Binding
                                                                                                                                                                                                                                                            2. Major Histocompatibility Complex (MHC) Proteins
                                                                                                                                                                                                                                                              1. MHC Class I
                                                                                                                                                                                                                                                                1. MHC Class II
                                                                                                                                                                                                                                                                  1. Antigen Presentation
                                                                                                                                                                                                                                                                  2. Complement Proteins
                                                                                                                                                                                                                                                                    1. Classical Pathway
                                                                                                                                                                                                                                                                      1. Alternative Pathway
                                                                                                                                                                                                                                                                        1. Lectin Pathway
                                                                                                                                                                                                                                                                        2. Antimicrobial Proteins
                                                                                                                                                                                                                                                                          1. Defensins
                                                                                                                                                                                                                                                                            1. Lysozyme
                                                                                                                                                                                                                                                                              1. Lactoferrin

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                                                                                                                                                                                                                                                                          4. Protein Folding, Misfolding, and Denaturation

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                                                                                                                                                                                                                                                                          6. Regulation of Protein Activity