Biophysics

  1. Molecular Biophysics
    1. Biophysics of Proteins
      1. Amino Acids and the Peptide Bond
        1. Structure of Amino Acids
          1. Peptide Bond Formation
            1. Properties of Side Chains
              1. Ramachandran Plots
              2. Protein Structure
                1. Primary Structure
                  1. Sequence Determination
                    1. Mutations and Variants
                      1. Sequence-Structure Relationships
                      2. Secondary Structure
                        1. Alpha-Helices
                          1. Beta-Sheets
                            1. Turns and Loops
                              1. Prediction Methods
                              2. Tertiary Structure
                                1. Folding Motifs
                                  1. Hydrophobic Core
                                    1. Disulfide Bonds
                                      1. Domain Organization
                                      2. Quaternary Structure
                                        1. Oligomerization
                                          1. Protein Complexes
                                            1. Symmetry in Protein Assemblies
                                          2. Protein Folding
                                            1. The Levinthal Paradox
                                              1. Folding Pathways and Funnels
                                                1. Energy Landscapes
                                                  1. Chaperones and Misfolding
                                                    1. Molecular Chaperones
                                                      1. Protein Aggregation and Disease
                                                        1. Amyloid Formation
                                                        2. Protein Denaturation
                                                          1. Denaturing Agents
                                                            1. Reversibility of Denaturation
                                                              1. Folding Intermediates
                                                            2. Protein Dynamics and Function
                                                              1. Conformational Changes
                                                                1. Induced Fit
                                                                  1. Dynamic Equilibria
                                                                    1. Breathing Motions
                                                                    2. Allostery and Cooperativity
                                                                      1. Allosteric Regulation
                                                                        1. Cooperative Binding
                                                                          1. Monod-Wyman-Changeux Model
                                                                          2. Enzyme Kinetics and Catalysis
                                                                            1. Michaelis-Menten Kinetics
                                                                              1. Catalytic Mechanisms
                                                                                1. Inhibition and Regulation
                                                                                  1. Single-Molecule Enzymology
                                                                                2. Protein-Ligand Interactions
                                                                                  1. Binding Affinity and Specificity
                                                                                    1. Kinetics of Binding
                                                                                      1. Thermodynamics of Binding
                                                                                        1. Structure-Activity Relationships
                                                                                      2. Biophysics of Nucleic Acids
                                                                                        1. Structure of DNA and RNA
                                                                                          1. The Double Helix
                                                                                            1. Watson-Crick Base Pairing
                                                                                              1. Helical Parameters
                                                                                                1. Major and Minor Grooves
                                                                                                2. A, B, and Z forms of DNA
                                                                                                  1. Structural Differences
                                                                                                    1. Biological Relevance
                                                                                                      1. Conditions for Formation
                                                                                                      2. RNA Structures
                                                                                                        1. Secondary Structures
                                                                                                          1. Tertiary Structures
                                                                                                            1. Pseudoknots and Complex Folds
                                                                                                          2. Physical Properties of DNA
                                                                                                            1. Persistence Length and Flexibility
                                                                                                              1. Supercoiling and Topology
                                                                                                                1. Linking Number
                                                                                                                  1. Topoisomerases
                                                                                                                    1. Writhe and Twist
                                                                                                                    2. DNA Compaction and Chromatin
                                                                                                                      1. Nucleosomes
                                                                                                                        1. Higher-Order Chromatin Structure
                                                                                                                          1. Histone Modifications
                                                                                                                        2. DNA-Protein Interactions
                                                                                                                          1. DNA Binding Proteins
                                                                                                                            1. Sequence Recognition
                                                                                                                              1. DNA Repair and Modification
                                                                                                                                1. Protein-Induced DNA Bending
                                                                                                                                2. RNA Folding and Ribozymes
                                                                                                                                  1. RNA Folding Pathways
                                                                                                                                    1. Catalytic RNA
                                                                                                                                      1. Riboswitches
                                                                                                                                        1. RNA-Protein Complexes
                                                                                                                                      2. Biophysics of Lipids and Membranes
                                                                                                                                        1. Lipid Molecules and Self-Assembly
                                                                                                                                          1. Types of Lipids
                                                                                                                                            1. Phospholipids
                                                                                                                                              1. Sterols
                                                                                                                                                1. Sphingolipids
                                                                                                                                                2. Micelles and Vesicles
                                                                                                                                                  1. Critical Packing Parameter
                                                                                                                                                  2. The Lipid Bilayer
                                                                                                                                                    1. Structure and Phases
                                                                                                                                                      1. Gel and Liquid-Crystalline Phases
                                                                                                                                                        1. Phase Diagrams
                                                                                                                                                        2. Fluidity and Phase Transitions
                                                                                                                                                          1. Factors Affecting Fluidity
                                                                                                                                                            1. Temperature Effects
                                                                                                                                                              1. Cholesterol Effects
                                                                                                                                                              2. Elasticity and Curvature
                                                                                                                                                                1. Bending Modulus
                                                                                                                                                                  1. Membrane Deformation
                                                                                                                                                                    1. Spontaneous Curvature
                                                                                                                                                                  2. Membrane Proteins
                                                                                                                                                                    1. Integral and Peripheral Proteins
                                                                                                                                                                      1. Structural Features
                                                                                                                                                                        1. Functional Roles
                                                                                                                                                                          1. Membrane Insertion
                                                                                                                                                                          2. Transmembrane Helices and Barrels
                                                                                                                                                                            1. Alpha-Helical Proteins
                                                                                                                                                                              1. Beta-Barrel Proteins
                                                                                                                                                                                1. Hydrophobic Matching
                                                                                                                                                                              2. Membrane Transport
                                                                                                                                                                                1. Passive Diffusion
                                                                                                                                                                                  1. Permeability of Small Molecules
                                                                                                                                                                                    1. Partition Coefficients
                                                                                                                                                                                    2. Facilitated Diffusion
                                                                                                                                                                                      1. Carrier Proteins
                                                                                                                                                                                        1. Channel Proteins
                                                                                                                                                                                          1. Kinetic Models
                                                                                                                                                                                          2. Active Transport
                                                                                                                                                                                            1. Pumps and ATPases
                                                                                                                                                                                              1. Coupling Mechanisms
                                                                                                                                                                                              2. Ion Channels and Pumps
                                                                                                                                                                                                1. Selectivity and Gating
                                                                                                                                                                                                  1. Electrogenic Transport
                                                                                                                                                                                                    1. Single-Channel Conductance

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                                                                                                                                                                                              4. Cellular Biophysics