Biochemistry

Biochemistry is the branch of science that explores the chemical processes within and related to living organisms, effectively bridging the fields of biology and chemistry. It focuses on the molecular level of life, investigating the structure, function, and interactions of biological macromolecules such as proteins, nucleic acids, carbohydrates, and lipids. By studying metabolic pathways, the flow of genetic information, and the conversion of energy, biochemists seek to understand how the collective activities of these molecules give rise to the complex phenomena of life, from the inner workings of a single cell to the physiology of an entire organism.

1. Foundations of Biochemistry
   1. The Chemical Basis of Life
      1. Elements in Living Systems
         1. Major Elements
            1. Carbon
            2. Hydrogen
            3. Oxygen
            4. Nitrogen
         2. Trace Elements
            1. Iron
            2. Zinc
            3. Copper
            4. Magnesium
            5. Calcium
            6. Phosphorus
            7. Sulfur
      2. Chemical Bonds in Biochemistry
         1. Covalent Bonds
            1. Single Bonds
            2. Double Bonds
            3. Triple Bonds
            4. Bond Polarity
            5. Electronegativity
            6. Resonance Structures
         2. Noncovalent Interactions
            1. Hydrogen Bonds
               1. Directionality
               2. Strength
               3. Biological Significance
            2. Ionic Interactions
               1. Salt Bridges
               2. Effects of Solvent
               3. Electrostatic Forces
            3. Van der Waals Forces
               1. London Dispersion Forces
               2. Dipole-Dipole Interactions
               3. Steric Complementarity
            4. Hydrophobic Effect
               1. Entropy and Water Structure
               2. Role in Protein Folding
               3. Role in Membrane Formation
   2. Water: The Solvent of Life
      1. Properties of Water
         1. Molecular Structure
         2. Hydrogen Bonding Network
         3. High Heat Capacity
         4. High Heat of Vaporization
         5. Solvent Properties
         6. Density Properties
      2. Ionization of Water
         1. Autoionization Constant (Kw)
         2. Proton Hopping
         3. Temperature Effects
      3. pH and pKa
         1. Definition of pH
         2. Calculation of pH
         3. Relationship Between pH and pKa
         4. Acid-Base Properties of Biological Molecules
         5. Strong vs Weak Acids and Bases
      4. Buffers and the Henderson-Hasselbalch Equation
         1. Buffer Definition
         2. Buffer Capacity
         3. Calculating pH of Buffer Solutions
         4. Henderson-Hasselbalch Equation
      5. Biological Buffer Systems
         1. Bicarbonate Buffer System
         2. Phosphate Buffer System
         3. Protein Buffering
         4. Histidine Buffering
   3. Thermodynamics in Biological Systems
      1. First Law of Thermodynamics
         1. Conservation of Energy
         2. Internal Energy Changes
         3. Heat and Work
      2. Second Law of Thermodynamics
         1. Entropy
         2. Disorder
         3. Spontaneity of Reactions
      3. Gibbs Free Energy
         1. Definition of ΔG
         2. Relationship to Enthalpy and Entropy
         3. Predicting Reaction Direction
         4. Temperature Dependence
      4. Standard Free Energy Change
         1. Biochemical Standard State
         2. ΔG°' Definition
         3. Relationship to Equilibrium Constant
      5. Coupling of Reactions
         1. Endergonic Reactions
         2. Exergonic Reactions
         3. Thermodynamic Coupling
         4. ATP Hydrolysis as Coupling Agent
      6. High-Energy Compounds
         1. ATP Structure
         2. Phosphoryl Group Transfer Potential
         3. GTP
         4. Creatine Phosphate
         5. Phosphoenolpyruvate