Chemical Foundation: Bonding Concepts

Chemical Foundation

• Covalent Bonds: Stable bonds formed when atoms share electrons.
• Nonpolar Covalent Bonds: Equal sharing of electrons; examples include hydrocarbons and hydrophobic molecules.
• Polar Covalent Bonds: Unequal sharing of electrons, creating partial positive and negative charges (dipoles); found in water.
• Non-Covalent Interactions: Weaker than covalent bonds, crucial for transient biological interactions.
• Ionic Bonds: Attraction between oppositely charged ions (e.g., Na+ and Cl-); involve complete electron transfer.
• Hydrogen Bonds: Weak bonds involving a partially positive hydrogen atom and an unpaired electron pair (commonly with O or N); found in water molecules.
• Van der Waals Forces: Weak, non-specific attractions between atoms that are close together; important for molecular packing and shape interactions.
• Hydrophobic Interactions: Nonpolar molecules cluster together in water to minimize energy (e.g., lipid bilayers).

Molecular Complementarity

• Definition: Molecules interact based on complementary shapes, charges, and properties.
• Parameters: Specificity (precision of fit between molecules) and affinity (strength of binding, measured by Kd).
• Examples: Receptor-ligand binding, antibody-antigen interactions.
• Proteins: Proteins can have multiple binding sites for different ligands (molecules).
• Covalent Bonds & Flexibility: Covalent bonds are strong and stable, but transient non-covalent bonds allow flexibility.

Chemical Building Blocks

• Macromolecules: Constructed from monomers via condensation reactions (removal of water).
• Protein Types: Composed of amino acids linked by peptide bonds.
• Nucleic Acid Types: Made of nucleotides linked by phosphodiester bonds.
• Carbohydrate Types: Built from monosaccharides linked by glycosidic bonds.
• Lipid Types: Non-polymeric, composed of hydrophobic tails (often fatty acids) and hydrophilic heads.
• Condensation Reaction: Combines monomers by removing water.
• Hydrolysis: Breaks down macromolecules by adding water.

Chemical Reactions and Equilibrium

• Chemical Equilibrium: Occurs when the rate of the forward reaction equals the rate of the reverse reaction.
• Equilibrium Constant (Keq): Reflects the ratio of products to reactants.
• Steady State vs. Equilibrium: In cells, reactions are in a steady state (intermediate formation and consumption at the same rate) rather than true equilibrium.
• Homeostasis: The steady state maintains stable conditions within cells.

pH and Buffers

• pH Scale: Measures the negative logarithm of hydrogen ion concentration.
• Cytoplasmic pH: Approximately 7.2-7.4 (neutral).
• Lysosomal pH: Approximately 4.5 (acidic).
• Acids and Bases: Acids release H+ ions; bases bind H+ ions.
• Buffers: Mixtures of weak acids and their conjugate bases that minimize pH changes.

Biochemical Energetics

• Energy Types: Kinetic energy (energy of motion), potential energy (stored energy).
• Concentration Gradients: Energy stored due to unequal distribution of molecules.
• Electric Potential: Energy from charge separation across a membrane.
• Free Energy (ΔG): Measure of energy available for a reaction; spontaneous reactions have negative ΔG.
• Chemical Coupling: Thermodynamically unfavorable reactions are driven by coupling with exergonic (energy-releasing) reactions.
• ATP: Universal energy currency in cells; energy stored in phosphoanhydride bonds, which release energy upon hydrolysis.
• Redox Reactions: Oxidation (loss of electrons) and reduction (gain of electrons) involve electron carriers (e.g., NAD+, NADP+, FAD).

Central Dogma

• Flow of Genetic Information: DNA → RNA → Protein. This flow controls cellular function and gene expression.

Explore the fundamentals of chemical bonding in this quiz. Learn about covalent, ionic, and non-covalent interactions, including hydrogen bonds and van der Waals forces. Understand how these concepts play a crucial role in biological systems and molecular interactions.