Biological Chemistry PDF

Here’s a detailed and comprehensive breakdown of the key topics from the presentation: 1. Chemical Foundation Covalent and Non-Covalent Interactions 1. Covalent Bonds: Stable bonds where atoms share electrons. Types: Nonpolar covalent bonds:...

Here’s a detailed and comprehensive breakdown of the key topics from the presentation: 1. Chemical Foundation Covalent and Non-Covalent Interactions 1. Covalent Bonds: Stable bonds where atoms share electrons. Types: Nonpolar covalent bonds: Equal sharing of electrons (e.g., hydrocarbons, hydrophobic molecules). Polar covalent bonds: Unequal sharing of electrons, creating partial positive and negative charges (dipoles), as in water. 2. Non-Covalent Interactions: Weaker than covalent bonds, essential for transient biological interactions. Types: Ionic Bonds: Attraction between oppositely charged ions (e.g., Na+ and Cl−). Involves complete electron transfer. Hydrogen Bonds: Weak bonds involving a partially positive hydrogen atom and an unpaired electron pair (commonly with O or N). Example: Water molecules forming H-bonds. Van der Waals Forces: Weak, non-specific attractions between close atoms. Significant in molecular packing and shape interactions. Hydrophobic Interactions: Nonpolar molecules cluster together in water to minimize energy (e.g., lipid bilayers). 2. Molecular Complementarity 1. Definition: Molecules interact based on complementary shapes, charges, and other properties. Facilitates dynamic biological processes through specificity and affinity. 2. Parameters: Specificity: Precision of fit between interacting molecules. Affinity: Strength of binding (measured as the dissociation constant, Kd). 3. Examples: Receptor-ligand binding. Antibody-antigen interactions. Proteins can have distinct binding sites for multiple ligands. 4. Notes: Covalent bonds are the strongest and most stable, but transient non-covalent bonds allow flexibility. 3. Chemical Building Blocks 1. Macromolecules: Constructed from monomers via condensation reactions (removal of water). Types: Proteins: Composed of amino acids linked by peptide bonds. Nucleic Acids: Made of nucleotides connected by phosphodiester bonds. Carbohydrates: Built from monosaccharides joined by glycosidic bonds. Lipids: Non-polymeric, composed of hydrophobic tails (often fatty acids) and hydrophilic heads. 2. Reactions: Condensation Reaction:  Combines monomers by removing water. Hydrolysis: Breaks down macromolecules by adding water. 4. Chemical Reactions and Equilibrium 1. Chemical Equilibrium: Occurs when the rate of the forward reaction equals the rate of the reverse reaction. Defined by the equilibrium constant (Keq), which reflects the ratio of products to reactants. 2. Steady State vs. Equilibrium: In cells, reactions are in a steady state, meaning intermediates form and are consumed at the same rate (no net accumulation). 3. Homeostasis: The steady state ensures stable conditions within cells. 5. pH and Buffers 1. pH Scale: Defined as the negative logarithm of hydrogen ion concentration. Cytoplasmic pH: ~7.2–7.4 (neutral). Lysosomal pH: ~4.5 (acidic). 2. Acids and Bases: Acids: Release hydrogen ions. Bases: Bind hydrogen ions. 3. Buffers: Mixtures of weak acids and their conjugate bases. Minimize pH changes when small amounts of acids or bases are added. 6. Biochemical Energetics  1. Energy Types: Kinetic Energy: Energy of motion (e.g., heat, light, mechanical). Potential Energy: Stored energy (e.g., in chemical bonds or gradients). Concentration Gradients: Energy stored due to unequal molecule distribution. Electric Potential: Energy from charge separation across a membrane. 2. Free Energy (ΔG): Measure of energy available for a reaction. Reactions with negative ΔG are spontaneous (exergonic). Catalysts (enzymes) lower activation energy, speeding up reactions without being consumed. 3. Chemical Coupling: Thermodynamically unfavorable reactions are driven by coupling them with exergonic reactions (e.g., ATP hydrolysis). 4. ATP: Universal energy currency in cells. Energy stored in phosphoanhydride bonds, which release energy upon hydrolysis. 5. Redox Reactions: Oxidation (loss of electrons) and reduction (gain of electrons). Electron carriers (NAD+, NADP, FAD) shuttle electrons for energy generation. 7. Central Dogma 1. Flow of Genetic Information: Information flows unidirectionally: DNA → RNA → Protein.  This flow controls cellular function and gene expression. These are the key points, distilled for clarity and detail, with your notes integrated. Let me know if you need elaboration on any topic!