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Principles of Biochemistry

Principles of Biochemistry

The Biochemistry of Life

  • Universal Nature: Biochemical processes are shared across all living organisms.

  • Key Discoveries: Both yeast and animal muscle cells metabolize glucose via glycolysis, highlighting a conserved metabolic pathway that generates ATP.

Differences Between Mineral and Biological Worlds

  • Mineral World (Inanimate Matter):

    • Composed of simple inorganic compounds (e.g., rocks, metals).

    • Elements include silicon, iron, aluminum, and oxygen.

    • Lacks growth, metabolism, or reproduction.

  • Biological World (Living Matter):

    • Composed of complex organic molecules (proteins, carbohydrates, lipids, nucleic acids).

    • Rich in carbon (C), oxygen (O), nitrogen (N), hydrogen (H), and phosphorus (P).

    • Exhibits metabolism, growth, and reproduction.

Historical Context

  • Antoine Lavoisier's contributions highlighted chemical complexities of life, paving the way for biochemistry by linking chemistry and biology.

Domains of Living Organisms

  • Three Domains (Carl Woese, 1990):

    • Bacteria: Prokaryotic, simple, binary fission, e.g., E. coli.

    • Archaea: Prokaryotic, genetically distinct, extreme environments, e.g., methanogens.

    • Eukarya: Eukaryotic, complex, can reproduce sexually or asexually, e.g., humans, plants.

General Requirements for Life

  1. Chemical Diversity:

    • Variety of compounds is crucial for biological functions (structural components, energy carriers, genetic material).

  2. Stability and Reactivity:

    • Molecules must be stable to persist but reactive enough for biochemical reactions.

  3. Presence of a Solvent:

    • Water is vital as it facilitates reactions and molecular movement.

Importance of Chemical Diversity

  • Diverse Molecular Forms: Enables the creation of simple and complex biomolecules, essential for life functions.

  • 3D Structures: Proper molecular conformation is necessary for biological activity.

Carbon as a Scaffolding Element

  • Carbon is ideal as it forms strong covalent bonds and supports diverse molecular shapes and sizes, critical for biological macromolecules.

  • Other Elements (e.g., Sulfur, Boron, Silicon) have limitations in forming stable, complex structures compared to carbon.

Role of Solvent in Biochemistry

  • Water: Unique solvent properties support life by dissolving biochemical molecules, enabling reactions, and stabilizing biomolecular structures.

Elements of Life

  • Major Elements in the Human Body:

    • Big 4: Carbon, Oxygen, Hydrogen, Nitrogen (96% of body mass).

    • Major Elements: Calcium, Phosphorus, etc. (3.5%).

    • Trace Elements: Such as Iron, Zinc, etc. (0.5%).

Small Molecules in Cells

  • Definition: Small molecules are compounds participating in cellular processes, crucial for metabolism and signaling.

  • Types: Water, inorganic ions (e.g., Na⁺, K⁺), metabolites (carbohydrates, lipids, amino acids), nucleotides.

Primary vs. Secondary Metabolites

  • Primary Metabolites: Essential for growth and survival (e.g., carbohydrates, amino acids).

  • Secondary Metabolites: Not essential for survival but play roles in defense and communication (e.g., Alkaloids, Terpenoids).

Introduction to Stereochemistry

  • Stereochemistry: Study of 3D arrangements of atoms in molecules.

  • Importance in molecular recognition, metabolic pathways, and drug design.

Isomerism in Biochemistry

  • Types of Isomerism: Structural isomerism (different connectivity) and stereoisomerism (different spatial arrangement).

  • Chirality: Molecules with chiral centers exhibit non-superimposable mirror images (enantiomers).

Configurations and Interactions

  • D and L Configuration: Determine orientation of chiral centers in sugars and amino acids.

  • R/S Configuration: Cahn-Ingold-Prelog rules for assigning configurations based on priority of attached groups.

Conclusion on Stereospecific Interactions

  • Biomolecular interactions are stereospecific, reflecting the necessity of proper molecular fit (like a lock and key) for biological functions such as enzyme-substrate binding and hormone-receptor interactions.

These in-depth notes encapsulate the essential biochemistry principles, distinctions between different worlds of matter, and the critical role of chemical diversity and molecular configurations in biological systems.