5BICH001W_Met_Biochem_Key concepts and themes_2024_25

Metabolic Biochemistry Overview

Key Concepts

  • Learning Outcomes:

    • Understand metabolism (catabolism & anabolism).

    • Grasp thermodynamics (1st and 2nd laws, redox reactions, biochemical calculations).

    • Knowledge of enzymes (function, specificity, regulation).

Metabolism

  • Metabolism comprises all chemical reactions within a cell, catalyzed primarily by enzymes.

  • Metabolites: Small molecule intermediates in the degradation/synthesis of macromolecules.

Metabolic Pathways and Networks

Reactome

  • Contains proteins and pathways crucial for metabolic processes.

  • Over 11,000 proteins are involved in approximately 2,600 metabolic pathways.

KEGG Database

  • Provides reference pathways like glycolysis and gluconeogenesis, showcasing complex interactions within cellular metabolism.

Types of Metabolic Reactions

  • Catabolic Reactions: Break down molecules, releasing energy (ATP, reduced carriers).

  • Anabolic Reactions: Construct complex molecules from simpler ones, requiring energy.

Thermodynamics in Metabolism

Laws of Thermodynamics

  1. 1st Law: Energy in a closed system remains constant.

  2. 2nd Law: Physical and chemical processes lead to increased disorder (entropy).

Key Terms

  • System: Part of the universe studied (cell, organism).

  • Surroundings: Environment impacting the system.

Types of Systems

  • Isolated: No exchange of energy/matter.

  • Closed: Exchange energy only.

  • Open: Exchange both energy and matter (typical for biological systems).

Energy Changes in Reactions

  • Changes in internal energy relate to heat and work in both thermodynamic equations:

    • Change in energy: ( ,\Delta E = \Delta q + \Delta w )

    • At constant pressure, use enthalpy: ( \Delta E = \Delta H + \Delta w )

Free Energy Changes

  • Gibbs Free Energy Equation: ( \Delta G = \Delta H - T\Delta S )

    • Predicts spontaneity of reactions:

      • ( \Delta G < 0 ): spontaneous

      • ( \Delta G = 0 ): equilibrium

      • ( \Delta G > 0 ): non-spontaneous

Coupled Reactions

  • Combine exergonic and endergonic reactions to drive biological processes (e.g., hydrolysis of ATP).

Enzyme Functionality

  • Enzymes are crucial for metabolic reactions:

    • Catalysis: Lowering activation energy, increasing reaction rates.

    • Specificity: Enzymes are selective for substrates.

    • Regulation: Allosteric and covalent modifications control activity.

Regulatory Mechanisms in Metabolism

  • Metabolic pathways are tightly regulated by:

    • Substrate concentration

    • Thermodynamic irreversibility

    • Feedback inhibition

    • Hormonal and genetic regulation

    • Compartmentalization (e.g., different cellular locations for synthesis and degradation).

Further Reading

  • Recommended texts for deeper understanding:

    • Biochemistry (10th edition) by Berg et al.

    • Lehninger Principles of Biochemistry (8th edition) by Nelson and Cox.