Lecture 1

Cell Chemistry and Bioenergetics

Overview

  • Course: BIOC212

  • Instructor: Maria Vera Ugalde

Chapter 2: Molecular Biology of the Cell

  • Key Areas Covered:

    • Cell chemistry and organic compounds

    • Chemical interactions

    • Assembly of macromolecules

    • Free Gibbs energy: Entropy and Enthalpy

    • Heat energy

    • Equilibrium

    • Enzymes

    • Cell reactions

Importance of Chemical Reactions in Living Organisms

  • Living creatures as chemical systems:

    • Life relies on chemical reactions that occur in aqueous solutions, primarily involving carbon compounds.

    • Macromolecules formed from carbon are essential for growth and function of cells.

    • Cell chemistry is complex, with many interlinked chemical reactions.

Chemical Interactions and Bond Types

Types of Chemical Bonds

  • Covalent Bonds:

    • Strong bonds (100x stronger than non-covalent).

    • Form macromolecules and resist thermal motion.

    • Broken only by biologically catalyzed reactions.

  • Non-Covalent Bonds:

    • Weaker than covalent bonds but crucial for molecular recognition and reversible associations.

Properties of Chemical Bonds

  • Bond strength determines the energy required to break it.

Chemical Components of Cells

  • 99% of cell atoms consist of:

    • Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O).

  • 0.9% of cell atoms include:

    • Phosphorus (P), Sulfur (S), Chlorine (Cl), Sodium (Na), Magnesium (Mg), Potassium (K), Calcium (Ca).

  • Common chemical groups in cells:

    • Methyl (-CH3), Hydroxyl (-OH), Carboxyl (-COOH), Carbonyl (-C=O), Phosphate (-PO3 -2), Sulfhydryl (-SH), Amino (-NH2).

Organic Compounds and Macromolecules

Characteristics of Organic Compounds

  • Typically carbon-based, found naturally in cells.

  • Classified into four major families:

    • Carbonyl, Methyl, Hydroxyl, Amino, Phosphate.

Role of Macromolecules

  • Serve as building blocks for cellular functions.

  • Formed by covalent linking of monomers to create polymers.

  • Versatile and perform numerous functions, including enzymatic activity.

Assembly of Macromolecules

  • Non-random assembly of subunits in a precise order.

  • Covalent bonds provide flexibility while non-covalent bonds constrain shapes.

Catalysis and Energy Usage in Cells

Types of Cellular Reactions

  • Catabolic Pathways: Break down larger molecules to release energy.

  • Anabolic Pathways: Build larger molecules and utilize energy.

Thermodynamics in Cellular Processes

  • Second law of thermodynamics indicates that disorder tends to increase (entropy).

  • Cells are not isolated systems; they maintain order by increasing total entropy of the system and surroundings.

  • Heat energy is released, facilitating cellular order.

Energy Conversion and First Law of Thermodynamics

  • Energy can change forms but is neither created nor destroyed.

  • Organisms harness energy from chemical bonds in organic molecules for growth and reproduction.

Gibbs Free Energy

  • Equation: ∆G = ∆H - T∆S

    •  ∆G: Change in free energy

    • ∆H: Change in enthalpy

    • T: Temperature in Kelvin

  • Favorable reactions occur when ∆G < 0.

Enzymatic Reactions

  • Enzymes lower activation energy, facilitating faster reactions.

  • Cannot make energetically unfavorable reactions occur (cannot drive reactions 'uphill').

Coupled Reactions

  • Reactions can be coupled such that an energetically unfavorable reaction is driven by a favorable one, maintaining overall negative free energy change.

ATP as an Activated Carrier

  • ATP hydrolysis powers the synthesis of biological polymers.

  • Steps in ATP-driven reactions involve the transfer of phosphate groups, creating high-energy intermediates.

Oxidation and Reduction Reactions

  • Oxidation: Removal of electrons, often indicates a partial positive charge.

  • Reduction: Addition of electrons, often indicates a partial negative charge.

  • Hydrogenation and Dehydrogenation are involved in these processes.

Electron Carriers and Energy Storage

  • NADH and NADPH serve as electron carriers in cellular oxidation-reduction reactions.

  • Table of activated carriers includes ATP, NADH, NADPH, FADH2, and Acetyl CoA with their respective high-energy links.

Summary of Key Concepts

Composition of Living Organisms

  • Rich in carbon and specific chemical groups.

  • Four essential subunits: sugars, amino acids, nucleotides, fatty acids.

  • Life involves complex interactions through covalent and non-covalent bonds.

Summary of Chemical Reactions

  • Equilibrium reflects no net change in concentrations of reactants and products.

  • Energy changes during reactions can be quantified using Gibbs free energy principles, emphasizing spontaneity and favorability.