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.