Activation Energy and the Metastable State

Activation Energy in Chemical Reactions

All chemical reactions, including those in biological systems, require an initial input of energy to begin, even if the overall reaction releases energy. This initial energy is known as activation energy (Ea).

• Activation energy is needed to:

  • Break existing chemical bonds in reactants

  • Distort reactant molecules to reach a transition state

  • Bring reactants into the correct orientation for reaction

• Transition state: A high-energy, unstable arrangement of atoms that occurs during a reaction.

The Metastable State

Many biological molecules exist in a metastable state, meaning they are thermodynamically favorable to react (products are lower in energy), but do not react spontaneously due to a high activation energy barrier.

• Example: The reaction of glucose and oxygen to form carbon dioxide and water is energetically favorable, but glucose does not spontaneously combust in cells because of the activation energy barrier.

Energy Diagrams

• Reaction coordinate diagrams illustrate the energy changes during a reaction:

  • Reactants must overcome the activation energy to reach the transition state before forming products.

  • The height of the energy barrier represents the activation energy.

Biological Importance of Activation Energy

• Prevents uncontrolled, spontaneous reactions in cells

• Allows cells to regulate when and where reactions occur

• Enables storage of energy in stable chemical bonds (e.g., glucose)

Enzymes as Biological Catalysts

What Are Enzymes?

Enzymes are biological catalysts, primarily proteins, that increase the rate of chemical reactions without being consumed in the process. They do not alter the overall free energy change (ΔG) of a reaction, but they lower the activation energy required.

• Enzymes are highly specific for their substrates.

• Most enzymes are proteins; some RNA molecules (ribozymes) also have catalytic activity.

Mechanisms of Enzyme Action

• Enzymes speed up reactions by:

  • Stabilizing the transition state

  • Bringing substrates together in the correct orientation

  • Straining bonds in substrates to facilitate breaking/forming

  • Creating a favorable microenvironment (e.g., optimal pH or charge)

  • Forming temporary enzyme–substrate complexes

Active Site and Specificity

• The active site is the region of the enzyme where the substrate binds and the reaction occurs.

• Enzyme specificity is explained by two models:

  • Lock-and-key model: The active site is a rigid shape that fits only specific substrates.

  • Induced-fit model: The enzyme changes shape upon substrate binding to better fit the substrate.

Factors Affecting Enzyme Activity

• Substrate concentration: Higher concentrations increase reaction rate up to a maximum (saturation).

• Enzyme concentration: More enzyme increases reaction rate if substrate is not limiting.

• Temperature: Increases rate up to an optimum; too high causes denaturation.

• pH: Each enzyme has an optimal pH; deviations reduce activity.

• Inhibitors:

  • Competitive inhibitors: Compete with substrate for the active site.

  • Noncompetitive inhibitors: Bind elsewhere, changing enzyme shape and reducing activity.

Cofactors and Coenzymes

• Some enzymes require non-protein helpers:

  • Cofactors: Inorganic ions (e.g., Mg2+, Fe2+)

  • Coenzymes: Organic molecules (e.g., NAD+, FAD, CoA)

Chemotrophic Energy Metabolism: Glycolysis and Fermentation

Overview of Chemotrophic Metabolism

Chemotrophs obtain energy by oxidizing chemical compounds, rather than from light. Glucose is a primary fuel molecule, and its breakdown provides energy for cellular processes.

• Energy is captured in the form of ATP and electron carriers (NADH, FADH2).

Glycolysis

Glycolysis is the metabolic pathway that converts glucose (6 carbons) into two molecules of pyruvate (3 carbons each). It occurs in the cytosol and does not require oxygen.

• Occurs in nearly all cells (prokaryotes and eukaryotes).

• Consists of two phases:

  • Energy Investment Phase: 2 ATP are used to phosphorylate glucose and its intermediates.

  • Energy Payoff Phase: 4 ATP and 2 NADH are produced, along with 2 pyruvate.

• Net yield per glucose:

  • 2 ATP (net gain)

  • 2 NADH

  • 2 pyruvate

Fermentation

When oxygen is absent, cells use fermentation to regenerate NAD+ from NADH, allowing glycolysis to continue.

• Lactic Acid Fermentation: Pyruvate is reduced to lactate (occurs in muscle cells and some bacteria; no CO2 released).

• Alcoholic Fermentation: Pyruvate is converted to ethanol and CO2 (occurs in yeast and some plant cells; CO2 causes bread to rise).

• Fermentation does not produce additional ATP beyond the 2 ATP from glycolysis.

Key Concepts

• Glycolysis is ancient, universal, and does not require oxygen.

• Fermentation keeps NAD+ available for glycolysis under anaerobic conditions.

• Each step of glycolysis is catalyzed by a specific enzyme, allowing for gradual and regulated energy release.

• Energy from glucose is transferred to ATP and NADH.

Cellular Respiration: Stages and ATP Yield

Overview of Cellular Respiration

The goal of cellular respiration is to convert the energy stored in glucose into ATP, the cell's usable energy currency. The process occurs in several stages:

1. Glycolysis (cytoplasm)

2. Pyruvate Oxidation (mitochondria)

3. Citric Acid Cycle (Krebs Cycle) (mitochondria)

4. Electron Transport Chain (ETC) and Oxidative Phosphorylation (inner mitochondrial membrane)

1. Glycolysis

• 1 glucose (6C) → 2 pyruvate (3C each)

• Products per glucose: 2 ATP (net), 2 NADH

• No oxygen required

• Only source of ATP under anaerobic conditions

2. Pyruvate Oxidation (Link Reaction)

• Each pyruvate (3C) → acetyl-CoA (2C) + CO2

• Per glucose (2 pyruvate): 2 acetyl-CoA, 2 CO2, 2 NADH

• Some carbons from glucose are lost as CO2 before the Krebs cycle begins

3. Citric Acid Cycle (Krebs Cycle)

• Acetyl-CoA is fully oxidized to CO2

• Energy is captured as NADH and FADH2

• Per glucose: 6 NADH, 2 FADH2, 2 ATP (or GTP), 4 CO2

• Most energy from glucose is now stored in NADH and FADH2

4. Electron Transport Chain (ETC) & Oxidative Phosphorylation

• Location: Inner mitochondrial membrane

• NADH and FADH2 donate electrons to the ETC

• Electrons move through complexes I → III → IV

• Oxygen is the final electron acceptor, forming water

• Protons are pumped across the membrane, creating a gradient used by ATP synthase to make ATP

• Final products: H2O, ~26–28 ATP from oxidative phosphorylation

NADH and ATP Yield

• NADH from the Krebs cycle enters the ETC at Complex I, resulting in more ATP per NADH

• NADH from glycolysis is produced in the cytosol and must be shuttled into mitochondria, entering the ETC less efficiently and yielding less ATP per NADH

Electron Carriers in the ETC

ATP Totals (Aerobic Respiration)

• Glycolysis: 2 ATP

• Krebs Cycle: 2 ATP

• Oxidative Phosphorylation: ~26–28 ATP

• Total: ≈ 30–32 ATP per glucose (varies depending on shuttle mechanisms)

Anaerobic Conditions (No Oxygen)

• ETC and Krebs cycle stop

• NADH accumulates

• Cells regenerate NAD+ by fermentation (pyruvate → lactate or ethanol)

• ATP yield: Only 2 ATP per glucose (from glycolysis)

Key Definitions

• Substrate-level phosphorylation: Direct transfer of a phosphate group to ADP to form ATP (occurs in glycolysis and Krebs cycle)

• Oxidative phosphorylation: ATP synthesis using the electron transport chain and proton gradient

• Stronger oxidizing agent: A molecule with higher electron affinity

Summary Flowchart

• Glucose → Pyruvate → Acetyl-CoA → Krebs Cycle → ETC → ATP

• Final electron acceptor: O2

• Final product: H2O

• Most ATP is produced by the ETC (oxidative phosphorylation)

• No oxygen: Only glycolysis operates (2 ATP per glucose)

Key Equations

• Overall cellular respiration (aerobic):

• ATP yield per glucose (aerobic):