Cellular Respiration, Enzyme Function, and Bioenergetics: Study Notes for General Biology

Enzyme Function and Bioenergetics

Energy Diagrams and Activation Energy

Biological reactions often require an input of energy, known as activation energy, to proceed. Enzymes lower this activation energy, making reactions more efficient.

• Transition State: The high-energy state that reactants must reach for a reaction to proceed.

• Activation Energy (without enzyme): The energy required to reach the transition state in the absence of an enzyme.

• Activation Energy (with enzyme): The reduced energy required when an enzyme is present.

Label	Description
A	Transition state
B	Activation energy in the absence of an enzyme
C	Activation energy in the presence of an enzyme

Example: The hydrolysis of sucrose is much faster in the presence of the enzyme sucrase because the activation energy is lowered.

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy. The active site is the specific region of an enzyme where the substrate binds and the reaction occurs.

• Substrate: The molecule upon which an enzyme acts.

• Active Site: The region on the enzyme where the substrate binds.

Example: In the reaction catalyzed by catalase, hydrogen peroxide binds to the active site of the enzyme.

Types of Energy in Biological Molecules

Chemical bonds, such as the C-H bonds in glucose, store potential energy that can be released during metabolic reactions.

• Potential Energy: Stored energy due to the position or structure of molecules.

• Kinetic Energy: Energy of motion (not stored in bonds).

Example: The energy released from glucose during cellular respiration is used to produce ATP.

Enzyme Inhibition

Enzyme activity can be regulated by inhibitors. Noncompetitive inhibitors bind to an allosteric site, causing a conformational change in the enzyme that reduces its activity.

• Noncompetitive Inhibition: Inhibitor binds to a site other than the active site, altering enzyme shape and function.

• Effect: Changes the conformation of the active site, preventing substrate binding.

Example: Heavy metals can act as noncompetitive inhibitors for many enzymes.

Factors Affecting Enzyme Activity

• pH: Each enzyme has an optimal pH range.

• Temperature: Enzyme activity increases with temperature up to a point, then decreases due to denaturation.

• Inhibitors: Molecules that decrease enzyme activity.

Example: Pepsin works best at acidic pH in the stomach.

Feedback Inhibition in Metabolic Pathways

Feedback inhibition is a regulatory mechanism where the end product of a metabolic pathway inhibits an earlier step, preventing overproduction.

• Mechanism: The product binds to an enzyme involved in the pathway, reducing its activity.

Example: In isoleucine biosynthesis, isoleucine inhibits the first enzyme in its pathway.

Cellular Respiration and ATP Production

Overview of Cellular Respiration

Cellular respiration is the process by which cells extract energy from glucose to produce ATP. It consists of several stages:

1. Glycolysis

2. Pyruvate Oxidation

3. Krebs Cycle (Citric Acid Cycle)

4. Electron Transport Chain (ETC) & Oxidative Phosphorylation

Correct Order: Glycolysis → Krebs Cycle → ETC & Oxidative Phosphorylation

Glycolysis

Glycolysis is the first step in cellular respiration, occurring in the cytoplasm. It breaks down glucose into pyruvate, producing ATP and NADH.

• Products: Pyruvate, ATP, NADH

Equation:

$\text{Glucose} + 2\,\text{NAD}^+ + 2\,\text{ADP} + 2\,\text{P}_i \rightarrow 2\,\text{Pyruvate} + 2\,\text{NADH} + 2\,\text{ATP} + 2\,\text{H}_2\text{O}$

Pyruvate Oxidation

Pyruvate produced in glycolysis is transported into the mitochondrial matrix, where it is converted to acetyl-CoA, producing NADH and releasing CO2.

• Location: Mitochondrial matrix

Krebs Cycle (Citric Acid Cycle)

The Krebs cycle completes the oxidation of glucose derivatives, generating NADH, FADH2, and ATP (or GTP).

• Main Reactions: Oxaloacetate to citrate, citrate to alpha-ketoglutarate, alpha-ketoglutarate to succinyl CoA, malate to oxaloacetate

• Oxidative Decarboxylation: Steps where CO2 is released and NAD+ is reduced to NADH

Electron Transport Chain & Oxidative Phosphorylation

The electron transport chain (ETC) is located in the inner mitochondrial membrane. Electrons from NADH and FADH2 are transferred through protein complexes, creating a proton gradient used to synthesize ATP via oxidative phosphorylation.

• Oxidative Phosphorylation: The process of ATP formation driven by the transfer of electrons through the ETC and the resulting proton gradient.

• ATP Synthase: The enzyme that uses the proton gradient to produce ATP from ADP and inorganic phosphate.

Equation:

$\text{ADP} + \text{P}_i + 4\,\text{H}^+_{\text{cytosol}} + \text{NADH} + \text{H}^+ \rightarrow \text{ATP} + \text{H}_2\text{O} + \text{NAD}^+ + 4\,\text{H}^+_{\text{matrix}}$

Substrate-Level vs. Oxidative Phosphorylation

Feature	Substrate-Level Phosphorylation	Oxidative Phosphorylation
ATP Yield	Less	More
Location	Glycolysis, Krebs Cycle	ETC (mitochondria)
Mechanism	Direct transfer of phosphate to ADP	Proton gradient and ATP synthase
Example	Phosphoglycerate kinase reaction	ATP synthase in mitochondria

Additional info: The exact mechanism of ATP formation in oxidative phosphorylation is called chemiosmosis.

Fermentation

When oxygen is not available, cells can produce ATP via fermentation. In lactic acid fermentation, NADH acts as a reducing agent to convert pyruvate to lactate.

• Products: Lactic acid (in animals), ethanol and CO2 (in yeast)

ATP Production Pathways

• Glycolysis: Universal pathway for ATP production in all living organisms.

• Oxidative Phosphorylation: Main ATP-producing process in aerobic organisms.

Order of Cellular Respiration Stages

1. Glycolysis

2. Krebs Cycle

3. Electron Transport Chain & Oxidative Phosphorylation

Redox Reactions and Oxidizing Agents

Redox reactions involve the transfer of electrons. The oxidizing agent is the substance that gains electrons and is reduced.

• Oxidizing Agent: Gains electrons

• Reducing Agent: Loses electrons

Bioenergetics and Thermodynamics

Bioenergetics

Bioenergetics is the study of energy flow and transformation in living systems.

Thermodynamics and Thermochemistry

• Thermodynamics: The study of energy and its transformations, including heat and work.

• Thermochemistry: The branch of thermodynamics that deals specifically with the heat changes during chemical reactions and physical changes.

Entropy and Spontaneous Reactions

Entropy (S) is a measure of disorder or randomness in a system. Most spontaneous reactions increase the entropy of the system.

• Spontaneous Reaction: A reaction that occurs naturally under given conditions, often increasing entropy.

Equation:

$\Delta S > 0$ (for most spontaneous reactions)

Additional Topics

Anabolism and Catabolism

• Anabolism: The synthesis of complex molecules from simpler ones (e.g., protein synthesis).

• Catabolism: The breakdown of complex molecules into simpler ones (e.g., cellular respiration).

Experimental Evidence in Cellular Respiration

Studies on bacteria producing magnetite support the role of the electron transport chain in cellular respiration. Inhibiting ETC enzymes prevents magnetite formation, indicating the importance of these enzymes in the process.

Chemiosmosis and ATP Synthase

Chemiosmosis is the movement of ions (usually H+) across a semipermeable membrane, down their electrochemical gradient. In mitochondria, this process is coupled to ATP synthesis via ATP synthase.

• ATP Synthase: The enzyme complex that synthesizes ATP as protons flow through it.