Cellular Metabolism, Energy, and Enzyme Function: Study Notes for General Biology

Metabolism and Metabolic Pathways

Overview of Metabolism

Metabolism encompasses all chemical reactions occurring within an organism, managing the material and energy resources of the cell. These reactions are organized into metabolic pathways, each beginning with a specific molecule and ending with a product, catalyzed by enzymes.

• Catabolic pathways: Break down larger molecules into smaller components, releasing energy (exergonic). Example: Hydrolysis of carbohydrates into monomers; cellular respiration catabolizes glucose and harnesses energy.

• Anabolic pathways: Use energy to build complex molecules from simpler ones (endergonic). Example: Synthesis of proteins from amino acids; dehydration synthesis reactions.

• Coupling of pathways: Catabolic and anabolic pathways are coupled in space and time. Catabolic reactions (e.g., ATP formation) provide energy for anabolic reactions.

Forms of Energy

Types of Energy Relevant to Biology

Energy is the capacity to cause change or perform work, and it exists in various forms within biological systems.

• Kinetic energy: Energy of motion (e.g., running water).

• Thermal energy: Kinetic energy associated with random movement of atoms or molecules; heat energy is thermal energy transferred between objects.

• Light energy: Can be harnessed to perform work (e.g., photosynthesis).

• Potential energy: Energy due to location or structure (e.g., water behind a dam, concentration gradients, electrical gradients).

• Chemical energy: Potential energy stored in chemical bonds, available for release in chemical reactions. Example: Breaking covalent bonds in glucose to release energy for ATP synthesis.

The Laws of Energy Transformation

Thermodynamics in Biological Systems

Thermodynamics studies energy transformations in matter. Biological systems are open systems, exchanging energy and matter with their surroundings.

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transferred or transformed. Example: Plants convert sunlight (light energy) to chemical energy; animals convert chemical energy to kinetic energy.

• Second Law of Thermodynamics: Every energy transfer increases entropy (disorder); some energy is lost as heat. Example: Only a fraction of food energy is transformed into kinetic energy; the rest is lost as heat.

• Entropy: Measure of molecular disorder; systems tend toward increased entropy.

Biological Order and Disorder

Cells and organisms create ordered structures from less ordered materials, but overall, energy flows through ecosystems and increases entropy.

• Example: Building proteins from amino acids (order); breaking proteins into amino acids (disorder).

Free Energy and Metabolism

Exergonic and Endergonic Reactions

Free energy change ($\Delta G$) determines whether a reaction occurs spontaneously.

• Exergonic reactions: Net release of free energy; spontaneous and energetically favorable. Example: Cellular respiration.

• Endergonic reactions: Absorb free energy; nonspontaneous and not energetically favorable. Example: Synthesis of macromolecules.

Equilibrium and Metabolism

Cells are open systems and do not reach equilibrium; constant flow of materials prevents equilibrium, which would result in cell death.

ATP: Cellular Energy Currency

ATP Powers Cellular Work by Coupling Reactions

ATP (adenosine triphosphate) is used to couple exergonic and endergonic reactions, enabling cells to perform chemical, transport, and mechanical work.

• Chemical work: Building polymers from monomers.

• Transport work: Pumping molecules across membranes.

• Mechanical work: Movement of flagella, muscle contraction.

Structure and Hydrolysis of ATP

ATP consists of ribose, adenine, and three phosphate groups. Energy is released when phosphate bonds are broken by hydrolysis:

• $\text{ATP} \rightarrow \text{ADP} + \text{P}_i$ Exergonic reaction

• $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$ Endergonic reaction

ATP hydrolysis releases large amounts of energy due to repulsion between negatively charged phosphate groups. The energy released is used to drive endergonic reactions by phosphorylation (adding a phosphate group to another molecule).

Enzymes: Biological Catalysts

Enzymes Speed Up Metabolic Reactions by Lowering Energy Barriers

Enzymes are proteins that act as catalysts, speeding up chemical reactions without being consumed. They lower the activation energy ($E_a$) required for reactions.

• Activation energy barrier: Energy required to start a reaction.

• Enzyme specificity: Each enzyme acts on a specific substrate, forming an enzyme-substrate complex (lock and key fit).

• Active site: Region on enzyme where substrate binds; chemical interactions facilitate reaction.

• Induced fit: Enzyme changes shape to better fit substrate upon binding.

How Enzymes Speed Up Reactions

• Orient substrates correctly

• Strain substrate bonds

• Provide favorable microenvironment

• Temporarily bond to substrate

Enzyme Rates and Saturation

Enzyme rate depends on enzyme and substrate concentration. When all enzyme molecules are bound to substrate, the enzyme is saturated; further increases in substrate do not increase reaction rate.

Effects of Local Conditions on Enzyme Activity

• Temperature: Each enzyme has an optimal temperature; too high or low can denature the enzyme.

• pH: Each enzyme has an optimal pH; e.g., pepsin in stomach (pH 2), trypsin in intestines (pH 8).

• Chemicals: Cofactors (nonprotein helpers) and inhibitors can affect enzyme activity.

Cofactors and Enzyme Inhibitors

• Cofactors: Nonprotein molecules that assist enzyme function. Inorganic: Metal ions (e.g., zinc, copper) Organic: Coenzymes (e.g., B vitamins)

• Inhibitors: Molecules that reduce enzyme activity. Reversible: Bind via weak bonds. Irreversible: Bind via covalent bonds.

• Competitive inhibitors: Bind to active site, blocking substrate.

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

Regulation of Enzyme Activity

Control of Metabolic Pathways

Cells regulate metabolic pathways and enzyme activity at genetic and enzyme levels.

• Genetic level: Switching genes on/off to control enzyme production.

• Enzyme level: Regulating activity of enzymes once formed, often via specific molecules.

• Allosteric regulation: Regulatory molecules bind to a protein at one site, affecting function at another site; may inhibit or stimulate enzyme activity.

Summary Table: Types of Enzyme Inhibition

Type	Binding Site	Effect on Enzyme
Competitive	Active site	Blocks substrate binding; reversible
Noncompetitive	Allosteric site (other than active site)	Changes enzyme shape; reduces activity; reversible or irreversible

Key Equations

• ATP Hydrolysis: $\text{ATP} \rightarrow \text{ADP} + \text{P}_i$

• ATP Synthesis: $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

• Free Energy Change: $\Delta G = \Delta H - T\Delta S$ Where $\Delta G$ is change in free energy, $\Delta H$ is change in enthalpy, $T$ is temperature in Kelvin, and $\Delta S$ is change in entropy.

Additional info: These notes expand on the original points with definitions, examples, and equations for clarity and completeness.