Microbial Metabolism

Introduction to Energy

Energy is fundamental to all biological processes, enabling organisms to perform work and drive chemical reactions. In biology, work refers to the transfer of energy that results in a change in the state of matter.

• Potential Energy: Stored energy available to do work, such as energy in chemical bonds or gravitational energy.

• Kinetic Energy: Energy of motion, such as muscle contractions or moving objects.

• Example: A glucose molecule contains potential energy, while water rushing over a waterfall demonstrates kinetic energy.

Thermodynamics in Biological Systems

Thermodynamics studies energy transfers between bodies of matter. Biological systems are defined as the specific portion of matter being studied, while surroundings are everything outside the system. Biological systems exchange both energy and mass with their surroundings.

• System: The organism or cell under study.

• Surroundings: The environment outside the system.

• Importance: Principles of thermodynamics govern chemical processes and energy exchange in all living organisms.

Laws of Thermodynamics

First Law of Thermodynamics

The first law states that energy can be transferred and transformed, but it cannot be created or destroyed. This is known as the Principle of Conservation of Energy. The total amount of energy in the universe remains constant.

• Example: Energy from sunlight is transferred to plants via photosynthesis and then to animals via cellular respiration.

Entropy

Entropy is a measure of disorder or randomness. The greater the disorder, the higher the entropy. Reactions tend to move the universe toward higher entropy, but energy input can decrease entropy locally.

• Low Entropy: Ordered systems (e.g., billiard balls arranged in a triangle).

• High Entropy: Disordered systems (e.g., billiard balls scattered).

Second Law of Thermodynamics

The second law states that energy conversions are never 100% efficient; some energy is always lost as heat, increasing universal entropy.

• Heat: A form of kinetic energy transferred between objects of different temperatures.

• Example: Energy transfer up the food chain results in heat loss at each step.

Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, leading to changes in matter. Reactants are the starting materials, and products are the resulting materials.

• Endergonic Reactions: Require an input of energy (energy enters the reaction).

• Exergonic Reactions: Release energy (energy exits the reaction).

• Example: Building up molecules (endergonic) vs. breaking down molecules (exergonic).

Adenosine Triphosphate (ATP)

ATP is the primary energy molecule used to power cellular activities. It consists of three phosphate groups, a ribose sugar, and an adenine nitrogenous base. ATP hydrolysis releases energy by breaking bonds between phosphate groups, generating ADP and inorganic phosphate (Pi).

• ATP Hydrolysis:

• Example: Energy from food is stored in ATP and used for cellular work.

Energy Coupling and Phosphorylation

Energy coupling occurs when energy released by an exergonic reaction is used to drive an endergonic reaction. ATP hydrolysis is often coupled to endergonic reactions to provide the necessary energy input. Phosphorylation is the transfer of a phosphate group from ATP to another molecule, activating it or changing its conformation.

• Example: ATP phosphorylates glucose to initiate glycolysis.

Enzymes and Catalysis

Enzymes are biological catalysts that speed up chemical reactions without being consumed. Substrates are the reactants in enzyme-catalyzed reactions. Enzymes are essential for building molecules, copying DNA, and digesting food.

• Example: Lactase breaks down lactose; DNA polymerase synthesizes DNA.

Activation Energy and Enzyme Function

Activation energy (EA) is the minimum energy required to start a chemical reaction. Enzymes lower the activation energy barrier, allowing reactions to occur faster.

• Transition State: Temporary high-energy state during a reaction.

• Example: Reaction coordinate diagrams show how enzymes lower EA.

Enzyme Binding and Cofactors

Substrates bind to the enzyme's active site, forming an enzyme-substrate complex. After catalysis, products are released, and the enzyme remains unchanged. Some enzymes require cofactors (non-protein substances) or coenzymes (organic cofactors) for activity.

• Example: Cofactors assist in substrate binding and catalysis.

Enzyme Inhibition

Enzyme inhibitors interfere with catalysis. Competitive inhibitors compete for the active site, while noncompetitive inhibitors bind to an allosteric site, changing the enzyme's shape.

• Example: Competitive vs. noncompetitive inhibition diagrams.

Metabolic Pathways

Metabolism is the sum of all an organism's chemical reactions. Metabolic pathways are series of reactions that alter a substrate multiple times before the final product. There are two types:

• Catabolic Pathways: Release energy by breaking down molecules.

• Anabolic Pathways: Consume energy to build larger molecules.

Feedback Regulation

Negative feedback occurs when the final product inhibits an earlier step in the pathway, while positive feedback stimulates an earlier step. Feedback regulation is crucial for maintaining metabolic balance.

• Example: Negative feedback acts as a "red light"; positive feedback acts as a "green light" in metabolic pathways.

Oxidation-Reduction (Redox) Reactions

Redox reactions transfer electrons between molecules. Oxidation is the loss of electrons, and reduction is the gain of electrons. These reactions always occur together.

• Mnemonic: "LEO the Lion goes GER" (Lose Electrons = Oxidation; Gain Electrons = Reduction).

• Example: Glucose is oxidized, NAD+ is reduced to NADH during cellular respiration.

Electron Carriers: NADH, FADH2, NADPH

Electron carriers such as NADH, FADH2, and NADPH transport electrons during metabolic processes. NADH and FADH2 shuttle electrons to the electron transport chain in cellular respiration, while NADPH is used in biosynthetic reactions.

• Example: NADH and FADH2 are "heavier" with electrons; NADPH is used in photosynthesis.

Summary Table: Types of Metabolic Pathways