Microbial Metabolism and Energy Pathways

Metabolism: All chemical and physical workings of a cell
- Two types of chemical reactions:
- Catabolism:
  - Definition: Degradative process breaking the bonds of larger molecules to form smaller ones; releases energy.
- Anabolism:
  - Definition: Biosynthesis process forming larger macromolecules from smaller molecules; requires energy input.

Enzymes: Biological catalysts that increase the rate of a chemical reaction by lowering the energy of activation.
Energy of Activation: Resistance to a chemical reaction; the energy required to start a reaction.
Characteristics of Enzymes:
- Not permanently altered in the reaction.
- Promotes reactions by serving as a physical site for substrate molecules to position.

Reaction with and without Enzymes:
- Activation energy without enzyme: Higher energy (energy peak) needed to initiate the reaction.
- Activation energy with enzyme: Lower energy requirement, allowing the reaction to proceed more easily.
Visual Representation:
- Graph with initial energy level, final energy level, and activation energy depicted.

Simple Enzymes: Consist of protein alone.
Conjugated Enzymes (Holoenzymes):
- Components:
- Apoenzyme: Protein portion.
- Cofactors: Non-protein portion.
  - Metallic Cofactors: Iron, copper, magnesium.
  - Coenzymes: Organic molecules, typically vitamins.

Catalase: Breaks down hydrogen peroxide
- Metallic Cofactor: Iron (Fe)
Oxidase: Adds electrons to oxygen
- Metallic Cofactor: Iron, copper (Cu)
Hexokinase: Transfers phosphate to glucose
- Metallic Cofactor: Magnesium (Mg)
Urease: Splits urea into an ammonium ion
Nitrate reductase: Reduces nitrate to nitrite
DNA polymerase: Synthesis of DNA
- Metallic Cofactors: Nickel (Ni), molybdenum (Mo), zinc (Zn), magnesium (Mg).

Structure: Exhibits primary, secondary, tertiary, and some quaternary structure.
Active Site: The site for substrate binding.
- Mechanism:
- Temporary enzyme-substrate union occurs upon substrate moving into the active site (induced fit).
- Appropriate reaction occurs; product is formed and released.

Exoenzymes: Transported extracellularly, breaking down large food molecules or harmful chemicals (e.g., cellulase, amylase, penicillinase).
Endoenzymes: Retained intracellularly and function there; most enzymes are endoenzymes.

Influencing Factors: Environment of cells (temperature, pH, osmotic pressure).
Denaturation: Changes in environmental conditions can destabilize enzymes, breaking weak bonds that maintain their structure.

Temperature:
- Increased temperature enhances activity until denaturation occurs. Graph shows increased enzymatic activity (rate of reaction) with rising temperature until denaturation leads to a steep fall.
pH:
- Each enzyme has an optimal pH range; activity decreases at pH levels significantly different from the optimum.

Competitive Inhibition:
- A substance resembling the normal substrate competes with it for the active site.
Noncompetitive Inhibition:
- Regulation by binding of molecules other than the substrate at an allosteric site, changing the conformation of the active site and blocking reactions.

Energy: The capacity to do work or to cause change.
Forms of Energy:
- Thermal, radiant, electrical, mechanical, atomic, and chemical.

Cells manage energy through chemical reactions that form or break bonds and transfer electrons.
- Endergonic Reactions: Consume energy; related to anabolism.
- Exergonic Reactions: Release energy; related to catabolism.

Oxidation: Removal of electrons.
Reduction: Gain of electrons.
Redox Reactions: An oxidation reaction paired with a reduction reaction; always occur in pairs.

Redox Reactions: Always involve an electron donor and an electron acceptor forming a redox pair.
The process salvages electrons and their energy, which can be used to phosphorylate ADP or another compound.

Function: Accept and release electrons and hydrogen to facilitate redox energy transfer.
Most Carriers: Coenzymes such as NAD, FAD, NADP, coenzyme A, and compounds of the respiratory chain.

Definition: Metabolic "currency" of the cell.
Structure: Composed of three parts:
- Adenine: A nitrogenous base.
- Ribose: A 5-carbon sugar.
- Three Phosphate Groups: The terminal phosphate bond releases energy when broken.

Mechanisms of ATP Formation:
- Substrate-level Phosphorylation: Direct transfer of a phosphate group from a substrate to ADP.
- Oxidative Phosphorylation: Involves a series of redox reactions in the respiratory pathway.
- Photophosphorylation: Uses light energy.

Bioenergetics: Study of the mechanisms of cellular energy release, involving both catabolic and anabolic reactions.
Primary Catabolic Pathways:
- Glycolysis: The breakdown of glucose into pyruvate.
- Kreb's Cycle: Also known as the citric acid cycle.
- Electron Transport Chain: Final stage of aerobic respiration.

Aerobic Respiration Process:
- Glycolysis: Begins with glucose (6C). Produces ATP and NADH, results in 2 pyruvate (3C).
- Kreb's Cycle: Acetyl-CoA enters the cycle, producing CO2, ATP, and more NADH.
- Electron Transport Chain: Oxygen is the final electron acceptor, enabling ATP production (total of 38 ATP produced).

Nutrient Processing: Varies but is typically based on three catabolic pathways that convert glucose to CO2 while releasing energy.
- Aerobic Respiration: Involves glycolysis, Kreb’s cycle, respiratory chain with O2 as the final electron acceptor.
- Anaerobic Respiration: Similar to aerobic but without O2 as the final electron acceptor.
- Fermentation: Includes glycolysis but concludes with organic compounds as the final electron acceptor.

Process: Breaks down glucose into pyruvate through several enzymatic steps. Produces ATP, NADH, and other intermediates.

Process: Starts with Acetyl CoA, goes through several steps resulting in CO2, ATP, NADH, and FADH2 production.

Function: Processes electrons and hydrogen ions, generating a major quantity of ATP through ATP synthase using energy released from the electron transport chain.

Final Reaction: Oxygen accepts 2 electrons and 2 hydrogen ions, forming water:
2H^+ + 2e^- + rac{1}{2}O2 ightarrow H2O