Microbial Metabolism: Chemical Reactions, Enzymes, and Energy Pathways

Chemical Reactions in Microbial Metabolism

Classification of Chemical Reactions

Chemical reactions in microbiology are fundamental to cellular metabolism and can be classified into two main types:

• Catabolic reactions: Involve the breakdown of molecules. These reactions are exergonic, meaning they release energy.

• Anabolic (biosynthetic) reactions: Involve the building of molecules. These reactions are endergonic, meaning they consume energy.

Metabolic processes often require reaction coupling, where an exergonic reaction is paired with an endergonic reaction to drive cellular functions.

Examples of Reaction Coupling

• ATP Synthesis: The breakdown of molecules releases chemical energy, which is stored in the biosynthesis of adenosine triphosphate (ATP). ATP consists of an adenine base, ribose sugar, and three phosphate groups. Energy is stored in the bonds between the phosphate groups.

• ATP Hydrolysis: The end phosphate bond of ATP is broken, releasing energy for cellular work such as building proteins, DNA, or powering cellular processes.

Enzymes and Their Function

Enzyme Catalysis

Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy required. They are essential for metabolic reactions in cells.

• Substrate: The reactant that binds to the enzyme's active site.

• Induced Fit Model: The enzyme changes shape slightly to mold to the substrate, facilitating the reaction.

Enzyme Activity and Environmental Factors

• Enzymes work best within specific temperature and pH ranges. Extreme conditions can cause denaturation, leading to loss of enzyme function.

• Enzyme activity can be affected by the presence of cofactors (inorganic ions) and coenzymes (organic molecules, often vitamins).

Enzyme Inhibition

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

• Noncompetitive inhibitors: Bind elsewhere on the enzyme, altering its shape and reducing activity.

Antibiotics and Enzyme Inhibition

Exogenous Inhibitors of Bacterial Enzymes

• Penicillin: Inhibits cell wall synthesis by blocking peptidoglycan cross-linking.

• Sulfonamide and Trimethoprim: Inhibit folic acid synthesis, affecting DNA and RNA production.

These antibiotics target bacterial enzymes, making them effective treatments for infections.

Aerobic Cellular Respiration (ACR)

Overview and Equation

Aerobic cellular respiration is a key process for energy release from organic molecules. It occurs in both eukaryotic and prokaryotic cells.

• General equation:

$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy}$

The energy released is stored in ATP. ACR is a complex pathway involving many chemical reactions.

Redox Reactions in Respiration

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Redox reactions: Transfer of electrons between molecules.

• Oxygen: Final electron acceptor, gets reduced.

Coenzymes in Respiration

• NAD+: Most common oxidized cofactor, carries high energy electrons.

• NADH: Reduced form, carries high energy electrons.

• FAD: Another cofactor, carries electrons as FADH2 when reduced.

ATP Production Mechanisms

• Substrate-level phosphorylation (SLP): Direct transfer of phosphate to ADP to make ATP.

• Oxidative phosphorylation: Uses electron transport chain and ATP synthase to produce most ATP.

Glycolysis and Alternative Pathways

Glycolysis

Glycolysis is the process of splitting glucose into pyruvate, generating ATP and NADH.

• Input: Glucose

• Outputs: 2 pyruvate, 2 ATP, 2 NADH

Entner-Doudoroff Pathway (EDP)

Some bacteria use the EDP as an alternative to glycolysis.

• One ATP produced (vs. two in glycolysis)

• One NADPH produced (used in biosynthetic reactions)

• Bacteria: Pseudomonas genus, Rhizobium

Pentose-Phosphate Pathway

This pathway produces important intermediates for biosynthesis.

• Two NADPH produced per glucose

• Ribose-5-phosphate: Used to make RNA and DNA

• Erythrose-4-phosphate: Used to make amino acids

Pyruvate Oxidation and Citric Acid Cycle

Pyruvate Oxidation

Pyruvate (3C) is converted to acetyl CoA (2C), which enters the citric acid cycle.

• Location in bacteria: Cytoplasm

• Location in eukaryotes: Mitochondrial matrix

• Summary: 2 pyruvate → 2 acetyl CoA + 2 NADH

Citric Acid Cycle (Krebs Cycle)

A series of reactions that further oxidize acetyl CoA, producing NADH, FADH2, and ATP.

• Location in bacteria: Cytoplasm

• Location in eukaryotes: Mitochondrial matrix

• After two turns: 6 NADH and 2 FADH2 are made

Oxidative Phosphorylation

Occurs in the electron transport chain, producing most ATP.

• Electrons are transferred from NADH and FADH2 to proteins in the electron transport chain.

• Protons (H+) are pumped across the membrane, creating a gradient.

• ATP synthase uses this gradient to make ATP from ADP and phosphate.

Summary Table: Key Metabolic Pathways

Pathway	Main Products	Location (Bacteria)	Location (Eukaryotes)
Glycolysis	2 ATP, 2 NADH, 2 pyruvate	Cytoplasm	Cytoplasm
Entner-Doudoroff	1 ATP, 1 NADPH, 2 pyruvate	Cytoplasm	Not present
Pentose-Phosphate	2 NADPH, ribose-5-phosphate, erythrose-4-phosphate	Cytoplasm	Cytoplasm
Pyruvate Oxidation	2 acetyl CoA, 2 NADH	Cytoplasm	Mitochondrial matrix
Citric Acid Cycle	6 NADH, 2 FADH2, 2 ATP	Cytoplasm	Mitochondrial matrix
Oxidative Phosphorylation	~34 ATP	Plasma membrane	Inner mitochondrial membrane

Additional info:

• Some context and terminology were inferred for clarity and completeness.

• Figures referenced (e.g., Figure 5.1, 5.2, etc.) are not included but their content is summarized in the notes.