Microbial Metabolism: Enzymes, Energy, and Pathways

Microbial Metabolism

Overview of Metabolism

Metabolism is the sum of all chemical reactions occurring within a cell. These reactions are organized into metabolic pathways, which are sequences of enzymatically catalyzed reactions. Metabolism is divided into two main types: catabolism (breakdown of molecules to release energy) and anabolism (synthesis of complex molecules using energy).

• Catabolic pathways break down macromolecules into simpler components, releasing energy.

• Anabolic pathways build up macromolecules from simpler molecules, consuming energy.

• Catabolic and anabolic pathways are linked by energy, typically in the form of ATP.

Metabolic Pathways and Enzymes

Metabolic pathways are determined by enzymes, which are proteins encoded by genes. Each step in a pathway is catalyzed by a specific enzyme, ensuring the proper transformation of substrates to products.

• Enzymes lower the activation energy required for reactions, increasing reaction rates without being consumed.

• Enzyme specificity ensures that only particular substrates are transformed.

Energy and Reaction Rates

Chemical reactions require a certain amount of energy to proceed, known as activation energy. Enzymes accelerate reactions by lowering this energy barrier.

• Factors influencing reaction rates include temperature, pH, substrate concentration, and the presence of inhibitors.

Enzymes: Structure and Function

Mechanism of Enzyme Action

Enzymes function by binding substrates at their active sites, forming an enzyme-substrate complex. The substrate is converted to product, and the enzyme is released unchanged.

• Enzyme specificity is due to the unique shape of the active site.

• Turnover number refers to the number of substrate molecules converted per second.

Enzyme Components

Enzymes may consist of a protein portion (apoenzyme) and a nonprotein component (cofactor or coenzyme). The active enzyme (holoenzyme) is the combination of both.

• Cofactor: Inorganic ions (e.g., Mg2+, Fe2+).

• Coenzyme: Organic molecules, often derived from vitamins.

Enzyme Classification

Enzymes are classified based on the type of reaction they catalyze.

Class	Type of Reaction Catalyzed	Examples
Oxidoreductase	Oxidation-reduction	Cytochrome oxidase, lactate dehydrogenase
Transferase	Transfer of functional groups	Acetate kinase, alanine deaminase
Hydrolase	Hydrolysis	Lipase, sucrase
Lyase	Removal of groups without hydrolysis	Oxalate decarboxylase, isocitrate lyase
Isomerase	Rearrangement within a molecule	Glucose-phosphate isomerase, alanine racemase
Ligase	Joining of molecules (using ATP)	Acetyl-CoA synthetase, DNA ligase

Vitamins as Coenzymes

Many vitamins serve as coenzymes or their precursors, playing essential roles in metabolism.

Vitamin	Function
Vitamin B1 (thiamine)	Part of coenzyme for metabolism of pyruvic acid
Vitamin B2 (riboflavin)	Coenzyme in electron transfers
Niacin (nicotinic acid)	Part of NAD molecule
Vitamin B6 (pyridoxine)	Coenzyme in amino acid metabolism
Vitamin B12 (cyanocobalamin)	Coenzyme in methyl group transfer
Pantothenic Acid	Part of coenzyme A, involved in metabolism of pyruvic acid and lipids
Biotin	Involved in carbon dioxide fixation reactions
Folic Acid	Coenzyme used in synthesis of purines and pyrimidines
Vitamin E	Needed for cellular and macromolecular synthesis
Vitamin K	Coenzyme in electron transport

Factors Influencing Enzyme Activity

Enzyme activity is affected by temperature, pH, substrate concentration, and inhibitors. Extreme conditions can denature enzymes, rendering them inactive.

• Optimal temperature and pH maximize enzyme activity.

• Increasing substrate concentration increases activity until saturation is reached.

Enzyme Inhibition

Enzyme inhibitors can be competitive (compete with substrate for active site) or noncompetitive (bind elsewhere, altering enzyme shape).

• Competitive inhibitors resemble the substrate and block the active site.

• Noncompetitive inhibitors bind to an allosteric site, changing the enzyme's conformation.

Example: Sulfa drugs act as competitive inhibitors of the enzyme involved in folic acid synthesis in bacteria.

Feedback Inhibition

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

• Helps maintain metabolic balance within the cell.

Oxidation-Reduction (Redox) Reactions

Redox Basics

Oxidation is the loss of electrons, while reduction is the gain of electrons. In biological systems, these reactions often involve the transfer of hydrogen atoms.

• Redox reactions are essential for energy extraction from nutrients.

• NAD+ and FAD are common electron carriers.

ATP: The Energy Currency

ATP Structure and Synthesis

ATP (adenosine triphosphate) stores and transfers energy in cells. It is generated by phosphorylation of ADP.

• ATP is produced by substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation.

Carbohydrate Catabolism

Overview of Respiration and Fermentation

Cells extract energy from glucose through a series of enzymatic reactions. The main pathways are glycolysis, the Krebs cycle, and the electron transport chain (ETC). Fermentation is an alternative pathway used when oxygen is absent.

Glycolysis

Glycolysis is the oxidation of glucose to pyruvate, producing ATP and NADH. It occurs in the cytoplasm and does not require oxygen.

• Net gain: 2 ATP, 2 NADH, and 2 pyruvate per glucose molecule.

• First half: energy investment; second half: energy payoff.

Preparatory Step and Krebs Cycle

Before entering the Krebs cycle, pyruvate is converted to acetyl CoA. The Krebs cycle (citric acid cycle) completes the oxidation of acetyl CoA, generating NADH, FADH2, ATP, and CO2.

• Each glucose yields 6 NADH, 2 FADH2, 2 ATP, and 4 CO2 (from two turns of the cycle).

Electron Transport Chain and Chemiosmosis

The ETC is a series of membrane-bound carriers that transfer electrons from NADH and FADH2 to oxygen (in aerobic respiration), generating a proton gradient used to synthesize ATP via ATP synthase.

• Proton-motive force drives ATP synthesis as protons flow through ATP synthase.

• Each NADH yields about 3 ATP; each FADH2 yields about 2 ATP.

Anaerobic Respiration

Some microbes use electron acceptors other than oxygen (e.g., nitrate, sulfate, carbonate) in the ETC, producing less ATP than aerobic respiration.

Electron Acceptor	Products
NO3–	NO2–, N2 + H2O
SO42–	H2S + H2O
CO32–	CH4 + H2O

Fermentation

Fermentation allows ATP production in the absence of oxygen by using organic molecules as final electron acceptors. It regenerates NAD+ for glycolysis and produces various end products.

• Lactic acid fermentation: Pyruvate is reduced to lactic acid (e.g., in Lactobacillus).

• Alcohol fermentation: Pyruvate is converted to ethanol and CO2 (e.g., in yeast).

Organism	Fermentation End-Product(s)
Streptococcus, Lactobacillus, Bacillus	Lactic acid
Saccharomyces (yeast)	Ethanol and CO2
Propionibacterium	Propionic acid, acetic acid, CO2, and H2
Clostridium	Butyric acid, butanol, acetone, isopropyl alcohol, CO2, and H2
Escherichia, Salmonella	Ethanol, lactic acid, succinic acid, acetic acid, CO2, and H2
Enterobacter	Ethanol, lactic acid, formic acid, butanediol, acetoin, CO2, and H2

Applications and Examples

• Cheese production: Lactic acid bacteria ferment milk sugars, producing lactic acid and curdling milk.

• Sauerkraut and pickles: Anaerobic fermentation by Lactobacillus and Leuconostoc produces acids and gases.

• Poi: Fermentative succession by various microbes, with acid byproducts accumulating over time.