Microbial Metabolism: Structured Study Notes for Microbiology Students

Microbial Metabolism

Overview of Metabolism

Metabolism encompasses all the chemical reactions that occur within a cell, involving both the breakdown and synthesis of nutrients. These reactions provide energy and generate substances essential for sustaining life. While microbial metabolism can contribute to disease and food spoilage, many metabolic pathways are beneficial and support various biological and industrial processes.

Catabolic and Anabolic Reactions

Metabolic reactions are classified as either catabolic or anabolic:

• Catabolism: The breakdown of complex molecules into simpler ones, releasing energy and providing building blocks for anabolic reactions. Catabolic reactions are exergonic (energy-releasing).

• Anabolism: The synthesis of complex molecules from simpler ones, requiring energy input. Anabolic reactions are endergonic (energy-consuming).

• Metabolic pathways: Sequences of enzymatically catalyzed reactions, determined by specific enzymes encoded by genes.

Collision Theory and Enzyme Function

The collision theory states that chemical reactions occur when atoms, ions, or molecules collide with sufficient energy (activation energy). The reaction rate can be increased by enzymes, temperature, pressure, or concentration.

• Catalysts: Substances that speed up reactions without being consumed.

• Enzymes: Biological catalysts that lower activation energy and act on specific substrates.

Enzyme Specificity, Efficiency, and Naming

Enzymes exhibit high specificity for their substrates and are highly efficient, with turnover numbers ranging from 1 to 500,000 substrate molecules per second. Enzyme names typically end in -ase and are grouped by the type of reaction they catalyze:

• Oxidoreductase: Oxidation-reduction reactions

• Transferase: Transfer of functional groups

• Hydrolase: Hydrolysis reactions

• Lyase: Removal of atoms without hydrolysis

• Isomerase: Rearrangement of atoms

• Ligase: Joining of molecules, often using ATP

Enzyme Components

Enzymes may require additional components for activity:

• Apoenzyme: Protein portion, inactive alone

• Cofactor: Nonprotein component (can be inorganic or organic)

• Coenzyme: Organic cofactor

• Holoenzyme: Apoenzyme plus cofactor, forming the active enzyme

• Common coenzymes include NAD+, NADP+, FAD, and Coenzyme A, which often act as electron carriers.

Factors Influencing Enzyme Activity

Several factors affect enzyme activity:

• Temperature: Enzyme activity increases with temperature up to an optimum, after which denaturation occurs.

• pH: Each enzyme has an optimal pH; extreme pH can denature proteins.

• Substrate concentration: Higher substrate concentrations increase reaction rate until saturation is reached.

• Inhibitors: Substances that decrease enzyme activity.

Enzyme Inhibition

Enzyme inhibitors can be classified as:

• Competitive inhibitors: Compete with the substrate for the active site.

• Noncompetitive inhibitors: Bind to an allosteric site, altering the enzyme's shape and function.

Feedback Inhibition

Feedback inhibition occurs when the end-product of a metabolic pathway allosterically inhibits an enzyme early in the pathway, regulating the pathway's activity.

Ribozymes

Ribozymes are RNA molecules that act as catalysts, binding to substrates and facilitating reactions such as RNA splicing and protein synthesis. Unlike enzymes, ribozymes are not consumed in the reaction.

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons:

• Oxidation: Removal of electrons

• Reduction: Gain of electrons

• Redox reaction: Paired oxidation and reduction

• In biological systems, electrons and protons are often removed together (dehydrogenation).

The Generation of ATP

ATP is generated by the phosphorylation of ADP, using energy from catabolic reactions. There are three main mechanisms:

• Substrate-level phosphorylation: Direct transfer of a high-energy phosphate group to ADP.

• Oxidative phosphorylation: Electrons are transferred through an electron transport chain, releasing energy for ATP synthesis via chemiosmosis.

• Photophosphorylation: Light energy is used to generate ATP in photosynthetic cells.

Metabolic Pathways of Energy Production

Microbial cells extract energy from organic compounds through a series of enzymatically catalyzed reactions, storing energy in ATP.

Carbohydrate Catabolism

The breakdown of carbohydrates to release energy typically occurs in three principal stages:

• Glycolysis

• Krebs cycle

• Electron transport chain

Glycolysis

Glycolysis is the oxidation of glucose to pyruvic acid, producing ATP and NADH. It consists of:

• Preparatory stage: 2 ATP are used; glucose is split into two molecules (GP and DHAP).

• Energy-conserving stage: GP is oxidized to pyruvic acid, producing 4 ATP and 2 NADH.

Additional Pathways

• Pentose phosphate pathway: Breaks down pentose sugars, produces NADPH, and provides intermediates for biosynthesis.

• Entner-Doudoroff pathway: Produces NADPH and ATP independently of glycolysis; found in certain bacteria.

Cellular Respiration

Cellular respiration involves the oxidation of molecules, liberating electrons to operate an electron transport chain. The final electron acceptor is inorganic:

• Aerobic respiration: Uses oxygen as the final electron acceptor.

• Anaerobic respiration: Uses a molecule other than oxygen.

Krebs Cycle

Pyruvic acid from glycolysis is oxidized and decarboxylated, forming acetyl CoA and NADH. Acetyl CoA enters the Krebs cycle, producing NADH, FADH2, ATP, and CO2.

Electron Transport Chain and Chemiosmosis

The electron transport chain consists of carrier molecules that are oxidized and reduced as electrons are passed down the chain. Energy released is used to produce ATP by chemiosmosis, where protons are pumped across a membrane, creating a gradient that drives ATP synthesis.

ATP Yield

Each NADH can produce 3 ATP, and each FADH2 can produce 2 ATP in the electron transport chain.

Anaerobic Respiration

In anaerobic respiration, the final electron acceptor is not O2, resulting in less energy yield compared to aerobic respiration.

Fermentation

Fermentation releases energy from the oxidation of organic molecules without using oxygen, the Krebs cycle, or the electron transport chain. It uses an organic molecule as the final electron acceptor and produces small amounts of ATP.

Types of Fermentation

• Lactic acid fermentation: Produces lactic acid; can be homolactic (only lactic acid) or heterolactic (lactic acid and other compounds).

• Alcohol fermentation: Produces ethanol and CO2.

Industrial Uses of Fermentation

Fermentation End-Product(s)	Industrial or Commercial Use	Starting Material	Microorganism
Ethanol	Beer, wine	Starch/sugar	Saccharomyces cerevisiae (yeast)
Acetic Acid	Vinegar	Alcohol	Acetobacter
Lactic Acid	Cheese, yogurt	Milk	Lactobacillus, Streptococcus
Propionic Acid and CO2	Swiss cheese	Lactic acid	Propionibacterium freudenreichii
Butyric Acid, Butanol, Acetone, CO2, H2	Pharmaceutical industrial uses	Molasses	Clostridium
Methane	Fuel	Acetic acid	Archaea (fungi)
Sorbose	Vitamin C (ascorbic acid)	Glucose	Gluconobacter

Lipid and Protein Catabolism

Lipids are broken down by lipases into glycerol and fatty acids, which enter glycolysis and the Krebs cycle. Proteins are degraded by proteases and peptidases into amino acids, which are deaminated, decarboxylated, or desulfurized to enter the Krebs cycle.

Biochemical Tests and Bacterial Identification

Biochemical tests identify bacteria by detecting specific enzymes involved in metabolic reactions. Fermentation tests detect acid production (color change in pH indicator) and gas production (Durham tube). The oxidase test identifies bacteria with cytochrome c oxidase.

Photosynthesis

Photosynthesis consists of light-dependent reactions (conversion of light energy to ATP and NADPH) and light-independent reactions (Calvin-Benson cycle, where ATP and NADPH reduce CO2 to sugar).

• Oxygenic photosynthesis: Produces O2 (plants, algae, cyanobacteria)

• Anoxygenic photosynthesis: Does not produce O2 (purple/green sulfur bacteria)

Metabolic Diversity among Organisms

Microorganisms are classified based on their energy and carbon sources:

• Phototrophs: Use light energy

• Photoautotrophs: Use light energy and CO2 as carbon source

• Photoheterotrophs: Use light energy and organic compounds as carbon source

• Chemoautotrophs: Use inorganic chemicals and CO2 as carbon source

• Chemoheterotrophs: Use organic chemicals for both energy and carbon

Characteristic	Eukaryotes (Algae, Plants)	Cyanobacteria	Green Bacteria	Purple Bacteria
Substance that Reduces CO2	H2O	H2O	Sulfur, sulfur compounds, H2	Sulfur, sulfur compounds, H2
Type of Chlorophyll	Chlorophyll a	Chlorophyll a	Bacteriochlorophyll a, c, d, e	Bacteriochlorophyll a, b
Site of Photosynthesis	Thylakoids	Thylakoids	Chlorosomes	Chromatophores
Environment	Aerobic	Aerobic (and anaerobic)	Anaerobic	Anaerobic

Biosynthesis and Integration of Metabolism

Cells synthesize polysaccharides, lipids, amino acids, and nucleotides from metabolic intermediates. Amphibolic pathways function in both anabolism and catabolism, allowing simultaneous operation and sharing of intermediates.