Microbial Metabolism: Structured Study Notes for College Microbiology

Microbial Metabolism

Metabolism Basics

Metabolism encompasses all chemical reactions that organisms use to break down substances to release energy and to build new substances using that energy. These reactions are organized into biochemical pathways, where intermediates are transformed stepwise to end products.

• Catabolic pathways: Break down substances, releasing energy; typically hydrolytic and exergonic.

• Anabolic pathways: Build new substances using energy and molecules; involve dehydration synthesis and are endergonic.

• Amphibolic pathways: Can function in both catabolic and anabolic roles.

• Catabolic and anabolic reactions are often coupled, allowing energy released from catabolism to drive anabolism.

Adenosine Triphosphate (ATP)

ATP is the primary energy currency in cells, produced by catabolic reactions and used to power anabolic reactions. Its structure consists of adenine, ribose, and three phosphate groups.

• Dephosphorylation: Removal of the terminal phosphate group releases energy and produces ADP.

• Phosphorylation: Addition of a phosphate group to ADP regenerates ATP.

Enzymes

Enzymes are protein catalysts that facilitate chemical reactions under cellular conditions. They increase reaction rates, are not consumed in the reaction, and lower activation energy by holding reactants in proper orientation.

• Enzyme names: Usually end in -ase.

• Substrate: The molecule an enzyme acts upon.

• Active site: The region where the substrate binds.

• Induced fit model: Enzymes mold to the substrate for optimal catalysis.

Enzyme Classification

Enzymes are classified by the type of chemical reaction they catalyze.

Class	Reactions Catalyzed	Examples
Oxidoreductase(	Oxidation-reduction	Cytochrome oxidase, Alcohol dehydrogenase
Transferase	Transfer of functional groups	DNA methyltransferase, Pyruvate kinase
Hydrolase	Hydrolysis(water break)	Lipase, Sucrase
Lyase	Removal of groups without hydrolysis	Pyruvate decarboxylase
Isomerase	Rearrangement within a molecule	Triose cphosphate isomerase
Ligase	Joining of two molecules	Acetyl-CoA synthase

Enzyme-Substrate Complex

The enzyme-substrate complex is formed when the substrate binds to the enzyme's active site, allowing the reaction to proceed.

• Proper positioning of reactants

• Provision of activation energy

• Stabilization of the transition state

Factors Affecting Enzyme Activity

• Cofactors: Nonprotein components required for enzyme function. Apoenzyme (inactive, no cofactor), holoenzyme (active, with cofactor).

• Temperature: Lowers activity at low temperatures, increases up to optimal, then decreases due to denaturation.

• pH: Alters hydrogen and ionic bonds, extreme pH leads to denaturation.

• Substrate concentration: Rate depends on available active sites and substrate amount.

• Inhibitors: Competitive (binds active site), noncompetitive (binds elsewhere), allosteric regulation, feedback inhibition.

Obtaining and Using Energy

Redox Reactions and Energy Extraction

Cells extract energy from nutrients using oxidation-reduction (redox) reactions. Oxidation is the loss of electrons, reduction is the gain of electrons. Oxygen is a common oxidizing agent, hydrogen is often a reducing agent.

• Enzymes rely on coenzymes like NAD+ and FAD as electron carriers.

• Redox reactions are often coupled to phosphorylation reactions that recharge ADP to ATP.

Phosphorylation Mechanisms

Mechanism	How ATP is made	Electron transport chain used?	Used in	Cell types
Substrate-Level	Direct transfer of phosphate	No	Glycolysis, Krebs cycle, fermentation	Prokaryotic & eukaryotic
Oxidative	Electron transport chain	Yes	Cellular respiration	Prokaryotic & eukaryotic
Photophosphorylation	Light-driven electron transport	Yes	Photosynthesis	Photosynthetic cells

Cellular Respiration

Pathways of Cellular Respiration

Cellular respiration is the primary process for extracting energy from carbohydrates, involving glycolysis, intermediate step, Krebs cycle, and electron transport chain.

• Glycolysis: Ten reactions, energy investment and payoff stages. Products: 2 pyruvic acid, 2 water, 2 NADH, 2 ATP. Does not require oxygen.

• Intermediate step: Pyruvic acid converted to acetyl-CoA, NADH, and CO2.

• Krebs cycle: Series of redox and decarboxylation reactions. Products: 3 NADH, 1 FADH2, 1 ATP, 2 CO2.

• Electron transport chain: NADH and FADH2 donate electrons, protons pumped, ATP synthesized by chemiosmosis.

ATP Yield

• Prokaryotes: 38 ATP per glucose

• Eukaryotes: 36 ATP per glucose (2 used in transport)

Final Electron Acceptors

Bacteria Type	Importance	Examples of Final Electron Acceptors
Nitrogen fixing	Nitrogen cycle	Nitrate (NO3-)
Methanogens	Carbon cycle	Carbonate (CO32-)
Sulfate reducing	Sulfur cycle	Sulfate (SO42-)

Glucose Breakdown and Alternative Pathways

Pentose Phosphate and Entner-Doudoroff Pathways

• Pentose Phosphate Pathway: Converts pentoses to trioses and hexoses, produces NADPH, used by many bacteria.

• Entner-Doudoroff Pathway: Produces 1 ATP per glucose, makes NADPH, found in Gram-negative obligate aerobes.

Fermentation

Types of Fermentation

Fermentation sustains ATP production by glycolysis when respiratory chains are unavailable. NADH transfers electrons to organic molecules, regenerating NAD+.

• Homolactic fermentation: Pyruvic acid reduced to lactic acid; 2 ATP produced; used by yogurt bacteria and human muscle cells.

• Heterolactic fermentation: Produces lactic acid, ethanol, CO2, and minor acids; 1 ATP produced; used by various bacteria and fungi.

• Alcohol fermentation: Pyruvic acid converted to ethanol and CO2; used by yeast and some bacteria.

• Mixed acid fermentation: Produces various acids and gases; used by enteric bacteria.

• Butanediol fermentation: Produces neutral end products like butanediol and ethanol.

Other Catabolic Pathways

Macromolecule Catabolism

• Lipases: Break lipids into glycerol and fatty acids. Glycerol enters glycolysis; fatty acids undergo beta-oxidation to acetyl-CoA for Krebs cycle.

• Proteases: Break proteins into peptides and amino acids. Amino acids can be recycled or deaminated for catabolism.

• Nucleases: Break nucleic acids into nucleotides, which are usually salvaged rather than catabolized for energy.

Biosynthesis (Anabolic Pathways)

Gluconeogenesis and Glycogenesis

• Gluconeogenesis: Building glucose from non-sugar materials using intermediates from glycolysis, Krebs cycle, and lipid/protein catabolism.

• Glycogenesis: Production of glycogen from glucose.

• Simple sugars can be assembled into polysaccharides.

Lipid and Amino Acid Biosynthesis

• Glycerol is made from glycolysis intermediate (DHAP).

• Fatty acids are synthesized by linking acetyl-CoA molecules.

• Cells make nonessential amino acids by amination (addition of NH2 to an intermediate).

• Degree of dependence on essential amino acids varies among species.

Nucleotide Biosynthesis

• Purines (adenine, guanine) and pyrimidines (uracil, thymine, cytosine) are essential for nucleic acids and energy molecules.

Classification by Metabolic Properties

Carbon, Energy, and Reducing Power Sources

• Autotrophs: Make organic carbon from inorganic sources via carbon fixation.

• Heterotrophs: Require external organic carbon.

• Phototrophs: Harvest energy from light.

• Chemotrophs: Harvest energy from chemical bonds.

• Lithotrophs: Use inorganic sources for reducing power.

• Organotrophs: Use organic sources for reducing power.

• Saprobes: Use dead organic material.

Tests to Identify Bacteria

Metabolic Profiling

• Metabolic profiles serve as biochemical fingerprints for microbial identification.

• Tests include specialized media, molecular, genetic, and metabolic assays.

• Panel of tests: Pure culture, staining, microscopy, culture characteristics, and biochemical tests.

Amino Acid Catabolism Tests

• Detect deaminases and decarboxylases.

• Phenylalanine deaminase, ornithine decarboxylase, sulfur reduction (black precipitate with iron).

Fermentation Tests

• Media contains protein, carbohydrate, pH indicator, and Durham tube.

• Acidic end products lower pH and change color; Durham tube captures gas.

Methyl Red/Voges-Proskauer (MRVP) Test

• MR: Detects mixed acid fermentation (acidic products lower pH).

• VP: Detects acetoin (intermediate of butanediol fermentation).

Oxidase and Catalase Tests

• Oxidase: Tests for cytochrome c oxidase.

• Catalase: Tests for catalase enzyme (breaks down hydrogen peroxide).

Rapid Identification Techniques

• API® system: Semi-automated process for multiple tests with a single inoculation.

Summary

Microbial metabolism is a complex interplay of catabolic and anabolic pathways, regulated by enzymes and influenced by environmental factors. Understanding these processes is essential for identifying microbes and their roles in health, disease, and biotechnology.