Microbial Metabolism: Study Notes for College Microbiology

Microbial Metabolism

Introduction to Metabolism

Metabolism encompasses all chemical reactions that occur within a cell, involving the buildup and breakdown of nutrients. These reactions provide energy and create substances essential for life. Microbial metabolism can cause disease, spoil food, and also benefit the environment and food production.

• Catabolism: Breaks down complex molecules, releasing energy.

• Anabolism: Builds complex molecules, requiring energy.

• Both processes are often coupled via energy intermediates like ATP.

Types of Metabolic Reactions

Metabolic reactions are classified as catabolic or anabolic, and are often interconnected.

• Catabolic reactions: Release energy by oxidation of molecules (e.g., glucose to CO2 and H2O).

• Anabolic reactions: Use energy to synthesize macromolecules (e.g., proteins from amino acids).

• ATP: Energy is stored and released via ATP hydrolysis and synthesis.

Metabolic Pathways

Metabolic pathways are sequences of enzymatically catalyzed chemical reactions in a cell, determined by enzymes encoded by genes.

• Pharmaceutical industry utilizes microbial metabolism for antibiotic production.

Enzymes & Reactions

Enzymes are specialized proteins that lower the activation energy for reactions, acting as catalysts without being altered.

• Enzymes act on specific substrates.

• They can be reused multiple times.

• Lower activation energy increases reaction rate.

How Enzymes Work

• Substrate contacts the enzyme's active site, forming an enzyme-substrate complex.

• Substrate is transformed into products, which are released from the enzyme.

• Enzyme remains unchanged and can react with other substrates.

Enzyme Characteristics

• Specificity: Enzymes are specific for particular substrates.

• Turnover number: Number of substrate molecules converted per second (generally 1 to 10,000, up to 500,000).

• Enzyme names usually end in -ase and are grouped by reaction type:

  • Oxidoreductase: Oxidation-reduction reactions

  • Hydrolase: Hydrolysis

  • Ligase: Joining of molecules, uses ATP

Enzyme Components

• Apoenzyme: Protein portion, inactive alone

• Cofactor: Non-protein component

• Coenzyme: Organic cofactor

• Holoenzyme: Apoenzyme plus cofactor (active form)

• Electron carriers:

  • NAD+ (Nicotinamide adenine dinucleotide)

  • NADP+ (Nicotinamide adenine dinucleotide phosphate)

  • FAD (Flavin adenine dinucleotide)

  • Coenzyme A

Factors Influencing Enzyme Activity

Temperature and pH

• Enzymes function at specific pH and temperature ranges.

• High temperature and extreme pH denature proteins, rendering enzymes inactive.

Substrate Concentration

• High substrate concentration leads to enzyme saturation, catalyzing at maximum rate.

Inhibitors

• Competitive inhibitors: Compete for the active site, blocking substrate binding.

• Noncompetitive inhibitors: Bind to allosteric site, altering enzyme shape and activity.

• Inhibition can be reversible or permanent.

Feedback Inhibition

• End product of a pathway inhibits an enzyme via noncompetitive feedback, regulating metabolic pathways.

Ribozymes

• RNA molecules that act as catalysts by binding to substrates and acting upon them.

• Not used up in the reaction.

• Frequently used in cells to cut and splice RNA; involved in protein synthesis in ribosomes.

Metabolic Terms

• Oxidation: Loss of electrons (e.g., Na → Na+).

• Reduction: Gain of electrons (e.g., Cl → Cl-).

• Redox reaction: Coupling of oxidation and reduction.

• Phosphorylation: Addition of phosphate (e.g., ADP → ATP).

• Dehydrogenation: Loss of hydrogen atom (e.g., NADH → NAD+).

Major Metabolic Processes

• Cellular respiration

• Fermentation

• Photosynthesis

Cellular Respiration

• Catabolic process converting glucose to ATP.

• ATP is a high energy carrier.

• Can be aerobic (uses oxygen) or anaerobic (does not use oxygen).

• NADH, NADPH, and FADH2 are electron carriers, accepting and donating electrons during reactions.

Glycolysis

• First pathway in cellular respiration (Embden-Meyerhof pathway).

• Glucose (6C) is broken into 2 pyruvic acid molecules (3C).

• Produces 4 ATP (Net 2) and 2 NADH.

Alternative Pathways to Glycolysis

Pathway	Features	Products
Pentose Phosphate Pathway	Used by bacteria; breaks down pentose and glucose	1 ATP & 2 NADPH per glucose
Entner-Doudoroff Pathway	Found in gram-negative bacteria; metabolizes glucose/pentose	1 NADPH, 1 NADH, 1 ATP

Krebs Cycle (Citric Acid Cycle)

• Occurs if oxygen is present; pyruvic acid enters the cycle.

• Produces 1 ATP, 3 NADH, 1 FADH2 per cycle.

• Releases CO2 as waste.

Electron Transport Chain

• Third step in aerobic respiration.

• Occurs in plasma membrane (prokaryotes) or inner mitochondrial membrane (eukaryotes).

• Carrier molecules (flavoproteins, cytochromes, ubiquinones) are oxidized/reduced as electrons are passed down the chain.

• Energy released is used to produce ATP by chemiosmosis.

• Final electron acceptor is oxygen (O2), forming water.

ATP Yield Table

Source	Electron Carrier	ATP Yield (Method)
Glycolysis	2 NADH	2 ATP (substrate-level phosphorylation)
Transition Step	2 NADH	2 GTP (equivalent to 2 ATP)
Krebs Cycle	6 NADH, 2 FADH2	2 ATP (substrate-level phosphorylation)
Electron Transport Chain	10 NADH, 2 FADH2	34 ATP (oxidative phosphorylation)

Total ATP yield per glucose (prokaryotic aerobic respiration): 38 ATP

Fermentation

• Occurs when final electron acceptor is not oxygen.

• Produces ATP via substrate-level phosphorylation only.

Types of Fermentation

Type	Products	Applications
Lactic Acid Fermentation	Lactic acid, ATP	Cheese, yogurt, food products
Alcoholic Fermentation	ATP, ethanol	Alcoholic beverages

Industrial Uses of Fermentation

Fermentation End-Product(s)	Industrial/Commercial Use	Starting Material	Microorganism
Ethanol	Beer, wine, fuel	Starch, sugar	Saccharomyces cerevisiae
Acetic Acid	Vinegar	Ethanol	Acetobacter
Lactic Acid	Cheese, yogurt	Milk	Lactobacillus, Streptococcus
Propionic Acid & CO2	Swiss cheese	Milk	Propionibacterium freudenreichii
Acetone & Butanol	Pharmaceuticals, industrial uses	Molasses	Clostridium acetobutylicum
Citric Acid	Food, pharmaceuticals	Molasses	Aspergillus niger
Methane	Fuel	Acetic acid	Methanobacterium
Sorbitol	Vitamins	Glucose	Gluconobacter

Catabolism of Various Organic Molecules

• Lipids are broken down into fatty acids, converted to Acetyl CoA, and enter the Krebs cycle.

• Proteins are degraded by extracellular proteases and peptidases into amino acids.

• Amino acids are deaminated, decarboxylated, and desulfurized to enter the Krebs cycle.

Biochemical Tests

• Identify bacteria by detecting enzymes.

• Fermentation test: Detects acid/gas production from carbohydrate/protein catabolism.

• Oxidase test: Identifies bacteria producing cytochrome c oxidase (e.g., Pseudomonas).

Photosynthesis

• Light energy and CO2 are converted to glucose and O2.

• Used by bacteria, protists, and plants.

• Two steps:

  • Light-dependent reactions (light reactions)

  • Light-independent reactions (dark reactions, Calvin Cycle)

Light Dependent Reactions

• Convert light energy into chemical energy (ATP and NADPH).

• Utilize chlorophyll as electron source.

• Electron transport chain produces ATP.

• Starting products: light and water; ending products: oxygen, ATP, NADPH.

Light-independent Reaction (Calvin Cycle)

• Do not require light.

• Starting products: CO2, 3 ATP, 6 NADPH.

• Ending products: 6 ATP (Net 3), 6 NADP+, glucose.

Nutritional Types of Microorganisms

Nutritional Type	Energy Source	Carbon Source	Example
Photoautotroph	Light	CO2	Cyanobacteria, plants
Photoheterotroph	Light	Organic compounds	Green bacteria, purple nonsulfur bacteria
Chemoautotroph	Inorganic chemical	CO2	Iron-oxidizing bacteria
Chemoheterotroph	Chemical	Organic compounds	Animals, protozoa, fungi, bacteria

Biosynthesis Pathways

Polysaccharides

• Glucose is converted to glycogen (in bacteria and animals) and peptidoglycan (in bacteria).

Simple Lipids

• Glycerol and fatty acids are synthesized from intermediates of glycolysis and the Krebs cycle.

Amino Acids

• Synthesized via pentose phosphate pathway, Krebs cycle, and Entner-Doudoroff pathway.

Purine and Pyrimidine Nucleotides

• Synthesized from intermediates of glycolysis and the pentose phosphate pathway.

Integration of Metabolism

• Amphibolic pathways: Pathways that function in both anabolism and catabolism.

• Many pathways function simultaneously with common intermediates.

Additional info: These notes provide a comprehensive overview of microbial metabolism, including enzymatic function, metabolic pathways, energy production, and biosynthetic processes, suitable for college-level microbiology students.