Microbial Metabolism: Study Guide and Key Concepts

Microbial Metabolism

Catabolism and Anabolism

Metabolic reactions in cells are broadly classified as catabolic (breaking down molecules to release energy) or anabolic (building complex molecules from simpler ones, requiring energy input).

• Catabolic reactions: Large molecules are broken down into smaller ones, releasing energy (often as ATP).

• Anabolic reactions: Small molecules are assembled into larger, more complex molecules, consuming energy.

• Linkage: The energy released from catabolism is used to drive anabolic reactions.

• Example: Glucose breakdown (catabolism) provides ATP for protein synthesis (anabolism).

Oxidation-Reduction (Redox) Reactions

Redox reactions involve the transfer of electrons between molecules, essential for energy transfer in metabolism.

• Oxidation: Loss of electrons from a molecule.

• Reduction: Gain of electrons by a molecule.

• Recognizing redox: In biological systems, often involves transfer of hydrogen atoms or addition/removal of oxygen.

• Example: In cellular respiration, glucose is oxidized and oxygen is reduced.

Carrier Molecules in Respiration

Cells use specific molecules to transfer electrons and energy during respiration.

• NAD+ (Nicotinamide adenine dinucleotide): Accepts electrons to become NADH.

• FAD (Flavin adenine dinucleotide): Accepts electrons to become FADH2.

• NADP+ (Nicotinamide adenine dinucleotide phosphate): Used mainly in anabolic reactions.

• When used: These carriers are reduced during glycolysis, Krebs cycle, and other metabolic pathways, then donate electrons to the electron transport chain.

Phosphorylation Methods

Cells generate ATP by adding phosphate groups to ADP through three main mechanisms:

• Substrate-level phosphorylation: Direct transfer of phosphate from a substrate to ADP (occurs in glycolysis and Krebs cycle).

• Oxidative phosphorylation: Uses energy from electron transport chain to add phosphate to ADP (occurs in cellular respiration).

• Photophosphorylation: Uses light energy to phosphorylate ADP (occurs in photosynthesis).

Enzymes: Structure, Function, and Specificity

Enzymes are biological catalysts that speed up chemical reactions without being consumed.

• Recognition: Enzyme names often end in "-ase" (e.g., streptokinase).

• Properties: Highly specific, increase reaction rates, function under mild conditions, can be regulated.

• How enzymes work: Lower activation energy by binding substrates at the active site, forming an enzyme-substrate complex.

• Example: Streptokinase digests fibrin clots but does not cause infection because it is not a whole bacterium, only the enzyme.

• Specificity: Each enzyme acts on a specific substrate due to the shape of its active site.

• Macromolecule type: Enzymes are proteins (some RNA molecules also have catalytic activity, called ribozymes).

• Substrate: The molecule upon which an enzyme acts.

Parts of an Enzyme

• Apoenzyme: The protein portion of an enzyme (inactive without cofactor).

• Cofactor: Non-protein component (e.g., metal ion or coenzyme) required for activity.

• Holoenzyme: The complete, active enzyme with its cofactor.

Factors Affecting Enzyme Activity

• Temperature: High temperatures can denature enzymes; low temperatures slow activity.

• pH: Extreme pH can denature enzymes or alter active site shape.

• Substrate concentration: Increased substrate increases activity up to a saturation point.

• Inhibitors: Chemicals that decrease enzyme activity.

Deamination

Deamination is the removal of an amino group from an amino acid, allowing the remaining molecule to enter energy-producing pathways.

Enzyme Inhibition

Enzyme activity can be regulated by inhibitors, which are classified as:

• Competitive inhibition: Inhibitor resembles substrate and binds to active site, blocking substrate.

• Noncompetitive inhibition: Inhibitor binds to an allosteric site, changing enzyme shape and reducing activity.

• Feedback inhibition (end-product inhibition): End product of a pathway inhibits an earlier enzyme, preventing overproduction.

• Need for inhibition: Prevents wasteful overproduction of products and conserves resources.

Glycolysis and Fermentation

• End-product of glycolysis: Pyruvate (pyruvic acid).

• Fermentation: Used when oxygen is absent or electron transport chain is not available; regenerates NAD+ for glycolysis.

Respiration Pathways

Respiration involves several pathways for energy extraction:

• Glycolysis: Glucose → Pyruvate; produces ATP and NADH.

• Krebs Cycle (Citric Acid Cycle): Pyruvate derivatives → CO2; produces ATP, NADH, FADH2.

• Electron Transport Chain (ETC): NADH/FADH2 donate electrons; produces most ATP via oxidative phosphorylation.

Respiration vs. Fermentation

• Respiration: Complete oxidation of glucose; high ATP yield; requires ETC.

• Fermentation: Incomplete oxidation; lower ATP yield; does not require ETC.

• Preference: Organisms prefer respiration due to higher energy yield.

Alternate Pathways to Glycolysis

• Pentose Phosphate Pathway: Generates NADPH and pentoses; used for biosynthesis.

• Entner-Doudoroff Pathway: Alternative to glycolysis in some bacteria; produces NADPH and ATP.

Catabolism of Fats and Proteins

• Fats: Broken down by beta-oxidation into acetyl-CoA, which enters Krebs cycle.

• Proteins: Deaminated to remove amino groups; carbon skeletons enter glycolysis or Krebs cycle.

• Order of use: Carbohydrates are used first, then lipids, then proteins.

Anabolic Reactions

• Requirements: Energy (usually ATP), reducing power (NADPH), and precursor metabolites.

• Photosynthesis: An important anabolic pathway using light energy to produce glucose and oxygen from CO2 and water.

Amphibolic Pathways

An amphibolic pathway is a metabolic pathway that functions in both catabolism and anabolism (e.g., glycolysis and Krebs cycle intermediates are used for both energy production and biosynthesis).

Pathway	Input	Output	Main Purpose
Glycolysis	Glucose	Pyruvate, ATP, NADH	Initial breakdown of glucose
Krebs Cycle	Acetyl-CoA	CO2, ATP, NADH, FADH2	Energy extraction from acetyl groups
Electron Transport Chain	NADH, FADH2, O2	ATP, H2O	Major ATP production
Pentose Phosphate Pathway	Glucose-6-phosphate	NADPH, Ribose-5-phosphate	Biosynthesis, reducing power
Entner-Doudoroff Pathway	Glucose	Pyruvate, NADPH, ATP	Alternative glycolysis in some bacteria

Key Equations

• ATP formation (substrate-level phosphorylation): $\mathrm{ADP} + \mathrm{P_i} \rightarrow \mathrm{ATP}$

• General redox reaction: $\mathrm{AH}_2 + \mathrm{B} \rightarrow \mathrm{A} + \mathrm{BH}_2$

• Glycolysis (overall): $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 2\ \mathrm{NAD}^+ + 2\ \mathrm{ADP} + 2\ \mathrm{P_i} \rightarrow 2\ \mathrm{C}_3\mathrm{H}_4\mathrm{O}_3 + 2\ \mathrm{NADH} + 2\ \mathrm{ATP} + 2\ \mathrm{H}_2\mathrm{O}$

Additional info: Some explanations and examples were expanded for clarity and completeness based on standard microbiology textbooks.