Lecture 3: Microbial Metabolism

Metabolism

The total sum of all chemical reactions in a cell that provide energy (ATP) and materials for growth, repair, and survival; includes catabolism and anabolism.

Catabolism

The breakdown of larger molecules into smaller ones, releasing energy (exergonic reactions).

Anabolism

The building of complex molecules from simpler ones, requiring energy (endergonic reactions).

ATP (Adenosine Triphosphate)

The universal energy currency of cells; energy is released when its third phosphate bond breaks.

Metabolic Pathway

A series of enzyme-controlled reactions that convert a starting molecule into a final product.

Enzyme

Protein catalyst that speeds up a chemical reaction by lowering activation energy without being consumed.

Activation Energy

The minimum energy needed for a reaction to begin; lowered by enzymes.

Substrate

The specific reactant that an enzyme binds to and acts upon.

Factors affecting enzyme activity

Amount of enzyme or substrate, temperature, pH, salt concentration, presence of cofactors or inhibitors.

Denaturation

Loss of an enzyme's proper shape due to heat, pH, or salt changes; causes loss of function.

Cofactor

A non-protein helper (metal ion or organic molecule) required by some enzymes for activity.

Coenzyme

An organic cofactor, usually a vitamin derivative such as NAD⁺, FAD, or Coenzyme A.

Apoenzyme

The inactive enzyme alone, without its cofactor.

Holoenzyme

The active enzyme formed when the apoenzyme binds its cofactor.

Examples of inorganic cofactors

Mg²⁺, Zn²⁺, Fe²⁺, Cu²⁺.

Examples of organic cofactors (coenzymes)

NAD⁺ (from niacin B₃), FAD (from riboflavin B₂), Coenzyme A (from pantothenic acid B₅).

Redox Reaction

A reaction involving electron transfer; one substance is oxidized (loses electrons) and another is reduced (gains electrons).

NAD⁺ / NADH

Electron carrier; NAD⁺ (oxidized) → NADH (reduced) when it gains electrons and hydrogen.

FAD / FADH₂

Electron carrier; FAD (oxidized) → FADH₂ (reduced) when it gains two electrons and two hydrogens.

Enzyme inhibition

Molecules that slow or stop enzyme activity by binding to the enzyme.

Competitive inhibition

Inhibitor binds to the enzyme's active site, blocking the substrate.

Allosteric inhibition

Inhibitor binds to another site, changing enzyme shape and preventing substrate binding.

Reversible inhibition

Inhibitor can detach and enzyme activity returns.

Irreversible inhibition

Inhibitor permanently disables enzyme (e.g. poisons).

Glycolysis

Catabolic pathway converting glucose → 2 pyruvate + 2 ATP + 2 NADH; occurs in cytoplasm without oxygen.

Glucose oxidation in glycolysis

Glucose is oxidized (loses electrons) while NAD⁺ is reduced to NADH.

Embden-Meyerhof Pathway

Most common glycolytic route; used by yeast and lactic acid bacteria.

Pentose Phosphate Pathway (HMP)

Produces NADPH and pentose sugars for DNA/RNA; used by facultative anaerobes like E. coli.

Entner-Doudoroff Pathway

Alternative glycolysis in some Gram-negative bacteria; yields 1 ATP + 2 ethanol + 2 CO₂.

Phosphoketolase Pathway

Found in some lactic acid bacteria; yields 1 lactate + 1 ethanol + 1 CO₂ + 1 ATP; important in dairy fermentation.

Fermentation

Energy-yielding process that regenerates NAD⁺ from NADH without oxygen.

Lactic acid fermentation

Produces lactic acid; used by Streptococcus and Lactobacillus species.

Mixed acid fermentation

Used by Escherichia coli; produces acids, gases, and alcohols.

2,3-Butanediol fermentation

Used by Enterobacter aerogenes; produces neutral end-products.

Facultative anaerobes

Organisms that can grow with or without oxygen; switch between aerobic respiration and fermentation (e.g. E. coli).

Respiration

Process where electrons are transferred through an electron transport chain to produce ATP; may be aerobic or anaerobic.

Chemiosmosis

Process where electron transport creates a proton (H⁺) gradient across a membrane; flow of H⁺ through ATP synthase generates ATP.

Autotrophs

Organisms that make their own organic molecules from CO₂.

Heterotrophs

Organisms that require pre-formed organic molecules for carbon and energy.

Photoautotrophs

Use light energy to convert CO₂ into organic compounds (photosynthesis).

Chemoautotrophs

Use chemical reactions as their energy source to fix CO₂.

Thylakoid membrane

Membrane inside chloroplasts where light reactions of photosynthesis occur; contains chlorophyll pigments.

Stroma

The fluid surrounding thylakoids in chloroplasts where the Calvin cycle (dark reactions) occurs.

Light-dependent reactions (photophosphorylation)

Light energy excites electrons in chlorophyll; electrons pass through carriers to form ATP and NADPH; oxygen is released when water is split.

Dark reactions (Calvin cycle)

Use ATP and NADPH to fix CO₂ into carbohydrates such as glucose.

Oxygenic photosynthesis

Photosynthesis that splits water to release O₂; occurs in cyanobacteria and chloroplasts using PSII and PSI.

Anoxygenic photosynthesis

Photosynthesis without oxygen production; uses H₂S or other donors; occurs in green and purple bacteria.

Photosystem II (PSII)

First photosystem in the thylakoid membrane; absorbs light, splits water into O₂, H⁺, and electrons; produces ATP.

Photosystem I (PSI)

Second photosystem; re-energizes electrons to reduce NADP⁺ → NADPH.

Oxygenic photosynthesis and light stage

O₂ is produced during the light-dependent stage when water is split at PSII.

Precursor of sugars

A molecule that serves as the starting material to build sugars; e.g. phosphoglyceric acid (PGA) or hexose phosphate.

Summary of key redox pairs

NAD⁺/NADH and FAD/FADH₂ carry electrons in metabolic pathways and must be recycled for metabolism to continue.