Microbial Metabolism

Microbial Metabolism • Overview of metabolism (you should know about TCA cycle, Embden-Meyerhof pathway-glycolysis, Proton motive force etc.) • Overview of nutrition • Culture media • Energetics • Enzyme catalysis • Oxidation and reduction • Electron carriers • Energy conservation Metabolism Energy classes of microbes • microbes need three things to grow: – Energy source – Nutrients (C) – Suitable environmental conditions • Energy source – Phototroph (light) – Chemotroph (chemicals) • Chemoorganotroph (organic chemicals) • Chemolithoautotroph (inorganic chemicals) Macronutrients • • • • • • • • • • • Carbon (CO2 or organic compounds) Hydrogen (H2O or organic compounds) Oxygen (H2O or organic compounds) Nitrogen (NH3, NO3-, organic N-compounds) Phosphorus (PO43-) Sulfur (H2S, SO42-, organic compounds) Potassium (K+) Magnesium (Mg2+, salts) Sodium (Na+) Calcium (Ca2+, salts) Iron (Fe3+, Fe2+, or salts) Iron as a nutrient • Needed for aerobic metabolism (cytochromes, iron-sulfur proteins) • Insoluble under aerobic conditions – Fe(OH)3, FeOOH – Solubilized by siderophores Siderophore Iron uptake Micronutrients and growth factors • Micronutrients: Metals and metalloids – Generally not necessary to add to medium – Deficiencies can arise when medium constituents are very pure • Growth factors: organic requirements – Vitamins, amino acids, purines, pyrimidines, acetate Culture media • Defined: all chemicals are ostensibly known • Complex (undefined): contains substances with unknown chemistries, such as peptones, yeast extract, lake water, soil extract, etc Energetics • Gibbs Free-Energy (G) • Reaction has a free-energy change – Negative: exergonic – Positive: endergonic – Zero: equilibrium • Standard concentrations—tables of ΔGf°’ Redox Reactions • Reactions can be written as half-reactions – Oxidation: removal of electrons • S → P + e- or H2 → 2H+ + 2e- – Reduction: addition of electrons • S + e- → P or O2 + 4H+ + 4e- → 2H2O • Energetics of redox reactions can be considered as electrical potentials (see electron tower) Calculation of reaction energetics • First, must write balanced equation – E.g., 2H2 + O2 → 2H2O • Calculation of ΔG°’ for a reaction – ΔG°’ = ΔGf°’products - ΔGf°’reactants – ΔG°’ = x (-237.2 kJ/mol) – (2 x + 0) • Calculation of ΔG for a reaction – ΔG = ΔG°’ + RT x ln(k) Electron Tower • A redox reaction needs a reducing and oxidizing half-reaction • Reactions with stronger tendency to give up electrons are higher (more negative) on the tower • To determine which direction the reactions go, see which is “higher” on the electron tower • Note the position of important electron carriers (NAD, FAD, cytochrome a) and external electron donors/acceptors (H2, organic compounds, O2) Chemical kinetics and enzyme catalysis Electron carriers: NAD NAD+ as co-enzyme NADH as co-enzyme NAD as electron carrier • NAD+ + ED → EDox + NADH • NADH + EA → EAred + NAD+ • Overall reaction: – ED +EA → EDox + EAred High-energy compounds • ATP is the energy currency of the cell – High energy released when phosphate is hydrolyzed (ATP, ADP, AMP) • Acetyl phosphate • Acetyl coenzyme A • Phospho-enol pyruvate Modes of E Conservation-ATP • Fermentation: in which redox reaction ocurs WITHOUT a terminal electron acceptor (couple oxiation with subsequent reduction of an organic product generated from initial substrate) • Respiration: in which O2 or another oxidant serves as an electron acceptor MORE Modes of E generation • Anaerobic Respiration • Chemolitho(auto)trophy • Photo(auto)trophy • WHAT DO ALL THESE HAVE IN COMMON? Overview of fermentation