Microbial Metabolism and Energetics

Vocabulary practice flashcards covering microbial nutrition classes, catabolic pathways (glycolysis, Entner-Doudoroff, pentose phosphate, TCA cycle), cellular respiration, fermentation, and lipid and amino acid catabolism.

Catabolism

The metabolic breakdown of complex molecules into smaller, simpler ones, releasing energy that is harnessed for cellular work or released as heat.

Anabolism

The metabolic process that requires energy input to synthesize complex cellular molecules from simpler precursors.

Autotroph vs. Heterotroph

Autotrophs use carbon dioxide ($CO_2$) as their sole or principal biosynthetic carbon source, whereas heterotrophs utilize reduced, preformed organic molecules from other organisms.

Phototroph vs. Chemotroph

Phototrophs capture light energy, whereas chemotrophs obtain energy from the oxidation of organic or inorganic chemical compounds.

Lithotroph vs. Organotroph

Lithotrophs use reduced inorganic molecules as their electron donors, while organotrophs extract electrons from organic molecules.

Photolithoautotroph

An organism that uses carbon dioxide ($CO_2$) as its carbon source, light as its energy source, and inorganic compounds as electron donors.

Chemoorganoheterotroph

A nutritional class that utilizes organic molecules simultaneously as carbon, energy, and electron sources; includes most nonphotosynthetic pathogens.

Photoorganoheterotroph

An organism that uses organic carbon for growth, light for energy, and organic electron donors (for example, purple nonsulfur bacteria).

Chemolithoautotroph

An organism that utilizes carbon dioxide ($CO_2$) as its carbon source and reduced inorganic compounds as electron donors.

Major Microbial Energy-Yielding Pathways

The three primary nutritional pathways for generating chemical energy: phototrophy (using light), chemoorganotrophy (using organic compounds), and chemolithotrophy (using inorganic compounds).

Aerobic Respiration

A respiratory catabolic pathway that uses oxygen ($O_2$) as an exogenous terminal electron acceptor.

Anaerobic Respiration

A respiratory process that uses an exogenous terminal electron acceptor other than oxygen, such as $NO_3^-$, $SO_4^{2-}$, or $CO_2$.

Fermentation

An anaerobic metabolic pathway that uses an endogenous electron acceptor (such as pyruvate or a derivative) rather than an exogenous terminal acceptor, lacks an electron transport chain, relies solely on substrate-level phosphorylation, and leaves the substrate only partially oxidized.

Stage 1 of Aerobic Catabolism

The initial step of catabolism where polymeric nutrients are hydrolyzed into their constituent monomers, yielding little to no energy.

Amphibolic Pathway

A metabolic pathway that functions reversibly in both catabolic (degradative) and anabolic (biosynthetic) directions.

Classic Amphibolic Carbohydrate Pathways

Glycolysis (the Embden-Meyerhof pathway) and the Tricarboxylic Acid (TCA) cycle.

Embden-Meyerhof Glycolysis Equation

$$\text{Glucose} + 2\text{ADP} + 2P_i + 2\text{NAD}^+ \rightarrow 2\text{Pyruvate} + 2\text{ATP} + 2\text{NADH} + 2H^+$$

6-Carbon Phase of Glycolysis

The initial investment phase in which glucose is phosphorylated twice at the expense of $2\text{ ATP}$ molecules to produce fructose 1,6-bisphosphate.

3-Carbon Phase of Glycolysis

The energy-conserving phase where $4\text{ ATP}$ molecules are produced by substrate-level phosphorylation, yielding a net gain of $2\text{ ATP}$ per glucose molecule.

Cellular Site of Bacterial Glycolysis

The cytoplasmic matrix.

Pentose Phosphate Pathway Biosynthetic Products

NADPH (which provides reducing power for biosynthesis) and 4- and 5-carbon sugars (such as ribose-5-phosphate for nucleic acids).

Glyceraldehyde-3-Phosphate

The intermediate generated in the pentose phosphate pathway that can directly enter the Embden-Meyerhof glycolytic pathway to produce ATP.

2-Keto-3-deoxy-6-phosphogluconate (KDPG)

The unique identifying intermediate formed in the Entner-Doudoroff pathway.

Entner-Doudoroff Pathway Net Yield

$1\text{ ATP}$, $1\text{ NADH}$, and $1\text{ NADPH}$ per glucose molecule oxidized.

Entner-Doudoroff Pathway Microorganisms

Certain Gram-negative soil bacteria, such as Pseudomonas and Rhizobium, that utilize this pathway instead of classic glycolysis.

TCA Cycle Single-Turn Yield

$2\,CO_2$, $3\text{ NADH}$, $1\,FADH_2$, and $1\text{ GTP}$ (or ATP) per acetyl-CoA oxidized.

Total Reduced Coenzymes from Complete Glucose Oxidation

$10\text{ NADH}$ (2 from glycolysis, 2 from pyruvate transition, 6 from the TCA cycle) and $2\,FADH_2$ (from the TCA cycle).

Anabolic Function of the TCA Cycle

Supplying critical precursor carbon skeletons used for amino acid synthesis and other biosynthetic pathways.

Oxidative Phosphorylation Mechanism

The process by which electrons flow sequentially from carriers with more negative reduction potentials ($E_0'$) to those with more positive $E_0'$, releasing free energy that is used to pump protons across a membrane.

Theoretical P/O Ratios

The theoretical maximum yield of ATP per electron pair in mitochondrial oxidative phosphorylation: $3\text{ ATP}$ per NADH and $2\text{ ATP}$ per $FADH_2$.

Prokaryotic Electron Transport Chain Location

The plasma membrane.

bo Branch (Escherichia coli ETC)

An electron transport branch utilized during high aeration (log phase) that possesses moderate affinity for oxygen and functions as a proton pump.

bd Branch (Escherichia coli ETC)

An electron transport branch utilized under low oxygen concentrations or during stationary phase that has a very high oxygen affinity but does not pump protons.

Prokaryotic vs. Eukaryotic ETC Differences

Prokaryotic electron transport chains are typically branched, shorter, utilize different electron carriers, and generally have lower P/O ratios than the eukaryotic mitochondrial chain.

Chemiosmotic Hypothesis

The hypothesis proposing that ATP synthesis is driven directly by the proton motive force (PMF), which is established by an electrochemical and concentration gradient of protons across a membrane.

Proton Motive Force Secondary Functions

Directly powers bacterial flagellar rotation and active transport across the plasma membrane, independent of ATP synthesis.

$F_0$ and $F_1$ Subunits of ATP Synthase

$F_0$ functions as the membrane-embedded proton-conducting channel, while $F_1$ acts as the catalytic multiprotein complex facing the matrix or cytoplasm that synthesizes ATP.

Cyanide and Azide

Respiratory chain inhibitors that bind to electron carriers such as cytochrome $a/a_3$, blocking electron transfer to oxygen and arresting both respiration and proton translocation.

Piericidin

An antibiotic that inhibits the electron transport chain by specifically blocking electron transfer at coenzyme Q (CoQ).

Uncouplers

Compounds such as 2,4-dinitrophenol (DNP) that make lipid membranes permeable to protons, thereby dissipating the proton motive force as heat without synthesizing ATP.

Energy Yield of Anaerobic vs. Aerobic Respiration

Anaerobic respiration generates less ATP because alternate terminal electron acceptors (such as $NO_3^-$ or $SO_4^{2-}$) possess standard reduction potentials ($E_0'$) that are less positive than that of oxygen ($O_2$).

Denitrification

Dissimilatory nitrate reduction, an anaerobic respiratory process wherein nitrate ($NO_3^-$) is reduced to nitrite ($NO_2^-$) and sequentially converted to gaseous nitrogen forms ($N_2O$, $N_2$).

Agricultural Impact of Denitrification

Depletes nitrogen from agricultural soil by converting bioavailable forms into gaseous nitrogen ($N_2$), lowering overall soil fertility.

Paracoccus denitrificans

A soil bacterium that serves as a primary model organism for studying the genetics and biochemistry of bacterial denitrification.

Biochemical Purpose of Fermentation

To regenerate $\text{NAD}^+$ by re-oxidizing NADH, thereby maintaining a pool of electron acceptors required for continued glycolytic flux.

Homolactic vs. Heterolactic Fermentation

Homolactic fermenters reduce pyruvate almost exclusively to lactic acid, while heterolactic fermenters produce a mixture of lactic acid, ethanol, and $CO_2$.

Alcoholic Fermentation Pathway

A two-step pathway where pyruvate is first decarboxylated to acetaldehyde by pyruvate decarboxylase, followed by the reduction of acetaldehyde to ethanol by alcohol dehydrogenase.

Methyl Red Test

A microbiological test that detects mixed organic acids produced during mixed acid fermentation, which cause a significant decrease in culture pH.

Voges-Proskauer Test

A diagnostic test that identifies acetoin, an essential intermediate produced in the 2,3-butanediol fermentation pathway.

Stickland Reaction

The coupled anaerobic fermentation of an amino acid pair, where one amino acid is oxidized while the other serves as the electron acceptor.

Alanine-Glycine Stickland Reaction

A Stickland reaction in which alanine is oxidized to pyruvate/acetate, while two glycine molecules act as electron acceptors and are reduced to acetate.

Phosphorolysis

The phosphorolytic cleavage of reserve polysaccharides like glycogen to form glucose-1-phosphate directly without consuming an ATP molecule, preserving metabolic energy.

Poly-$\beta$-hydroxybutyrate (PHB) Catabolism

The enzymatic degradation of the bacterial intracellular storage polymer PHB into acetyl-CoA via 3-hydroxybutyrate.

Lipases

Extracellular or intracellular hydrolytic enzymes that cleave ester bonds in triglycerides to liberate glycerol and free fatty acids.

Glycerol Entry into Catabolism

Glycerol is phosphorylated and oxidized to form dihydroxyacetone phosphate (DHAP), which directly enters the glycolytic pathway.

$\beta$-Oxidation

A recurring catabolic pathway for fatty acids that removes a 2-carbon acetyl-CoA unit per turn while generating $1\,FADH_2$ and $1\text{ NADH}$.

Extracellular Proteases

Hydrolytic enzymes secreted by microbes to break down environmental proteins into small peptides and amino acids that are small enough to pass across the plasma membrane.

Deamination

The removal of an amino group from an amino acid, resulting in the release of ammonia ($NH_3$) and the generation of an organic keto acid.

Transamination

The enzymatic transfer of an amino group from an amino acid to an $\alpha$-keto acid acceptor, yielding a new amino acid and a corresponding keto acid.

Chemolithotrophic Energy Sources

Reduced inorganic molecules, including $H_2$, $H_2S$, $NH_4^+$, and $Fe^{2+}$, that donate electrons to an electron transport system.

Chemolithotrophic ATP Synthesis

Oxidative phosphorylation driven by a proton motive force that is established as electrons from inorganic donors travel through an electron transport chain.

Major Chemolithotrophic Bacterial Groups

Hydrogen-oxidizing bacteria, nitrifying bacteria, and sulfur-oxidizing bacteria.