Comprehensive Microbial Metabolism, Genetics, Biotechnology, and Growth Review

300 vocabulary flashcards reviewing microbial metabolism, genetics, molecular microbiology, cell growth, and biotechnology from five lecture sources.

Nutrients

Supply of monomers or chemical precursors required by cells for growth and cellular function.

Macronutrients

Chemical elements and nutrients required by microorganisms in large amounts.

Micronutrients

Nutrients and trace elements required by microorganisms in small or trace amounts.

Carbon (C)

Major element present in all classes of biological macromolecules, constituting approximately $50\%$ of a typical bacterial cell by dry weight.

Heterotrophs

Organisms that require organic compounds as their primary source of carbon.

Autotrophs

Organisms that utilize carbon dioxide ($CO_2$) as their primary carbon source.

Nitrogen (N)

Key element found in proteins, nucleic acids, and cell wall constituents, making up about $13\%$ of a bacterial cell by dry weight.

Phosphorus (P)

Essential macronutrient required for the synthesis of nucleic acids and membrane phospholipids.

Sulfur (S)

Macronutrient contained in amino acids such as cysteine and methionine, as well as vitamins like thiamine, biotin, lipoic acid, and coenzyme A.

Potassium (K)

Macronutrient required as an enzymatic cofactor for several cellular enzymes.

Magnesium (Mg)

Macronutrient that stabilizes ribosomes, membranes, and nucleic acids, and is required for many enzymatic activities.

Calcium (Ca)

Macronutrient that helps stabilize microbial cell walls and plays a key role in the heat stability of bacterial endospores.

Sodium (Na)

Macronutrient specifically required by certain microbes, such as marine microorganisms.

Iron

Key micronutrient component of cytochromes and iron-sulfur ($Fe-S$) proteins involved in electron transport chains.

Growth Factors

Organic compounds required in small amounts by certain organisms, including vitamins, amino acids, purines, and pyrimidines.

Vitamins

The most commonly required growth factors, which mostly function as coenzymes in cellular metabolism.

Culture Media

Nutrient solutions prepared and used to grow microorganisms in the laboratory.

Defined Media

Culture media in which the precise chemical composition is known.

Complex Media

Culture media composed of digests of chemically undefined substances, such as yeast and meat extracts.

Enriched Media

Complex media supplemented with highly nutritious substances like blood or serum to cultivate nutritionally demanding (fastidious) organisms.

Selective Media

Culture media containing compounds that selectively inhibit the growth of some microbes while allowing others to grow.

Differential Media

Culture media containing an indicator, usually a dye, that detects particular chemical reactions occurring during growth.

Pure Culture

A culture that contains only a single strain or species of microorganism.

Contaminants

Unwanted microorganisms present within a culture.

Colonies

Visible, isolated masses of microbial cells formed on solid culture media derived from single cells or small clusters.

Metabolism

The sum total of all chemical reactions that occur within a cell.

Catabolism

Energy-releasing metabolic reactions that break down complex molecules.

Anabolism

Energy-consuming metabolic reactions involved in biosyntheses and building complex cell components.

Chemoorganotrophs

Organisms that obtain energy from the oxidation of organic chemicals.

Chemolithotrophs

Organisms that obtain energy from the oxidation of inorganic chemicals.

Phototrophs

Organisms that utilize light as their energy source.

Kilojoule ($kJ$)

The standard unit of heat energy used to measure bioenergetic changes in metabolic reactions.

Free Energy ($G$)

The energy released in a chemical reaction that is available to perform work.

$$\Delta G^{0'}$$

The change in free energy during a reaction calculated under standard conditions ($25\,^\circ\text{C}$, $1\,\text{atm}$, $pH\,7$).

Exergonic Reactions

Reactions with a negative $\Delta G^{0'}$ that release free energy.

Endergonic Reactions

Reactions with a positive $\Delta G^{0'}$ that require energy input to proceed.

Free Energy of Formation ($G_f^0$)

The energy released or required during the formation of a given molecule from its constituent elements.

Activation Energy

The minimum energy required to bring all molecules in a chemical reaction into the reactive state.

Catalyst

A substance that lowers the activation energy of a reaction and increases reaction rate without affecting reaction energetics or equilibrium.

Enzymes

Highly specific biological catalysts, typically proteins (or RNA molecules), that increase chemical reaction rates.

Active Site

The specific region of an enzyme that binds substrate molecules and carries out catalysis.

Prosthetic Groups

Small nonprotein molecules that bind tightly and usually covalently/permanently to enzymes to participate in catalysis.

Coenzymes

Loosely bound nonprotein organic molecules that participate in enzymatic reactions and are typically vitamin derivatives.

Oxidation-Reduction Reaction

Paired chemical reactions involving the loss of electrons (oxidation) by one substance and gain of electrons (reduction) by another.

Electron Donor

The substance oxidized in a redox reaction, which serves as the energy source.

Electron Acceptor

The substance reduced in a redox reaction by accepting electrons.

Reduction Potential ($E_0'$)

The inherent tendency of a substance to donate or accept electrons, expressed in volts ($V$).

Redox Tower

A conceptual vertical ranking of standard reduction potentials ($E_0'$) placing strongest electron donors at the top and strongest acceptors at the bottom.

$$NAD^+ / NADH$$

A ubiquitous redox coenzyme pair ($E_0' = -0.32\,V$) that shuttles two electrons and one proton between metabolic reactions.

Poly-$\beta$-hydroxybutyrate (PHB)

An insoluble lipid-like carbon and energy storage polymer produced by prokaryotes under excess carbon conditions.

Fermentation

Anaerobic catabolic process in which an organic compound serves as both electron donor and acceptor, generating ATP via substrate-level phosphorylation.

Respiration

Catabolic process where electron transport from an oxidized donor to an external acceptor generates a proton motive force that drives ATP synthesis.

Substrate-Level Phosphorylation

Direct synthesis of ATP through the transfer of a phosphate group from an energy-rich organic intermediate to ADP.

Oxidative Phosphorylation

Synthesis of ATP from ADP and inorganic phosphate driven by the dissipation of a proton motive force across a membrane.

Glycolysis (Embden-Meyerhof Pathway)

A major catabolic pathway consisting of three stages that breaks down glucose into two pyruvates, producing two ATP and two NADH.

Stage I of Glycolysis

The preparatory stage of glycolysis where glucose is phosphorylated using two ATP molecules to form fructose 1,6-bisphosphate.

Stage II of Glycolysis

The oxidation stage of glycolysis where 3-carbon intermediates yield four ATP and two NADH, ending in two pyruvate molecules.

Stage III of Glycolysis

The redox-balancing stage of fermentation where pyruvate is reduced by NADH to yield fermentation products and recycle $NAD^+$.

Aerobic Respiration

Respiration mechanism utilizing molecular oxygen ($O_2$) as the terminal electron acceptor.

Anaerobic Respiration

Respiration mechanism utilizing electron acceptors other than oxygen (such as $NO_3^-$, $SO_4^{2-}$, or $Fe^{3+}$) under anoxic conditions.

Electron Transport System

A membrane-bound chain of electron carriers arranged in order of increasingly positive reduction potential that pumps protons out of the cell.

Quinones ($Q$)

Nonprotein, hydrophobic, lipid-soluble electron carriers that move freely within the cytoplasmic membrane.

Cytochromes

Membrane-bound proteins containing iron-bearing heme prosthetic groups involved in single-electron transport.

Flavoproteins

Enzymes containing flavin prosthetic groups (such as FMN or FAD) that accept two electrons and two protons.

Iron-Sulfur ($Fe-S$) Proteins

Non-heme iron proteins containing clusters of iron and sulfur atoms that carry electrons only.

NADH Dehydrogenase

Membrane-bound enzyme complex that accepts electrons and protons from NADH and transfers electrons to flavoproteins.

Proton Motive Force (PMF)

An electrochemical potential and pH gradient established across the cytoplasmic membrane during electron transport.

ATP Synthase (ATPase)

A reversible multiprotein membrane complex that utilizes proton motive force dissipation ($3\,H^+$ per ATP) to synthesize ATP from ADP and $P_i$.

$F_1$ Component of ATP Synthase

The multi-subunit extramembrane catalytic domain of ATP synthase located on the cytoplasmic side of the membrane.

$F_0$ Component of ATP Synthase

The proton-conducting intramembrane channel complex of ATP synthase.

Citric Acid Cycle (TCA / Krebs Cycle)

Cyclic pathway in which pyruvate is completely oxidized to $CO_2$, generating NADH, $FADH_2$, GTP/ATP, and key biosynthetic precursors.

$\alpha$-Ketoglutarate

A 5-carbon citric acid cycle intermediate that serves as the precursor for the glutamate family of amino acids.

Oxaloacetate (OAA)

A 4-carbon citric acid cycle intermediate that condenses with acetyl-CoA and serves as a precursor for aspartate family amino acids and phosphoenolpyruvate.

Succinyl-CoA

A 4-carbon citric acid cycle intermediate required for the biosynthesis of cytochromes, chlorophylls, and other tetrapyrroles.

Acetyl-CoA

A 2-carbon energy-rich thioester compound that enters the citric acid cycle and serves as the starting unit for fatty acid synthesis.

Gluconeogenesis

The biosynthetic synthesis of glucose-6-phosphate from phosphoenolpyruvate ($PEP$) by reversing glycolysis steps.

Pentose Phosphate Pathway

A metabolic pathway that converts hexoses into 5-carbon sugars (pentoses) and NADPH needed for nucleic acid and fatty acid synthesis.

Ribose 5-Phosphate

A 5-carbon sugar intermediate generated via the pentose phosphate pathway that forms the sugar backbone of nucleotides.

Glutamine Synthetase

A key enzyme that assimilates inorganic ammonia ($NH_3$) into glutamate to form glutamine during nitrogen metabolism.

Transaminase

An enzyme that transfers amino groups from an amino donor molecule to a keto-acid precursor during amino acid biosynthesis.

Acyl Carrier Protein (ACP)

A carrier protein that holds the growing fatty acid chain during its step-by-step assembly.

Palmitate

A 16-carbon saturated fatty acid synthesized in cells through repetitive additions of malonyl-ACP units.

Aerobic Respiration Net Yield

The maximum theoretical yield of $38\text{ ATP}$ generated per glucose molecule oxidized through glycolysis and the citric acid cycle.

Complex I (NADH:Ubiquinone Oxidoreductase)

An electron transport complex that oxidizes NADH, transfers two electrons to quinone, and pumps four protons across the membrane.

Complex II (Succinate Dehydrogenase)

A citric acid cycle enzyme and membrane complex that transfers electrons from succinate to quinone without pumping protons.

Photosynthesis

The biological conversion of light energy into chemical energy to drive cellular metabolism.

Chlorophylls

Light-sensitive magnesium-porphyrin pigments required for oxygenic photosynthesis in plants, algae, and cyanobacteria.

Bacteriochlorophylls

Light-absorbing photosynthetic pigments specific to anoxygenic phototrophic bacteria.

Oxygenic Photosynthesis

Photosynthesis in which water ($H_2O$) serves as the electron donor, resulting in the evolution of molecular oxygen ($O_2$).

Anoxygenic Photosynthesis

Photosynthesis that does not produce oxygen, utilizing alternative electron donors such as $H_2S$, $S^0$, or $Fe^{2+}$.

Reaction Center

A photosynthetic membrane complex containing special chlorophyll/bacteriochlorophyll pairs directly involved in light-driven charge separation.

Antenna Pigments

Light-harvesting complexes that absorb photons and transfer excitation energy via resonance energy transfer to the reaction center.

Thylakoids

Internal membrane systems containing photosynthetic pigments, reaction centers, and electron transport chains.

Stroma

The matrix fluid surrounding thylakoids inside eukaryotic chloroplasts where carbon fixation reactions occur.

Cyclic Photophosphorylation

Light-driven electron flow in anoxygenic phototrophs where electrons travel in a closed circuit to generate a proton motive force without net reductant consumption.

Reverse Electron Transport

Energy-consuming movement of electrons against the thermodynamic gradient driven by PMF to generate NADH in purple phototrophs.

Photosystem II ($PSII$)

The photosystem in oxygenic phototrophs that oxidizes water to generate $O_2$ and donates electrons to the quinone pool.

Photosystem I ($PSI$)

The photosystem in oxygenic phototrophs that absorbs light to generate low-potential electrons used to reduce $NADP^+$ to NADPH.

Noncyclic Photophosphorylation

Unidirectional electron flow in the Z-scheme of oxygenic photosynthesis from $H_2O$ through PSII and PSI to $NADP^+$.

Calvin Cycle

The primary autotrophic carbon fixation pathway that converts $CO_2$ into fructose-6-phosphate using ATP, NADPH, RubisCO, and phosphoribulokinase.