Comprehensive Microbiology: Foundations, Biochemistry, Cell Biology, Microscopy, and Metabolism

Flashcard study set covering core vocabulary and foundational concepts from OpenStax Microbiology chapters on microbial metabolism, biochemistry, cell biology, microscopy, and history.

Metabolism

The complete set of all chemical reactions that occur inside a living cell, encompassing both catabolic and anabolic pathways.

Catabolism

Exergonic metabolic pathways that break down complex organic molecules into simpler compounds, releasing stored chemical energy.

Anabolism

Endergonic metabolic pathways involved in biosynthesis, assembling simple molecular building blocks into complex cellular molecules using cellular energy.

Autotroph

An organism that converts inorganic carbon dioxide ($\text{CO}_2$) into organic carbon compounds for nutrition and cellular structures.

Heterotroph

An organism that relies on complex organic carbon compounds provided initially by autotrophs as its source of nutrients.

Phototroph

An organism that obtains its energy for cellular work and electron transfer from light (sunlight).

Chemotroph

An organism that derives its energy for electron transfer by breaking the chemical bonds of chemical compounds.

Organotroph

A chemotroph that obtains high-energy electrons from organic compounds, such as glucose, proteins, or lipids.

Lithotroph

A chemotroph unique to the microbial world that extracts energy from inorganic molecules, such as hydrogen sulfide ($\text{H}_2\text{S}$) or reduced iron ($\text{Fe}^{2+}$).

Apoenzyme

An inactive protein component of an enzyme that requires an associated cofactor or coenzyme to become catalytically active.

Holoenzyme

An active enzyme formed by the binding of an apoenzyme to its necessary nonprotein cofactor or organic coenzyme.

Competitive Inhibitor

A regulatory molecule structurally similar to a substrate that competes for and blocks substrate binding directly at the enzyme's active site.

Noncompetitive (Allosteric) Inhibitor

A regulatory molecule that binds to an allosteric site rather than the active site, inducing a conformational change that reduces the enzyme's substrate affinity.

Feedback Inhibition

A regulatory mechanism where the end product of a metabolic pathway binds allosterically to an early enzyme in the pathway, slowing its own continued synthesis.

Embden-Meyerhof-Parnas (EMP) Pathway

The most common glycolytic pathway in animals and microbes, consuming $2\text{ ATP}$ in its investment phase to generate a net yield of $2\text{ ATP}$, $2\text{ NADH}$, and $2\text{ pyruvate}$ per glucose molecule.

Entner-Doudoroff (ED) Pathway

An alternate glycolytic pathway found in certain prokaryotes, including Pseudomonas aeruginosa and optionally Escherichia coli, used to catabolize glucose to pyruvate.

Pentose Phosphate Pathway (PPP)

An ancient, universal glycolytic pathway (hexose monophosphate shunt) that generates phosphorylated pentose intermediates for nucleotide and amino acid biosynthesis.

Substrate-Level Phosphorylation

A mechanism of ATP synthesis in which a high-energy phosphate group is directly transferred from a phosphorylated organic intermediate to ADP.

Oxidative Phosphorylation

The synthesis of ATP from ADP and inorganic phosphate ($\text{P}_i$) fueled by the potential energy stored within an electrochemical proton gradient generated across a membrane.

Proton Motive Force (PMF)

An electrochemical and pH gradient formed across a biological membrane by the selective pumping of hydrogen ions ($\text{H}^+$) by electron transport complexes.

Chemiosmosis

The flow of hydrogen ions down their electrochemical gradient across a membrane through ATP synthase to generate ATP.

ATP Synthase

A membrane-bound protein complex that functions like a molecular turbine, utilizing the downhill diffusion of protons ($\text{H}^+$) to phosphorylate ADP into ATP.

Fermentation

An anaerobic metabolic process that uses an organic molecule (commonly pyruvate) as the final electron acceptor to reoxidize NADH to $\text{NAD}^+$, producing no ATP beyond glycolysis.

Homolactic Fermentation

A type of lactic acid fermentation carried out by bacteria such as Lactobacillus delbrueckii and Streptococcus thermophilus where lactic acid is the sole fermentation product.

Heterolactic Fermentation

Fermentation that uses the branched pentose phosphate pathway to yield a mixture of lactic acid, ethanol, acetic acid, and $\text{CO}_2$, exemplified by Leuconostoc mesenteroides.

Alcohol Fermentation

A two-step fermentation pathway where pyruvate is decarboxylated by pyruvate decarboxylase to form acetaldehyde and $\text{CO}_2$, followed by reduction of acetaldehyde to ethanol by alcohol dehydrogenase.

$\beta$-Oxidation

The lipid catabolic process that sequentially cleaves two-carbon acetyl units from fatty acid chains, producing NADH, $\text{FADH}_2$, and acetyl-CoA for the Krebs cycle.

Calvin-Benson Cycle

The light-independent biochemical cycle occurring in chloroplast stroma or bacterial cytoplasm comprising three stages—fixation, reduction, and regeneration—to fix $\text{CO}_2$ into sugars.

RuBisCO

Ribulose bisphosphate carboxylase/oxygenase; the enzyme that catalyzes the initial fixation of $\text{CO}_2$ to ribulose bisphosphate (RuBP), composing $30\%\text{--}50\%$ of soluble protein in plant chloroplasts.

Nitrogen Fixation

The conversion of tightly bonded atmospheric triple-covalent nitrogen gas ($\text{N}_2$) into ammonia ($\text{NH}_3$), performed by free-living or symbiotic diazotrophic prokaryotes like Rhizobium.

Sulfur Cycle

The biogeochemical cycle in which prokaryotes oxidize hydrogen sulfide ($\text{H}_2\text{S}$) to elemental sulfur ($\text{S}^0$) and sulfate ($\text{SO}_4^{2-}$), or reduce sulfate in anaerobic respiration.

Bioremediation

The targeted use of microbial metabolism to degrade, remove, or neutralize environmental pollutants and xenobiotics either in situ (on-site) or ex situ (off-site).

Xenobiotics

Synthetic chemical compounds produced by human activities that are introduced into the natural environment at unnaturally high concentrations and typically resist microbial degradation.

Miller-Urey Experiment

A 1952 experiment that passed electric sparks through a simulated prebiotic atmosphere containing $\text{H}_2\text{O}$, $\text{CH}_4$, $\text{H}_2$, and $\text{NH}_3$, demonstrating the abiotic synthesis of amino acids.

Macronutrients

The six most abundant chemical elements in living cells (H, C, O, N, P, and S) that together account for approximately $99\%$ of the dry weight of a cell.

Structural Isomers

Compounds that share an identical chemical molecular formula (such as glucose, galactose, and fructose, $\text{C}_6\text{H}_{12}\text{O}_6$) but differ in the covalent bonding sequence of their atoms.

Enantiomers

Stereoisomers that are nonsuperimposable mirror images of one another due to molecular chirality, capable of rotating polarized light in opposite directions.

Dehydration Synthesis

A chemical reaction in which two monomers become covalently bonded together with the simultaneous loss of a water molecule ($\text{H}_2\text{O}$) as a reaction byproduct.

Glycosidic Bond

The covalent bond established between hydroxyl groups of two monosaccharide units formed during a dehydration synthesis reaction.

Phospholipid Bilayer Assemblies

Structures formed in aqueous environments by amphipathic phospholipids, where hydrophilic polar heads face outward toward water while hydrophobic tails orient inward away from water.

Isoprenoids (Terpenoids)

Branched lipid molecules formed by chemical modifications of five-carbon isoprene units that function as plant pigments, fragrances, and sebum components.

Hopanoids

Multiringed hydrophobic lipid compounds synthesized by bacteria that integrate into bacterial plasma membranes to reinforce membrane structural rigidity.

Peptide Bond

The covalent bond connecting the carboxylic acid group of one amino acid to the amino group of an adjacent amino acid, releasing water via dehydration synthesis.

Denaturation (Protein)

The loss of a protein's functional native secondary, tertiary, and quaternary three-dimensional conformations without breaking primary peptide bonds, induced by extreme pH or temperature.

FAME Analysis

Fatty acid methyl ester analysis; an identification technique where bacterial membrane fatty acids are extracted, converted into volatile methyl esters, and analyzed by gas chromatography.

MALDI-TOF Mass Spectrometry

A rapid diagnostic method that irradiates bacterial matrix preparations with pulsed UV laser light to separate gaseous ions by their mass-to-charge ($m/z$) ratio to produce a spectral fingerprint.

Alcanivorax borkumensis

A naturally occurring marine oil-eating bacterium whose population surged following the 2010 Deepwater Horizon oil spill to assist in biodegradation of petroleum hydrocarbons.

Antonie van Leeuwenhoek

A Dutch draper known as the 'Father of Microbiology' who in 1674 used simple, single-lens microscopes of high resolution to discover microscopic life ('animalcules').

Inoculation Loop

A handheld laboratory tool terminating in a small wire loop, used to aseptically streak microbes onto agar surfaces or transfer cultures between vessels.

Common Bacterial Shapes

The standard morphological classifications of prokaryotes: spherical (coccus), rod-shaped (bacillus), curved rod (vibrio), short rod (coccobacillus), rigid wave (spirillum), and loose helix (spirochete).

Taxonomy

The formal biological science encompassing the classification, description, identification, and naming of living organisms into standardized hierarchical groupings.

Binomial Nomenclature

A two-word scientific naming system established by Carolus Linnaeus identifying each organism by its capitalized genus name followed by its lowercase specific epithet.

Three-Domain Tree of Life

A phylogenetic classification system developed by Carl Woese and George Fox based on comparative small subunit ribosomal RNA (rRNA) gene sequences, establishing Archaea, Bacteria, and Eukarya.

Pseudopeptidoglycan (Pseudomurein)

A structural polymer comprising the cell walls of certain archaea that lacks N-acetylmuramic acid and D-amino acids found in bacterial peptidoglycan.

Helminths

Multicellular parasitic worms, including flukes, tapeworms, and nematodes, studied within microbiology because their diagnostic stages involve microscopic eggs and larvae.

Viruses

Acellular, ultramicroscopic infectious entities composed strictly of a protein capsid enclosing either DNA or RNA (never both) that require a host cell for replication.

Prions

Acellular infectious particles lacking nucleic acids, composed entirely of misfolded abnormal proteins that cause transmissible spongiform encephalopathies such as Creutzfeldt-Jakob disease.

Spontaneous Generation

The historical, now-disproven theory proposing that living organisms can arise spontaneously from nonliving matter containing vital 'pneuma' or 'life force'.

Biogenesis

The fundamental tenet of modern cell theory summarized as 'Omne vivum ex vivo' ('life only comes from life'), affirming that all living cells originate from preexisting cells.

Endosymbiotic Theory

The evolutionary theory asserting that eukaryotic mitochondria and chloroplasts originated when ancestral host cells engulfed aerobic and photosynthetic prokaryotes in endosymbiosis.

Germ Theory of Disease

The clinical principle established in the 19th century stating that specific human and animal diseases are caused by infections with microscopic pathogens.

Miasma Theory

An ancient medical paradigm asserting that infectious diseases originated from poisonous noxious mists or emanations ('bad air') rising from rotting organic matter and sewage.

Pneumonia

An inflammatory condition of the lungs where alveolar pockets become infiltrated with fluid and mucus, visible as radio-opaque white 'shadows' on chest X-rays.

Plasmolysis

The physiological shrinkage and detachment of the bacterial plasma membrane from its rigid cell wall when placed in a hypertonic environment due to water loss.

70S Ribosome

The sedimentation coefficient of prokaryotic, mitochondrial, and chloroplast ribosomes, each assembled from a small $30\text{S}$ subunit and a large $50\text{S}$ subunit.

Endospore

A dormant, highly resistant, dehydrated bacterial survival structure surrounded by a thick cortex and protein coat, produced by genera like Bacillus and Clostridium.

Bacterial Cell Wall Types

Distinct envelope architectures: Gram-positive walls feature thick peptidoglycan ($30\text{--}100\,\text{nm}$) rich in teichoic acids; Gram-negative walls feature thin peptidoglycan ($\approx 4\,\text{nm}$) and an outer membrane with lipopolysaccharide.

Lipopolysaccharide (LPS)

A complex endotoxin embedded in the outer leaflet of Gram-negative outer membranes, composed of toxic Lipid A, a core polysaccharide, and an antigenic O side chain.

Pili (Singular: Pilus)

Longer, less numerous proteinaceous appendages projecting from bacterial cell surfaces that mediate attachment to surfaces and facilitate conjugation via the F pilus (sex pilus).

Chemotaxis

Directional bacterial movement mediated by alternating counterclockwise flagellar rotation ('runs') and clockwise rotation ('tumbles') in response to environmental chemical gradients.

Golgi Apparatus

An endomembrane organelle made of stacked membranous cisternae (dictyosomes) that receives ER transport vesicles at its cis face, modifies glycoproteins, and buds secretory vesicles from its trans face.

9+2 Array

The characteristic eukaryotic microtubule arrangement in cilia and flagellar axonemes, consisting of nine outer doublet microtubules encircling a central singlet pair.

Refractive Index

A measure of the extent to which a transparent medium slows the transmission speed of light relative to empty space, governing the angle of light refraction.

Resolution

The capacity of a microscope lens to distinguish two closely spaced points or objects as distinct and separate entities, governed by light wavelength and numerical aperture.

Immersion Oil

A high-refractive-index oil placed between a microscope slide and a specialized $100\times$ objective lens to prevent light scattering caused by air-glass index differences.

Darkfield Microscope

A microscope featuring an opaque light stop below the condenser that blocks direct illumination, directing only scattered or reflected light into the objective to view living specimens.

Phase-Contrast Microscope

An optical microscope utilizing an annular condenser stop and an objective phase ring to exploit destructive interference, creating contrast in unstained living specimens.

Fluorochrome

A fluorescent dye molecule (such as FITC, DAPI, or Texas red) that absorbs high-energy short-wavelength excitation light and emits lower-energy, longer-wavelength visible light.

Scanning Probe Microscope

A class of non-optical microscopes (STM and AFM) that scan physical probes across a specimen's surface to construct atomic-level surface topographical images with magnifications up to $100,000,000\times$.

Gram Stain

A differential staining procedure utilizing crystal violet, Gram's iodine mordant, an alcohol decolorizer, and safranin counterstain to distinguish thick-walled Gram-positive cells (purple) from Gram-negative cells (pink).

Acid-Fast Stain

A differential staining protocol that uses carbolfuchsin and methylene blue to differentiate bacteria bearing waxy mycolic acid cell walls (red) from non-acid-fast cells (blue).

Schaeffer-Fulton Endospore Stain

A differential staining technique that applies heat to drive primary malachite green into dormant bacterial endospores, followed by water washing and vegetative counterstaining with pink safranin.