Microbiology
October 2, 2026
Microbiology Key Terms by Unit
A unit-by-unit glossary of the key microbiology terms and definitions, from microscopy and cell structure to genetics, drugs, immunity and disease.
Microbiology is a vocabulary-heavy course. Most exam questions are really asking whether you can tell two similar terms apart, so the fastest way to improve is a clean list of definitions you can test yourself on. This glossary follows the order of the units in Encodr's free Microbiology deck , and every definition comes from the deck's chapter notes. Use it as a checklist: cover the right-hand column, say the definition aloud, then check.
Foundations and microscopy
Term Definition Binomial nomenclature Naming by Genus species: genus capitalized, species lowercase, both italicized; abbreviated to the first letter after first use (E. coli) Three-domain system Bacteria, Archaea and Eukarya (Woese and Fox, using rRNA gene comparison); the first two are prokaryotic Resolution The ability to distinguish two points as separate; better with shorter wavelength and higher numerical aperture Differential stain Uses multiple dyes or steps so different organisms or structures end up different colors Gram stain Crystal violet, Gram's iodine mordant, decolorizer, safranin counterstain; gram-positive is purple and gram-negative is pink or red Acid-fast stain Carbolfuchsin resisted by waxy walls (Mycobacterium); acid-fast cells are red or pink, others blue Koch's postulates Four criteria linking a specific microbe to a specific disease
The microbial cell
Term Definition Peptidoglycan Alternating NAG and NAM subunits cross-linked by peptide bridges into a mesh forming the bacterial wall Lipopolysaccharide (LPS) Component of the gram-negative outer membrane that acts as endotoxin Glycocalyx Capsule (organized, tightly attached, resists phagocytosis) or slime layer (loosely attached) Endospore Dormant, highly resistant structure that protects the genome in unfavorable conditions Plasmid Small extrachromosomal, typically circular DNA, often carrying antibiotic resistance genes Nucleoid Region of cytoplasm holding the circular, haploid prokaryotic chromosome, with no nuclear membrane Plasmolysis Membrane detaching from the wall in a hypertonic environment Fimbriae and pili Fimbriae are short and numerous, for attachment; F pili mediate DNA transfer in conjugation
Prokaryotic diversity
Term Definition Proteobacteria Five classes (Alpha through Epsilon); Gamma is the most diverse Spirochetes Long, thin, spiral and motile via axial filaments (Treponema, Borrelia) Cyanobacteria Oxygenic photosynthesizers; heterocysts fix nitrogen Methanogens Archaea that reduce CO2 with H2 to produce methane Mutualism, commensalism, parasitism Both benefit; one benefits and the other is unaffected; one benefits and the other is harmed Nitrogen fixation Converting atmospheric N2 into usable ammonia
Eukaryotic microbes
Term Definition Yeast and mold Yeasts are unicellular and bud; molds are multicellular, built from hyphae forming a mycelium Dimorphic fungus Grows as yeast or mold depending on the environment Mycosis A fungal infection Lichen A fungus living symbiotically with a green alga or cyanobacterium Trophozoite and cyst The active, feeding protozoan form and the dormant, protective form Helminth A parasitic worm: nematode, trematode (fluke) or cestode (tapeworm)
Acellular pathogens
Term Definition Virion A nucleic acid genome (DNA or RNA, never both) inside a protein capsid Lytic cycle Attachment, penetration, biosynthesis, maturation, release; kills the host Lysogenic cycle Phage genome integrates as a prophage and is copied passively without killing the host Induction A stressor such as UV triggers a prophage to excise and switch to the lytic cycle Plaque assay Phage lysis of bacteria in a soft-agar lawn leaves clear plaques Viroid, virusoid, prion Naked circular RNA; ssRNA needing a helper virus; infectious misfolded protein with no nucleic acid
Microbial biochemistry
Term Definition Glycosidic bond Links monosaccharides into disaccharides and polysaccharides by dehydration synthesis Peptide bond Joins amino acids by dehydration synthesis Denaturation Destroys secondary and tertiary structure and function; primary sequence stays intact Amphipathic Having a hydrophobic tail and a hydrophilic head, as in a phospholipid Hopanoids, cholesterol, ergosterol Membrane-strengthening molecules of bacteria, eukaryotes and fungi/protozoa respectively MALDI-TOF Identifies an isolate by comparing its mass spectrum with a reference database
Microbial metabolism
Term Definition Anabolism and catabolism Building molecules (endergonic net) and breaking them down (exergonic net) Redox Oxidation removes electrons and reduction adds them; the two are always paired Glycolysis (EMP) Energy investment then payoff phases, converting glucose to 2 pyruvate Entner-Doudoroff pathway An alternative to EMP; Pseudomonas aeruginosa uses only this one Krebs cycle Amphibolic: extracts energy and supplies biosynthetic intermediates Fermentation Nets only 2 ATP per glucose, from glycolysis alone Oxygenic and anoxygenic photosynthesis Splits H2O releasing O2; uses H2S or thiosulfate releasing sulfur
Microbial growth and culture
Term Definition Binary fission Division in which FtsZ forms a Z ring, a divisome builds the septum and the cell splits Growth curve phases Lag, log (exponential), stationary and death Generation time Time for a population to double through one round of fission; a synonym of doubling time CFU/mL (Colonies counted x dilution factor) / volume plated; count only plates with 30-300 colonies Selective and differential media Selective inhibits unwanted organisms; differential visually distinguishes types Biofilm A cluster of microbes in a self-produced matrix (EPS) Quorum sensing Cells detect local density through autoinducers Obligate aerobe to microaerophile The five oxygen-requirement classes, along with obligate anaerobes, facultative anaerobes and aerotolerant anaerobes
The growth and counting formulas have their own guides: bacterial growth curve and generation time and serial dilutions and CFU calculations . The bacterial growth calculator checks your arithmetic.
Microbial genetics
Term Definition Central dogma DNA to RNA (transcription) to protein (translation) Codon A 3-nucleotide unit; 64 possible, 61 code for amino acids and 3 are stop codons Semiconservative replication Each daughter molecule keeps one old strand and one new strand Operon Structural genes plus a shared promoter and operator, transcribed as one polycistronic mRNA Inducible and repressible operon Normally off, needs an inducer (lac); normally on, needs a corepressor (trp) Transformation, transduction, conjugation Uptake of naked DNA; phage-mediated transfer; pilus-mediated transfer Missense, nonsense, frameshift Different amino acid; premature stop; insertion or deletion not divisible by 3
Applications of microbial genetics
Term Definition Restriction enzyme Cuts DNA at a specific, usually palindromic sequence, leaving sticky or blunt ends DNA ligase Seals the backbone nicks, joining insert to vector Blue-white screening White colonies carry an insert (disrupted lacZ); blue colonies are empty vector PCR Amplifies a target sequence by cycles of denaturation (~95 C), annealing (~50 C) and extension (~72 C) Taq polymerase Heat-stable DNA polymerase from Thermus aquaticus Gel electrophoresis Separates DNA by size; smaller fragments migrate farther Somatic and germ-line gene therapy Targets body cells, not inherited; targets reproductive cells or embryos
Control of microbial growth
Term Definition Sterilization Kills or removes all vegetative cells, endospores and viruses Disinfection Reduces microbial load on inanimate surfaces; endospores often survive Antisepsis Antimicrobial chemicals safe for living tissue -cidal and -static Kills; only inhibits growth D-value Time to produce a 90% reduction in a microbial population Autoclave 121 C (or 132 C), 15-20 psi, 20+ minutes; kills endospores Phenol coefficient Highest dilution of test agent killing in 10 but not 5 minutes, divided by the same for phenol
Antimicrobial drugs
Term Definition Selective toxicity Harming the pathogen while sparing host cells Narrow- and broad-spectrum Limited target range; wide range but higher superinfection risk MIC Lowest antibiotic concentration in a dilution series showing no visible growth MBC Lowest concentration that kills at least 99.9% of the original inoculum Kirby-Bauer test Disks on a bacterial lawn; zone of inhibition sorts isolates as susceptible, intermediate or resistant Beta-lactamase Enzyme that hydrolyzes the beta-lactam ring, inactivating the drug
Mechanisms of pathogenicity
Term Definition Pathogenicity and virulence Ability to cause disease; how severe that disease is Sign and symptom Objective, measurable evidence; subjective patient-reported experience Five disease periods Incubation, prodromal, illness, decline, convalescence Adhesin Pathogen surface molecule that binds host receptors to establish colonization Endotoxin and exotoxin Lipid A of LPS, gram-negative only; secreted proteins, mainly gram-positive Superantigen Toxin causing nonspecific T-cell activation and a cytokine storm Antigenic drift and shift Gradual point mutation; sudden segment reassortment behind pandemic flu strains
Disease and epidemiology
Term Definition Sporadic, endemic, epidemic, pandemic Occasional; constantly present at a low level; more cases than expected in a region; epidemic worldwide Prevalence and incidence Proportion with an illness at one time; proportion of new cases in a period Reservoir Where a pathogen persists: human, animal (zoonotic) or environmental Mechanical and biological vector The vector only carries the pathogen; the pathogen reproduces in the vector HAI Healthcare-associated infection Emerging and reemerging disease New to humans or sharply increased; increasing again after a decline
Innate immunity
Term Definition PAMP and PRR Pathogen-associated molecular pattern and the pattern recognition receptor (including Toll-like receptors) that detects it Phagocytosis steps Chemotaxis, adhesion, ingestion, fusion, destruction, exocytosis Cardinal signs of inflammation Erythema, edema, heat, pain, altered or lost function Complement pathways Classical, alternative and lectin, all ending in the membrane attack complex Interferon Type I (alpha/beta) protects neighbors of virus-infected cells; type II (gamma) activates other immune cells Pyrogen Substance that resets the hypothalamic thermostat higher, causing fever
Adaptive immunity
Term Definition Specificity and memory The two hallmarks of adaptive immunity Humoral and cellular immunity B cells making antibodies; T cells orchestrating and killing infected cells MHC I and MHC II On all nucleated cells, presenting intracellular antigen; on macrophages, dendritic cells and B cells, presenting exogenous antigen CD4 and CD8 T cells Helper T cells, activated through MHC II; cytotoxic T cells, activated through MHC I, killing with perforin and granzyme Immunoglobulin classes IgG, IgM, IgA, IgD and IgE Four immunity types Natural active, artificial active, natural passive and artificial passive Herd immunity Too few susceptible individuals remain for a disease to spread effectively
Immune disorders and testing
Term Definition Hypersensitivity types I to IV IgE-mediated immediate; antibody-mediated cytotoxic; immune-complex; T-cell-mediated delayed Autoimmune disease Loss of immune tolerance Autograft, isograft, allograft, xenograft Self; identical twin; nonidentical person; animal GVHD Donor immune cells attacking host tissue Agglutination Visible clumping when antibodies cross-link antigen-bearing cells or particles ELISA Enzyme-conjugated antibody converts a substrate to a visible signal Seroconversion The point at which antibody becomes detectable
Infectious diseases by body system
Term Definition Sepsis A body-wide inflammatory response to infection Arbovirus A virus transmitted by an arthropod vector Zoonosis A disease transmitted from animals to humans Meningitis and encephalitis Inflammation of the meninges; inflammation of the brain tissue itself Dermatophyte A fungus that infects keratinized tissue, causing tinea Koplik's spots Small white spots on the inner cheek, uniquely diagnostic of measles Dimorphic fungus Mold in the environment, yeast in the body
How to use this glossary
Reading a glossary is the weakest way to learn it. Instead, cover the definitions, say each one from memory, mark the ones you miss, and come back to those. Active recall beats passive review , and the Encodr deck schedules the repeats for you. Some pairs are worth comparing directly, for example gram-positive vs gram-negative bacteria and bacteria vs viruses vs fungi . For the plan behind it all, see how to study for microbiology and what's in microbiology .
Encodr turns this into a habit: study anything in a feed, and it schedules the rest.
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