Microbiology: Structure, Taxonomy, and Microscopy

Vocabulary flashcards covering key terms and concepts from microscopy, bacterial taxonomy, and prokaryotic cell biology.

Focal length ($f$)

The distance between the center of a lens and its focal point ($F$); a short focal length provides higher magnification.

Transmission electron microscope

An electron microscope that uses an electron beam and electromagnets to examine the internal structures of microorganisms, magnifying up to 500 000X.

Scanning electron microscope

An electron microscope that uses an electron beam and electromagnets to examine the surfaces of objects.

Bright-Field Microscope

A compound microscope that produces a dark image against a brighter background by passing light directly through the specimen.

Dark-Field Microscope

A microscope that produces a bright image of the object against a dark background, commonly used to observe living, unstained preparations.

Phase-Contrast Microscope

A microscope that enhances contrast between intracellular structures with slight differences in refractive index without requiring staining.

Fluorescence Microscope

A microscope that exposes specimens to ultraviolet, violet, or blue light and shows a bright image formed by light emitted from fluorochrome-stained specimens.

Refractive index

A measure of how greatly a substance slows the velocity of light.

Resolution

The ability of a lens to separate or distinguish small objects that are close together.

Heat fixing

A fixation technique that preserves overall cell morphology and firmly attaches the organism to a slide by killing it, though internal structures are not preserved.

Chemical fixing

A fixation technique that protects fine cellular substructure and the morphology of larger, more delicate organisms.

Chromophore

Chemical groups with conjugated double bonds that impart color to a dye.

Basic dyes

Dyes possessing positive charges (such as crystal violet, methylene blue, basic fuchsin, safranin, and malachite green) that bind to negatively charged cellular components.

Acid dyes

Dyes containing negatively charged groups ($-COOH$), such as eosin, rose bengal, and acid fuchsin.

Gram staining

A differential staining procedure developed in 1884 by Christian Gram that divides bacteria into Gram-positive and Gram-negative groups based on cell wall structure.

Mordant

A substance (such as Gram's iodine) that intensifies color by increasing the interaction between the primary stain and the specimen.

Acid-fast staining

A differential stain requiring heat that uses carbol fuschin to identify organisms with thick waxy cell walls high in lipid content, such as Mycobacterium tuberculosis and Mycobacterium leprae.

Schaeffer-Fulton stain

An endospore staining method requiring heat to penetrate the cell wall, rendering bacterial endospores green and vegetative cells red.

Negative staining

A technique that stains the background while leaving cells and capsules colorless, allowing visualization of bacterial morphology without cell distortion.

Taxonomy

The science of biological classification consisting of classification, nomenclature, and identification.

Classification

The arrangement of organisms into groups (taxa) based on mutual similarities or evolutionary relationships.

Nomenclature

The branch of taxonomy concerned with assigning names to taxonomic groups.

Identification

The process of determining whether a particular isolate belongs to a recognized taxon.

Species (prokaryotic)

A collection of strains that have a similar G+C composition and 70\text{\rule{0pt}{0pt}\text{\textpercent}} or greater similarity.

Strain

A population of organisms distinguishable phenotypically from at least some other populations.

Genus

A well-defined group of one or more species that is clearly separate from other genera.

Binomial System

The naming system created by Carolus Linnaeus where each organism receives a two-part Latinized, italicized name consisting of a capitalized genus name and an uncapitalized specific epithet.

Phenetic system

A classification system that groups organisms together based on mutual similarity of their phenotypic characteristics.

Phylogenetic system

A classification system that groups organisms together based on probable evolutionary relationships rather than general resemblance.

Bergey's Manual of Systematic Bacteriology

A foundational bacterial taxonomy reference that used a phenetic system in its 4-volume 1st edition and a phylogenetic system in its 5-volume 2nd edition.

Cocci

Roughly spherical bacterial cells that may occur in pairs (diplococci), chains (streptococci), grape-like clusters (staphylococci), squares of 4 (tetrads), or cuboidal packages of 8.

Bacilli

Rod-shaped bacterial cells.

Coccobacilli

Very short, rod-shaped bacterial cells.

Vibrios

Curved rod-shaped bacterial cells.

Spirilla

Rigid, helical bacterial cells.

Spirochetes

Flexible, helical bacterial cells.

Pleomorphic

Organisms that naturally vary in shape.

Mycelium

A network of long, multinucleate filaments produced by certain prokaryotes like Actinomyces.

Fluid mosaic model

A model of cell membrane structure depicting a lipid bilayer with embedded integral proteins and associated peripheral proteins.

Amphipathic lipids

Molecules having both polar, hydrophilic ends that interact with water and nonpolar, hydrophobic ends that are insoluble in water.

Peripheral proteins

Membrane proteins (20\text{--}30\text{\rule{0pt}{0pt}\text{\textpercent}} of total membrane proteins) that are loosely associated with the membrane, easily removed, and soluble in aqueous solutions.

Integral proteins

Membrane proteins (70\text{--}80\text{\rule{0pt}{0pt}\text{\textpercent}} of total membrane proteins) that are embedded within the lipid bilayer, difficult to remove, and insoluble in aqueous solutions.

Cytoplasmic Matrix

The substance inside the cell between the membrane and nucleoid that is 70\text{\rule{0pt}{0pt}\text{\textpercent}}\text{ H}_2\text{O} and packed with ribosomes and inclusion bodies.

70S ribosome

The prokaryotic ribosome responsible for protein synthesis, composed of protein and RNA, where S stands for Svedburg unit.

Nucleoid

An irregularly shaped, non-membrane-bound region in prokaryotes that contains the chromosome and consists of 60\text{\rule{0pt}{0pt}\text{\textpercent}}\text{ DNA}, 30\text{\rule{0pt}{0pt}\text{\textpercent}}\text{ RNA}, and 10\text{\rule{0pt}{0pt}\text{\textpercent}}\text{ proteins}.

Plasmids

Small, closed circular DNA molecules that replicate independently of the chromosome and carry non-essential genes that may confer selective advantages like drug resistance.

Gram-positive cell wall

A thick cell wall composed primarily of peptidoglycan and large amounts of teichoic acids, which provide rigidity to the cell.

Gram-negative cell wall

A cell wall consisting of a thin layer of peptidoglycan lacking peptide interbridges, enclosed by an outer membrane made of lipids, lipoproteins, and lipopolysaccharides (LPS).

Osmotic lysis

Cell swelling and rupture resulting from water entering the cell when exposed to a hypotonic solution.

Plasmolysis

Shrinkage of the cytoplasm away from the cell wall caused by water leaving the cell when exposed to a hypertonic solution.

Capsules

Well-organized polysaccharide layers outside the cell wall that are not easily removed and provide protection against phagocytosis, viral infection, and desiccation.

Fimbriae

Short, thin, hairlike proteinaceous appendages (up to 1,000 per cell) that mediate attachment to surfaces and motility.

Sex pili

Hairlike appendages that are longer, thicker, and less numerous (1 to 10 per cell) than fimbriae and are required for bacterial mating.

Monotrichous

A flagellar arrangement consisting of a single flagellum, which is termed polar if located at one end of the cell.

Amphitrichous

A flagellar arrangement with a single flagellum located at each end of the cell.

Lophotrichous

A flagellar arrangement featuring a cluster of flagella at one or both ends of the cell.

Peritrichous

A flagellar arrangement where flagella are distributed randomly over the entire surface of the cell.

Chemotaxis

The directional movement of a cell toward a chemical attractant or away from a chemical repellent detected by chemoreceptors.

Bacterial endospore

A dormant, extremely resistant structure formed by some bacteria to survive extreme environmental conditions such as heat, radiation, chemicals, and desiccation.

Germination

The second stage in spore transformation characterized by spore swelling, rupture or absorption of the spore coat, loss of resistance, and increased metabolic activity.