Chapter 3: Observing organisms through a microscope

Vocabulary flashcards covering key concepts, terms, and methods from the microscopy and staining notes.

Compound Light Microscopy

A light microscope where the image from the objective lens is magnified again by the ocular lens; total magnification equals ocular X objective.

Light Microscopy

Any microscope that uses visible light to observe specimens; includes compound, darkfield, phase-contrast, DIC, fluorescence, and confocal microscopy.

Brightfield Illumination

A type of light microscopy where dark objects are seen against a bright background; light reflected off the specimen does not enter the objective lens.

Darkfield Microscopy

Light objects are visible on a dark background; uses an opaque disk in the condenser; only light reflected from the specimen enters the objective lens.

Phase-Contrast Microscopy

A technique that allows detailed viewing of living organisms and internal cell structures without fixation or staining.

Differential Interference Contrast (DIC) Microscopy

Similar to phase-contrast but uses two light beams and prisms to provide higher contrast and often a three-dimensional appearance.

Fluorescence Microscopy

Uses UV light to excite fluorescent substances (fluorochromes) that emit visible light, enabling visualization of labeled structures.

Auramine O

A fluorochrome used to stain certain microbes (e.g., Mycobacterium tuberculosis) for fluorescence microscopy.

Confocal Microscopy

Cells are stained with fluorochromes; blue light excites a single plane, yielding exceptionally clear 2D images and enabling 3D reconstruction with a computer.

Two-Photon Microscopy

Uses two photons of long-wavelength light to excite fluorochromes, allowing imaging of living cells up to about 1 millimeter deep in real time.

Super-Resolution Light Microscopy

A method that uses two laser beams and computer processing to achieve resolution beyond the diffraction limit, effectively imaging at ~1 nm scales.

Scanning Acoustic Microscopy

Measures sound waves reflected from a specimen to study cells attached to surfaces, providing information on cellular structures and properties.

Electron Microscopy

Uses electrons instead of light; electrons have a shorter wavelength, allowing much higher resolution; images are black-and-white and often color-enhanced digitally.

Transmission Electron Microscope (TEM)

Electrons pass through a thin specimen; magnets lenses focus electrons onto a screen to form an image; reveals internal ultrastructure.

Scanning Electron Microscope (SEM)

A beam of electrons scans the specimen’s surface; secondary electrons are detected to produce a 3‑D appearance of surface structures.

Scanned Probe Microscopy

Uses various probes to examine a specimen’s surface without altering it; enables mapping of atomic shapes and properties; includes STM and AFM.

Scanning Tunneling Microscopy

A type of scanned probe microscopy that uses a conductive tip to image surfaces at the atomic level by measuring tunneling current.

Atomic Force Microscopy

A scanned probe technique that uses a cantilever with a sharp tip to map surface topography at the atomic scale by measuring forces.

Smear

A thin film of material containing microorganisms spread over a slide for staining and examination.

Fixing a smear

Process to attach microorganisms to a slide, kill them, and preserve cell structures; can be done by heat or chemical fixation.

Simple Stain

A staining method using a single basic dye to visualize the entire microorganism and its shape.

Mordant

A substance that helps a stain adhere to the specimen or coats it to enlarge the stain's effect.

Chromophore

The colored part of a stain; in basic dyes the chromophore is a positively charged ion (cation).

Basic Dye

A dye whose chromophore is a cation; commonly used to stain bacteria (e.g., crystal violet, methylene blue, safranin).

Acidic Dye

A dye whose chromophore is an anion; used to stain the background rather than cells (eosin, acid fuchsin, nigrosin).

Negative Staining

A staining method that colors the background rather than the cell, often using acidic dyes; capsules appear as halos around cells.

Gram Stain

A differential stain classifying bacteria as Gram-positive or Gram-negative based on cell wall structure and staining characteristics.

Gram-Positive

Bacteria with thick peptidoglycan cell walls that retain the crystal violet–iodine complex and appear purple.

Gram-Negative

Bacteria with thin peptidoglycan and an outer membrane; they decolorize and take up the counterstain, appearing pink/red.

Crystal Violet

Primary stain in Gram staining; a purple dye that stains all cells initially.

Mordant (Gram Stain context: Iodine)

Iodine acts as a mordant in Gram staining, forming a complex with crystal violet to trap dye in Gram-positive cell walls.

Alcohol (decolorization)

Decolorizing step in Gram staining that removes dye from Gram-negative cells while Gram-positives retain it.

Safranin

Counterstain in Gram staining that stains decolorized Gram-negative cells pink/red.

Capsule

A gelatinous outer covering of some bacteria that does not readily take up most dyes; visualized by negative staining or special stains.

Capsule Stain

A staining technique used to visualize capsules surrounding certain bacterial cells.

Endospore Stain

A stain specifically designed to visualize endospores, which are resistant dormant structures within some bacteria.

Schaeffer-Fulton Stain

Endospore staining method using malachite green as primary stain, water decolorization, and safranin as counterstain; spores appear green.

Malachite Green

Primary stain in the Schaeffer-Fulton endospore stain that penetrates endospores with heat.

Flagella Staining

A staining method to visualize the slender flagella by thickening them with a mordant and dye (carbolfuchsin) for light microscopy.