Microbiology Essentials: Microscopy, Cellular Structures, and Infectious Entities

Vocabulary flashcards covering microbiology topics including microscopy types, cell wall structures, organelles, eukaryotic protists and fungi, viral life cycles, and acellular entities.

Microbe Size Ranges

Viruses range from $20 - 400\,nm$; Bacteria & Archaea range from $0.2 - 5\,\mu m$; Eukaryotic Microbes range from $5 - 100\,\mu m$.

Endosymbiont Theory (Endomembrane Origin)

Infoldings of the plasma membrane in an ancestral prokaryote created early endomembrane structures such as the nucleus and endoplasmic reticulum (ER).

Mitochondria Event

An evolutionary event where an ancestral eukaryote engulfed an aerobic bacterium that evolved into mitochondria.

Chloroplast Event

An evolutionary event where early eukaryotes engulfed photosynthetic bacteria (cyanobacteria) that evolved into chloroplasts.

Bright-Field Microscopy

Microscopy where light passes through the specimen; usually requires staining (which kills cells). Used for routine bacterial morphology and cell layout.

Dark Field Microscopy

Microscopy where light scatters off the specimen to create a bright image on a dark background. Used for unstained live cells and identifying spirochetes like Treponema pallidum.

Phase Contrast / DIC Microscopy

Microscopy that uses refraction and interference to enhance contrast without staining. Used for viewing internal organelles and structures in live eukaryotic cells.

Fluorescence Microscopy

Microscopy using UV or excited light to detect fluorophores or tagged antibodies. Used for specific protein/pathogen tagging, such as the Rabies DFA assay.

Confocal Microscopy

Microscopy using lasers for optical sectioning of thick specimens. Used for 3D visual analysis of complex structures.

TEM (Transmission Electron Microscopy)

Microscopy where an electron beam passes through thin sections, achieving $0.1\,nm$ resolution. Used to observe fine internal cell organelles and ultrastructure.

SEM (Scanning Electron Microscopy)

Microscopy where an electron beam scans a metal-coated surface to create a 3D surface view. Used for high-resolution 3D surface topology.

Magnification Formula

$$\text{Magnification} = \frac{\text{Measured Image Size (using ruler)}}{\text{Actual Scale Bar / Object Size}}$$

Actual Size Formula

$$\text{Actual Size} = \frac{\text{Measured Object Size (using ruler)}}{\text{Magnification}}$$

Resolution

The ability to distinguish two closely spaced points as separate entities (image clarity).

Resolving Power (d)

Calculated as $d = \frac{\lambda}{2 \times \text{NA}}$. Shorter wavelengths ($\lambda$) improve resolution.

Basic Dyes

Positively charged dyes ($+$ charge) that bind to negatively charged cell components such as nucleic acids and cell surfaces.

Acid Dyes

Negatively charged dyes ($-$ charge) repelled by cell surfaces that stain the background (negative staining).

Capsule Stain

A combination of acidic and basic dyes where the neutral capsule repels dye, appearing as a clear halo.

Coccus / Cocci

Round-shaped bacterial cells.

Bacillus / Bacilli

Rod-shaped bacterial cells.

Vibrio

Curved rod-shaped bacterial cells.

Coccobacillus

Short, oval rod-shaped bacterial cells.

Spirillum

Rigid spiral-shaped bacterial cells.

Spirochete

Flexible, long helical spiral-shaped bacterial cells.

Bacterial Cytoskeleton Proteins

Internal protein structures including FtsZ, MreB, and Crescentin.

Gram-Positive Cell Wall

Characterized by a thick peptidoglycan layer ($20 - 80\,nm$, many layers), presence of teichoic and lipoteichoic acids, a very narrow/small periplasmic space, and absence of an outer membrane and LPS.

Gram-Negative Cell Wall

Characterized by a thin peptidoglycan layer ($2 - 7\,nm$, 1-3 layers), an outer membrane containing LPS/endotoxin (Lipid A, Core, O-antigen, Porins), and a large periplasmic space with abundant exoenzymes.

Acid Fast Cell Wall

Characterized by a peptidoglycan layer linked to mycolic acids and arabinogalactan, lacking an outer membrane, LPS, and teichoic acids.

Gram Staining Mechanism

Four-step procedure: 1. Crystal Violet (primary stain), 2. Iodine (mordant forming CV-I complex), 3. Alcohol decolorization (dehydrates Gram-positive peptidoglycan; washes CV-I out of Gram-negative outer membrane), 4. Safranin counterstain (Gram-positive remains purple; Gram-negative turns pink/red).

Secretory Pathway Sequence

Rough ER $\rightarrow$ Transport Vesicle $\rightarrow$ Cis-Golgi $\rightarrow$ Trans-Golgi $\rightarrow$ Secretory Vesicle $\rightarrow$ Plasma Membrane.

Eukaryotic Cytoskeleton Filaments

Microfilaments (actin, $7\,nm$), Intermediate filaments (keratin/vimentin, $8 - 12\,nm$), and Microtubules (tubulin, $25\,nm$).

Protists Taxonomic Status

Not a true taxonomic classification because it is a polyphyletic group lacking a single shared common evolutionary origin or unique unifying characteristics; grouped primarily by what they lack.

Primary Algae

Autotrophic direct descendants of early endosymbiosis with double-membrane chloroplasts containing chlorophylls or accessory pigments (e.g., green and red algae).

Secondary Algae

Mixotrophic products of secondary endosymbiosis (engulfed primary algae), such as diatoms with silica walls and dinoflagellates.

Dimorphic Fungi

Fungi that switch between a single-celled yeast form in human hosts and a mycelial/mold form at environmental temperatures.

Cestodes

Parasitic flatworms (tapeworms) that lack digestive tracts and absorb nutrients directly through their skin.

Scolex

Head structure of a tapeworm equipped with suckers or hooks for attachment to the host intestinal wall.

Proglottids

Sequential body segments of a tapeworm that each contain both male and female reproductive organs.

Viral Life Cycle Steps

1. Attachment (adsorption) $\rightarrow$ 2. Entry/Penetration $\rightarrow$ 3. Uncoating $\rightarrow$ 4. Biosynthesis $\rightarrow$ 5. Assembly (Maturation) $\rightarrow$ 6. Release.

Virulent Phages

Bacteriophages that undergo only the lytic cycle, multiplying immediately upon host entry and lysing the bacterial cell to release virions.

Temperate Phages

Bacteriophages capable of lytic or lysogenic cycles, which can integrate their DNA into the bacterial genome as a prophage during lysogeny.

Viroids

Naked infectious circular ssRNA molecules lacking protein components that exclusively target plant hosts.

Prions

Misfolded infectious proteins (PrP$^{\text{Sc}}$ isoform) lacking genetic material that induce normal proteins (PrP$^{\text{C}}$) in mammalian brain tissue to misfold.