Comprehensive Microbiology Exam 1 Study Notes

Bacterial Morphology & General Size Reference

Microscopic vs. macroscopic shape
- Colonies on agar ≈ circular, flat or raised.
- Individual cells under the microscope may be rods (bacilli), spheres (cocci), curved (vibrios), spirals, etc.
Typical dimensions
- Smallest observed range: 200\text{–}500\ \text{nm} \,(2 \times 10^{-7}\text{–}5 \times 10^{-7}\,\text{m}).
- “Average” bacterium ≈ 1\,\mu m \;(=10^{-6}\,\text{m}) – literally the size of the dot in a printed sentence.

Cell Membrane (Plasma Membrane)

Phospholipid bilayer – highly selective barrier.
- Maintains internal homeostasis; regulates nutrient & waste traffic.
- Contributes to membrane fluidity → allows internal components to move.
Only small, non-polar molecules diffuse freely; larger/charged species require
- Protein channels (porins), carriers, or receptors.

External Bacterial Appendages

Flagella – motility
- Single = monotrichous.
- Tuft at one pole = lophotrichous.
- One flagellum at each pole = amphitrichous.
- All around cell = peritrichous (mentioned implicitly).
- More flagella → faster, multidirectional movement → ↑ ability to cross host barriers.
Fimbriae / Fibrae – numerous, thin; key for adhesion to surfaces/host cells → ↑ pathogenicity.
Pili (sing. pilus) – thicker, longer; “conjugation bridge.”
- Transfers plasmids → generates genetic diversity, antibiotic resistance (“super-bugs”).
- Looks like a thin line connecting two cells under TEM.

Glycocalyx Variants

Slime Layer
- Loosely attached, porous → antibiotics can permeate through visible “tunnels.”
Capsule
- Thick, well-organized, non-porous → drugs/immune factors have little entry.
- Prominent virulence factor; enhances survival in harsh environments.

Cell Wall Architectures: Gram (+) vs Gram (−)

Key contrasts (memorize ≥5 for Exam 1):

Peptidoglycan (PG)
- Gram (+) – thick, surface-exposed; retains crystal-violet dye.
- Gram (−) – thin, sandwiched between outer & inner membranes.
Outer membrane
- Absent in Gram (+).
- Present in Gram (−); contains lipopolysaccharide (LPS), porins, receptors.
Lipopolysaccharide (LPS)
- Exclusive to Gram (−); endotoxin (lipid A region is most toxic) → triggers macrophages, monocytes, dendritic cells.
Teichoic / lipoteichoic acids
- Present in Gram (+) cell wall → overall acidic surface charge.
Sensitivity to antibiotics
- β-lactams & drugs that target PG more effective against Gram (+) (PG exposed).
- Gram (−) harder to treat (dual membrane blocks access).

Peptidoglycan chemical motif:
\text{Repeating}\;\bigl[ N!\text{-acetyl-} \beta\text{-D-glucosamine}\,(G) \leftrightarrow N!\text{-acetyl-} \beta\text{-D-muramic acid}\,(M) \bigr]_{n}

Gram-Stain Protocol (4 Critical Steps)

Crystal violet (≈30 s) – stains all cells purple.
Gram’s iodine (mordant) – complexes dye with PG.
Alcohol/acetone decolorizer – removes unbound dye.
- Gram (+) remain purple; Gram (−) become colorless.
Safranin counterstain – Gram (−) appear pink/red; Gram (+) stay purple.

Remember: Some organisms (e.g., Mycobacterium) possess waxy mycolic acids → acid-fast stain required.

Internal Structures & Genetics

Ribosomes (70 S) – translation; antibiotic target.
Chromosome – single, circular dsDNA.
Plasmids – extrachromosomal, non-essential DNA; replicate independently; instrumental in genetic engineering.
Endospores (mainly Bacillus, Clostridium)
- Two-phase cycle: vegetative → endospore.
- Highly resistant; formed under stress (nutrient depletion, heat, UV).

Archaea Snapshot

Prokaryotic domain distinct from Bacteria.
Thrive in extreme habitats (thermophiles, halophiles, acidophiles).

Eukaryotic Cell Components (Brief Review)

Membrane-bound organelles universal.
- Lysosome: hydrolytic digestion.
- Golgi apparatus: “Amazon warehouse” – sorts, modifies, ships proteins/lipids.
- Mitochondria: inner membrane folds = cristae; site of ETC/ATP synthesis.

Fungi

Nutrition: heterotrophic; saprobes (dead) or parasitic (living hosts).
Growth anatomy
- Hyphae – filaments; collectively mycelium.
- Simple extension vs. fragmentation (piece breaks off → new colony).
Reproduction: spore formation (NOT bacterial endospores!)
- Sporangiospores – produced inside sac (sporangium); sac ruptures to release.
- Conidiospores – pinch off openly; no enclosing sac.

Viruses: Fundamentals

Obligatory intracellular parasites.
Core = DNA or RNA (never both) + capsid (protein coat).
May possess envelope (lipid) outside capsid → “enveloped” vs “naked.”
Surface spikes/peplomers = glycoproteins → host-cell receptor binding.
Bacteriophage – specialized virus infecting bacteria; complex capsid with tail fibers & base plate for injection.

Baltimore Classification (know examples)

Class I – dsDNA (e.g., Herpesviridae).
Class II – ssDNA → needs dsDNA intermediate.
Class III – dsRNA.
Class IV – (+) ssRNA (sense).
Class V – (−) ssRNA (antisense) – e.g., influenza.
Class VI – ssRNA-RT (retroviruses, HIV) → RNA-DNA intermediate.
Class VII – dsDNA-RT (not explicitly in transcript but completes chart; e.g., HBV).

General Replication Cycle (6 Steps)

Adsorption – virion attaches to host receptor via spikes.
Penetration – enters by endocytosis or membrane fusion.
Uncoating – capsid removed; genome released.
Synthesis – genome replication & protein translation.
- RNA viruses replicate/translate in cytoplasm.
- DNA viruses send DNA to nucleus → mRNA → cytoplasm.
Assembly – new nucleocapsids form.
Release
- Budding (enveloped) → acquires host membrane.
- Lysis (naked) → host cell bursts.

Infection Patterns

Acute vs. Persistent/latent – genome remains, periodic reactivation when conditions favor.
Examples discussed (implied): HSV, HIV, Hepatitis viruses.

Non-Traditional Agents

Prions – infectious proteins only; no nucleic acid; cause spongiform encephalopathies.
Viroids – naked ssRNA; infect plants exclusively.

Chemotaxis & Host Interaction (Applied Concept)

Bacteria move toward/away from chemical gradients.
- Surface receptors detect attractants/repellents.
- Flagellar rotation bias (run vs. tumble) → net migration to favorable site (e.g., lung mucus during infection).

Practical / Exam Tips

Master ≥5 distinctions Gram (+) vs Gram (−).
Memorize Gram-stain reagents, timing, color outcomes.
Distinguish sporangiospore vs conidiospore (fungi) and spores vs. bacterial endospores.
Viral DNA vs RNA replication locales (nucleus vs cytoplasm) – be explicit in answers.
Recall that plasmids accelerate antibiotic resistance; pili facilitate plasmid transfer.
Sizes: nm vs μm; flagella patterns vocabulary.
LPS as endotoxin; lipid A = most toxic portion.

Quick Numerical / Formula Highlights

Size hierarchy: \text{Virus} < 0.2\,\mu m < \text{Bacteria}~(0.2\text{–}1\,\mu m) < \text{Fungal spores/mycelia}.
Bacterial PG repeating unit (alternating G–M sugars).
Unit conversions: 1\,\mu m = 10^{-6}\,\text{m},\quad 1\,\text{nm} = 10^{-9}\,\text{m}.

Branches of Microbiology (mentioned in passing)

Medical, Industrial, Agricultural, Environmental, Immunology, Food & Dairy (standard six-branch list to reinforce).