Microbiology — BIOL 4640 cheat sheet · Rowen · UNomaha Fall 2026

Domains & Gram

• 3 domains: Bacteria · Archaea · Eukarya (Woese, 16S/18S rRNA).
• Archaea sister to Eukarya, not Bacteria.
• Gram stain: CV → I₂ → EtOH → safranin. G+ purple (thick PG); G− pink (thin PG + outer membrane).
• Koch postulates: present, isolated, reproduces, re-isolated.

Cell envelope

Feature	Bacteria	Archaea
Wall	Peptidoglycan (NAG-NAM)	Pseudopep (NAG-NAT) or S-layer
Membrane	Ester FA bilayer	Ether isoprenoid; sometimes monolayer
Outer mem	G− has it (LPS)	None
RNA pol	5 subunits	8-12 (eukaryotic-like)

• LPS: lipid A (endotoxin) + core + O-antigen → TLR4 → septic shock.
• Teichoic acids in G+ wall.
• Capsule resists phagocytosis; S-layer = paracrystalline protein.
• Endospore (Bacillus, Clostridium): DPA-Ca²⁺ core, heat resistant.
• Pili: type IV (twitch + biofilm); F-pilus (conjugation).
• Mycoplasma = NO wall → β-lactam resistant.

Growth

• FtsZ Z-ring → binary fission. N = N₀ × 2ⁿ.
• Phases: lag · log · stationary · death.
• T: psychro <15 · meso 20-45 · thermo 45-80 · hyper >80.
• O₂: obligate aerobe · facultative · microaero · aerotolerant · obligate anaerobe.
• Halophiles use compatible solutes (K⁺, betaine, ectoine).

Metabolism

• Chemoorgano · chemolitho · phototroph (oxy + anoxy).
• SLP (glycolysis) vs OxPhos (ETC + ATP synthase).
• Anaerobic resp acceptors: NO₃⁻ → SO₄²⁻ → Fe³⁺ → CO₂ (lowest energy).
• Fermentation = SLP + organic e⁻ acceptor; no ETC.
• Methanogenesis: Archaea only; CO₂+H₂ or acetate → CH₄.
• N-fix: nitrogenase (Mo-Fe), 16 ATP/N₂; O₂-sensitive.
• Nitrification: NH₃ → NO₂⁻ (Nitrosomonas) → NO₃⁻ (Nitrobacter).
• Denitrification: NO₃⁻ → N₂.

Genome & HGT

• 1 circular chr (most); plasmid optional.
• oriC + DnaA → DnaB helicase → primase → pol III → ligase.
• Gyrase = Topo II (target of quinolones); Topo IV decatenates.
• HGT: transformation (naked DNA) · transduction (phage) · conjugation (pilus, F+/Hfr).
• R-M defense; CRISPR-Cas adaptive immunity.

Regulation

• lac: catabolic, inducible; allolactose releases LacI; CAP-cAMP (low glucose) needed.
• trp: anabolic, repressible; Trp + TrpR represses; attenuation via leader peptide stalling.
• σ factors: σ70 hk · σ32 heat · σS stat · σ54 N · σF flagella · σE extracyto.
• Two-component: His-kinase autoP → response regulator → DNA.
• Quorum sense: AHLs (G−, LuxI/R) · AIPs (G+, Agr in S. aureus).
• Riboswitch: 5'UTR binds metabolite directly.
• sRNA via Hfq → blocks translation or recruits RNase E.

Viruses

• Genome + capsid ± envelope; helical, icosahedral, complex.
• Lytic: adsorb → penetrate → replicate → assemble → lyse.
• Lysogeny: integrate as prophage → induced → lytic.
• Retrovirus: +ssRNA → RT → dsDNA → integrase → provirus.
• Baltimore I (dsDNA), II (ssDNA), III (dsRNA), IV (+ssRNA), V (−ssRNA), VI (RT-RNA), VII (RT-DNA).

Bacterial diversity

• Proteobacteria (G−): α Rhizobium, Rickettsia · γ E. coli, Pseudomonas, Vibrio · ε Helicobacter, Campylobacter.
• Firmicutes (G+ low GC): Bacillus, Clostridium, Staphylo, Strepto, Listeria, Lacto.
• Actinobacteria (G+ high GC): Mycobacterium, Streptomyces (antibiotics), Coryne.
• Cyanobacteria: oxygenic photo, chloroplast ancestor.
• Spirochaetes: Treponema, Borrelia, Leptospira.

Archaea

• Crenarchaeota: thermo + acidophiles (Sulfolobus).
• Euryarchaeota: methanogens, halophiles, thermoacido.
• Thaumarchaeota: ammonia oxidizers (marine, soil).
• Bacteriorhodopsin = light-driven H⁺ pump in Halobacterium.
• Hyperthermophiles: Pyrolobus 113°C; Methanopyrus 122°C.

Pathogenesis (ROWEN)

• Virulence: adhesion · toxins · secretion · biofilm · immune evasion.
• A-B exotoxins: B binds + delivers, A is enzymatic.
• Diphtheria: ADP-rib EF-2 → no protein synth.
• Cholera: ADP-rib Gαs → cAMP↑ → diarrhea.
• Botulinum/tetanus: cleave SNAREs → no NT release.
• Shiga: depurinates 28S rRNA.
• Endotoxin = LPS lipid A → TLR4.
• T3SS: needle injectisome → effectors into host. Yersinia, Salmonella, Pseudomonas, Shigella, EPEC.
• T4SS: H. pylori CagA, Agrobacterium T-DNA, Legionella Dot/Icm.
• T6SS: phage-tail "harpoon" — bacterium vs bacterium.
• P. aeruginosa: G−, motile, opportunistic, MDR. Quorum sensing LasI/R + RhlI/R.
• Mucoid: mucA mutation → σ22 (AlgT/U) → alginate → biofilm in CF lungs.
• Biofilm 100-1000× antibiotic tolerant (slow growth + persisters + EPS).

Antibiotics

Class	Target	Cidal/Static
β-lactams (PCN, ceph, carba)	Transpeptidase / PBPs	Cidal
Vancomycin	D-Ala-D-Ala (G+ only)	Cidal
Aminoglycosides	30S → mistranslation	Cidal
Tetracyclines	30S tRNA entry	Static
Macrolides, Cm, lincosamides	50S	Static
Quinolones	Gyrase + Topo IV	Cidal
Rifampin	RpoB (RNA pol)	Cidal
TMP-SMX	DHFR + DHPS (folate)	Cidal combo

Resistance

• (1) Inactivation: β-lactamase (ESBL, KPC, NDM-1).
• (2) Efflux: AcrAB-TolC, MexAB-OprM (Pseud).
• (3) Target alteration: PBP2a (MRSA, mecA); D-Ala-D-Lac (VRE, vanA); RpoB mut (rifampin); gyrase mut (quinolone).
• (4) Reduced uptake: porin loss (carbapenem R in Pseud, KPC carriers).
• MIC = lowest [drug] inhibiting visible growth.

Lab + applied

• 16S rRNA = phylogenetic + microbiome marker.
• MALDI-TOF = species ID from colony in minutes.
• Catalase: Staph (+) vs Strep (−). Coagulase: S. aureus (+) vs CoNS (−).
• Sterilization: autoclave 121°C/15 psi/15 min, gamma, EtO.
• Vaccines: live att (MMR), inactivated (IPV, flu), subunit (HBV), toxoid (DT, TT), conjugate (Hib, pneumococcal), mRNA (COVID).