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

Units & exam dates

Unit	Slonczewski 6e	Exam
Unit 1 · Methods	notes · 4.3–4.4 · 2.1–2.6	Exam 1 · Oct 5
Unit 2 · Genomes & phylogeny	7.1–7.6, 6.3 · A3.6, 9.5 · 9 · 17.3/17.5, 18.1	Exam 1 · Oct 5
Unit 3 · Structure & viruses	3.2–3.6 · 6	Exam 2 · Oct 28
Unit 4 · Metabolism	13 · 14 · 15.1–15.2	Exam 3 · Nov 23
Unit 5 · Regulation & adaptation	8.1–8.5 · 10, 12.1 · 4.5, 12.2 · 4.6, 5.1–5.6	Exam 4 · Dec 16, 10–11:59 AM

Optional comprehensive final Dec 16–18 replaces one of exams 1–3. Grades: best 4 of 5 exams = 400 pts (~73%) + homework ~150 pts (~27%). Late HW −3%/day, max −50%.

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 (off-syllabus — Rowen research)

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 (off-syllabus)

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 (off-syllabus)

(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).