Cellular Biology — BIOL 4140 cheat sheet · Johnson + Northam · UNomaha Fall 2026

Cells & microscopy

• Endosymbiosis: mito ← α-proteobact; chloro ← cyanobact.
• Light limit ~200 nm (Abbe). Confocal = optical sections. Super-res STED/STORM/PALM ~20 nm. EM: TEM ~0.1 nm, SEM ~1 nm.
• IF: 1°Ab unlabeled → fluorescent 2°Ab + DAPI nuclei.
• Cell lines: HeLa, HEK293, MCF-7, NIH-3T3.

Chemistry & proteins

• ΔG<0 spontaneous; ATP hydrolysis ΔG ~−7.3 kcal/mol.
• Michaelis-Menten v=V_max[S]/(K_m+[S]).
• Structure: 1° AA, 2° α-helix/β-sheet, 3° fold, 4° multimer.
• Chaperones Hsp70/90/GroEL-ES; ubiquitin-proteasome (K48 polyUb).
• Phosphorylation Ser/Thr/Tyr by kinases; phosphatases reverse.

DNA & replication

• AT 2 H-bonds, GC 3. Semiconservative replication.
• Helicase → primase → pol III; Okazaki on lagging strand.
• Telomerase RNP extends 3' overhang; active in stem + cancer.
• Repair: MMR, BER, NER, HR (BRCA1/2 + Rad51), NHEJ (Ku, Lig4).
• Nucleosome = 146 bp + histone octamer (2× H2A,B,3,4); H1 linker.

Gene expression

• RNA pol II → mRNA. Cap (m7G) + poly-A + splicing.
• Alternative splicing → proteome diversity.
• Active marks H3K4me3, H3K27ac. Repressive H3K27me3, H3K9me3.
• miRNA in RISC → 3'UTR → repression / decay.

Membranes & transport

• Bilayer: amphipathic phospholipids; cholesterol buffers fluidity.
• Lipid raft = sphingolipid + chol + GPI proteins.
• Na⁺/K⁺-ATPase: 3 Na⁺ out, 2 K⁺ in / ATP.
• Symport (same direction) vs antiport (opposite).
• Aquaporin = water channel; AQP2 in kidney via ADH.

Compartments

• ER co-translational import via SRP + Sec61 + signal peptide.
• Smooth ER: lipids, Ca²⁺, P450 detox.
• Golgi: cis→medial→trans; M6P tags lysosomal hydrolases.
• Lysosome pH ~4.5 (V-ATPase).
• Mito: post-translational; TOM/TIM; matrix sequence.
• NLS lys/arg-rich → importin α/β → NPC; RanGTP releases.

Vesicles

• COPII ER→Golgi (Sar1); COPI Golgi→ER (Arf1).
• Clathrin + AP1/2 — endocytosis + Golgi→endosome.
• SNAREs v + t → 4-helix → fusion. NSF/SNAP recycle.
• Endo: phagocytosis · pinocytosis · receptor-mediated (LDL, transferrin).

Energy

• Glycolysis (cyto) glucose → 2 pyr + 2 ATP + 2 NADH.
• TCA per acetyl: 3 NADH, 1 FADH₂, 1 GTP, 2 CO₂.
• ETC: I, II, III, IV; pumps H⁺ I/III/IV; e⁻ → O₂ → H₂O.
• Chemiosmosis: ATP synthase (F₀F₁) ~30-32 ATP/glucose.
• UCP1 (brown fat) → heat by H⁺ leak.

Signaling

• GPCR: Gαβγ → AC/cAMP/PKA OR PLCβ → IP₃ (Ca²⁺)/DAG (PKC).
• RTK: dimer → autoP → SH2 adaptors. EGFR, insulin, VEGFR.
• MAPK: Ras→Raf→MEK→ERK → Elk1, Fos. Ras mutated 30% cancers.
• PI3K→PIP₃→AKT→mTORC1; PTEN reverses.
• Notch: γ-secretase → NICD → CSL → HES/HEY.
• Wnt → Frizzled → Dvl → β-catenin stabilized → TCF/LEF.
• TGF-β/BMP → SMAD pathway.

Cytoskeleton

Filament	Width	Subunit	Motor
Actin	7 nm	G-actin	Myosin
Microtubule	25 nm	αβ-tubulin (13 protofil)	Kinesin (+) / Dynein (−)
IF	10 nm	Coiled-coil	None — structural

• Actin nucleators: Arp2/3 (branched), formin (linear).
• MT dynamic instability: GTP cap → grow, catastrophe → shrink.
• Cilia/flagella 9+2 axoneme; dynein-driven.

Cycle & death

• Phases G1→S→G2→M; G0 quiescent.
• D/CDK4/6 → E/CDK2 → A/CDK2 → B/CDK1.
• Restriction (R) point: Rb→E2F. p53→p21 inhibits CDK on damage.
• APC/C-Cdc20 → degrades securin → separase cleaves cohesin → anaphase.
• SAC blocks APC/C until all kinetochores attached.
• Apoptosis intrinsic: BAX/BAK → cyt c → apoptosome → casp9 → casp3/7.
• Extrinsic: FasL/TNFα → DISC → casp8 → casp3/7.
• Bcl-2 anti vs Bax/Bak pro; BH3-only triggers (Bid, Bim, Puma).
• Autophagy: phagophore → autophagosome → lysosome. mTORC1 inhibits.
• Pyroptosis: gasdermin pores after caspase-1/11 (inflammasome).

Junctions (JOHNSON)

Junction	Protein	Cytoskel
Tight	Claudin/occludin/ZO-1	Actin
Adherens	E-cadherin → β/α-catenin	Actin
Desmosome	Desmocollin/glein → plakoglobin/desmoplakin	Keratin IF
Gap	Connexin × 6 = connexon	—
Hemides.	Integrin α6β4	Keratin IF
Focal adh.	Integrin → talin/vinc/pax	Actin

• Gap junction: small mol <1 kDa (ions, cAMP, IP₃).
• EMT: E-cad ↓, N-cad ↑ → migratory phenotype.
• β-catenin doubles as Wnt TF when cytosolic.

Cancer / ECM

• Hallmarks (10): proliferation, evade growth supp, evade death, immortality, angiogenesis, invasion+metastasis, deregulated metab, immune evasion, inflammation, genome instability.
• Oncogene gain-of-fxn (Ras, Myc, EGFR, BRAF). Tumor supp loss-of-fxn (p53, Rb, APC, PTEN, BRCA1/2).
• Metastasis: EMT → intravas → circ → extravas → colonize.
• ECM: collagen, elastin, proteoglycans, fibronectin, laminin.
• Basal lamina: type IV collagen + laminin + perlecan + nidogen.

Lab (NORTHAM)

• Tissue culture: medium + FBS, sterile, passage. Trypsinize to detach.
• Transfect: lipofection / electroporation / lentivirus.
• IF: fix → perm → block → 1°→ 2° → DAPI → image.
• Western: SDS-PAGE → transfer → 1°→ HRP-2°→ ECL.
• RT-qPCR ΔΔCt: normalize to housekeeping + control. Fold = 2^(−ΔΔCt).
• FACS = sort by fluor markers.
• Knockdown siRNA (transient) / shRNA (stable) / CRISPR-Cas9 (edit).
• FRAP = diffusion. FRET = <10 nm proximity.
• MTT viability: tetrazolium → formazan; absorbance ∝ live cells.