Cellular Biology — Study Guide

U1 · Cells, model organisms & microscopy

📖 Lodish 9e · related chapters

CH 01

Evolution: Molecules, Genes, Cells, and Organisms

Cell theory

All organisms are made of cells; cells are the basic units of life; cells arise from preexisting cells (Schleiden, Schwann, Virchow).

Prokaryotes vs eukaryotes

Prokaryotes lack a nucleus and membrane organelles; eukaryotes have both. Eukaryotic cells originated by endosymbiosis (mitochondria from α-proteobacteria, chloroplasts from cyanobacteria).

Model organisms

E. coli (bacteria), S. cerevisiae (yeast), C. elegans (worm — Karen Kim Guisbert uses this), Drosophila, zebrafish, mouse, human cell culture lines (HeLa, HEK293).

Light microscopy

Resolution limit ~200 nm (Abbe). Bright-field, phase contrast, DIC, fluorescence (matters for Johnson's lab).

Confocal microscopy

Pinhole excludes out-of-focus light → optical sections of thick samples.

Super-resolution microscopy

STED, STORM, PALM beat the diffraction limit (~20-50 nm).

Electron microscopy

TEM (transmission, ~0.1 nm) and SEM (surface, ~1 nm). Requires fixation, sections.

Immunofluorescence (IF)

Primary antibody binds antigen; fluorescent secondary antibody binds primary. Used to localize proteins in cells.

U2 · Cell chemistry & biosynthesis

📖 Lodish 9e · related chapters

CH 02

Chemical Foundations

CH 03

Protein Structure and Function

Water properties

Polar; H-bonds give high specific heat, surface tension, cohesion. Hydrophobic effect drives folding + membrane assembly.

Macromolecules

Proteins (AA), nucleic acids (nucleotides), polysaccharides (sugars), lipids (FAs + glycerol/sterol).

ΔG (free energy change)

ΔG < 0 = spontaneous (exergonic); ΔG > 0 = nonspontaneous (endergonic). Cells couple endergonic to exergonic via ATP hydrolysis.

ATP

Energy currency. Hydrolysis of γ-phosphate releases ~−7.3 kcal/mol under standard conditions; much more in cells.

Enzyme catalysis

Lower activation energy. Michaelis-Menten: v = V_max[S] / (K_m + [S]). K_m = [S] at half V_max.

Allosteric regulation

Effector binds non-active site, changes conformation + activity. Foundation of cell-signaling switches.

U3 · Proteins

📖 Lodish 9e · related chapters

CH 13

Moving Proteins into Membranes and Organelles

Primary structure

Amino acid sequence (peptide bonds).

Secondary structure

Local folds — α-helix, β-sheet — stabilized by backbone H-bonds.

Tertiary structure

3D fold of one polypeptide; stabilized by H-bonds, ionic, hydrophobic interactions, disulfides.

Quaternary structure

Multi-subunit assembly (hemoglobin = 2α + 2β).

Chaperone

Hsp70, Hsp90, GroEL/ES — assist folding; rescue misfolded proteins.

Ubiquitin-proteasome

Tags damaged/regulated proteins with poly-Ub chain → 26S proteasome degrades.

Motor proteins

Myosin (actin), kinesin + dynein (microtubules); ATP-driven directional movement.

Phosphorylation

Kinase adds phosphate (Ser/Thr/Tyr), phosphatase removes. Most common reversible regulatory PTM.

U4 · DNA, chromosomes & replication

📖 Lodish 9e · related chapters

CH 07

Genes, Chromatin, and Chromosomes

DNA structure

Antiparallel double helix; AT (2 H-bonds), GC (3). 10.5 bp/turn, major + minor grooves.

DNA replication

Semiconservative. Helicase unwinds, primase lays RNA primer, DNA pol III extends 5'→3'. Leading vs lagging strand (Okazaki fragments). Telomerase extends telomeres.

DNA repair

Mismatch repair (MMR), base excision (BER), nucleotide excision (NER), homologous recombination (HR), non-homologous end joining (NHEJ).

Chromosome structure

DNA + histones = nucleosome (~146 bp around 8 histones). 30-nm fiber → loops → chromatid in mitosis.

Centromere / kinetochore

Heterochromatic region where spindle attaches via kinetochore protein complex.

Telomere

(TTAGGG)n caps; shortens with each replication. Telomerase active in germ + stem + many cancer cells.

U5 · Gene expression

📖 Lodish 9e · related chapters

CH 08

Transcriptional Control of Gene Expression

CH 16

Growth Factor and Cytokine Signaling Pathways That Control Gene Expression

CH 09

Post-Transcriptional Gene Control

Transcription

RNA pol II makes mRNA from DNA template. Promoter (TATA, etc.) + general TFs + enhancers + activators.

RNA processing

5' cap (m7G), poly-A tail, splicing (spliceosome removes introns; alternative splicing diversifies proteome).

Translation

Ribosome reads mRNA codons via tRNA anticodons. Initiation (Met-tRNA, eIFs) → elongation → termination (release factors at stop codon).

Genetic code

Triplet, redundant (degenerate), nearly universal. Wobble at 3rd codon position.

Transcription factor (TF)

DNA-binding protein that activates/represses transcription (e.g., p53, Myc, NF-κB).

Epigenetic marks

DNA methylation (CpG), histone modifications (H3K4me3 active, H3K27me3 repressive, H3K9ac active).

miRNA

~22 nt; binds 3'UTR → translational repression or mRNA decay (RISC complex).

U6 · Membranes & transport

📖 Lodish 9e · related chapters

CH 11

Transmembrane Transport of Ions and Small Molecules

CH 13

Moving Proteins into Membranes and Organelles

Lipid bilayer

Amphipathic phospholipids; fluid mosaic. Cholesterol modulates fluidity; sphingolipids cluster in lipid rafts.

Membrane proteins

Integral (transmembrane), peripheral (cytosolic-facing), lipid-anchored (GPI-anchored, prenylated).

Passive transport

Diffusion (down gradient, no ATP); facilitated diffusion through channels or carriers.

Active transport

Against gradient, requires ATP. Primary: Na⁺/K⁺-ATPase, Ca²⁺-ATPase, H⁺-ATPase. Secondary: symport/antiport coupled to ion gradient.

Na⁺/K⁺-ATPase

3 Na⁺ out, 2 K⁺ in per ATP. Sets resting potential, drives secondary transport.

Aquaporin

Water-selective channel; key in kidney, RBCs.

Action potential prep

Voltage-gated channels open in response to depolarization. (Cross-reference NEUR 1520 U4!)

U7 · Internal compartments & sorting

📖 Lodish 9e · related chapters

CH 13

Moving Proteins into Membranes and Organelles

CH 14

Vesicular Traffic, Secretion, and Endocytosis

ER (rough)

Studded with ribosomes; site of secretory + membrane protein synthesis. Co-translational import via SRP + signal sequence.

ER (smooth)

Lipid synthesis, Ca²⁺ storage, detox (P450 enzymes in liver).

Golgi apparatus

Cis → medial → trans cisternae. Modifies glycoproteins, sorts to lysosomes / plasma / secretion.

Lysosome

Acidic (pH ~4.5) hydrolytic compartment; hydrolases tagged with mannose-6-phosphate.

Peroxisome

β-oxidation of very-long-chain fatty acids; H₂O₂ neutralized by catalase.

Mitochondrion

Double membrane; matrix has TCA cycle + mtDNA; inner membrane houses ETC + ATP synthase. Imports nuclear-encoded proteins post-translationally via TOM/TIM.

Nuclear localization signal (NLS)

Lys/Arg-rich sequence recognized by importin α/β; transport through nuclear pore.

U8 · Vesicle traffic

📖 Lodish 9e · related chapters

CH 14

Vesicular Traffic, Secretion, and Endocytosis

COPII

ER → Golgi anterograde traffic; Sar1 GTPase coordinates assembly.

COPI

Golgi → ER (retrograde) and intra-Golgi; Arf1 GTPase.

Clathrin

Plasma membrane endocytosis + Golgi → endosome. Adaptor proteins (AP1/2) link cargo to coat.

SNARE

v-SNARE (vesicle) + t-SNARE (target) zip into 4-helix bundle → membrane fusion. Specificity for compartment pairing.

Endocytosis types

Phagocytosis (large particles, immune cells), pinocytosis (fluid uptake), receptor-mediated endocytosis (LDL, transferrin).

Exocytosis

Constitutive (continuous) or regulated (Ca²⁺-triggered, e.g., insulin secretion, neurotransmitters).

U9 · Mitochondrial energy conversion

📖 Lodish 9e · related chapters

CH 12

Cellular Energetics

Glycolysis

Cytosolic, glucose → 2 pyruvate, net 2 ATP + 2 NADH.

TCA / Krebs cycle

Mitochondrial matrix. Acetyl-CoA → CO₂ + 3 NADH + 1 FADH₂ + 1 GTP per acetyl-CoA.

Electron transport chain

Complex I (NADH-DH), II (succinate-DH), III (cyt bc1), IV (cyt c oxidase). Electrons from NADH/FADH₂ → O₂ → H₂O. Pumps H⁺ to intermembrane space.

Chemiosmosis

Proton gradient drives ATP synthase (Complex V): F₀ rotor + F₁ catalytic head. ~32 ATP per glucose total.

Uncoupling protein (UCP1)

Brown adipose; dissipates proton gradient as heat (thermogenesis).

U10 · Cell signaling

📖 Lodish 9e · related chapters

CH 15

Receptors, Hormones, and Cell Signaling

CH 16

Growth Factor and Cytokine Signaling Pathways That Control Gene Expression

Receptor classes

Cell-surface: GPCR, RTK, ion-channel-coupled, integrins. Intracellular: nuclear receptors (steroid, thyroid).

GPCR signaling

Ligand → Gα-GTP → effectors (adenylyl cyclase → cAMP → PKA; PLCβ → IP₃/DAG → Ca²⁺/PKC). Desensitization by GRKs + arrestins.

RTK signaling

Ligand → dimerization → trans-autophosphorylation → SH2/PTB-domain adaptors (Grb2, Shc, PI3K). Examples: EGFR, insulin receptor, VEGFR.

MAPK cascade

Ras → Raf → MEK → ERK → nuclear TFs (Elk1, Fos). Drives proliferation. Mutated in many cancers.

PI3K-AKT-mTOR

Survival + growth. PIP₂ → PIP₃ recruits AKT; PTEN reverses. mTORC1 controls translation/autophagy.

Notch

Juxtacrine; intramembrane proteolysis releases NICD → nucleus → CSL → HES/HEY targets. Lateral inhibition.

Wnt/β-catenin

Wnt → Frizzled/LRP → Dishevelled → inhibits destruction complex (APC, GSK3, axin) → β-catenin to nucleus → TCF/LEF target genes.

TGF-β / BMP

Receptor Ser/Thr kinase phosphorylates SMADs → nucleus.

Second messengers

cAMP, cGMP, IP₃, DAG, Ca²⁺, NO.

U11 · Cytoskeleton

📖 Lodish 9e · related chapters

CH 17

Cell Organization and Movement I: Microfilaments

CH 18

Cell Organization and Movement II: Microtubules and Intermediate Filaments

Actin (microfilaments)

~7 nm; G-actin polymerizes (ATP-dependent) to F-actin. Polar (+/-). Regulators: profilin, cofilin, Arp2/3, formins. Cell shape, migration.

Microtubules

~25 nm; α/β-tubulin dimers (GTP-dependent). 13 protofilaments. Polar — minus end at centrosome, plus end outward. Dynamic instability (catastrophe / rescue).

Intermediate filaments

~10 nm; non-polar; coiled-coil dimers → tetramers → filaments. Mechanical support. Examples: keratins (epithelia), vimentin (mesenchymal), nuclear lamins.

Myosin

Actin-based motor. Myosin II = muscle + cytokinesis. Myosin V = vesicle transport.

Kinesin

MT + end-directed motor (anterograde transport, mitotic spindle).

Dynein

MT − end-directed (retrograde), also drives cilia/flagella.

Cilia/flagella

9+2 axoneme. Beat by dynein-driven sliding of doublets.

U12 · Cell cycle & cell death

📖 Lodish 9e · related chapters

CH 19

The Eukaryotic Cell Cycle

CH 22

Stem Cells, Cell Asymmetry, and Regulated Cell Death

Cell-cycle phases

G1 → S (DNA replication) → G2 → M (mitosis + cytokinesis). G0 = quiescent.

Cyclin/Cdk

CDKs are kinases; cyclins are regulatory subunits, periodically expressed. G1: cyclin D + CDK4/6; S: cyclin E/A + CDK2; M: cyclin B + CDK1.

Cell-cycle checkpoints

G1/S (Restriction): DNA damage → p53 → p21 → CDK inhibition. G2/M: damage / unreplicated DNA. M (SAC): unattached kinetochores hold APC/C.

Mitosis stages

Prophase → prometaphase → metaphase (alignment) → anaphase (cohesin cleaved by separase) → telophase → cytokinesis.

Apoptosis

Programmed cell death. Intrinsic (mitochondrial cyt c → apoptosome → caspase-9 → effector caspase-3/7); extrinsic (death receptor Fas/TNFR → caspase-8). Bcl-2 family balance.

Necroptosis / pyroptosis

Lytic forms of cell death — RIPK + MLKL; gasdermin pores (matters for Chivero's NEUR 1520 inflammasome content!).

Autophagy

Self-degradation via autophagosome → lysosome. mTORC1 inhibits, ATG genes execute.

U13 · Cell-cell junctions — Johnson focus

📖 Lodish 9e · related chapters

CH 20

Integrating Cells into Tissues

Tight junctions (zonula occludens)

Apical seal; claudins + occludin form paracellular barrier. Define apical/basolateral polarity.

Adherens junctions

E-cadherin (Ca²⁺-dependent) homophilic binding. Cytoplasmic tail binds β-catenin → α-catenin → actin. Johnson's specialty.

Desmosomes

Spot-weld between cells; desmocollins/desmogleins → plakoglobin/desmoplakin → intermediate filaments (keratin).

Gap junctions

Connexin hexamer = connexon; two connexons span the gap → channel for small molecules (<1 kDa: ions, cAMP, IP₃). Johnson's specialty.

Hemidesmosomes

Cell-to-ECM (basal lamina) via integrin α6β4 → keratin IFs.

Focal adhesions

Integrins + actin; mechanosensing; signal via FAK + Src.

Cadherin switching in EMT

E-cadherin ↓, N-cadherin ↑ during epithelial-to-mesenchymal transition (development + cancer metastasis).

Catenins as signals

β-catenin doubles as a Wnt-pathway TF when not sequestered at adherens junctions.

U14 · Cancer + tissues + ECM

📖 Lodish 9e · related chapters

CH 20

Integrating Cells into Tissues

CH 25

Cancer

Hanahan-Weinberg hallmarks

Sustained proliferation, evasion of growth suppressors, resisting cell death, replicative immortality, angiogenesis, invasion + metastasis, deregulated metabolism, immune evasion + inflammation, genome instability.

Oncogenes

Gain-of-function mutations in proto-oncogenes (Ras, Myc, EGFR, BRAF). Dominant.

Tumor suppressors

Loss-of-function (p53, Rb, APC, PTEN, BRCA1/2). Recessive (Knudson 2-hit).

Metastasis

EMT → local invasion → intravasation → circulation → extravasation → colonization.

ECM

Collagen (most abundant), elastin, proteoglycans (heparan/chondroitin sulfate), fibronectin, laminin (basal lamina).

Basal lamina

Sheet of laminin + type IV collagen + perlecan. Separates epithelium from CT. Barrier disrupted in carcinoma invasion.

Stem cells

Self-renewal + multipotency. Niche-dependent. Adult (intestinal crypt, bone marrow, hair follicle).

U15 · Lab techniques (Northam's lab block)

📖 Lodish 9e · related chapters

CH 06

Molecular Genetic Techniques

Tissue culture

Maintain mammalian cells in vitro: medium with FBS, sterile technique, passaging. Common lines: HeLa, HEK293, NIH-3T3, MCF-7.

Trypsinization

Protease detaches adherent cells for splitting/passaging.

Transfection

Introduce DNA/RNA: lipofection, electroporation, viral vectors (lentivirus).

Immunofluorescence (IF)

Fix → permeabilize → block → primary Ab → fluorescent secondary Ab → DAPI for nuclei → image. Localize proteins.

Western blot

SDS-PAGE → transfer → primary + secondary HRP Ab → ECL detection. Quantify protein.

RT-qPCR

RNA → cDNA (reverse transcriptase) → SYBR/TaqMan qPCR. Quantify mRNA. ΔΔCt analysis vs housekeeping gene.

Flow cytometry / FACS

Fluorescent markers + cytometer → analyze or sort cells by surface or DNA-content phenotypes.

siRNA / shRNA / CRISPR

Loss-of-function: siRNA transient, shRNA stable, CRISPR-Cas9 genomic edit.

Live-cell imaging

Fluorescent proteins (GFP/mCherry) + confocal/spinning disk; FRAP for diffusion; FRET for protein-protein interaction.

High-throughput assays

Multi-well plate readouts: viability (MTT, ATP), reporter, image-based phenotyping. Used in drug discovery.

📚 Textbook companion · Lodish MCB 9e

Each unit above maps to chapters in the locally-OCR'd Lodish MCB 9e. Use the cards below as a quick visual jump into the embedded textbook reader — one figure per chapter, click to read the full chapter:

CH 01

Evolution: Molecules, Genes, Cells, and Organisms

CH 02

Chemical Foundations

CH 03

Protein Structure and Function

CH 04

Culturing and Visualizing Cells

CH 05

Fundamental Molecular Genetic Mechanisms

CH 06

Molecular Genetic Techniques

CH 07

Genes, Chromatin, and Chromosomes

CH 08

Transcriptional Control of Gene Expression

CH 09

Post-Transcriptional Gene Control

CH 10

Biomembrane Structure

CH 11

Transmembrane Transport of Ions and Small Molecules

CH 12

Cellular Energetics

CH 13

Moving Proteins into Membranes and Organelles

CH 14

Vesicular Traffic, Secretion, and Endocytosis

CH 15

Receptors, Hormones, and Cell Signaling

CH 16

Growth Factor and Cytokine Signaling Pathways That Control Gene Expression

CH 17

Cell Organization and Movement I: Microfilaments

CH 18

Cell Organization and Movement II: Microtubules and Intermediate Filaments

CH 19

The Eukaryotic Cell Cycle

CH 20

Integrating Cells into Tissues

CH 21

Responding to the Cellular Environment

CH 22

Stem Cells, Cell Asymmetry, and Regulated Cell Death

CH 23

Cells of the Nervous System

CH 24

Immunology

CH 25

Cancer

📖 Open the full Textbook landing →