Cell Biology Fundamentals: Cell Structure, DNA, and Gene Expression

Big ideas & learning goals

• Life shares common ancestry (LUCA) and core biochemistry; what we learn in one cell often generalizes.

• Distinguish prokaryotes (no nucleus) vs eukaryotes (membrane-bound organelles).

• Know cell structures and the central dogma (DNA → RNA → protein).

• Track how DNA is packaged and replicated; how RNA is transcribed/processed; how proteins are translated and regulated.

• Compare cytoskeletal systems (microtubules vs actin) and their motors (kinesin/dynein vs myosin).

• Understand light, electron, and fluorescence microscopy, including GFP and immunofluorescence.

Cells & organelles (Lecture 1)

Prokaryotes: single-celled, no nucleus; Bacteria and Archaea. Eukaryotes: nucleus + organelles; compartmentalize functions. Plasma membrane (PM): boundary with environment. Cytoplasm vs cytosol: cytoplasm = interior of PM (minus nucleus); cytosol = aqueous solution between organelles. Nucleus: genome storage, replication & transcription; double membrane with nuclear pores. Endoplasmic reticulum (ER): lipid synthesis; rough ER has ribosomes for membrane/secreted proteins. Golgi apparatus: vesicle sorting and processing. Mitochondria: two membranes, own genome; ATP production; metabolic hubs.

Microscopy & resolution (concepts):

• Resolving power = ability to distinguish close objects.

• Light microscopy: lower resolution than EM; live imaging possible.

• Electron microscopy (EM): nanometer-scale detail; fixed samples.

• Fluorescence microscopy: label specific molecules (e.g., GFP from jellyfish or antibody tags) to visualize location/dynamics.

Quick checks

• Why is compartmentalization useful?

• Which organelle sorts vesicles? (Golgi)

• What does “resolving power” mean?

Central dogma & macromolecules

Macromolecules (most of cell mass) are polymers made by condensation reactions of monomers:

• Proteins ← amino acids

• Nucleic acids (DNA/RNA) ← nucleotides

• Polysaccharides ← sugars

DNA structure & replication

DNA basics: sugar-phosphate backbone (uniform), bases (A,T,G,C) pair via H-bonds; antiparallel strands; major groove is a protein-binding hotspot. Humans: 23 chromosome pairs. DNA is tightly packaged with histones → chromatin fibers.

Replication:

• Semiconservative: each duplex = 1 old + 1 new strand.

• DNA polymerase extends 3′ end and is highly accurate.

• Many origins of replication fire to speed copying; primase lays RNA primers; lagging strand forms Okazaki fragments.

• Telomerase extends ends to limit shortening.

Practice prompts

• Explain why a primer is needed.

• Label leading vs lagging strand and direction of synthesis.

RNA & transcription (Lecture 3)

DNA strands: template read by RNA Pol; coding matches RNA (T→U). RNA polymerase: binds promoter, synthesizes 5′→3′, stops at terminator; error-rate higher than DNA Pol (tolerable). Regulation: transcription factors tune initiation to meet cellular needs/signals.

RNA processing (eukaryotes):

1. Splicing: introns removed; exons joined by snRNPs (spliceosome); enables alternative splicing.

2. 5′ cap & 3′ poly(A) tail: stabilize/prevent degradation; aid export/translation.

3. Export: mature mRNA → cytosol for translation.

Translation

• Codons: triplets; AUG (start), three stop codons; frame matters.

• tRNA: anticodon (written antiparallel) + matched amino acid.

• Aminoacyl-tRNA synthetases: enforce correct aa↔tRNA pairing.

• Ribosome: aligns tRNAs, catalyzes peptide bond formation.

Quick checks

• What swaps in RNA compared to DNA? (U for T; ribose vs deoxyribose)

• Who ensures the “right amino acid”? (aminoacyl-tRNA synthetase)

Enzymes, metabolism & regulation (Lecture 5)

Protein-ligand binding: specific, shaped by 3D structure; noncovalent interactions dominate. Enzymes: lower activation energy; do not make thermodynamically unfavorable reactions favorable. Coupling: drive unfavorable steps by coupling to favorable ones (often ATP hydrolysis). Carbohydrates: built by condensation (can branch); storage as glycogen; hydrolysis breaks glycosidic bonds (e.g., lysozyme cleaves polysaccharides).

Regulation of protein activity

• Compartmentalization (separate incompatible reactions).

• Change amount (synthesis/degradation) or activity (allostery).

• Feedback inhibition: product inhibits an early enzyme.

• Phosphorylation: kinases add phosphate; phosphatases remove.

• GTP-binding switches: GEF turns on (adds GTP), GAP turns off (stimulates GTP hydrolysis).

Cytoskeleton & motors (Lecture 6)

Microtubules (MTs): α/β-tubulin dimers assemble into protofilaments → hollow tubes; plus end (growth) and minus end (often disassembly). Tubulin binds GTP/GDP; if addition lags, filaments can depolymerize. Functions: cell division, long-range transport, organelle positioning.

Motors on MTs

• Kinesins: typically to + end; move ER outward; processive (one head always bound).

• Dyneins: to – end; move Golgi centrally.

• Mechanism (kinesin): ATP binding docks the neck-linker and “throws” the partner head forward → hand-over-hand walking.

Actin filaments: ATP-bound actin assembles; also polar. Myosin (muscle/myosin-II): motor on actin; not processive—heads act independently; ATP binding causes detachment from actin, then power stroke after hydrolysis/Pi release. Sarcomere = contractile unit.

Practice (from worksheet themes)

• Kinesin parts & functions: N-terminal motor heads; neck linker (force transmission/stepping); stalk (dimerization/rod); C-terminal tail (cargo binding).

• Define processivity (motor takes many steps without detaching).

• Myosin moves toward the + (barbed) end of actin.

• Contrast ATP effects: kinesin ATP → step forward; myosin ATP → detachment.

Imaging & labels: fluorescence & antibodies

Fluorescence: fluorophore absorbs shorter-λ light, emits longer-λ light (after relaxing excess energy). Optical setup: excitation filter → beam-splitter → emission filter to detector. Sensitivity vs specificity: fluorescent labeling boosts signal; antibody choice determines target specificity. Immunofluorescence: primary Ab binds target; secondary Ab (fluor-tagged) binds primary to amplify signal. GFP fusion proteins: genetically tag your protein for live imaging; many color variants exist.

Mini reference

Key terms: LUCA, prokaryote, eukaryote, resolving power, GFP, promoter/terminator, intron/exon, spliceosome, aminoacyl-tRNA synthetase, kinase/phosphatase, GEF/GAP, microtubule, kinesin, dynein, actin, myosin, processive.

Concept connections

• Splicing & alternative splicing → proteome diversity.

• Motor directionality maps to cell architecture: dynein (– end) centers Golgi; kinesin (+ end) extends ER.

• ATP/GTP as molecular switches in both motor mechanics and signaling.