Cell Biology

What a cell is made of, how it runs, and how it divides

About this course

The cell from membrane to genome — transport and membrane potential, energy organelles, protein traffic and the cytoskeleton, then the cell cycle, signalling, cell death and cancer.

What you will be able to do

  • Explain how membranes control transport and set up a potential across the membrane
  • Describe how mitochondria and chloroplasts supply the cell's energy
  • Trace a protein from synthesis to its destination through the secretory and recycling pathways
  • Compare mitosis and meiosis and place each in the cell cycle
  • Connect failures of signalling and cell-cycle control to cell death and cancer

What this course covers

  • ATP turnover: recycling rate and daily production
  • ATP value as a ratio, not a bond
  • Proton motive force and the mitochondrial gradient
  • ATP synthase: a rotary motor geared to the gradient
  • Chloroplast photosystems and the cost of splitting water
  • Endosymbiotic origin of mitochondria and chloroplasts
  • Jagendorf–Uribe experiment: pH jump makes ATP
  • Cytoskeleton as dynamic steady state
  • Microtubule structure and dynamic instability
  • Actin treadmilling and cell crawling
  • Cytoskeletal drugs as rate modulators
  • Myosin stroke and muscle speed via series/parallel arithmetic
  • Intermediate filaments and composite cell mechanics
  • Sliding filament experiment (1954) as a model of scientific reasoning
  • DNA replication speed and parallelism
  • Three-stage replication fidelity
  • CDK–cyclin bistable switch and hysteresis
  • Cell-size control: the adder rule
  • Cell-cycle checkpoints and p53
  • Cell cycle as a chain of engineering solutions
  • Cooper–Helmstetter model of bacterial DNA content
  • Cell Theory: Three Claims and Their Evidence
  • Exponential Growth from Virchow's Third Claim
  • Cell Size Set by Surface-to-Volume and Diffusion
  • Prokaryotes vs. Eukaryotes: The Factor-of-400 Volume Difference
  • The Diffraction Limit of Light Microscopy
  • Epistemic Habits: Measuring, Checking, and Ranging Biology Numbers
  • Pasteur's Swan-Neck Experiment as Decisive Evidence
  • Signal arithmetic: molecules, receptors, and gain
  • Noise floor of receptor counting
  • Second messengers: cyclic AMP and calcium
  • Cascade ultrasensitivity: dimmers become a switch
  • Signal reach: diffusion, decay, and spatial range
  • Adaptation and the off switch: responding to fold change
  • Sutherland's fractionation: discovery of cyclic AMP
  • Apoptosis: budget, mechanism, and switch
  • Fractional killing from threshold variation
  • Hayflick's counter derived from telomeres
  • Three-lock architecture of the apoptotic switch
  • Cancer as multi-step arithmetic with clonal expansion
  • Peto's paradox and the six hallmarks
  • Hayflick mixing experiment as experimental design
  • Mitosis overview and three physics problems
  • The spindle search: random growth, failure, and bias
  • Failure as a design principle in the search
  • The spindle checkpoint: chemical AND-gate for anaphase
  • The pull: force capacity versus disassembly rate
  • The cut, the count, and stacked error filters
  • Reader et al. 1995: laser ablation experiment
  • The DNA packing problem: length and scale
  • Chromatin structure and the nucleosome
  • The nuclear envelope, lamina, and nuclear pore complex
  • Search time for a protein to find a nuclear pore
  • Genome content and the C-value paradox
  • The nucleolus as a membrane-less ribosome factory
  • Hershey-Chase experiment: DNA as the genetic archive
  • Cellular turnover: the steady-state numbers
  • Lysosomal acid: proton counting and the pump's thermodynamic ceiling
  • V-ATPase and ATP synthase as one reversible machine
  • Protein turnover machinery: proteasome and autophagy
  • The peroxisome and catalase kinetics
  • Lysosomal recycling, storage diseases, and the lysosome as nutrient sensor
  • De Duve's discovery of the lysosome by bookkeeping
  • Hydrophobic effect and bilayer self-assembly
  • Gorter and Grendel experiment and the 'right answer, wrong argument' lesson
  • Counting bilayer molecules two independent ways
  • Membrane permeability ladder and the price of admission
  • Born-energy check on the ion barrier
  • Membrane fluidity and FRAP measurement
  • Fluid mosaic membrane as a workplace
  • Protein production rate and signal addresses
  • Reconstitution as experimental strategy
  • Membrane map and budget of a liver cell
  • Motor proteins versus diffusion
  • Co-translational threading and quality control
  • Pulse-chase timing of the secretory conveyor
  • The secretory pathway as continuous directed flow
  • Meiosis: one copy, two divisions
  • Independent assortment and combinatorial diversity
  • Crossing over: mechanism, counts, and spacing rules
  • Sibling genome sharing and crossover count
  • Meiosis I vs. mitosis: a distinct invention
  • The egg's decades-long pause and cohesin decay
  • Worked example: reading crossover count from sibling data
  • Membrane potential is almost free to set
  • Osmosis and osmotic pressure
  • Channels, carriers, and the sodium-potassium pump
  • The Nernst equation: a concentration gradient is a voltage
  • The Goldman equation and the nerve impulse
  • Synthesis: steady state, energy cost, and the lecture's central result
  • Hodgkin–Horowicz experiment: testing and bounding Nernst
  • Multicellularity: what was easy and what was hard
  • Junctions, matrix mechanics, and bundle strength
  • Diffusion limit and the hollow-sphere or fold solution
  • Positional gradient reading and precision limits
  • Toggle switch and epigenetic memory of cell identity
  • Gregor et al. 2007: measuring gradient precision
  • The spine: fourteen clauses and five course habits

Syllabus

  1. The Cell and Its Membrane

    1. L1 · What a Cell Is, and How We Know
    2. L2 · The Membrane
    3. L3 · Transport, and the Potential Across the Membrane

  2. Energy, Genome and Protein Traffic

    1. L4 · Energy, and the Two Organelles That Make It
    2. L5 · The Nucleus and the Genome
    3. L6 · Protein Traffic

  3. Structure and Recycling

    1. L7 · The Cytoskeleton
    2. L8 · Lysosomes, Peroxisomes and Recycling

  4. The Cell Cycle and Division

    1. L9 · The Cell Cycle
    2. L10 · Mitosis
    3. L11 · Meiosis

  5. Signalling, Death and Multicellularity

    1. L12 · Cell Signalling
    2. L13 · Cell Death, and Cancer
    3. L14 · Multicellularity, and Where This Leads