13.1 Programmed cell death #
The study of Programmed cell death provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
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Simple Of Plant Cell ()
13.1.1 Why cells die on purpose #
Development and adult life both require cell death. The tadpole loses its tail. The sculpting of digits separates fingers by killing the cells between them. Lymphocytes that recognise self antigens are deleted. Epithelia shed cells at the same rate as they are born. This death is active, encoded, and tidy. Kerr, Wyllie, and Currie named the morphological pattern apoptosis in 1972. The genes were found later in C. elegans, where Horvitz and colleagues showed that a small set of ced genes kills a defined 131 cells during development and that the same molecular logic operates in humans.
13.1.2 Morphology #
An apoptotic cell shrinks. Chromatin condenses and often marginates against the nuclear envelope, and the nucleus may fragment. The cell blebs into membrane-bounded apoptotic bodies that keep the contents inside until a phagocyte eats them. Because the contents do not spill, inflammation is not triggered. Phosphatidylserine, normally held on the inner leaflet, appears on the outside and is one of the “eat me” signals. In culture, where phagocytes are absent, the bodies eventually rupture (secondary necrosis), which is an artifact of the dish and not the fate in a tissue.
13.2 Pathways of apoptosis #
The study of Pathways of apoptosis provides fundamental principles governing cellular architecture, molecular interactions, and physiological regulation.
Apoptosis (Nih Bioart 21 626915)
13.2.1 Caspases #
Apoptosis is carried out by caspases, cysteine proteases that cut after aspartate residues. They are made as inactive zymogens. Initiator caspases (caspase-8, caspase-9, and others) are activated by being brought together in a complex, which lets them cut one another. They then cleave and activate executioner caspases (caspase-3 and caspase-7), which cut hundreds of cellular proteins: an inhibitor of the DNase that fragments DNA, cytoskeletal proteins, nuclear lamins. The cleavage pattern produces the morphology. Caspases are specific. They do not liquify the cell at random, which is why the apoptotic body stays intact.
13.2.2 The extrinsic pathway #
Death ligands on one cell, such as Fas ligand, bind death receptors on another, such as Fas (CD95). The occupied receptor recruits the adaptor FADD, which recruits procaspase-8, forming the death-inducing signalling complex (DISC). Caspase-8 activates executioner caspases. In cells where that direct route is weak, caspase-8 also cleaves the BH3-only protein Bid. Truncated Bid goes to mitochondria and engages the intrinsic pathway. Cytotoxic T cells use this route, through Fas and through perforin and granzyme, to kill infected or transformed cells.
13.2.3 The intrinsic pathway #
Internal stresses — irreparable DNA damage (via p53), loss of survival signals, excessive unfolded protein, or withdrawal of trophic factors — converge on the mitochondrial outer membrane. The Bcl-2 family controls its permeability.
- Anti-apoptotic members, Bcl-2 and Bcl-xL, hold the membrane closed.
- Pro-apoptotic effectors, Bax and Bak, oligomerise and permeabilise the outer membrane when the restraints come off.
- BH3-only proteins, such as Bid, Bad, and Puma, sense the stresses and tip the balance toward Bax and Bak.
The result is mitochondrial outer-membrane permeabilisation. Cytochrome c leaves the intermembrane space and, in the cytosol, binds Apaf-1. With dATP, Apaf-1 oligomerises into the apoptosome and recruits procaspase-9, which activates caspase-3. Smac/DIABLO, released at the same time, blocks the IAPs, proteins that would otherwise inhibit caspases. This is why cytochrome c in the cytosol means something entirely different from cytochrome c in the respiratory chain.
Bcl-2 was discovered as the oncogene at a chromosomal translocation in follicular lymphoma. Too much Bcl-2 does not make cells proliferate faster. It makes them refuse to die, so damaged cells accumulate. That distinction, proliferation versus survival, is why apoptosis belongs in the cancer discussion.
13.3 Necrosis #
Necrosis is uncontrolled death after acute injury: trauma, ischaemia, toxin, complement lysis. The cell and its organelles swell, the plasma membrane ruptures, and the contents, including damage-associated molecules, spill and inflame the tissue. There is no orderly DNA ladder of the apoptotic kind as the primary event, and caspases are not the executors.
The contrast:
| Feature | Apoptosis | Necrosis |
|---|---|---|
| Trigger | Developmental programme or regulated stress response | Acute injury |
| Cell volume | Shrinks | Swells |
| Membrane | Intact until phagocytosis; phosphatidylserine exposed | Ruptures early |
| Nucleus | Condensed, fragmented, DNA cut between nucleosomes | Karyolysis, random degradation |
| Inflammation | Absent when clearance is normal | Present |
| Energy | Requires ATP | Often the result of ATP failure |
The dichotomy is useful and not absolute. Necroptosis is a programmed, caspase-independent death with necrotic morphology, driven by RIP kinases, used in some viral infections when caspases are blocked. Naming it is enough; the machinery is beyond this course. The exam distinction remains apoptosis versus necrosis.
13.4 Renewal and stem cells #
13.4.1 Turnover must balance death #
A tissue in steady state produces cells at the rate it loses them. The rates differ enormously. The intestinal epithelium replaces itself in a few days. Skin epidermis turns over in weeks. Red blood cells circulate for about four months and are then cleared. Hepatocytes divide rarely unless part of the liver is removed, in which case the remainder proliferates and then stops. Neurons of the central nervous system are mostly lifelong. A description of a tissue that ignores its turnover rate misstates how its stem cells are used.
13.4.2 Potency and the niche #
A stem cell divides and can produce both a replacement stem cell and a cell that will differentiate. That is the operational definition. Potency describes the range of what the daughters can become.
| Potency | What it can produce | Example |
|---|---|---|
| Totipotent | Every embryonic and extra-embryonic cell | The zygote, and early blastomeres in mammals |
| Pluripotent | Every cell of the embryo proper, not the extra-embryonic membranes | Inner-cell-mass cells; embryonic stem cells in culture |
| Multipotent | The cell types of one tissue | Haematopoietic stem cell; intestinal stem cell at the crypt base |
| Unipotent | One differentiated type, plus its own replacement | Spermatogonial stem cells, in the strict sense |
Differentiation is usually a sequence of progenitors with narrowing potency, not one jump from stem cell to finished cell. The finished cell often leaves the cycle and becomes structurally specialised: a keratinocyte full of keratin, a red blood cell without a nucleus, a neuron with an axon.
The niche is the microenvironment that keeps the stem cell a stem cell: particular neighbours, matrix, and signals (Wnt in the intestinal crypt, for example). A daughter that leaves the niche loses those signals and differentiates. Many stem-cell divisions are asymmetric in outcome, whether or not the division itself partitions determinants unequally. The niche, not a mystical internal property, explains why a stem cell transplanted to the wrong place may not behave as one.
13.4.3 Induced pluripotency #
Differentiated cells are not irreversibly locked in every case. Yamanaka and colleagues showed that expressing four transcription factors — Oct4, Sox2, Klf4, and c-Myc — can return a differentiated mouse or human cell to a pluripotent state. The products, induced pluripotent stem cells, can then be directed into other lineages. The result confirmed that potency is a gene-regulatory state, maintained by transcription factors, and not a loss of genes. c-Myc is dispensable in later protocols and is the most dangerous of the four because it is an oncogene. Reprogramming is inefficient and can leave epigenetic memory of the starting cell type. It is a genuine route to patient-matched cells and a genuine source of tumours if the pluripotent state is not fully extinguished before transplantation.
13.5 The transformed cell #
13.5.1 What “transformed” means in culture #
Transformation, as cell biologists use the word, is the set of heritable changes that make a cultured cell behave like a cancer cell. The observable properties are:
- reduced dependence on growth factors (the signalling pathways of Chapter 12 are locked on, or the requirement is bypassed);
- loss of contact inhibition — normal cells stop dividing when they touch their neighbours; transformed cells pile up;
- loss of anchorage dependence — normal cells die or arrest if denied matrix attachment; transformed cells grow in soft agar;
- an indefinite number of divisions, often through reactivation of telomerase, which maintains telomeres that would otherwise shorten to a crisis (the Hayflick limit of ordinary somatic cells);
- genomic instability, so that further mutations accumulate;
- in the organism, the ability to recruit blood vessels, invade, and colonise distant sites, which culture only partly reports.
Hanahan and Weinberg’s hallmarks organise these properties: sustained proliferative signalling, evasion of growth suppressors, resistance to cell death, replicative immortality, angiogenesis, and invasion and metastasis, with later additions of altered metabolism, evasion of the immune system, genome instability, and tumour-promoting inflammation. Each hallmark is a cell-biological chapter already in these notes, broken.
13.5.2 Oncogenes and tumour suppressors #
A proto-oncogene is a normal gene that promotes division or survival (Ras, Myc, a growth-factor receptor, Bcl-2). A gain-of-function mutation, amplification, or translocation makes it an oncogene. One altered copy is enough, because the product is overactive.
Tumour Stroma And Extracellular Matrix In Hypoxia
A tumour suppressor restrains the cycle or promotes repair or apoptosis (Rb, p53, PTEN, BRCA1). Both copies must usually be lost before the restraint disappears. Rb holds E2F until CDK phosphorylation releases it; loss of Rb lets E2F drive S phase without the proper signal. The retinoblastoma of children is the historical example, and Knudson’s two-hit hypothesis came from its inheritance pattern.
Cancer is therefore not one disease and not one mutation. It is clonal evolution: a cell acquires a combination of oncogene activations and tumour-suppressor losses, expands, and its descendants acquire more. The cell-biology course stops at the cellular properties and the pathways. Pathology and immunology take up invasion, metastasis, and immune evasion in their own right.
13.6 Flow cytometry #
13.6.1 What the instrument does #
A flow cytometer suspends cells in a stream so fine that they pass a laser one at a time. Detectors record:
- forward scatter, roughly proportional to size;
- side scatter, sensitive to internal complexity and granularity;
- fluorescence at chosen wavelengths, from dyes or labelled antibodies bound to the cell.
Thousands of cells are measured per second, which makes the method statistical. A rare cell present at one in a thousand is visible as a population, which microscopy would struggle to count fairly. If the instrument is a sorter (FACS, fluorescence-activated cell sorting), droplets containing chosen cells are charged and deflected into a tube. The sorted cells are alive if the staining was gentle, and can be cultured or analysed further.
13.6.2 Cell-cycle and apoptosis measurements #
DNA content is measured with a dye such as propidium iodide, which fluoresces in proportion to DNA once the cell is permeabilised.
Smad Apoptosis
- G0/G1 cells have 2C DNA.
- S-phase cells have intermediate values and fill the space between the peaks.
- G2 and mitotic cells have 4C DNA and cannot be distinguished by DNA content alone. A second marker, such as phosphorylated histone H3 for mitosis, separates them.
Apoptosis is read in the same machine. Annexin V labelled with a fluorophore binds exposed phosphatidylserine on cells whose membrane is still intact. A membrane-impermeant DNA dye, added at the same time, enters only cells whose membrane has failed. The combination separates live cells (negative for both), early apoptotic cells (annexin only), and late apoptotic or necrotic cells (both). A sub-G1 DNA peak, from fragments that have left the cell, is a coarser apoptotic signature.
The method belongs in this chapter because the questions it answers — is this population dividing, arrested, or dying, and which surface markers does it carry — are the questions of renewal and transformation.
13.7 Key terms, summary, and self-check #
Key terms. Apoptosis; apoptotic body; caspase; DISC; Bcl-2; Bax; apoptosome; necrosis; potency; niche; iPSC; contact inhibition; anchorage dependence; oncogene; tumour suppressor; flow cytometry; annexin V.
Summary. Apoptosis is an ATP-dependent, caspase-executed death that packages the cell for phagocytosis. The extrinsic pathway starts at death receptors and caspase-8; the intrinsic pathway starts at mitochondria under Bcl-2-family control and activates caspase-9. Necrosis ruptures the cell and inflames. Stem cells maintain tissues according to their potency and their niche, and differentiated cells can be returned to pluripotency by a small set of transcription factors. A transformed cell has escaped the controls on division, attachment, death, and finite lifespan. Flow cytometry counts those states cell by cell.
Self-check.
1. Why does apoptosis not cause inflammation, whereas necrosis does?
2. Cytochrome c has two jobs. Where is it during respiration, and where must it be to drive apoptosis?
3. A lymphoma overexpresses Bcl-2 but does not cycle especially fast. Why does the clone still expand?
4. What is the difference between multipotent and pluripotent, and which word applies to a haematopoietic stem cell?
5. A DNA-content histogram shows a large 2C peak, almost no S-phase cells, and a small 4C peak. What does that population’s cycling look like? If those cells are also annexin-V positive and impermeant-dye negative, what process is underway?
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# Closing: how the chapters fit together
A cell is a membrane-bounded compartment that copies its DNA and divides. Everything else in these notes is a solution to a problem that follows from that sentence.
The bilayer (Chapter 3) creates an inside, and immediately creates the problem of transport. Eukaryotes add internal bilayers (Chapter 4), which creates the problem of sorting (Chapters 7 to 9). A large fragile cell needs a wall or a matrix and junctions (Chapter 5) and an internal skeleton with motors (Chapter 6). Division has to be ordered, so cyclins, checkpoints, and a spindle exist (Chapters 10 and 11). Other cells and the environment have to be heard, so receptors exist (Chapter 12). And because a tissue is a population, not a single cell, there are regulated ways to die and to replace the dead (Chapter 13).
Methods (Chapter 2) are not a separate science. Every structure in the list was established by a microscope, a centrifuge, or a genetic experiment with an artifact that had to be ruled out. When you revise a pathway, revise the observation that supports it.
Revision checklist #
Use this as a last pass before an examination.
1. State the cell theory in three sentences and name the person attached to the third.
2. Draw, from memory, a Gram-negative envelope and a plant primary wall, labelling the selective barrier in each.
3. Write the route of a secreted protein from the ribosome to the outside of the cell, naming SRP, Sec61, COPII, the Golgi, and a SNARE.
4. Write the route of a mitochondrial matrix protein, and say why it cannot use the first route.
5. Give the diameter, subunit, and one motor of each cytoskeletal polymer.
6. List mitotic stages by what the nuclear envelope and the cohesin are doing.
7. Name the cyclin–CDK pair at G1/S and at G2/M, and the two substrates the APC/C must destroy for anaphase and mitotic exit.
8. Draw either the cAMP pathway or the Ras–MAPK pathway as a chain of five arrows, and mark where it is turned off.
9. Contrast apoptosis and necrosis in four rows: trigger, membrane, inflammation, proteases.
10. For any organelle, name the marker enzyme or marker protein you would assay in a centrifugal fraction.
Selected sources #
These notes are an original teaching summary, not a transcript of any textbook or of the block PDFs stored alongside them.
- Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 6th–7th editions. Garland Science / W. W. Norton.
- Alberts B, Hopkin K, Johnson A, Morgan D, Raff M, Roberts K, Walter P. Essential Cell Biology. W. W. Norton.
- Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Martin KC, Yaffe M, Amon A. Molecular Cell Biology. W. H. Freeman.
- Cooper GM, Hausman RE. The Cell: A Molecular Approach. Sinauer / Oxford University Press.
- Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 144:646–674 (2011).
- Mitchell P. Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature 191:144–148 (1961).
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# Part C. Visual Figures & Scientific Diagrams Gallery
Comprehensive high-resolution visual reference repository for Cell Biology from the B10logy Visual Atlas.
202403 Meiosis Ii Maternal Origin
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# Part C. Visual Figures & Scientific Diagrams Gallery
Essential high-resolution reference diagrams for Cell Biology from the B10logy Visual Atlas.
