Multicellular Lifeforms

A multicellular lifeform is a number of cooperating cells (of about 10³ — 10¹² — 10¹⁶ cells), in which each individual cell cannot live separately. This 'undivided loyalty' to the multi-unit comes from them being all identical genetically (they all develop from a single cell), so there is no competition between them to reproduce.

Multicellularity has its advantages:

All these advantages allow for higher metabolic rates (from $0.2-1.2-3\; W/kg$ while inactive to peaks of $12\; W/kg$).

Multicellularity requires new mechanisms to

• connect cells together
• communicate between cells
• regulate genes of different cells; e.g., an external signal may need affect only a particular tissue;
• differentiate and develop from a single cell

Multicellularity probably evolved from colonial eukaryotes which specialize into "vegetative" and "reproductive" cells.

Cell Connections

Cells are kept together by a composite matrix of polysaccharides and proteins outside the cells, produced by membrane proteins.

In animals, this extracellular matrix consists of cross-linked 3-stranded fibers of collagen or chitin in a "gel" of glycoproteins. These ionized polymers keep hydrated.

1µm

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Various proteins join cells together at specialized points called junctions. These either anchor the cells together and to the surrounding matrix, or else facilitate the transmission of molecules between them. Variants of such proteins are expressed by different cell types.

Different cell types express different varieties of integrins, which attach a cell's cytoskeleton to the correct extracellular matrix like "Velcro".

The outer epithelial cells have special tight-binding bands of cadherin junctions that make it a tough outer skin, separating the outside of the multicellular from its inside.

The extracellular matrix of plants is called a cell wall. It is permeable and acts as a structural container for cells. It becomes rigid when water fills up a vacuole, and prevents the cell from bursting.

The cell wall is made up mostly of polysaccharides (without much N, since plants cannot produce it readily):

• cellulose fibers, a glucose polymer of 0.5 – 14k atoms,
• xylan, a polymer of xylose,
• pectin, a polymer of galactose,
• glycoproteins, which attach cells to the cell wall ("middle lamella"),
• sometimes stiffened by lignin and extra cellulose.

Plasmodesmata join cells together, connecting even the endoplasmic reticulum; up to small proteins can pass through.

Cell Types

Specialized cells do their jobs much better than generic eukaryotic cells:

• they can pack the relevant proteins in each cell,
• they can have a specialized shape
• they can be stacked into tissues

Classification of cell types:

• Epithelial cells:
  • attached tightly to each other and the basal lamina (thick extracellular matrix)
  • prevent other cells from entering
• Sensory cells:
  • have receptors to detect specific molecules (e.g., O₂) or light or heat; or
  • cilia to detect touch
• Germ cells:
  • perform meiosis to produce gametes
  • may also produce a "fruiting body" for this
• Contractile cells: contract, e.g., muscle cells, "guard" cells
• Stem cells:
  • can divide with one cell specializing and the other remaining a stem cell;
  • specialized to reduce DNA damage
• Secretory, absorption cells:
  • secrete hormones, enzymes, or poisons in vesicles, or
  • aborb nutrients and pass them to other cells.
• Macrophages: clean up debris of dead cells, and attack parasites such as viruses, bacteria, fungi
• Connective cells:
  • produce proteins for the matrix or as a pigment, or
  • store/produce food, or
  • let fluids pass through
• Neurons: pass a signal fast across to other cells

The DNA of multicellulars is about fifty times larger than that of unicellular eukaryotes: $0.5-2-100Gb$ containing $5-30k$ genes. About $3-4k$ genes are essential eukaryote genes; the rest are for cell connection, cell communication, and cell differentiation.

All cells have the same genome, but they differ in which genes are in/active:

Even specialized cells retain a stress response — to O₂ deprivation, heat shock, ....

Cell Communication

Cells use signal molecules to communicate with other cells.

A signal is sent by either

• pumping the molecules out through transporters or releasing vesicles full of stored molecules, or
• passing through cell gap junctions directly into other cells, or
• exhibiting signal proteins on their surface.

1nm pore

Receptors at the cell membrane sense the water-soluble signal molecules (up to 100 different types); some non-polar signals (e.g., growth hormones) diffuse through the membrane and activate transcription factors directly without receptors. Surface protein signals bind to receptors on neighboring cells (e.g., Notch) that pass on the signal inside the cell.

Many cell types can trigger a signal, but sensory cells are specialized to detect certain molecules or events, e.g., food, touch, heavy metals, heat, light, tension in the membrane integrins, etc.

Logical processing: The signal, or combination of signals, triggers off certain signalling pathways. All cell types share the same pathways (Ca²⁺, cAMP,...) but each has different receptors and target effects. So different cells may respond differently to the same signal. One cell may use Ca²⁺ for one signal pathway to turn on one set of genes, while another uses it to contract a muscle cell, etc.

A signal may either act quickly (milliseconds) on already existing proteins, or more slowly as transcription factors (minutes) to switch on different genes.

The effect is usually temporary — how fast signal molecules are removed determines the latency of the signal; but it can be permanent — when the signal triggers mitosis or determines the cell type.

Cell Division

Cell division has to be controlled securely, as one cell can overwhelm the rest: In just 40 cell generations, a single cell becomes 2⁴⁰, or 1kg of cells; even the largest tree does not require more than 60 cell generations.

Most cells are only able to divide for 20-50 times to prevent uncontrolled division — the telomeres that cap chromosomes are not lengthened, so they shorten with each mitosis. When they are too short, the cell stops dividing.

There are many proteins that promote or suppress mitosis, triggered by signals from integrins that sense 'tensed' or 'compressed' neighbouring cells and give out a local 'growth' signal. To replace the $0.1\%$ of cells that die every day, stem cells retain the ability to divide indefinitely — they can lengthen their telomeres.

Programmed Cell Death (Apoptosis)

When the cell detects that something is seriously wrong, e.g.,

• a defective mitosis,
• an unrepaired chromosome break, or too much DNA damage,
• cell is disattached from extra-cellular matrix,
• no growth factor,
• the end of a telomere is reached,

then the cell is prepared for death by the formation of the apoptosome protein:

• DNA, proteins are cleaved into 180bp pieces by caspase proteins,
• a protein mixes the cell membrane lipids,
• the cytoskeleton is dismantled, so the cell breaks into small spheres without rupturing,
• external phagocytes recognize them by their membrane and engulf them.

Ageing

Although the DNA repair mechanism of cells is very efficient, about every 1 to 10 divisions, a gene in the whole genome of a cell mutates.

So every cell accumulates errors as it continues to replicate; when $15-20$ genes have errors, the cell is likely to be seriously affected and dies.

Cells accumulate mutations; the earlier they get one, the more widespread it becomes.

If a mutation happens to

• the gamete, then the entire individual carries the mutation (genetic disability),
• a cell of a developing zygote at an essential gene, then only the resulting tissue is affected; if it happens to an inessential gene, then there is no effect;
• a cell of an adult, then only that cell is affected; the mutated gene dies with the cell;
• a gamete-producing gonad cell, then all its gametes/children inherit the mutation.

Cancer

In large long-lived multicellulars, a few mutated cells survive and may lead to cancer:

1. Some (stem) cells have mutations in 'oncogenes': these are genes that encourage mitosis or suppress apoptosis, so they multiply to form a polyp in a tissue.
2. When one of these cells gets 2–5 mutated oncogenes, it does not die readily if something else goes wrong. As it proliferates, something will go wrong — a mutation to a gene like p53 or RB1 that stops mitosis when it is defective.
3. With these important checkpoint proteins gone, the cell can divide even if mitosis produces unbalanced genomes. Some daughter cells are now likely to lose other essential genes such as
   • DNA repair systems
   • Chromosome maintenance (condensation, etc.) so translocations, deletions etc. accumulate
   • Activation of Telomerase, so telomere is lengthened periodically.
4. From now on, it is survival of the fastest-replicating cell, engulfing the remaining cells.

Development and Differentiation

The initial cell gives rise to the possibly hundreds of different cell types and tissues.

Morula

The first task is to establish the 3 axes of

• front / back
• up / down
• right / left

The large egg cell has a concentration gradient of the initial morphogen: this determines front/back. When it is fertilized, the sperm activates it, and the egg completes meiosis. The sperm entry determines up/down.

The cell now goes through 5 rounds of division into a ball of 32 cells; each cell ends up with a different concentration of this morphogen. A set of genes (Wnt, Fz) switch on different development genes for the different axes. (For now, differentiation genes are repressed.)

Blastula

Two more rounds of division gives 128 cells; cells start to pump water into the center so they form a hollow open sphere; two more rounds give 512 cells: the ovum mRNA is destroyed and differentiation genes are turned on (repressors for them are removed and methylation patterns appear); a head-tail asymmetry forms because of:

• Externally created gradient in transcription factor
• Internally created gradient

For each cell division, one remains a stem cell and the other differentiates (because some transcription factors segregate along the spindle). While a cell's fate is not yet determined, it may reverse differentiation and remain some sort of stem cell. When its fate is irreversibly determined, it differentiates into a specialized cell — it becomes committed, with a number of genes permanently switched off, and it does not divide again normally.

Cells show their type by the integrins they exhibit.

Gastrula

In animals, one side of the blastula folds inward and the cells form two or three specialized layers:

• ecto → skin, nerves;
• meso → connective, muscles, gonads;
• endo → gut

Sponge and Plant embryos do not form a gastrula but elongate (e.g., to form the shoot and root).
In animals, the cells are able to migrate to their correct position.

Developmental genes must be permanently switched off. A simple way to do this is to have the gene network code for its own transcription factor; once the network is switched off, it cannot switch on again spontaneously.

Cells develop by interacting with morphogens. Homeobox genes produce and export morphogens to nearby cells. The various combinations of morphogens from different tissues at different stages give rise to cells with different patterns of switched development genes.

Move the morphogen centers (on the right; nearby cells receive more of a center's morphogen) and click on the network (left) to modify the effect of their combination.

Reproduction

Sex

Multicellulars can totally eliminate self-fertilization by specializing into two sex types: males produce only sperm gametes and females only ova gametes (although in a few species, individuals can be both — hermaphrodites). To achieve this distinction, each sex has its own chromosome X or Y: the default XX combination gives one sex type (e.g., female for mammals, male for reptiles), but the Y chromosome, if present, triggers a development path that produces the other sex. They are homologous on about 1/4 of the chromosome, but of different size on the rest (cross-overs are prevented in this area.)

X inactivation

The X chromosome is unlike any other chromosome because individuals have either one copy of it XY or two XX. So either the main part of one of the two XX chromosomes is downregulated or even switched off during late blastula stage (e.g., mammals), or the main part of the single X chromosome in XY individuals is upregulated (e.g., insects).

Bad alleles on the active X are dominant, since they have no counterpart.

Normally, missing or extra chromosomes (from mitosis) lead to death; but an extra X or Y chromosome does not kill; so X, XXY, XYY are all viable.

Life Cycle

Development into adult multicellulars can occur from the zygotes and/or the gametes.

Branching

A common pattern created by multicellular lifeforms is the branching structure. It is often used for the transport of air or water, or may act as a filter trap.

Plants

Plants form a major division of multicellular forms; they are autotrophic and phototrophic, i.e., require only water, air, minerals, and sunlight.

Leaves use photosynthesis in their cells' chloroplasts to convert the air's CO₂ and ground/dew water into carbohydrates, powered by sunlight.

The stem connects the roots to the leaves and supports the leaves.

The roots absorb water and salts by

• osmosis / capillarity / evaporation (transpiration pull) and
• active intake (root pressure).

Being immobile, plants' primary needs are to get enough sunshine and water, especially not to overheat, freeze, or dry out. Transpiration of water from the roots to the leaves is usually continuous or diurnal.

Plants cannot survive in dry climates or permafrost (with very cold winds). In hot climates, they produce isoprene for protection.

Parenchyma consists of filler cells that store water and starch. When full of water, or when fortified by a cellulose cell wall, they support the stem, which would otherwise wilt.

Xylem (wood) is lignified dead cells acting as vessels to transport water and its minerals from the roots, at 15-250 g/h/m², powered by capillarity and root pumping pressure (at night). Cellulose or lignin fibres are produced by cells that then die. They provide the main support for the stem.

Cambium cells are undifferentiated stem cells. Growth is guided by signals from 'phototropin' receptors triggered by light.

Phloem cells transport sugary sap (including soluble proteins) from the leaves/store at 5mm³/hour. They lack a nucleus and depend completely on neighboring cells.

Growth is promoted by 'hormones', e.g., auxins (for direction of growth) and gibberellins (for stem).

Leaves: Waxy cuticle; epidermal cells; stomata with guard cells; leaf shape and layering;

Defence/Pigmentation

When plants detect disease or grazing, they produce poisons, specifically against bacteria, fungi, and herbivores:

• passive, e.g., tannin, lignin, phytoliths (that abrade insect mouths),
• or active,
  • terpenes (against insects' nerves, e.g., herbs; oubain / digitalis inactivate sodium pumps; saponin against fungal cell walls)
  • alkaloids (react with enzymes, e.g., caffein, vanillin),
  • pheromones that attract predatory wasps; etc.

Germination and Growth

Cells at first use glyoxilation and beta-oxidation (in the peroxisomes) for the initial supply of glucose, until leaves form.

Storage

In strong seasonal variation (too hot/cold/dry), the plant stores carbohydrates (mannose, starch etc.) and loses its leaves during the hard season.

Reproduction

Plants reproduce mostly by flowers which grow at the end of an initial growth stage at a particular season (controlled by a suite of genes).

Seed Dispersal

Size

• Trees and shrubs (with large seeds, long growth period; K-strategy), or
• Grasses (many seeds, short growth period).

Fungi

Fungi have a cell wall of chitin (a polymer of acetyl-glucos-amine), glucan (a polymer of glucose), and glycoproteins, surrounded by more glucan. Cells are inter-connected by large pores, to facilitate fluid flow; but large protein 'stoppers' can close off these pores when a cell is damaged, or to allow neighboring cells to differentiate.

The cells form long hyphae that branch out. At favorable places, they branch deeper in towards nutrients, where they release enzymes to absorb them, or outward to the surface to form fruiting bodies; many can penetrate plant epithelia.

Fungi are haploid, i.e., have one copy of each chromosome. When two individuals meet, their hyphae fuse, produce a small fruiting body (some species grow a large mushroom) that produces spores (diploid → meiosis → gametes); a "rain" of spores or even an "explosion" scatters them away.

Animals

Animals are multicellular consumers. Generically they have a gut to digest food, blood to distribute molecules to all cells, nephridia to keep it clean, nerves to control activity, muscle for movement, and senses to detect light and chemicals.

Extracellular Digestion

An advantage for animals over unicellular consumers is an internal gut into which more powerful enzymes can be secreted (carbohydrases, lipases, proteases e.g., pepsin, trypsin) that break up carbohydrates, fats, and proteins, respectively.

Vitamins

As consumers, many species lost the ability to synthesize key compounds that are found often enough in their food. Examples:

• TPP (vitamin B1 thiamine),
• FAD (B2 riboflavin),
• NAD (B3 niacin),
• Carboxylase (biotin B7)
• pyridoxine (B6),
• retinol (A),
• quinone (K),
• some amino acids (e.g., those that involve the chorismate, pyruvate, valine and aspartate pathways)

Nutrient Diffusion

A disadvantage for multicellulars is that oxygen and nutrients need to be transported to the cells. So, such animals are either elongated / flattened for a high surface area, or have a branched internal canal carrying internal blood with oxygen-storing proteins (usually a porphyrin with Fe or Cu, e.g., haemoglobin). Blood also contains various lymphocytes for defence against invaders, and a clotting mechanism in case of rupture.

There may also be air trachaea for land animals for the direct diffusion of oxygen. Cilia may be present on the outside or inside to enable fluid flow.

Excretion

Intercellular fluid and blood need to be filtered, usually by active reabsorption; ammonia has a fast enough rate of diffusion in water not to require any special excretion mechanism.

Reproduction

Gonads produce gametes: testis → sperm, ovaries → ova. Some have both, but they mature at different times and place to avoid self-fertilization.

With very few exceptions, all animals are diploid.

Neural Network

Neurons are specialized cells that transmit signals (at $1m/s$ up to $100m/s$ if axons have a myelin sheath).

Na⁺Na⁺K⁺K⁺60mVStimulate this neuron to start an impulse

Na-K pumps work continuously (using ATP) to swap 3 Na⁺ inside with 2 K⁺ outside the cell. (Neurons use up the most energy among all cells because of this.)

The impulse is basically a domino effect of Na and K channels triggering each other.

1. Na-channels are triggered to open when the exterior voltage falls sufficiently, allowing an inrush of Na⁺ into the neuron.
2. When the interior voltage becomes positive, the Na-channels close and the K-channels open to let K⁺+ out.

Many neurons have a parallel but separate transmission of Ca²⁺ waves inside the cell.

At the end of an axon are several synapses full of vesicles containing a type of neurotransmitter molecules. When a nerve impulse reaches them, these are immediately released outside the cell and detected by receptors on adjacent neurons or muscle cells. Neurotransmitters can be either:

• excitatory ('stimulants') e.g., glutamate, open the Na⁺ channels; or
• inhibitory ('tranquillizers') e.g., glycine or GABA, open the K⁺ channels.

Each neuron may fire a train of impulses about every 0.1s.

Neural networks

Neural networks regulate the various tissues. Each neuron may connect to thousands of other neurons or muscle cells.

In the simulation below, a very small network controls the muscles of a swimmer.

Press the keys $J,K,L$ to activate the corresponding neurons.
The network then fires the other neurons in a specific order.
Neurons $1,2,3$ and $4,5,6$ control the left/right muscle cells of the swimmer.

A network forms when 'modulatory' neurons secrete special neurotransmitters (e.g., dopamine, serotonin,...) that activate genes in the neighboring neurons encouraging the growth of synapses. Synapses tend to concentrate in localized areas called ganglia.

Sensory Receptors are modified neurons that trigger an impulse when activated by an external stimulus:

Response Behavior: 'Motor' neurons mostly affect muscle cells: the final part of the impulse consists of Ca²⁺ which triggers the muscle cell to contract. A reflex is a quick direct response to avoid danger, but usually muscles need to be coordinated for effective motion. Inside muscle cells, an elastic titin protein holds myosin; as myosin moves across actin fibers, the whole cell structure is compressed.

Other responses:

Electric discharge cells give shocks of up to 700V.

In general, the response to danger is either

• no motion; defensive mechanism applied instead, or
• a haphazard motion (kinesis) until the stress lessens, or
• a directional motion (taxis) to/from the stimulus.

Feeding: Animals often specialize in the type of food they eat:

• herbivores — plants
• carnivores — animals
• omnivores — unspecialized
• scavengers — dead organics

Sleep is needed to rest the nerves (so that they can anabolize and recover?)

Reproduction: Breeding (mating) varies; it can occur

• once only with many young, or
• many times with fewer young.

Dispersion of young animals is not usually a problem since they simply move away; very small animals may be blown by the wind or by water currents; parasites use an intermediate host for dispersion.