Cell communication and the cytoskeleton

Cells are not isolated. A bacterium senses food and its neighbors; the 30 trillion cells of a human body coordinate growth, metabolism, defense and behavior through a constant traffic of chemical messages. Cells also have to hold their shape, move their contents to the right places and, in many cases, crawl or swim. This lesson introduces both topics: how cells send, receive and amplify signals, and the cytoskeleton of protein filaments and motors that gives cells structure and movement. Both are large fields; BIOL-214 develops them in depth and neurobiology (BIOL-420) and immunology (BIOL-380) apply them.

How cells talk

Cells communicate mostly with chemical signals, molecules released by one cell and detected by another. Signals differ in how far they travel:

Bacteria signal too. In quorum sensing, each bacterium releases a small molecule; when the population is dense enough that the signal builds up, the bacteria switch on genes together, for example to glow (in the marine bacterium Vibrio fischeri, which lights up the organ of a small squid) or to form a biofilm on a medical device.

Three stages: reception, transduction, response

In the 1950s Earl Sutherland, studying how the hormone adrenaline makes liver cells release glucose, found that the hormone never entered the cell. Instead, binding at the surface triggered a chain of events inside, which he described in three stages, a framework still used today (he received the 1971 Nobel Prize in Physiology or Medicine).

Reception is the binding of a signal molecule (a ligand) to a specific receptor protein, which changes shape. Transduction converts that shape change into a form that can produce a response, usually a relay of several molecules inside the cell. Response is the final cellular activity: an enzyme switched on, a gene expressed, a channel opened, the cell dividing or dying. Because each step can involve many molecules, signals are amplified and can be adjusted along the way.

Receptors

Where the receptor sits depends on the signal. Large or water-soluble signals, such as peptide hormones and most neurotransmitters, cannot cross the membrane and bind receptors on the cell surface. Small, hydrophobic signals, such as steroid hormones (estrogen, testosterone, cortisol), thyroid hormone and nitric oxide, cross the membrane and bind receptors inside the cell.

Receptors bind their signals reversibly, and how many are occupied depends on the signal's concentration relative to the receptor's dissociation constant, Kd, the concentration at which half the receptors are occupied. The relation has the same shape as the Michaelis–Menten curve from lesson 8:

# Fraction of receptors occupied at different hormone concentrations
Kd = 1.0          # nanomolar (a typical high-affinity hormone receptor)
for L in [0.1, 0.5, 1, 2, 5, 10, 100]:
    occ = L / (Kd + L)
    print(f"[hormone] = {L:6.1f} nM  ->  {occ*100:5.1f} % occupied")
# Hormones circulate at very low concentrations, often nanomolar or below

[hormone] =    0.1 nM  ->    9.1 % occupied
[hormone] =    0.5 nM  ->   33.3 % occupied
[hormone] =    1.0 nM  ->   50.0 % occupied
[hormone] =    2.0 nM  ->   66.7 % occupied
[hormone] =    5.0 nM  ->   83.3 % occupied
[hormone] =   10.0 nM  ->   90.9 % occupied
[hormone] =  100.0 nM  ->   99.0 % occupied

Transduction: second messengers and phosphorylation

Two mechanisms dominate signal transduction. The first is protein phosphorylation. Enzymes called protein kinases transfer a phosphate group from ATP to specific amino acids on target proteins, changing their shape and activity; protein phosphatases remove the phosphates, switching the proteins back. Many pathways are phosphorylation cascades in which one kinase activates the next. The human genome encodes more than 500 protein kinases, and many cancer drugs, such as imatinib for chronic myeloid leukemia, work by blocking an overactive kinase.

The second is small molecules called second messengers, produced inside the cell in response to the first messenger outside. Cyclic AMP (cAMP), made from ATP by the enzyme adenylyl cyclase, was the first discovered. Calcium ions are another: cells keep calcium in the cytosol about 10,000 times lower than outside, so opening calcium channels produces a sudden, strong signal that triggers muscle contraction, neurotransmitter release and much else. Second messengers diffuse quickly through the cytosol, spreading the signal.

Amplification: a small signal, a big response

One of the most important features of signaling pathways is amplification. When adrenaline binds a liver cell, each activated receptor activates many G proteins; each activated enzyme makes many cAMP molecules; each kinase phosphorylates many copies of the next protein. Over several steps, a handful of hormone molecules can lead to the release of millions of glucose molecules within seconds, preparing the body for fight or flight.

# Amplification through a signal cascade (illustrative factors)
steps = [("receptor -> G proteins", 10),
         ("G protein -> cAMP (via adenylyl cyclase)", 100),
         ("cAMP -> protein kinase A (2 cAMP each)", 0.5),
         ("PKA -> phosphorylase kinase", 10),
         ("phosphorylase kinase -> glycogen phosphorylase", 10),
         ("phosphorylase -> glucose per minute", 1000)]
n = 1
for name, factor in steps:
    n *= factor
    print(f"{name:<48} x{factor:<6}  running total {n:,.0f}")

receptor -> G proteins                           x10      running total 10
G protein -> cAMP (via adenylyl cyclase)         x100     running total 1,000
cAMP -> protein kinase A (2 cAMP each)           x0.5     running total 500
PKA -> phosphorylase kinase                      x10      running total 5,000
phosphorylase kinase -> glycogen phosphorylase   x10      running total 50,000
phosphorylase -> glucose per minute              x1000    running total 50,000,000

Responses and switching off

Signals produce two broad kinds of response. Some act in the cytoplasm within seconds, by activating enzymes or opening channels, like glycogen breakdown or muscle contraction. Others change gene expression in the nucleus, taking minutes to hours, like steroid hormones switching on genes for development or growth factors telling a cell to divide.

Just as important as switching signals on is switching them off. Enzymes such as phosphodiesterase break down cAMP; phosphatases remove phosphates; G proteins switch themselves off by splitting their bound GTP; receptors are taken into the cell by endocytosis (lesson 7). Caffeine partly works by blocking adenosine receptors and, at high doses, phosphodiesterase. Failure to switch off has consequences: cholera toxin locks G proteins in the on state in intestinal cells, causing massive secretion of salt and water, and mutations that lock the growth-signaling protein Ras in its active form are found in many cancers. A related form of signaling tells cells to die: apoptosis, programmed cell death, removes unneeded or damaged cells in a controlled way, and its failure also contributes to cancer (lesson 12).

The cytoskeleton

Electron microscopy and fluorescence imaging reveal that the cytoplasm is threaded by a network of protein filaments, the cytoskeleton. It gives cells their shape and mechanical strength, anchors organelles, provides tracks for transport, separates chromosomes during division and drives cell movement. Unlike a skeleton of bone, it is highly dynamic: its filaments are constantly assembled and disassembled from protein subunits, so a cell can remodel it in minutes.

Microtubules grow from an organizing center near the nucleus, the centrosome, which in animal cells contains a pair of centrioles. They switch unpredictably between growing and shrinking, a behavior called dynamic instability, which lets the cell search its interior and quickly rebuild its network. During cell division they form the spindle that separates chromosomes (lesson 12). Drugs that interfere with microtubules stop dividing cells, which is why paclitaxel (Taxol, first isolated from the bark of the Pacific yew) and vinca alkaloids (from the Madagascar periwinkle) are used to treat cancer, and colchicine (from the autumn crocus) is used for gout.

Motor proteins and movement

Motor proteins convert the chemical energy of ATP into movement along filaments. Kinesins generally walk along microtubules toward the cell's periphery, carrying vesicles and organelles; dyneins walk the other way, toward the center. Each step of kinesin moves about 8 nm and uses one ATP. Myosins move along actin filaments; in muscle, sliding of myosin along actin shortens the cell, and the 1950s sliding filament model explained how.

# Transport along a long nerve axon by kinesin (fast axonal transport)
speed_um_per_s = 1.0               # kinesin cargo speed, about 1 um per second
steps_per_s = speed_um_per_s * 1000 / 8   # 8 nm per step, one ATP per step
axon_m = 1.0                       # sciatic nerve: spine to foot
seconds = axon_m * 1e6 / speed_um_per_s
print(f"Steps (and ATP) per second per motor: {steps_per_s:.0f}")
print(f"Time to carry a vesicle 1 m: {seconds/86400:.1f} days")
D = 1e-12                          # a vesicle diffusing in cytoplasm, m^2/s (rough)
print(f"Diffusion over 1 m would take about {1**2/(2*D)/86400/365:,.0f} years")

Steps (and ATP) per second per motor: 125
Time to carry a vesicle 1 m: 11.6 days
Diffusion over 1 m would take about 15,855 years

Motor-driven transport moves a vesicle down a one-meter nerve in less than two weeks; diffusion alone would take thousands of years (lesson 7). Defects in axonal transport are linked to several neurological diseases.

Cilia and eukaryotic flagella are built around a ring of nine pairs of microtubules surrounding a central pair (the 9 + 2 arrangement), and dynein motors make them bend. Cilia beating in coordinated waves sweep mucus and trapped particles out of your airways; smoking paralyses them. A sperm cell swims with a flagellum. Crawling cells, such as white blood cells chasing bacteria and cells moving in a healing wound, push their front edge forward by assembling actin filaments and pull the rear along with myosin.