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Flashcards in cell biology 6 Deck (184):

Epithelial cells

There are many different epithelial tissues in the body, including the G.I. tract, kidneys, all exocrine glands, gall bladder, choroid plexus, ciliary body, corneal epithelium, and mucous membranes (but not the lungs ). Epithelial cells are organized into sheets of cells, often forming tubular structures, like the epithelium lining the G.I. tract. The apical surface faces the ‘special’ fluid (e.g., food in the gut, urine in the kidney, saliva in the parotid duct) and usually contains the special transporters that endow the epithelium with its specialized transport properties. The basolateral surface is exposed to the interstitial fluid and usually has generic transport properties like the plasma membranes of non-epithelial cells (neurons, for example). Synonyms for apical include mucosal and lumenal; synonyms for basolateral include serosal and peritubular. The cells that compose the epithelial sheet are glued to their neighbors by tight junctions. The glue is indeed tight is some epithelia, such as sweat glands and the distal parts of kidney tubules, preventing virtually any substance from passing from one side to the other by passing in between the cells. In most epithelia, however, the tight junctions are not very tight. For example, tight junctions of the small and large intestine, gall bladder, and proximal part of the kidney tubules are relatively leaky, and provide a pericellular shunt pathway for the movement of water and solutes. Leaky tight junctions are somewhat selective in their leakiness; some are relatively more permeable to cations, others to anions.


transport in the lungs

The main task of the lungs is to transport O2 into and CO2 out of the blood. There are no membrane transporters (active or otherwise) for O2 and CO2; they are lipid soluble molecules that diffuse freely through all membranes. Thus, the endothelial cells in the lung that separate blood from air in the alveoli of the lungs do not possess special transporters like those in epithelia to transport O2 or CO2.


Epithelial Transport

In general, epithelia engaged in massive transport of substances are leaky, while those epithelia doing the finishing work (‘fine tuning’) are tight. Leaky epithelia cannot maintain energy gradients as large as those produced by tight epithelia, because solutes and water leak back across the epithelium through the pericellular shunt. Thus, to get across an epithelium, a substance must follow one (or both) of two possible routes: it may either cross two membranes by entering the epithelial cell on one side and leaving on the other, or it may cross no membranes at all by passing in between cells through the pericellular shunt pathway. The driving force for nearly all transport – water, salts, nutrients, non-volatile metabolic wastes – is the Na/K pump (always located in the basolateral membrane). By keeping intracellular sodium ion concentration low, the Na/K pump provides the energy to drive a host of secondary transporters. Protons are the main exception to the otherwise universal dependence of epithelial pumping on the Na/K pump, because primary active transporters have evolved for protons, most notably in the stomach (to secrete acid into the lumen of the stomach) and kidney (to excrete protons, which are a metabolic waste product.)


basolateral membrane

surface is exposed to the interstitial fluid and usually has generic transport properties like the plasma membranes of non-epithelial cells Note that the basolateral membrane is just like many other cells, containing relatively low sodium permeability and high potassium permeability. What value of membrane potential would you expect to record across the basolateral membrane? Answer: because it’s like the plasma membrane of a neuron, Vm would be about -70 mV. The basolateral membrane also contains some chloride channels, and the Na/K pump.


apical membrane

faces the ‘special’ fluid (e.g., food in the gut, urine in the kidney, saliva in the parotid duct) and usually contains the special transporters that endow the epithelium with its specialized transport properties. It is relatively highly permeable to sodium, not potassium. What would be the potential across this membrane? (Answer: Vm would be more positive, perhaps +10 mV.) In addition, there is no Na/K pump in the apical membrane.


how salt and water are transported from apical to basolateral solution

Assume that identical NaCl solutions are placed on either side of the epithelium. Sodium ions leak into the cell across the apical membrane, down their electrochemical gradient. They are then pumped out of the other side of the cell by the Na/K pump, across the basolateral membrane. This results in the net transport across the epithelium of a positive charge, and chloride follows passively, drawn by the electrical force. The net transport of NaCl produces an osmotic gradient, which in turn draws water along. What would happen to the transport if the Na/K pump were blocked? As the cell filled with sodium (leaking in across the apical membrane), the driving force for further sodium entry across the apical membrane would be reduced, and net transport of sodium, chloride, and water would decrease.


What is the transepithelial potential difference (transPD)?

TransPD = Vm (Basolateral) – Vm (Apical). Keep in mind a couple of rules: i) all membrane potentials are written as the potential of the inside of the cell with respect to the outside (i.e., outside = zero); ii) the transepithelial potential is written as the potential of the apical solution with respect to the basolateral (i.e., basolateral = zero); iii) the cell is isopotential (all voltage drops are at membranes, so all lines showing electric potential are horizontal – no change over distance, except across membranes). Start at the basolateral side. The basolateral solution is defined as zero. You are given that Vm (B) = -50 mV, so in crossing the basolateral membrane from outside to inside, you must drop down 50 mV. The cell is isopotential (this is only an approximation, but a good one), so the line across the cell is horizontal. In leaving the cell by crossing the apical membrane, you must change by 10 mV, because Vm (A) = +10 mV. Do you move up or down? Because the inside is 10 mV more positive than the outside, you must move down, emerging at a potential of - 60 mV, compared to the basolateral solution.


leaky epithelium

allows significant fluxes through the paracellular shunt pathway. This would be characteristic of an epithelium like the one lining the G.I. tract, where relatively large fluxes occur. The shunt pathway in this case is relatively more permeable to chloride than to sodium, but is by no means totally impermeable to sodium (the molecular mechanisms by which tight junctions achieve selective permeabilities are not well understood). The major difference is that the leaky epithelium is usually capable of moving a larger amount of material. In addition, the leaky tight junctions partially ‘short out’ the transepithelial potential difference, so that a lower transepithelial voltage would be measured.


electroneutral cotransporter

e.g. carries one potassium, two chloride, and one sodium ions into the cell each cycle (it sounds more like pinocytosis than membrane transport!). This transporter is found in several important epithelia, including the kidney loop of Henle and the respiratory tract. Qualitatively, though, the end result is no different than other scenerios.


Secretion of fluid by epithelia

Not all cells in a given epithelium are identical. On the contrary, individual cells may be highly specialized, some for absorption, some for secretion. The mechanisms described so far concern absorption by epithelia – moving solutes from lumen to blood. Things can travel the other direction, too. One secretion pathway is of special clinical importance, for it underlies important diseases, including some types of diarrhea (including the worst of all, cholera), and also cystic fibrosis. The key to understanding epithelial secretion in general and the main defect in those diseases is a chloride channel in the apical membrane (especially in the GI tract and lungs). Normally, in a resting cell, this Cl- channel is closed. However, when this Cl- channel is activated, the cell begins to secrete electrolytes and water into the lumen. The secretion is driven by Cl- leaking out of the cell into the lumen. The Cl- concentration in the cell is high, thanks to a Cl- pump in the basolateral membrane. The pump is a Na-K-2Cl cotransporter that uses the downhill leakage of Na+ into the cell to drive the uptake of Cl- from the interstitial fluid. As the Cl- leaks out of the cell into the lumen, the electrical negativity that it creates draws Na+ along passively. The Na+ flows mostly through the intercellular shunt pathway. The resulting osmotic gradient draws water along, too, giving a net secretion of an isotonic solution of NaCl.


Turning on the Cl- channel

So eptithelia have mechanisms both to absorb and to secrete. Which one wins? At rest, the apical Cl- channels are closed, so absorption wins. A variety of stimuli can open the Cl- channel and turn on secretion. In the GI tract, it happens physiologically during digestion (parasympathetic nerve stimulation, hormones in the blood), as chemicals activate receptors in the basolateral membrane (the signal is carried across the inside of the cell from the basolateral receptors to the apical membrane by ‘cell signaling’ mechanisms (Ca++ ions, activated protein kinases, cyclic AMP, etc.). Pathogens also can activate the Cl- channels. Cholera toxin, for example, acts by locking open this channel, causing a massive efflux of fluid from the cell, leading to profound diarrhea and dehydration. While there are probably multiple types of Cl- channels (different gene products) involved in fluid secretion by epithelia, one of the most important is the ‘Cystic Fibrosis Transmembrane Conductance Regulator.’ (CFTCR, or more commonly CFTR). Cystic fibrosis is a genetic disease; it is this Cl- channel that is mutated, which reduces the ability of epithelia to secrete ‘serous’ (watery) fluid, leading to thickened mucous secretions, infections, and other life-shortening complications.


Absorption of nutrients

In the G.I. tract, enzymes secreted by digestive glands hydrolyze ingested proteins and polysaccharides, and the resulting amino acids and sugars are pumped from the G.I. lumen into the blood by the G.I. epithelium. Virtually identical mechanisms operate in the kidney, where glucose and amino acids are reabsorbed by the epithelial cells of the proximal tubule after being filtered from the plasma in the glomerulus. each nutrient is pumped across the apical membrane, and then passively moves out of the cell into the interstitial fluid. The sugar and amino acid pumps are examples of sodium-dependent secondary active transport systems. If [Na+] in the mucosal solution is removed (replaced by non-permeating choline+), sugar and amino acid pumping stops. Conversely, removing sugars and amino acids reduces the movement of Na+ from mucosal to serosal fluid. The transporter captures some of the energy released as Na+ moves down its electrochemical gradient into the cell, and uses this energy to pump the sugar or amino acid against its gradient into the cell. Note that the transport of glucose by epithelial apical membranes is different from the transport across the plasma membranes of nonepithelial cells (e.g., muscle), where glucose is transported by "facilitated diffusion", which is not a pump.


regulation of absorbing nutrients

In one sense, the transporters are not regulated, at least not by the ECF composition. Instead, they seem geared for maximum transport of nutrients any time, day or night. Thus, if a person drinks a glass of water, whether thirsty or not, all of the water will be absorbed by the G.I. epithelium and put into the blood. If a person eats five grams (that’s a lot) of table salt, virtually all of it enters the blood plasma. Same for glucose, and virtually all other common nutrients. (There is great chemical specificity of the transporters, however. For example, L-amino acids and D-sugars are selectively transported, but not their stereoisomers. Eating L-glucose or D-amino acids (which are not absorbed) is likely to produce an osmotic diarrhea as the unabsorbable solutes suck water into the GI lumen.) The G.I. tract works so avidly probably because the transport mechanisms evolved in far less abundant environments than the one we live in, nutritionally speaking, and it was adaptive to be able to absorb all available nutrients. By not regulating ECF composition at the input end, it falls by necessity to the kidneys, at the output end, to regulate the composition of the ECF. Not very efficient.


Transport of Water

It is curious, given the importance of water, that no water pumps exist in the body (or anywhere else). This means that water always moves passively down osmotic gradients. As described above, absorption (by active transport) of salts, sugars, amino acids, and other solutes by the G.I. tract epithelium is accompanied by water absorption (as the solutes are absorbed, the lumenal contents become slightly hypo-osmotic to plasma, and so water is absorbed, always passively). In a few places (sweat gland ducts, some parts of tubules in the kidney), epithelia are relatively impermeable to water. In these special cases, osmotic gradients can be maintained by pumping solute across the water-impermeable epithelium. Consider, for example, sweat glands. Their job is to ‘excrete heat’. To do that, they deliver water to the body surface where its evaporation (an endothermic process) cools the body. Nascent sweat forms deep in the gland (by a secretory process); it has a salt composition that is similar to plasma (about 300 mosM, mainly NaCl). As the fluid travels along the sweat duct on its way to the surface, NaCl is (re)absorbed by the epithelium lining the duct and returned to the blood. Because the ducts are impermeable to water, water cannot follow the salt, and the fluid in the lumen of the duct becomes more and more dilute (it can be as low as about 50 mosM). This is useful, because the solute in sweat does not help at all in the process of heat loss, and just leaves an unsightly white crust on your tee shirt.


Ridding the body of metabolic wastes

Each day the cells in an adult human produce about 15 moles of metabolic waste solute. That is enough to more than double the osmolarity of the body fluids! (45 liters of body fluids * 0.3 osmoles/liter = 13.5 osmoles present in body fluids at any one time). And yet, a rise in plasma osmolarity of a few percent is enough to make a person thirsty, and severe dehydration raises plasma osmolarity by less than ten percent. In other words, there is a stupendous amount of metabolic waste to get rid of each day. The problem is largely solved by an extraordinarily simple chemical fact: the end product of carbon metabolism, CO2, which composes 14.5 of the 15 moles of waste, is volatile. Consequently, it is simply exhaled via the lungs, and requires no special transporters at all (CO2 permeates all membranes easily, by dissolving in them). A little water - less than a liter – is lost as exhaled water vapor with the CO2 . What about the remaining 0.5 moles (500 mmoles) of metabolic waste? They are non- volatile molecules, and of course cannot be expelled by the lungs. Even though they account for a small fraction of the total, getting rid of these non-volatile metabolic waste products is a big problem. It falls to the magnificent kidney to solve the problem, and while it is responsible for many other tasks (such as regulating the concentration of just about everything in the ECF), the most important function of the kidney is to get rid of these non-volatile metabolic wastes, because no other organ can do it. When kidney function is lost, death from uremia can follow. Uremia literally means “urine in the blood.”


What kinds of metabolic waste molecules are non-volatile?

The majority (about 450 of the 500 mmoles) are the end product of nitrogen metabolism, urea. Most of the remainder (about 50 mmoles) are protons, H+.


How does the kidney do it?

The fundamental anatomical arrangement of the kidney is just like the lungs, which get rid of the volatile waste product, CO2. That is, in both the lungs and the kidney, blood capillaries pass close to the ends of dead-end tubules (glomeruli in the kidney, alveoli in the lungs), and various chemical substances move from the blood into the tubules, eventually becoming urine in the kidney, and expired air in the lungs. Functionally speaking, however, matters are entirely different in the two organs. In the lungs, CO2 diffuses passively from blood to air. The equivalent arrangement in the kidney would be to have molecular transporters at the blood-tubule interface, and have them pump metabolic wastes (mostly urea) out of the blood, into the tubules, and letting them, together with some water, pass on. However, urea transporters do not exist. Consequently, rather than trying selectively to pump waste products out of the plasma, it forms an ultrafiltrate of plasma in the glomerulus, which contains water, salts, sugars, amino acids, and all other beneficial compounds, as well as the non-volatile metabolic waste products. Then, as this plasma ultrafiltrate passes along the renal tubules, the epithelial cells lining the tubules reabsorb (pump back into the blood) the things that it wants to keep (glucose, salts, bicarbonate, etc), allowing the wastes to pass on. It’s incredibly expensive, energetically speaking, to do it this way, requiring a great deal of ATP to drive the reabsorbing pumps. That’s enough responsibility for any organ, but the kidney does so much more. Earlier we noted that the kidney regulates the ECF composition (by adjusting the activity of the transporters that do the reabsorbing). This additional chore arises because the undisciplined GI tract absorbs just about everything presented to it (see box below), regardless of the needs of the ECF. So the list of functions of the kidney includes excreting non-volatile metabolic wastes and regulating the composition of virtually all ECF solutes – nutrients and electrolytes – as well as water.


the GI tract

While its output, feces, comprises mainly bacteria and substances eaten but not absorbable, about 30 mmoles per day of non-volatile metabolic wastes are excreted via the G.I. tract (compared to 500 by the kidney). These wastes are mostly breakdown products of red blood cells (delivered from the liver to the GI lumen), and are highly toxic if not promptly eliminated. Moreover, as noted earlier, the transporters in the GI tract are incredibly specific. For example, the stereo isomer D-glucose in absorbed, but L-glucose is not. On the other hand, while most big molecules (e.g., whole proteins) that we eat are of course not absorbed intact, but are broken down (digested) to much smaller molecules (e.g., amino acids) before being absorbed into the blood, the most deadly substance on earth, botulinum toxin, if ingested in food-gone-bad, is absorbed as an intact protein (and it’s a big protein), and once in the blood it goes about its fiendish business.


water balance

Naturally, the kidney regulates water (like everything else) balance in the body. Getting rid of extra water is relatively easy: solutes in the lumen of the kidney tubule are reabsorbed as usual, but the epithelium is made water-impermeable, so water cannot follow the solutes osmotically. Thus, the extra water stays in the lumen, and passes into the urine. (The epithelium is made impermeable to water when the hypothalamus, sensing extra water on board as a drop in plasma osmolarity, stops secreting anti-diuretic hormone (vasopressin), which causes certain kidney epithelial cells to remove water channels (aquaporins) from their apical membranes, thereby reducing water reabsorption.) Conserving water in times of dehydration, like when stranded in the desert, is another matter altogether. Remember, there are no water pumps, so the kidney cannot just pump water back into the blood from the tubules. This makes for a huge physiological problem. You can guess what organ has had to solve the problem. Lacking water pumps, the renal tubules have had to evolve a far more complicated mechanism to conserve water. It works pretty well: human urine can be as concentrated as 1200 mosM.


Conserving water

Conceptually, the simplest way would be to pump water out of the ultrafiltrate in the renal tubules, back into the blood. But water pumps do not exist in biology, so a more complex process has evolved that accomplishes the same thing. It involves separating in space the removal of solute and the removal of water from the ultrafiltrate in the tubule. There are three steps to the process. First, NaCl is actively transported out of the ascending limb of the loop of Henle as it rises through the renal medulla. The tubule here has a very low permeability to water, so the fluid in the tubule lumen becomes hypo-osmotic to plasma (it's about 50 mosM at the top of the loop). In addition, the surrounding interstitial fluid is poorly vascularized in the medulla, so the salt accumulates in the ECF and is not washed away, creating a hyperosmotic interstitium. This is a key point. Second, the distal tubule is permeable to water, and the interstitium here (in the renal cortex) is well vascularized. Consequently, water passively leaves the tubule and is returned to the blood. Thus, the fluid arriving at the end of the distal tubule is isosmotic with plasma (about 300 mosM). The volume of fluid in the lumen has been greatly reduced though. In other words, five- sixths of the salt was removed by the ascending loop of Henle (remember: no volume change, because no water movement), and five-sixths of the water (and volume) left the distal tubule and returned to the blood. to the blood. Third, the tubule (now called the collecting duct) plunges back down into the renal medulla, through the hyperosmotic interstitium. The fluid in the lumen is isosmotic with plasma as it begins its passage. But the collecting duct tubule is permeable to water, and so water leaves the lumen, thereby making the lumenal fluid (urine) hyperosmotic to plasma. (Of course, water leaving the collecting duct will dilute the medullary interstitium, partially defeating the system. But because most (about 5/6) of the water was previously removed, the amount of water entering the collecting duct is greatly reduced.) In summary, the keys to this ingenious device is that most salt and water are removed from the tubule at separate locations, and the salt is kept around to provide a special, hyperosmotic interstitium to draw a little extra water from the lumen of the collecting duct. All because there are no water pumps.


what happens is permeability for Na increases?

(this happens during an action potential). We can say right away that EK and ENa will not change (no changes in concentrations, at least in the short term). To say it in words, when PNa increases, Na+ ions are able to move into the cell much more easily; the inward movement of positive charge depolarizes the membrane. As Vm moves closer to ENa, the driving force on the Na+ ions is reduced, while the driving force on K+ is increased as Vm moves away from EK (remember, the driving force on any ion is just the difference between Vm and the ion's equilibrium potential). The new steady potential is reached when the total amount of Na+ entering equals the total amount of K+ leaving the cell. In other words, when the Na+ and K+ currents are equal and opposite, Vm doesn't change.


what happens if external Na is reduced? (that is, most Na+ is replaced with a nonpermeating cation, such as choline+)

ENa will move closer to zero, because the change in [Na+]o has made the Na+ concentrations in the ICF and ECF more nearly equal (when [Na+]o= [Na+]i, ENa= 0, because the log of 1 is zero). From the Nernst equation, ENa= 0 mV.


what happens if external K is increased?

Intuitively, we can see that an increase in [K+]o will reduce the efflux of K+ from the cell. Because less K+ leaves, the cell will depolarize. EK will move closer to zero (we have made the internal and external concentrations more nearly equal); from the Nernst equation: EK= -60 mV. That's a big change (almost 30 mV), and reflects the fact that the ratio of [K+]o to [K+]i determines EK, and we have tripled the ratio with only a 10 mM change in [K+]o. Clinically, this can be very important. First, it's easy to imagine how blood potassium could increase if a little bit of the K+ leaked out of cells (remember, over 98% of the total K+ in the body is in the ICF). And second, a 20-30 mV depolarization of cells in the heart can quickly lead to cardiac arrest. In summary, external Na+ has little effect, and external K+ has a marked effect on membrane potential in nerve and muscle cells. This is simply because the plasma membrane of nerve cells and muscle cells is much more permeable to K+ than to any other ion: wherever EK goes, Vm follows in these cells.


Clinical notes on Hyperkalemia

a rather modest rise in ECF potassium ion concentration has a big effect on Vm. This can have serious clinical consequences. The reason that such a small change (only 4 mM) has such a big effect goes back to the Nernst equation: the potassium equilibrium potential, EK, depends on the ratio of external to internal potassium ion concentrations, and the ECF potassium concentration has doubled. So we expect a big change in EK. In cells that have a relatively high potassium permeability, Vm will slavishly follow EK, and so the membrane potential will depolarize a lot. A large depolarization of cells can be life threatening. In acute hyperkalemia, the main danger concerns the reliable conduction of electircal signals (action potentials) in the heart. As you will study a little later, the heart relies on a special electrical conduction system (intrinsic to the heart) to coordinate the contraction of its muscle fibers each heartbeat. These synchronized electrical signals can become disrupted during acute hyperkalemia, causing cardiac arrhythmias as conduction blocks occur and maverick pacemakers arise in various locations of the conduction system. The causes of hyperkalemia, as you might expect (knowing that 98% of all of the potassium in the body fluids is in the ICF) mostly concern loss of potassium from cells. Crush injuries, burns, and other trauma that disrupt cell membranes can do it. So can immunological attack of red blood cells (causing hemolysis). One of the most important determinants of the clinical course of the hyperkalemia is the status of the kidney, whose normal job it is to excrete excess potassium. If kidney function is compromised, hyperkalemia can be much more serious than if the kidney is functioning normally.


diagnosis of hyperkalemia

usually is via an electrocardiogram (EKG) to detect cardiac arrhythmias, followed by measuring plasma potassium ion concentration.


treatment of acute hyperkalemia

involves attempts first to relieve any cardiac arrhythmias, usually by giving intravenous calcium ions (you will study the mechanism by which calcium ions quiet the conduction system later). Next, efforts are made to reduce the concentration of potassium in the plasma. This can be done by encouraging cells to take up potassium by alkalinizing the blood by giving sodium bicarbonate (Alka Seltzer), or by juicing up the energy supply (ATP) for the sodium-potassium pump by giving insulin and glucose. Finally, potassium can be removed from the body by administering an ion exchanger (oral or enema) like Kayexalate (the exchanger is a big anion that is given as the sodium salt, but it has a higher affinity for potassium than it does for sodium, so the it selectively binds up potassium ions). A nice mnemonic always helps: when you CBIGK in a patient, what should you give, in order? (answer: Calcium, Bicarb, Insulin + Glucose, Kayexalate). In actual practice, bicarbonate is used less often. Finally, a more drastic way to cleanse the blood of potassium is dialysis by an ‘artificial kidney’. Blood is taken out of the body and passed through plastic capillary tubing, which allows free exchange of ions and small molecules between the blood and the dialysate that bathes the tubing. Because the dialysate contains a lower concentration of potassium than the plasma, potassium leaves the blood, which is then returned to the patient, cleansed artificially of its excess potassium ions. (Of course, the dialysate also contains normal concentrations of other salts.)


facilitated diffusion

Some transporters act like ion channels, shuttling a single solute species in either direction. (a historic term applied to molecules that shouldn’t be able to diffuse across lipid membranes because of their large size or charge, but do get across). The best known example of this is the glucose transporter. The glucose transporter will transport glucose in either direction, and burns no energy in the process. Thus, it is not a pump. You might then wonder how cells accumulate glucose. The answer is that as soon as a glucose molecule gets into the cell, it is phosphorylated to Glucose-6-Phosphate, which doesn't fit on the transporter, and so is "trapped" inside. Glucose uptake by cells is regulated by insulin, a hormone secreted by specialized cells in the pancreas when plasma glucose levels rise. How does insulin turn on the transporter? It turns out that in the absence of glucose, the transporter is not even present in the plasma membrane; it is sequestered inside the cell, in the membrane of intracellular vesicles. Insulin triggers a biochemical cascade that causes the vesicle membranes to fuse with the surface membrane (exocytosis), exposing the glucose transporter to the ECF. The transporter then gets busy and ‘carries’ glucose inside. When insulin subsides, the transporter molecules are reinternalized (endocytosis).


Primary active transporters

like the Na/K pump, derive their energy directly from the splitting of ATP. There are no other ubiquitous primary active transporters in the plasma membrane of cells. Some specialized cells have them, and you will study them later. For example, the cells in the stomach that secrete acid, and certain cells in the kidney geared for excreting protons from the body possess proton pumps in their plasma membranes that rely directly on ATP for their energy source. Inside cells (as opposed to the surface membrane) there are other primary active transporters. One pumps protons into intracellular membrane-bound organelles (endosomes, vesicles, lysosomes). Another pumps calcium ions into membrane-bound compartments. Inside mitochondria is a very special proton pump (the F1-ATPase) that, when running backwards, lets protons leak across a membrane and synthesizes, rather than hydrolyzes ATP.


Secondary active transport

the mechanism by which most substances are pumped. In this case, the energy to do the direct work of pumping comes not from metabolism (ATP), but from a secondary source. Usually this energy source is the 'downhill leak' of Na+ into the cell. For example, cells can accumulate amino acids against their energy gradients. This active uptake is dependent on external Na+; if external Na+ is removed, amino acid uptake is abolished. Conversely, removing the amino acid reduces the entry of Na+. The carrier ingeniously captures the energy released by the inward leak of Na+ and instead of letting it escape as heat, uses it to pump the amino acid into the cell. There are two basic types of secondary active transporters, those that move different solute species in the same direction (cotransport), and those that move solute in opposite directions (antiport, or exchange). Secondary active transporters do not necessarily always run in the same direction. They will always tap the bigger leak to drive the smaller pump. Consequently, they can reverse direction sometimes. One of the most important examples of this is the sodium-calcium exchanger, which reverses direction in heart muscle cells every time the heart beats (more on this later). All secondary transport mechanisms depend ultimately on the Na+/K+ pump (and therefore on ATP). For example, if the Na+/K+ pump is blocked, cells fill up with Na+, and thus the Na+ electrochemical gradient is reduced. Because this is the energy source for secondary active transport, all of these transport mechanisms suffer. Some secondary active transporters are electrogenic, in that one cycle produces a net charge transfer across the membrane. For example, Na/amino acid transporters are electrogenic, because one cycle transfers a net positive charge (Na+) into the cell. Other secondary active transporters are not electrogenic; an example is the Na/K/2Cl cotransporter, which each cycle moves one sodium ion, one potassium ion, and two chloride ions into the cell. The main feature of electrogenic secondary active transporters is that their activity is governed by the membrane potential. Electrically silent transporters could not care less about membrane potential.


Calcium transport

There is a huge electrochemical gradient for calcium ions across cell membranes. In fact, no other ion is further from equilibrium than calcium. The extracellular (ionized) calcium concentration (about 1 mM) is nearly 10,000 times greater than the intracellular concentration (about 0.0002 mM, or 200 nM); thus its concentration gradient is inward. And the electrical gradient is also inward, of course, because the ICF is electrically negative and calcium is positively charged. From the Nernst equation, ECa is calculated to be about +111 mV (ECa = (60/2)*log(1/0.0002) = +111 mV). Thus, given the opportunity (i.e., an open calcium channel), Ca++ ions will always leak into cells, so there must be a pump to extrude them. The Na/Ca exchanger’s main job is to pump calcium ions out of the cell. The inward leak of sodium ions provides the energy source. The Na/Ca exchange pump takes on a special significance in the heart, where it actually switches direction during each heartbeat. (You will study muscle contraction shortly, and will learn that calcium ions are necessary for contraction.) At rest (while the ventricles are refilling with blood during diastole), the exchanger runs forward, pumping Ca++ out (keeping the muscle relaxed) as Na+ leaks in. When the ventricles contract (systole), the exchanger switches direction, letting Ca++ leak into the cell, where it strengthens the force of contraction. The direction of Ca++ movement is controlled by the value of the membrane potential; when Vm is more negative than about -60 mV, the sodium leak rules, and drives the outward pumping of calcium; when Vm is more positive than -60, the pump reverses direction, and calcium leaks in (pumping sodium out).



For centuries it has been known that an extract of the beautiful purple foxglove can help a weak heart beat stronger. Digitalis (and related drugs) exert their action by acting directly on, not the Na/Ca exchanger, but the Na/K pump! In fact, digitalis blocks the Na/K pump. How does this lead to an increase in the strength of contraction of heart muscle? Blocking the Na/K pump of course allows intracellular sodium ion concentration to increase. In turn, this reduces the energy available to all sodium-driven secondary active transporters, including the Na/Ca exchanger. Thus, digitalis indirectly inhibits the Na/Ca exchanger, allowing intracellular calcium ion concentration to rise, which increases cardiac contractility.


Hydrogen ions

are also pumped out of most cells by a Na+/H+ exchange carrier, which operates under the same principles as the Na/Ca exchanger. Protons are harder to study than UFO's, because they capriciously vanish and reappear as they bind to and unbind from various buffers. Typically, only about 1 in a million protons is free, as H+; the rest are hiding, bound to buffers. The free concentration of protons in the ICF is about 100 nM (pH=7.0); in the ECF it’s even lower, about 40 nM (pH=7.4). From the Nernst equation, EH = -24 mV. That means in cells with membrane potentials more negative than -24 mV (most cells), H+ must be pumped out of the cell. The mechanism is a secondary active transport system, in which the inward leak of Na+ drives the outward pumping of H+.


Chloride ions

are pumped into some cells by a secondary active transport process (Na/K/2Cl cotransporter). As a result, ECl moves in a positive direction, away from the resting membrane potential.


H+/K+ exchanger’

There are several clinical situations that suggest the presence of a system that will exchange K+ for H+, and vice versa. For example, infusing K+ causes acidemia (the K+ is taken up by cells ‘in exchange’ for H+), and infusing acid causes hyperkalemia (elevated (hyper-) potassium (-kal- for Latin kalium) in the blood (-emia)). While it is conceptually simple (and useful) to think in terms of an H/K exchanger, the reality is that such a transporter probably does not exist. Rather, the process evidently involves different transporters, perhaps working in pairs in parallel, the upshot being hydrogen/potassium exchange. For example, hyperkalemia will cause extra K+ uptake via the Na/K pump. Hyperkalemia also will depolarize cells (by shifting EK in a positive direction), and the change in membrane potential can affect the rate of activity of electrogenic transporters. One such transporter, which transports 3 bicarbonate ions and one sodium ion from the ICF to the ECF, is inhibited by depolarization. Thus, the reduction in activity will reduce bicarbonate extrusion. Because bicarbonate is a base, its slower extrusion will cause acidemia.



The cytoskeleton provides cell shape, mechanical strength, the structures needed for locomotion, support for the plasma membrane, the scaffold for the spatial organization of organelles, and the means for intracellular transport of organelles and other cargo. The cytoskeleton is formed by three different families of proteins that assemble to form large filamentous or tubular, non-covalent polymers, each with distinct mechanical properties, dynamics and functions. The three types of cytoskeletal element are: microfilaments, microtubules, and intermediate filaments. Microfilaments (synonymous with actin cytoskeleton)


Microtubules (MTs)

are tubular (or hollow-fiber) structures, up to many μm long, with an outer diameter of 25nm. They are flexible but not very resistant to stretching. They function primarily as scaffolds for the spatial organization of organelles in the cell, for organelle movement, and for the movement of cilia and flagella. They typically have one end attached to a centrosome, also known as perinuclear microtubule organizing center (MTOC).



The building blocks of MTs are heterodimers of the protein tubulin (α and β). Each tubulin has a binding site for GTP. The GTP bound to a tubulin is a trapped at the tubulin interface of the dimer and is not hydrolized. It is a constant heterodimer component. The GTP bound to β tubulin can be hydrolized and is exchangeable. There are many isoforms. the main difference is the tail, which is the charged domain These tails are not part of the conserved tubulin fold; instead, they protrude from the surface of polymerized microtubules and are thus readily accessible for interacting molecules. To form microtubules, the dimers of α- and β-tubulin bind to GTP and assemble onto the (+) ends of microtubules while in the GTP-bound state. The β-tubulin subunit is exposed on the plus end of the microtubule while the α-tubulin subunit is exposed on the minus end. After the dimer is incorporated into the microtubule, the molecule of GTP bound to the β-tubulin subunit eventually hydrolyzes into GDP through inter-dimer contacts along the microtubule protofilament. Whether the β-tubulin member of the tubulin dimer is bound to GTP or GDP influences the stability of the dimer in the microtubule. Dimers bound to GTP tend to assemble into microtubules, while dimers bound to GDP tend to fall apart; thus, this GTP cycle is essential for the dynamic instability of the microtubule.



MTs are hollow cylinders composed of 13 parallel "protofilaments" consisting of alternating α and β subunits, i.e., of chains of heterodimers in which the top of one b tubulin interacts with the bottom of the a tubulin of the next heterodimer. Laterally, the protofilaments are slightly displaced (forming a spiral), but the interactions are mostly α−α and β−β. Because intermolecular interactions are strong within the assembled tubule, there is little exchange of dimers within. The ends, however, exhibit (controlled) rapid assembly and disassembly. Because of their architecture, MTs exhibit on one end α tubulin, on the other β tubulin and, thus, have polarity.



Because GTP-bearing β subunits favor polymerization, that end of the tubule, known as plus-end, is the one that predominantly grows. The opposite end, or minus-end, tends to be disassembling or shrinking. As GTP- containing dimers become incorporated more deeply in MTs, GTP is hydrolized to GDP, which weakens the tubulin interaction in the protofilament. This results ultimately in a "treadmilling" phenomenon (MT growth at the plus-end, MT disassembly at the minus-end).


dynamic instability

However in the response to a particular cellular activity, the plus-end may loose its GTP-rich cap, which causes rapid shrinkage from the plus-end until GTP-containing dimers are added back. This phenomenon of rapid MT dynamics is known as "dynamic instability". MT associating proteins can control MT stability by either protecting or removing GTP-cap. MT capping proteins that bind to the ends of microtubules, usually increase their stability. In contrast, microtubule severing proteins (such as spastin, katanin) increase microtubule instability by exposing GDP- rich parts of microtubules.


perinuclear microtubule organizing center (MTOC)

a structure found in eukaryotic cells from which microtubules emerge. MTOCs have two main functions: the organization of eukaryotic flagella and cilia and the organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division. Most animal cells contain a single MTOC, called the centrosome and located near the nucleus. It is composed of a pair of centrioles embedded in a matrix and of nucleation sites for MTs. These nucleation sites, consisting of rings of γ-tubulin, can initiate MT polymerization, and the minus-ends of MTs are anchored in them.



a cylindrical cell structure composed mainly of a protein called tubulin that is found in most eukaryotic cells. are a pair of cylindrical structures arranged at right angles to each other and consist of short modified tubules plus accessory proteins. Centrioles also form the basal bodies of cilia and flagella. During each cell cycle the centrosome duplicates and splits into equal parts, each containing a centriole pair. The centrosomes move to opposite ends of the cell at the onset of mitosis, and the MTs growing between them form the mitotic spindle for the separation of chromosomes.


Drugs that modify MT polymerization dynamics

have been isolated from plants. Colchicine (from the fall-flowering, crocus-like Colchicum autumnale) inhibits MT polymerization. Vinblastine and vincristine also are MT polymerization blockers, derived from the Madagascar periwinkle (Vinca rosea). Paclitaxel (Taxol®) was first isolated from the Pacific yew tree (Taxus brevifolia) and also binds to MTs, but it stabilizes them, which causes tubule and tubulin aggregates. These compounds and their derivatives block mitosis and, thus, are of great interest for cancer treatment.


Microtubule Functions

a) Scaffold for organelle positioning in the cell: Various organelles, such as ER and Golgi, are anchored to MTs. b) Intracellular transport. c) Cell division. d) Cilia formation and movement


MTs role in Intracellular transport

Many organelles (vesicles, mitochondria) travel long distances within cells, using MTs as "tracks". This is possible in conjunction with microtubule motor proteins. These proteins can transform the energy from ATP hydrolysis into motion (or walking) along MTs (molecular motors). They contain a cargo-binding domain and a "head" region or motor domain that hydrolyzes ATP and reversibly binds to MTs. Coordinated with ATP hydrolysis, the motor domain goes through a mechanochemical cycle of MT binding, conformational change, MT release, conformational relaxation, and MT re-binding. This moves motor protein and cargo along the MT in a stepwise fashion. These principles are shared with the myosins discussed further below. Two different classes of MT motors exist, kinesins, which move cargo toward the plus-end, and dyneins, which move cargo toward the minus-end.


MTs role in Cell division

The mitotic spindle is constructed from MTs and associated proteins and serves to segregate the replicated chromosomes during mitosis. Three types of MTs can be distinguished: "astral MTs" that radiate out from the centrosomes; "kinetochore MTs" that are attached to the kinetochore formed at the centromere of each duplicated chromosome; and "overlap MTs" that interdigitate at the equator of the spindle. In all cases, MT plus-ends point away from the centrosomes (or spindle poles). Multimeric plus-end-directed, kinesin-like motor proteins bind to overlap MTs from opposite poles. These motors, as well as the elongation of overlap MTs, cause the spindle to grow and the centrosomes to become more distant. This is enhanced by pulling forces transmitted by astral MTs. At the same time, minus-end directed motors, accompanied by kinetochore MT shortening, separate daughter chromosomes and move them along MTs to the centrosomes.



Kinesins are motor proteins that transport such cargo by walking unidirectionally along microtubule tracks hydrolysing one molecule of adenosine triphosphate (ATP) at each step. It was thought that ATP hydrolysis powered each step, the energy released propelling the head forwards to the next binding site. However, it has been proposed that the head diffuses forward and the force of binding to the microtubule is what pulls the cargo along. Motor proteins travel in a specific direction along a microtubule. This is because the microtubule is polar and the heads only bind to the microtubule in one orientation, while ATP binding gives each step its direction through a process known as neck linker zippering. Most kinesins walk towards the plus end of a microtubule which, in most cells, entails transporting cargo from the centre of the cell towards the periphery. This form of transport is known as anterograde transport/orthrograde transport.



The force-generating ATPase activity of each dynein heavy chain is located in its large doughnut-shaped "head", which is related to other AAA proteins, while two projections from the head connect it to other cytoplasmic structures. One projection, the coiled-coil stalk, binds to and "walks" along the surface of the microtubule via a repeated cycle of detachment and reattachment. The other projection, the extended tail (also called "stem"), binds to the intermediate and light chain subunits which attach the dynein to its cargo. The alternating activity of the paired heavy chains in the complete cytoplasmic dynein motor enables a single dynein molecule to transport its cargo by "walking" a considerable distance along a microtubule without becoming completely detached. Several mutations in the dyneim motor forms a subclass of “primary ciliary dyskinesia syndromes”. Due to a mutation the outer dynein arms in cilia and flagella are missing. When explaining the syndrome, note that photoreceptor outer segments are modified monocilia, that such cilia may operate as chemosensors (anosmia; probable explanation for cyst formation in developing kidney), and that establishment of left/right identity requires normal function of monocilia on nodal cells during gastrulation


Mitotic spindle

A notable structure involving microtubules is the mitotic spindle, used by most eukaryotic cells to segregate their chromosomes correctly during cell division. The mitotic spindle includes the spindle microtubules, microtubule-associated proteins (MAPs), and the MTOC. The microtubules originate in the MTOC and fan out into the cell; each cell has two MTOCs, as shown in the diagram. The process of mitosis is facilitated by three main subgroups of microtubules, known as astral, overlap and kinetochore microtubules.


astral microtubule

a microtubule originating from the MTOC that does not connect to a chromosome. Astral microtubules instead interact with the cytoskeleton near the cell membrane and function in concert with specialized dynein motors, which pull the MTOC toward the cell membrane, thus assisting in correct positioning and orientation of the entire apparatus.


Kinetochore microtubules

directly connect to the chromosomes, at the kinetochores. To clarify the terminology, each chromosome has two chromatids, and each chromatid has a kinetochore; the two kinetochores are linked. The complex created by the two kinetochores on a chromosome is called the centromere.


overlap microtubules

extend from one MTOC and intertwine with the microtubules from the other MTOC; motor proteins then make them push against each other and assist in the separation of the two daughter cells. Keinesin attached to both MTs will help seperate the centrosome by having two motor heads attached to each MT and walk towards + end.


MTs role in Cilia formation and movement

Cilia and flagella are wide-spread, hair-like cellular appendages that have a uniform diameter and contain a MT core, the axoneme. Flagella are long and serve to propel sperm by their undulating motion. Cilia are shorter and tend to occur in large numbers on the apical surface of various epithelial cells, especially those of the respiratory tract. By beating with a whip-like motion (in a staggered pattern across the cell surface) they move fluids over the surfaces of cells. In the respiratory tract, this serves to move dust particles, bacteria and mucus towards the mouth for elimination.


Intermediate filaments (IFs)

are rope-like, fibrous structures of about 10nm diameter. Unlike MTs and microfilaments, they are an invention of metazoans. IFs are prominent in cells exposed to mechanical stress. The main function of IFs is to provide intracellular mechanical support. IFs fall into two categories: cytoplasmic IFs and nuclear lamins. Several cell-type-specific cytoplasmic IF proteins exist: keratins, vimentins and vimentin-related proteins (including glial fibrillary acidic protein), and neurofilament proteins. In other words, IF proteins are far more heterogeneous than those of microfilaments and MTs. All IF proteins are elongated molecules with an extended central α-helical domain that forms a parallel coiled-coil with another monomer. Pairs of dimers then associate in anti-parallel fashion to form staggered tetramers. These tetramers are the soluble subunits that participate in IF polymerization. They are not polarized. IF polymerization is nucleotide-independent. Tetramers assemble into protofilaments, and eight such protofilaments pack together laterally to form the IF. Thus, at all levels IF cross- sections contain 32 individual α-helical coils that provide great tensile strength. IFs often are anchored in intercellular junctions. Is not polar therefore is more stable



only in epithelia. a family of about 50 proteins, are dominant components of the epidermis and its appendages, providing mechanical strength. a family of fibrous structural proteins. Keratin is the key structural material making up the outer layer of human skin. It is also the key structural component of hair and nails. Keratin monomers assemble into bundles to form intermediate filaments, which are tough and form strong unmineralized tissues found in reptiles, birds, amphibians, and mammals. Keratin mutations may interfere with filament assembly. The resulting epidermis is highly sensitive to mechanical stress and blisters easily, causing a severe disorder called epidermolysis bullosa simplex. Mutations in some of the associated proteins (e.g., those that anchor the filaments in desmosomes) may result in similar clinical syndromes. It is a heterodimer (acidic and basic keratins). Can be a marker for cancer cells because it will maintain the type of keratin expressed by the cell that it derieved from. hepatocytes only have one set of keratins, therefore keratin mutations in these proteins will lead to liver failure. Other types of cells have more than one set and therefore can compensate better with such mutations.



are in connective tissue, muscle cells, and neuroglial cells. Vimentins are present in a majority of cell types. a type III intermediate filament (IF) protein that is expressed in mesenchymal cells. Vimentin plays a significant role in supporting and anchoring the position of the organelles in the cytosol. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally



(three types) co-assemble to form neurofilaments, which are found in high concentration in vertebrate axons. Neurofilament abundance appears to control axonal diameter. They are a major component of the neuronal cytoskeleton, and are believed to function primarily to provide structural support for the axon and to regulate axon diameter. Mutations in the light chain may interfere with axonal transport of neurofilament subunits and cause a peripheral neuropathy called Charcot-Marie-Tooth syndrome. Abnormal neurofilament assembly seems to be involved in the neurodegenerative disease, amyotrophic lateral sclerosis (ALS or Lou Gehrig's Disease).


nuclear lamins

are filamentous proteins that form a stabilizing meshwork lining the inner membrane of the nuclear envelope to provide anchorage for chromosomes and nuclear pores. Mutations in lamins can result in nuclear instability. Lamin mutations are linked to various progeria syndroms.


Glial fibrillary acidic protein (GFAP

the IF protein characteristic of astrocytes in the CNS. It is involved in many important CNS processes, including cell communication and the functioning of the blood brain barrier. Glial scarring is a consequence of several neurodegenerative conditions, as well as injury that severs neural material. The scar is formed by astrocytes interacting with fibrous tissue to re-establish the glial margins around the central injury core and is partially caused by up-regulation of GFAP. Therefore, GFAP IFs are abundant in connection with inflammatory and/or degenerative processes in the brain. For example, Alzheimer plaques are surrounded by GFAP-rich reactive astrocytes.


epidermolysis bullosa simplex

a disorder resulting from mutations in the genes encoding keratin 5 or keratin 14. Blister formation of EBS occurs at the dermoepidermal junction. Sometimes EBS is called epidermolytic


Microtubules as drug targets

MT toxins block mitosis and, thus, are important therapeutic tools for cancer treatment. However, they may adversely affect other MT functions, such as axoplasmic transport. Thus, side effects (e.g. peripheral neuropathy) may be serious.



and associated proteins (actin cytoskeleton) form the third structural component of the cytoskeleton. They are structurally and functionally distinct from microtubules (MTs) and intermediate filaments. Microfilaments are essential for amoeboid motility. Microfilaments are filamentous polymers (~7 nm diameter) of actin monomers ("globular actin" = G-actin). In the presence of divalent cations and ATP, G-actin assembles to form two- stranded, helical filaments (F-actin). Most of these filaments contain additional actin-binding proteins. Microfilaments (MFs) are critical for cell shape, movement and polarity.



a globular multi-functional protein that forms microfilaments. It is found in all eukaryotic cells (the only known exception being nematode sperm), where it may be present at concentrations of over 100 μM. An actin protein's mass is roughly 42-kDa and it is the monomeric subunit of two types of filaments in cells: microfilaments, one of the three major components of the cytoskeleton, and thin filaments, part of the contractile apparatus in muscle cells. Most obvious are actin's roles in muscle contraction and amoeboid cell movement; however, these are not the only microfilament functions. MFs, just like MTs, are polarized (due to orientation in the filament and molecular asymmetry of the subunits). Some 60 accessory proteins - a huge number - participate in the regulation of polymerization and disassembly. These include proteins that bind G-actin, others that stabilize, crosslink, sever or cap F-actin, and proteins that enable F-actin branching to form MF networks.



This structure represents the “ATPase fold”, which is a centre of enzymatic catalysis that binds ATP and Mg2+ and hydrolyzes the former to ADP plus phosphate. This fold is a conserved structural motif that is also found in other proteins that interact with triphosphate nucleotides such as hexokinase (an enzyme used in energy metabolism) or in Hsp70 proteins (a protein family that play an important part in protein folding).[21] G-actin is only functional when it contains either ADP or ATP in its cleft but the form that is bound to ATP predominates in cells when actin is present in its free state



The F-actin polymer is considered to have structural polarity due to the fact that all the microfilament’s subunits point towards the same end. This gives rise to a naming convention: the end that possesses an actin subunit that has it’s ATP binding site exposed is called the "(-) end", while the opposite end where the cleft is directed at a different adjacent monomer is called the "(+) end"



extracted from the highly toxic fungus Amanita phalloides ("death cap"), which binds to and stabilizes F-actin (causing a net increase in actin polymerization). Actin filament nucleation typically occurs at the plasma membrane, which accounts for the high density of MFs in the cell periphery.



a seven-subunit protein that plays a major role in the regulation of the actin cytoskeleton. It is a major component of the actin cytoskeleton and is found in most actin cytoskeleton-containing eukaryotic cells. Two of its subunits, the Actin-Related Proteins ARP2 and ARP3 closely resemble the structure of monomeric actin and serve as nucleation sites for new actin filaments. The complex binds to the sides of existing ("mother") filaments and initiates growth of a new ("daughter") filament at a distinctive 70 degree angle from the mother. Branched actin networks are created as a result of this nucleation of new filaments. The ARP (or Arp2/3) complex nucleates MF polymerization from the minus-end, allowing rapid elongation at the plus-end. Arp2/3 activation results in branched actin filaments (required for lamellipodia formation).



the first step in the formation of either a new thermodynamic phase or a new structure via self-assembly or self-organisation. Nucleation is typically defined to be the process that determines how long we have to wait before the new phase or self-organised structure, appears. Nucleation with microfilaments is catalyzed by several regulatory proteins. One of them is a protein complex that includes two “actin-related proteins” (ARPs). Second regulator of actin nucleation regulator is forming. Activation of forming leads to parallel actin bundle formation (mirovilli, filopodia, actomyosin ring).


Actin and epithelial cell polarity

Actin plays a key role in polarization of epithelial cells. One of the most important functions of actin is anchoring proteins that are involved in Tight junction (TJ) and Adherens junction (AJ) formation. An unusual type of actin anchoring is observed in brush border microvilli: A tight MF bundle forms the core of these microvilli. All actin plus-ends are anchored in the apical protein cap of the microvillus. Actin bundles are held together by the cross-linking proteins villin and fimbrin, and bundles are linked laterally to the plasma membrane by myosin-I. Loss of microvilli is observed in microvilli inclusion disease.


Adherens junction (AJ)

are protein complexes that occur at cell–cell junctions in epithelial and endothelial tissues,[2] usually more basal than tight junctions. An adherens junction is defined as a cell junction whose cytoplasmic face is linked to the actin cytoskeleton. Decreased association of AJ proteins (cadherins and catenins) with actin leads to internalization of candherins and loss of cell-cell adhesion, the step that is a prerequisite for epithelial-to-mesenchimal (EMT) transition and cancer formation.


epithelial-to-mesenchimal (EMT) transition

a process by which epithelial cells lose their cell polarity and cell-cell adhesion, and gain migratory and invasive properties to become mesenchymal stem cells; these are multipotent stromal cells that can differentiate into a variety of cell types. EMT is essential for numerous developmental processes including mesoderm formation and neural tube formation. EMT has also been shown to occur in wound healing, in organ fibrosis and in the initiation of metastasis for cancer progression. Epithelial and mesenchymal cells differ in phenotype as well as function. Epithelial cells are closely connected to each other by tight junctions, gap junctions and adherens junctions, have an apico-basal polarity, polarization of the actin cytoskeleton and are bound by a basal lamina at their basal surface. Mesenchymal cells, on the other hand, lack this polarization, have a spindle-shaped morphology and interact with each other only through focal points. Epithelial cells express high levels of E-cadherin, whereas mesenchymal cells express those of N-cadherin, fibronectin and vimentin. Thus, EMT entails profound morphological and phenotypic changes to a cell. Based on the biological context, EMT has been categorized into 3 types - developmental (Type I), fibrosis and wound healing (Type II), and cancer (Type III).


microvilli inclusion disease

Microvillus inclusion disease is a condition characterized by chronic, watery, life-threatening diarrhea typically beginning in the first hours to days of life. Rarely, the diarrhea starts around age 3 or 4 months. Food intake increases the frequency of diarrhea. a rare genetic disorder of the small intestine that is inherited in an autosomal recessive pattern. Mutations in the MYO5B gene cause microvillus inclusion disease. The MYO5B gene provides instructions for making a protein called myosin Vb. This protein helps to determine the position of various components within cells (cell polarity). Cell loses polartiy. Myosin Vb also plays a role in moving components from the cell membrane to the interior of the cell for recycling. Don't for ARP2/3 structures.



a class of type-1 transmembrane proteins. They play important roles in cell adhesion, forming adherens junctions to bind cells within tissues together. They are dependent on calcium (Ca2+) ions to function, hence their name.



a family of proteins found in complexes with cadherin cell adhesion molecules of animal cells. The first two catenins that were identified[2] became known as α-catenin and β-catenin. A-catenin can bind to β-catenin and can also bind actin. B-catenin binds the cytoplasmic domain of some cadherins.


Tight junction (TJ)

the closely associated areas of two cells whose membranes join together forming a virtually impermeable barrier to fluid. It is a type of junctional complex present only in vertebrates. The corresponding junctions that occur in invertebrates are septate junctions. Tight junctions are composed of a branching network of sealing strands, each strand acting independently from the others. Therefore, the efficiency of the junction in preventing ion passage increases exponentially with the number of strands. Each strand is formed from a row of transmembrane proteins embedded in both plasma membranes, with extracellular domains joining one another directly. Although more proteins are present, the major types are the claudins and the occludins. These associate with different peripheral membrane proteins such as ZO-1 located on the intracellular side of plasma membrane, which anchor the strands to the actin component of the cytoskeleton. Thus, tight junctions join together the cytoskeletons of adjacent cells.


Actin-associated motor proteins

Like MTs, MFs support mechanical activity through the use of motor proteins. Actin-binding motor proteins belong to the myosin family.



comprise a family of ATP-dependent motor proteins and are best known for their role in muscle contraction and their involvement in a wide range of other eukaryotic motility processes. They are responsible for actin-based motility. The term was originally used to describe a group of similar ATPases found in striated and smooth muscle cells. (heavy chain) are structurally related to the kinesins and, thus, consist of a head region, containing ATPase activity and actin binding sites, and a tail region. The ATPase is actin-activated and moves to the plus-end of the MF. The tail region is involved in binding to other molecules. Myosin II, characteristic of striated muscle (see there), forms hetero-oligomers involving two heavy chains and two copies of each of two light chains. The coiled tails of myosin II bundle with the tails of other myosin molecules to form large bipolar assemblies (several hundred myosins), the "thick filaments" in muscle. The ATP-driven walk of myosin heads along actin filaments results in the sliding-filament mechanism responsible for muscle contraction. Other non-conventional myosins, such as I and V, are associated with membranes and, thus, are involved in the F-actin-mediated movement of organelles.



are microscopic cellular membrane protrusions that increase the surface area of cells and minimize any increase in volume, and are involved in a wide variety of functions, including absorption, secretion, cellular adhesion, and mechanotransduction. Microvilli are covered in plasma membrane, which encloses cytoplasm and microfilaments. Though these are cellular extensions, there are little or no cellular organelles present in the microvilli.



slender cytoplasmic projections that extend beyond the leading edge of lamellipodia in migrating cells. They contain actin filaments cross-linked into bundles by actin-binding proteins, e.g. fascin and fimbrin. Filopodia form focal adhesions with the substratum, linking it to the cell surface. Many types of migrating cells display filopodia, which are thought to be involved in both sensation of chemotropic cues, and resulting changes in directed locomotion.



a cytoskeletal protein actin projection on the leading edge of the cell. It contains a quasi-two-dimensional actin mesh; the whole structure propels the cell across a substrate. Within the lamellipodia are ribs of actin called microspikes, which, when they spread beyond the lamellipodium frontier, are called filopodia. The lamellipodium is born of actin nucleation in the plasma membrane of the cell and is the primary area of actin incorporation or microfilament formation of the cell.


Actin and cell shape

A MF-rich layer underlying the plasma membrane, the cell cortex, helps stabilize the plasma membrane and determine shape and movement of the cell surface. This includes cell surface projections. A mammalian cell in tissue or in culture usually has an irregular shape with specialized appendages, such as microvilli, filopodia and lamellipodia. The former are spike- like thin projections that contain tight parallel bundles of F-actin whereas the latter are veil-like, flat extensions or protrusions. Gel-like F-actin networks are found in many parts of the cell (the cell cortex), including lamellipodia. Filopodia and lamellipodia can adhere or detach to/from a cell substratum (the ECM or another cell) via appropriate adhesion molecules. F-actin also forms contractile bundles, so-called stress fibers (prominent in cultured cells). Stress fibers are inserted into large adhesive patches known as focal adhesions that are observed in culture conditions only. Most attached cells spontaneously form stress fibers and focal adhesions in culture. Together these devices anchor cells to the substratum and exert tension across the cell -- rather than being involved in amoeboid movement. In other words, focal-adhesion-anchored cells exhibit low motility.


Regulation of Cell Shape and Movement

Actin organization and, thus, cell shape are controlled, in part, by extracellular signals that act via signaling molecules. Of particular importance are molecular switches of the Rho family. These are members of the large superfamily of Ras GTPases. In their GTP-bound state they are active, in the GDP-bound state inactive. Three Rho family members play distinctive roles: Rho (itself) activation causes the formation of stress fibers and focal adhesions; Rac activation the formation of veils; and Cdc42 activation the protrusion of fillopodia. Such control mechanisms are critical for cell motility.


Rho family of GTPases

a family of small (~21 kDa) signaling G proteins, and is a subfamily of the Ras superfamily. The members of the Rho GTPase family have been shown to regulate many aspects of intracellular actin dynamics, and are found in all eukaryotic organisms. One of the most obvious changes to cell morphology controlled by rho proteins is the formation of lamellipodia and filopodia. In addition to the formation of lamellipodia and filopodia, it has been shown that intracellular concentration and cross-talk between different rho proteins drives the extensions and contractions that cause cellular locomotion. a proposed model based on differential equations, which helps explain the activity of rhos and their relationship to motion. This model encompassed the three proteins Cdc42, RhoA, and Rac. Cdc42 was assumed to encourage filopodia elongation and block actin depolymerization. RhoA was considered to encourage actin retraction. Rac was treated to encourage lamellipodia extension but block actin depolymerization. These three proteins, although significantly simplified, covered the key steps in cellular locomotion. Through various mathematical techniques, solutions to the differential equations that described various regions of activity based on intracellular activity were found. The paper concludes by showing that the model predicts that there are a few threshold concentrations that cause interesting effects on the activity of the cell. Below a certain concentration, there is very little activity, causing no extension of the arms and feet of the cell. Above a certain concentration, the rho protein causes a sinusoidal oscillation to occur, much like the extensions and contractions of the lamellipodia and filopodia. In essence, this model predicts that increasing the intracellular concentration of these three key active rho proteins causes an out-of-phase activity of the cell, resulting in extensions and contractions that are also out of phase.


stress fibers

Are high order structures in non-muscle cells which consist of actin filaments (aka microfilaments), crosslinking proteins (proteins that bind two or more filaments together), and myosin II motors. Originally thought to arise from the effects of tension,[1] stress fibers have since been shown to play an important role in cell motility and contractility, providing force for a number of cell functions such as cell adhesion and morphogenesis.


focal adhesions

are large macromolecular assemblies through which mechanical force and regulatory signals are transmitted between the extracellular matrix (ECM) and an interacting cell. More precisely, focal adhesions are the sub-cellular structures that mediate the regulatory effects (i.e., signaling events) of a cell in response to ECM adhesion.[



a small (~21 kDa) signaling G protein (more specifically a GTPase), and is a member of the Rac subfamily of the family Rho family of GTPases. Members of this superfamily appear to regulate a diverse array of cellular events, including the control of cell growth, cytoskeletal reorganization, and the activation of protein kinases


Amoeboid cell motility

Mammalian cells can move by swimming in a fluid medium, propelled by flagella (spermatozoa; see Cytoskeleton I), but much more common is amoeboid movement, the crawling along a surface, the process that requires actin cytoskeleton and cell adhesion. Amoeboid cell migration is very common in both normal conditions and disease. Overall, motility depends on adhesion in a biphasic manner: (i) Tightly adhering cells cannot migrate. (ii) As cell adhesion decreases, motility increases (up to a maximum). (iii) As adhesion decreases further, motility declines (traction no longer possible). And (iv) eventually, cells detach completely. Attachment and detachment processes, together with MF polymerization and depolymerization, must be coordinated precisely to allow for efficient cell migration. They seem to cycle seamlessly. They also are regulated by extracellular factors (attractants, etc.; the migration matrix, etc.).


Amoeboid role in development

In development, many cell types move over long distances to reach their destination. The classic example is the cells of the neural crest. These give rise, for example, to pigment cells and the peripheral nervous system. Neural crest cells originate from the ectoderm immediately adjacent to the forming neural tube and have to reach destinations in many parts of the body, including its entire surface (in the case of pigment cells). During nervous system development, nerve fibers (axons) grow over long distances. Axons are tipped by an amoeboid structure, the nerve growth cone, that moves just like an amoeboid cell, spinning out behind it the nerve fiber (the nerve cell body typically remains stationary).


Amoeboid role in Host defense

Upon infection of a tissue, polymorphonuclear leukocytes have to exit blood vessels and migrate into the tissue to reach the infection site


Amoeboid role in Cancer

As cancer cells become more malignant they often begin to migrate and invade healthy tissues (metastatic progression). By this process they may establish new tumor sites at a distance from the primary tumor (metastases).


Important attributes of amoeboid locomotion

As explained below in detail, amoeboid cell motility is the result of modulation of the actin cytoskeleton and changes in cell adhesion. Changes in the actin cytoskeleton involve the function of Rho GTPases. They respond to factors that regulate (random) migratory activity (chemokinesis) and directed migration (chemotaxis). Cells may respond to attractants (positive chemotaxis) or repellents (negative chemotaxis) by migrating toward or away from the sources of such factors. For example, infection/inflammation sites in a tissue release a strong attractant that enables leukocytes to migrate to these sites. In the nervous system, repellents and attractants play major roles in pathfinding of the growth cones of growing axons. Amoeboid cell migration in the context of a tissue is an invasive process. The invading cells or cell processes release proteases (see ECM).



is chemically prompted kinesis, a motile response of unicellular prokaryotic or eukaryotic organisms to chemicals that cause the cell to make some kind of change in their migratory/swimming behaviour. Changes involve an increase or decrease of speed, alterations of amplitude or frequency of motile character, or direction of migration. However, in contrast to chemotaxis, chemokinesis has a random, non-vectorial moiety, in general



movement of an organism in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food (e.g., glucose) by swimming toward the highest concentration of food molecules, or to flee from poisons (e.g., phenol). In multicellular organisms, chemotaxis is critical to early development (e.g., movement of sperm towards the egg during fertilization) and subsequent phases of development (e.g., migration of neurons or lymphocytes) as well as in normal function. In addition, it has been recognized that mechanisms that allow chemotaxis in animals can be subverted during cancer metastasis. Positive chemotaxis occurs if the movement is toward a higher concentration of the chemical in question. However, negative chemotaxis occurs if the movement is in the opposite direction. Chemically prompted kinesis (randomly directed or nondirectional) can be called chemokinesis.


Key elements of amoeboid locomotion.

During locomotion, amoeboid cells go through repeated cycles of -protrusion (of lamellipodia, fillopodia) attachment (of these protrusions), traction (to pull the cell forward), detachment (of adhesion toward the rear). In other words, tight coordination between actin cytoskeleton dynamics and cell adhesion is a prerequisite for migration.


Wiskott–Aldrich Syndrome protein (WASp)

The Wiskott–Aldrich syndrome (WAS) family of proteins share similar domain structure, and are involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton. The presence of a number of different motifs suggests they are regulated by a number of different stimuli, and interact with multiple proteins. These proteins, directly or indirectly, associate with the small GTPase CDC42, known to regulate formation of actin filaments, and the cytoskeletal organizing complex, Arp2/3. The WASp family includes both WASp, which is expressed exclusively in hematopoietic cells, and neuronal WASp (N-WASp), which is expressed ubiquitously. In its inactive state, N-WASp is autoinhibited and bound to Arp2/3. Cooperative binding of CDC42 and PIP2 relieve the autoinhibition of N-WASp, causing Arp2/3 to carry out actin polymerization.


Wiskott-Aldrich syndrome

WAS is a rare, X-linked immunodeficiency disease. It results from WASp mutations. Clinical symptoms include thrombocytopenia (reduced platelet number and size) and recurrent infections. Platelets are, in essence, sloughed-off lamellipodia of megakaryocytes, so that thrombocytopenia may result from defective lamellipodia/platelet formation. WAS macrophages and neutrophil leukocytes have been shown to be migration- and chemotaxis-deficient.



Protrusion of fillopodia and lamellipodia is driven by polymerization of actin meshworks at the leading edge. The meshwork's MFs have their plus-ends facing forward. Minus-ends often are linked to the sides of other MFs via ARP complexes (branched web). This is controlled by Rac and also involves WASp, the Wiskott-Aldrich syndrome protein (see below), which stimulates Arp2/3 complexes. As filament assembly of these meshworks takes place (at the leading edge) it pushes the plasma membrane forward. Simultaneously some treadmilling of the meshwork occurs, with MF disassembly taking place further back. As cell protrusions advance and the cell elongates MTs appear to grow in that direction and to stabilize the changed cell shape. However, they do not reach into filopodia or lamellipodia.


Mechanisms of actin polymerization by Arp2/3

Many actin-related molecules create a free barbed end for polymerization by uncapping or severing pre-existing filaments and using these as actin nucleation cores. However, the Arp2/3 complex stimulates actin polymerization by creating a new nucleation core. Actin nucleation is an initial step in the formation of an actin filament. The nucleation core activity of Arp2/3 is activated by members of the Wiskott-Aldrich syndrome family protein (WASP, N-WASP, WAVE, and WASH proteins). The V domain of a WASP protein interacts with actin monomers while the CA region associates with the Arp2/3 complex to create a nucleation core. However, de novo nucleation followed by polymerization is not sufficient to form integrated actin networks, since these newly synthesized polymers would not be associated with pre-existing filaments. Thus, the Arp2/3 complex binds to pre-existing filaments so that the new filaments can grow on the old ones and form a functional actin cytoskeleton. Capping proteins limit actin polymerization to the region activated by the Arp2/3 complex, and the elongated filament ends are recapped to prevent depolymerization and thus conserve the actin filament. The Arp2/3 complex simultaneously controls nucleation of actin polymerization and branching of filaments. Moreover, autocatalysis is observed during Arp2/3-mediated actin polymerization. In this process, the newly formed filaments activate other Arp2/3 complexes, facilitating the formation of branched filaments. The mechanism of actin filament initiation by Arp2/3 has been disputed. The question is where the complex binds the filament and nucleates a "daughter" filament. Historically two models have been proposed. Recent results, and the balance of opinion in the field, favour the side branching model, in which the Arp2/3 complex binds to the side of a pre-existing ("mother") filament at a point different from the nucleation site. Although the field lacks a high-resolution crystal structure, data from electron microscopy, together with biochemical data on the filament nucleation and capping mechanisms of the Arp2/3 complex, favour side branching. In the alternative barbed end branching model, Arp2/3 only associates at the barbed end of growing filaments, allowing for the elongation of the original filament and the formation of a branched filament. This model, which is based on kinetic analysis and optical microscopy, is decreasingly favoured by the field.


Attachment and traction

Protrusions are equipped to form attachments with the substratum as they advance. These new, dynamic attachment sites serve as anchorage points to pull the cell body forward. The necessary traction forces seem to be generated by myosins in conjunction with actin MFs.



As traction forces are applied to the cell, adhesions formed earlier and located further back must be released or detached to allow for translocation of the cell body.


Actin cytoskeleton, amoeboid motility, and medicine

In view of the fundamental importance of the actin cytoskeleton for normal cell function significant changes in the actin cytoskeleton are not compatible with life (e.g., phalloidin poisoning). However, the large number of actin-associated proteins seems to provide some redundancy in function. Two examples of diseases based on actin-associated proteins follow.



This describes a severe defect of brain development resulting in a smooth cortical surface, i.e., the absence gyri. Neuronal migration is a critical process for establishing the normal, complex cytoarchitecture of the brain. Loss-of-function of n-cofilin, an actin filament depolymerizing factor, results in lissencephaly and the associated severe mental retardation.



Most of the terminal cancers are characterized by the spread of the tumors from the primary site, the process known as metastasis. The migration of cancer cells from the primary tumor to the blood stream and setting up secondary tumors at the other tissues is at the core off metastasis. Multiple drugs are being developed and used to either prevent or at least slow-down cell movement as a means of preventing spread of tumors.


actomyosin ring

A cytoskeletal structure composed of actin filaments and myosin that forms beneath the plasma membrane of many cells, including animal cells and yeast cells, in a plane perpendicular to the axis of the spindle, i.e. the cell division plane. Ring contraction is associated with centripetal growth of the membrane that divides the cytoplasm of the two daughter cells. In animal cells, the contractile ring is located inside the plasma membrane at the location of the cleavage furrow. Is composed of formin. If done too early, chromosomes have not yet been seperated and can cause chromosome cleaving This is all regulated of Rho GTP/GDP. when RHO is GTP bound, which activates both formin and myosin creating contractile ring. RHO is activated in regions where there is a lot of MTs (in the middle).


Actin and cell division

Actin also plays a key role during last stages of cell division, known as cytokinesis. The formation and contraction of actomyosin ring drives the formation of the cleavage furrow and separation of the daughter cells. The site of actomyosin ring formation and the timing of its contraction are highly regulated events that determine the symmetry of cell division.



a group of proteins that are involved in the polymerization of actin and associate with the fast-growing end (barbed end) of actin filaments. Most formins are Rho-GTPase effector proteins. Formins regulate the actin and microtubule cytoskeleton and are involved in various cellular functions such as cell polarity, cytokinesis, cell migration and SRF transcriptional activity. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins also directly bind to microtubules via their FH2 domain. This interaction is important in promoting the capture and stabilization of a subset of microtubules oriented towards the leading edge of migrating cells. Formins also promote the capture of microtubules by the kinetochore during mitosis and for aligning microtubules along actin filaments.


receptor tyrosine kinase (RTK)

are essential components of signal transduction pathways that mediate cell-to-cell communication. These single-pass transmembrane receptors, which bind polypeptide ligands — mainly growth factors — play key roles in processes such as cellular growth, differentiation, metabolism and motility. Recent progress has been achieved towards an understanding of the precise (and varied) mechanisms by which RTKs are activated by ligand binding and by which signals are propagated from the activated receptors to downstream targets in the cell. The enzymes that catalyze phosphoryl transfer to tyrosine residues in protein substrates, using ATP as a phosphate donor, are the protein tyrosine kinases, of which there are 58 receptor types (RTKs) and 32 non-receptor types in the human genome [1]. The RTK family includes, among others, epidermal growth factor receptor (EGFR), platelet-derived growth factor receptors, fibroblast growth factor receptors (FGFRs), vascular endothelial growth factor receptors, Met (hepatocyte growth factor/scatter factor [HGF/SF] receptor), Ephs (ephrin receptors), and the insulin receptor. RTKs are essential components of cellular signaling pathways that are active during embryonic development and adult homeostasis. Because of their roles as growth factor receptors, many RTKs have been implicated in the onset or progression of various cancers, either through receptor gain-of- function mutations or through receptor/ligand overexpression. The c-terminal tail folds up into the active P site, inhibiting it. When RTK dimerizes, it changes C-terminal tail, activating phosphorlating site and P tyrosine on tail. Which serve as docking sites for other molecules


mechanism of receptor tyrosine kinase (RTK) activation

Generally, RTKs are activated through ligand-induced oligomerization, typically dimerization, which juxtaposes the cytoplasmic tyrosine kinase domains. For most RTKs, this juxtaposition facilitates autophosphorylation in trans of tyrosine residues in the kinase activation loop or juxtamembrane region, inducing conformational changes that serve to stabilize the active state of the kinase. These and other phosphotyrosine residues serve as recruitment sites for a host of down-stream signaling proteins — enzymes and adapter/scaffolding proteins — typically through Src homology-2 (SH2) or phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine residues in specific sequence contexts. Whether the ‘inactive’ state is monomeric or oligomeric, activation of the receptor still requires the bound ligand to stabilize a specific relationship between individual receptor molecules in an ‘active’ dimer or oligomer. Depending on the ligand present, RTK can either form homodimerization or heterodimerization to activate different signaling pathways. Different tyrosine residues are P or de-P based on different kinetics.


Ligand-induced dimerization of RTK extracellular regions

Early studies of RTKs and cytokine receptors suggested a conceptually straightforward mechanism for ligand-induced dimerization: a bivalent ligand interacts simultaneously with two receptor molecules and effectively cross-links them into a dimeric complex. the ligand is itself a dimer and simply cross-links the ligand-binding fragments of two receptor molecules. Recent structures of more complete extracellular regions of RTKs have provided important additional insight into the range of mechanisms used for ligand-induced dimerization. At one extreme, receptor dimerization is entirely “ligand-mediated” and the two receptors make no direct contact. At the other extreme, dimerization is instead entirely “receptor-mediated” (and the ligand makes no direct contribution to the dimer interface. Alternatively, dimerization can involve both ligand-mediated and receptor-mediated components


The Signaling Pathway

An extracellular signaling molecule binds to a receptor and activates it. (The receptor is usually but not always located on the cell membrane). The activated receptor activates a down-stream signaling molecule, which in return can activate another down-stream signaling molecule, and so on... until an effector protein is activated that regulates a cellular function.



Can be named after their natural ligand (usually an activator = agonist; for example acetylcholine), or after a pharmacological ligand (agonist or antagonist; for example dehydropyridine). Receptor Types: Ligand (or Voltage)-gated Ion Channels, GPCRs (G-protein coupled receptors), Enzyme-linked receptors – including receptor tyrosine-kinases, Nuclear receptors – transcription factors activated by cell-penetrating signaling molecules.


Second Messengers

Small molecules generated or released within the cell in response to the first messenger, the extracellular signaling molecule. Can bind to intracellular signaling molecules and regulate their activity. Second Messenger examples: Ca2+ enters through ion channels from extracellular space or intracellular stores, cAMP (cyclic Adenosine Mono Phosphate) is generated by AC (Adenylate Cyclase) IP3 (inositol triphosphate; released into the cytosol) and DAG (diacylglycerol; stays in membrane) are generated by PLC (Phospholipase C), NO (nitric oxide) generated by NOS (Nitric oxide synthase) is cell permeable.


Other signaling steps

Signaling proteins, activated by receptors or second messengers, can activate other signaling or effector proteins (including enzymes that generate second messengers) in a variety of ways. Such as: Protein modification, Protein-Protein Binding, GTP/GDP exchange


signalling through protein modification

Protein phosphorylation (or dephosphorylation) mediated by kinases (or phosphates) is most prominent. But there is also: Acetylation (histones), Glycosylation (trafficking through ER, Golgi, etc.), Ubiquitinylation (marking for degradation... and more) -Proteolytic Cleavage (of inactive precursors)


signalling through Protein-Protein Binding

Can directly regulate activity and/or target a signaling protein to specific cellular locations. Targeting often involves protein-protein binding, but can include other mechanisms as well. Targeting can regulate signaling enzymes by promoting access to nearby downstream substrates, and by preventing access to other substrates.


signalling through GTP/GDP exchange

In G-proteins coupled to receptors and in small GTPases such as ras. Note that GTP is NOT a second messenger, as signaling through GTP does NOT depend on its concentration.


Signal Amplification and Termination

Amplification and termination occurs in every signaling pathway. A signal can be terminated at any point in a signaling pathway, starting with the extracellular signaling molecule (which can be taken up into cells and reused; broken down extracellularly; or simply diffuse to reach a too low concentration). Termination of a signal can be initiated by another signal (for instance, phopshorylation by a kinase can be reversed by dephosphorylation by a phosphatase). Some enzymes are dedicated to turn off signals (for instance, phosphodiesterases –PDEs- hydrolyze cAMP or cGMP). Some signaling proteins have built in terminators (G-proteins and ras-like proteins are slow GTPases, thereby reversing their active GTP-bound state). Amplification occurs when one upstream signaling molecule activates more than one downstream signaling molecule. If this occurs at multiple consecutive steps, the amplification is further amplified. This is often called a signaling cascade. In reality almost every signal transduction step involves amplification to some degree or other (even though pathway diagrams usually do not indicate the degree of amplification). Amplification often depends on the time it takes to terminate activity of a signaling molecule. One form of amplification is a positive feed-back loop (signal 1 enhances signal 2 which in turn enhances signal 1 again). This type of regulation is “dangerous” as it can get out of hand easily. Thus, in signaling, a positive feed-back loop is usually coupled with a negative feed-back loop that stops the signal before it gets out of control.


The Signaling Network

If you picture all possible intra-cellular signaling at the same time, the result will not be countless parallel pathways, but a very complex network. A consequence of the network is a vast potential for cross-talk in signaling. For instance, simultaneous activity (and/or non-activity) of several receptor types may be necessary to achieve a certain signaling outcome (this is called coincidence detection, important in immunology and neuroscience). One obvious problem with a network is the following question: In a given pathway, why are some of the possible connections used while other possible connections are not? There are many different possibilities, including the following. Some connections may require an additional input stimulation (see coincidence detection). The signaling protein in question may not be expressed in the cell type currently examined. Or it might be expressed in this cell type, but in a location that does not allow activation by the upstream signal in question (only by other signals). Or it may be activated, but the downstream signaling pathway does not result in a function, or it results in a function that we are not interested in for now or do not know about. In additions to pathways, there are two other patterns found in networks, nodes and modules. Awareness of both can make understanding of signal transduction and pathways easier.



are points in a network that receive multiple inputs and/or multiple outputs. Ca2+ is likely the most extensive node in signaling. But how does this make understanding easier compared to thinking of linear pathways? It becomes very unsatisfying when you learn about six pathways were Ca2+ links “specific” upstream signals with “specific” downstream outputs... but the “specific” link is different in each case. It is much better to know that Ca2+ is a signaling node, and that there is some reason for the specific link seen in each pathway (see end of first paragraph of this chapter), even if we might not know the reason at the moment.



groups of components (or building blocks) that function together; in signaling they are often proteins physically associated to form complexes. Don’t worry about what exactly you can or can not group into a module (nobody has defined this exactly for signaling... or most other cases). For instance, “kitchen” may be a module in helping to understand the problem “house” (or “stove” in “kitchen”, or “hot-plate” in “stove”). Let your intuition guide you: If it makes sense to group things into a module... then it makes sense. How does this help understanding? Well, initially it may be additional work, but it will force you to functionally analyze and better understand your signaling example at hand, and help to recognize similar modules in future examples. Once you have an understanding of a module (“kitchen”), you don’t need to consider all its components (stove->hot-plate, oven, etc.; refrigerator->..., etc) each time when considering the overall problem (“house”).


Signal transduction with RTK

Through diverse means, extracellular ligand binding will typically cause or stabilize receptor dimerization. This allows a tyrosine in the cytoplasmic portion of each receptor monomer to be trans-phosphorylated by its partner receptor, propagating a signal through the plasma membrane. The phosphorylation of specific tyrosine residues within the activated receptor creates binding sites for Src homology 2 (SH2) domain- and phosphotyrosine binding (PTB) domain-containing proteins. Specific proteins containing these domains include Src and phospholipase Cγ. Phosphorylation and activation of these two proteins on receptor binding lead to the initiation of signal transduction pathways. Other proteins that interact with the activated receptor act as adaptor proteins and have no intrinsic enzymatic activity of their own. These adaptor proteins link RTK activation to downstream signal transduction pathways, such as the MAP kinase signalling cascade. An example of a vital signal transduction pathway involves the tyrosine kinase receptor, c-met, which is required for the survival and proliferation of migrating myoblasts during myogenesis. A lack of c-met disrupts secondary myogenesis and—as in LBX1—prevents the formation of limb musculature. This local action of FGFs (Fibroblast Growth Factors) with their RTK receptors is classified as paracrine signalling.


epidermal growth factor receptor

a receptor tyrosine kinases: the cell-surface receptor for members of the epidermal growth factor family (EGF-family) of extracellular protein ligands. EGFR (epidermal growth factor receptor) exists on the cell surface and is activated by binding of its specific ligands, including epidermal growth factor and transforming growth factor α (TGFα) (note, a full list of the ligands able to activate EGFR and other members of the ErbB family is given in the ErbB article). ErbB2 has no known direct activating ligand, and may be in an activated state constitutively or become active upon heterodimerization with other family members such as EGFR. Upon activation by its growth factor ligands, EGFR undergoes a transition from an inactive monomeric form to an active homodimer. EGFR dimerization stimulates its intrinsic intracellular protein-tyrosine kinase activity. This autophosphorylation elicits downstream activation and signaling by several other proteins that associate with the phosphorylated tyrosines through their own phosphotyrosine-binding SH2 domains. These downstream signaling proteins initiate several signal transduction cascades, principally the MAPK, Akt and JNK pathways, leading to DNA synthesis and cell proliferation. Such proteins modulate phenotypes such as cell migration, adhesion, and proliferation. Activation of the receptor is important for the innate immune response in human skin. The kinase domain of EGFR can also cross-phosphorylate tyrosine residues of other receptors it is aggregated with, and can itself be activated in that manner.


EGFR role in cancer

Mutations that lead to EGFR overexpression (known as upregulation) or overactivity have been associated with a number of cancers, including lung cancer, anal cancers and glioblastoma multiforme. These somatic mutations involving EGFR lead to its constant activation, which produces uncontrolled cell division. In glioblastoma a more or less specific mutation of EGFR, called EGFRvIII is often observed. Mutations, amplifications or misregulations of EGFR or family members are implicated in about 30% of all epithelial cancers.


EGFR targeted cancer treatments

The identification of EGFR as an oncogene has led to the development of anticancer therapeutics directed against EGFR (called "EGFR inhibitors"), including gefitinib, erlotinib, afatinib, and icotinib for lung cancer, and cetuximab for colon cancer. Many therapeutic approaches are aimed at the EGFR. Cetuximab and panitumumab are examples of monoclonal antibody inhibitors. However the former is of the IgG1 type, the latter of the IgG2 type; consequences on antibody-dependent cellular cytotoxicity can be quite different. Other monoclonals in clinical development are zalutumumab, nimotuzumab, and matuzumab. The monoclonal antibodies block the extracellular ligand binding domain. With the binding site blocked, signal molecules can no longer attach there and activate the tyrosine kinase. Another method is using small molecules to inhibit the EGFR tyrosine kinase, which is on the cytoplasmic side of the receptor. Without kinase activity, EGFR is unable to activate itself, which is a prerequisite for binding of downstream adaptor proteins. Ostensibly by halting the signaling cascade in cells that rely on this pathway for growth, tumor proliferation and migration is diminished. Gefitinib, erlotinib, and lapatinib (mixed EGFR and ERBB2 inhibitor) are examples of small molecule kinase inhibitors.


tyrosine-kinase inhibitor (TKI)

a pharmaceutical drug that inhibits tyrosine kinases. Tyrosine kinases are enzymes responsible for the activation of many proteins by signal transduction cascades. The proteins are activated by adding a phosphate group to the protein (phosphorylation). TKIs are typically used as anti-cancer drugs. TKIs operate by four different mechanisms: they can compete with adenosine triphosphate (ATP), the phosphorylating entity, the substrate or both or can act in an allosteric fashion, namely bind to a site outside the active site, affecting its activity by a conformational change. Recently TKIs have been shown to deprive tyrosine kinases of access to the Cdc37-Hsp90 molecular chaperone system on which they depend for their cellular stability, leading to their ubiquitylation and degradation. Signal transduction therapy can in principle also apply for non-cancer proliferative diseases and for inflammatory conditions. Until now TKIs have not been developed for the treatment of such conditions.


mechanisms of resistance of TKIs

The most common and prevalent mechanism leading to against TKIs therapy is point mutations within the kinase domain, which decrease the affinity of the TKIs to binding domain. Some mutations may occur around the binding site, which make extensive conforma- tional changes, thereby impeding TKIs approach through steric hindrance. Moreover, some mutations may render the predo- minance of ATP to competitive binding to the kinase compare with the second generation TKIs, such as Dasatinib, Nilotinib or Bosutinib. Gene copy number alteration and protein expression level change are another two major mechanisms of oncogenic activa- tion or signaling pathway modification. Cancer cells can survival and replace the lack of signal in target therapy by activating modified signaling pathway, leading to the acquisition of drug resistance. In tumor cell lines, multidrug resistance (MDR) is often associated with an ATP-dependent decrease in cellular drug accumulation, which is attributed to the overexpression of certain ATP-binding cassette (ABC) transpor- ter proteins.


SH2 (Src Homology 2) domain

SH2 domains bind to Phospho-Tyr-containing peptides. SH3 domains bind to Pro-containing peptides. a structurally conserved protein domain contained within the Src oncoprotein and in many other intracellular signal-transducing proteins. SH2 domains allow proteins containing those domains to dock to phosphorylated tyrosine residues on other proteins. SH2 domains are commonly found in adapter proteins that aid in the signal transduction of receptor tyrosine kinase pathways. SH2 domains typically bind a phosphorylated tyrosine residue in the context of a longer peptide motif within a target protein, and SH2 domains represent the largest class of known pTyr-recognition domains. Phosphorylation of tyrosine residues in a protein occurs during signal transduction and is carried out by tyrosine kinases. In this way, phosphorylation of a substrate by tyrosine kinases acts as a switch to trigger binding to an SH2 domain-containing protein. Many tyrosine containing short linear motifs that bind to SH2 domains are conserved across a wide variety of higher Eukaryotes. The intimate relationship between tyrosine kinases and SH2 domains is supported by their coordinate emergence during eukaryotic evolution.


microtubule capping proteins

bind to GTP cap and stabilizes the microtubule


microtubule severing proteins

severes the the GTP cap therefore the whole microtubule is GDP bound, GDP causes a kink, causing the microtubule to fall apart. If the tails are clipped these proteins are not functional because they work by pulling on the tails.



a microtubule-severing AAA protein. Structural analysis using electron microscopy has revealed that microtubule protofilaments change from a straight to a curved conformation upon GTP hydrolysis of β-tubulin. However, when these protofilaments are part of a polymerized microtubule, the stabilizing interactions created by the surrounding lattice lock subunits into a straight conformation, even after GTP hydrolysis. In order to disrupt these stable interactions, katanin, once bound to ATP, oligomerizes into a ring structure on the microtubule wall - in some cases oligomerization increases the affinity of katanin for microtubules and stimulates its ATPase activity. Once this structure is formed, katanin hydrolyzes ATP, and likely undergoes a conformational change that puts mechanical strain on the tubulin subunits, which destabilizes their interactions within the microtubule lattice. The predicted conformational change also likely decreases the affinity of katanin for tubulin as well as for other katanin proteins, which leads to disassembly of the katanin ring structure, and recycling of the individual inactivated proteins.



The human gene SPAST codes for the microtubule-severing protein of the same name, commonly known as spastin. This gene encodes a member of the AAA (ATPases associated with a variety of cellular activities) protein family. Members of this protein family share an ATPase domain and have roles in diverse cellular processes including membrane trafficking, intracellular motility, organelle biogenesis, protein folding, and proteolysis. The encoded ATPase may be involved in the assembly or function of nuclear protein complexes. Two transcript variants encoding distinct isoforms have been identified for this gene. Other alternative splice variants have been described but their full length sequences have not been determined. Mutations associated with this gene cause the most frequent form of autosomal dominant spastic paraplegia 4.


hereditary spastic paraplesia

Mutations in the AAA adenosine triphosphatase (ATPase) Spastin (SPG4) cause an autosomal dominant form of hereditary spastic paraplegia, which is a retrograde axonopathy primarily characterized pathologically by the degeneration of long spinal neurons in the corticospinal tracts and the dorsal columns.


AAA proteins

an abbreviation for ATPases Associated with diverse cellular Activities. They share a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules. AAA proteins couple chemical energy provided by ATP hydrolysis to conformational changes which are transduced into mechanical force exerted on a macromolecular substrate.



n cell biology, the centrosome is an organelle that serves as the main microtubule organizing center (MTOC) of the animal cell as well as a regulator of cell-cycle progression.


gamma tubulin

not incorporated in MT, but forms rings around centrosome, allowing other tubulin to grow out of it. Thus acts to stabilize the negative end of MT.


microtubule dependent motors

composed of molecular motor (does not bind directuly to cargo vesicle), adaptor molecule (where regulations and specificity takes place). They also move RNA, proteins, and can slide microtubules (important in mitotic cell devision).


The kinetic cycles of kinesin

When bound to ATP it binds to filament. ATP hydrolysis leads to dettachement and kink. Kinesin accomplishes transport by "walking" along a microtubule. Two mechanisms have been proposed to account for this movement. In the "hand-over-hand" mechanism, the kinesin heads step past one another, alternating the lead position. In the "inchworm" mechanism, one kinesin head always leads, moving forward a step before the trailing head catches up. Despite some remaining controversy, mounting experimental evidence points towards the hand-over-hand mechanism as being more likely. ATP binding and hydrolysis cause kinesin to travel via a "seesaw mechanism" about a pivot point. This seesaw mechanism accounts for observations that the binding of the ATP to the no-nucleotide, microtubule-bound state results in a tilting of the kinesin motor domain relative to the microtubule. Critically, prior to this tilting the neck linker is unable to adopt its motor-head docked, forward-facing conformation. The ATP-induced tilting provides the opportunity for the neck linker to dock in this forward-facing conformation. This model is based on CRYO-EM models of the microtubule-bound kinesin structure which represent the beginning and end states of the process, but cannot resolve the precise details of the transition between the structures.


Lamin associated diseases

Emery-Dreifuss muscular dystrophy - A muscle wasting disease, Progeria - Premature aging, Restrictive dermopathy - A disease associated with extremely tight skin and other severe neonatal abnormalities.


CaaX box

Protein prenylation involves the transfer of either a farnesyl or a geranyl-geranyl moiety to C-terminal cysteine(s) of the target protein. There are three enzymes that carry out prenylation in the cell, farnesyl transferase, Caax protease and geranylgeranyl transferase I.



the addition of hydrophobic molecules to a protein or chemical compound. It is usually assumed that prenyl groups (3-methyl-but-2-en-1-yl) facilitate attachment to cell membranes, similar to lipid anchor like the GPI anchor, though direct evidence is missing. Prenyl groups have been shown to be important for protein-protein binding through specialized prenyl-binding domains.


IF structure

The N and C-termini of IF proteins are non-alpha-helical regions and show wide variation in their lengths and sequences across IF families. The basic building-block for IFs is a parallel and in-register dimer. The dimer is formed through the interaction of the rod domain to form a coiled coil. Cytoplasmic IF assemble into non-polar unit-length filaments (ULF). Identical ULF associate laterally into staggered, antiparallel, soluble tetramers, which associate head-to-tail into protofilaments that pair up laterally into protofibrils, four of which wind together into an intermediate filament



Prelamin A contains a CAAX box at the C-terminus of the protein (where C is a cysteine and A is any aliphatic amino acids). This ensures that the cysteine is farnesylated and allows prelamin A to bind membranes, specifically the nuclear membrane. After prelamin A has been localized to the cell nuclear membrane, the C-terminal amino acids, including the farnesylated cysteine, are cleaved off by a specific protease. The resulting protein, now lamin A, is no longer membrane-bound, and carries out functions inside the nucleus. In progeria, the recognition site that the enzyme requires for cleavage of prelamin A to lamin A is mutated. Lamin A cannot be produced, and prelamin A builds up on the nuclear membrane, causing a characteristic nuclear blebbing. This results in the symptoms of progeria, although the relationship between the misshapen nucleus and the symptoms is not known.


Actin Filament Structure and Regulation

1. G-actin concentration (profilin) 2. ADP to ATP exchange (profilin) 3. Capping
(Capping protein; gelsolin) 4. Depolymerization/severing (ADF/cofilin). The only productive end is the pluse end because the polyermerization rate at plus end is about 10* greater when ATP bound as compared to ADP bound.



an actin-binding protein that is a key regulator of actin filament assembly and disassembly.



a family of actin-binding proteins which disassembles actin filaments. The protein binds to actin monomers and filaments, G actin and F actin, respectively. Cofilin causes depolymerization at the minus end of filaments, thereby preventing their reassembly. The protein is known to sever actin filaments by creating more positive ends on filament fragments. Cofilin/ADF(destrin) is likely to sever F-actin without capping and prefers ADP-actin.


stages of actin nucleation

1. nucleation center- three actin bind together. Spontaneous induction is too slow. This is the regulated site. The two ways of regulation is ARP2/3 and formin. They both pretend to be an actin dimer and will bind a single actin and will act as nucleation site. Formin base are long and parallel.(cable like crucial for cell division). Arp2/3 will branch. (network like crucial for cell motility) 2. growth will occur spontenously.


Actin Roles in Cell Function

epithelia cell polarity, contraction, cell motility (Arp2/3), cell division (formin based)


actin role in cell motility

1. Arp2/3 complex regulates lamellipodia formation 2. Formins complex regulate filopodia formation. Actin polymerization at plus end protrudes lamellipodium, actin cortex stabilizes cell and allows movement of unpolymerized actin, focal contacts (contain integrins) attach cell. Can change directions by changing where polymerization occurs. Net filament assembly occurs at leading edge (helped with capping and net filament disassembly (helped with cofilin) behind leading edge. the lagging end is formin.


asymetric cell division

enucleation process in RBCs, regulated by Rho. Polypoid megakaryocyte (create platelets),do not undergo division, inhibit Rho. Spermatogonia arrests cell division creating ring canal, incomplete cytokinesis. Division of epithealial cells only occur along a certain axis. All of these are accomplished by regulating actin ring.


paracrine signaling

a local mediatior binds to a receptor on target cell near by.



when the mediator binds to receptor on signaling cells


endocrin signaling

hormone is released in blood and binds to traget cell far away


contact dependent signaling

mediator is membrane bound


two major classes of signaling

lipophilic- hydrophobic, eg steriod hormones, can penetrate membrance and receptor can be intra-cellular, cannot store and can only control release through synthesis, it is slow. Hyrophilic- eg peptides, proteins and amino acids, cannot penetrate membrane, receptor has to be on cell surface, can be stored and release can be controlled by vesicle release, is fast


excitation/contraction coupling

The neuromuscular junction is where a neuron activates a muscle to contract. This is a step in the excitation-contraction coupling of vertebrate skeletal muscle. Upon the arrival of an action potential at the presynaptic neuron terminal, voltage-dependent calcium channels open and Ca2+ ions flow from the extracellular fluid into the presynaptic neuron's cytosol. This influx of Ca2+ causes neurotransmitter-containing vesicles to dock and fuse to the presynaptic neuron's cell membrane through SNARE proteins. Fusion of the vesicular membrane with the presynaptic cell membrane results in the emptying of the vesicle's contents (acetylcholine) into the synaptic cleft, a process known as exocytosis. Acetylcholine diffuses into the synaptic cleft and can bind to the nicotinic acetylcholine receptors on the motor endplate. This causes sodium/ calcium channels to open. This depolarisation activates non-gated voltage sensors, DHPRs (differing from the Cardiac DHPR, which is a gated Calcium channel). This activates RyR type 1 via foot processes (involving conformational changes that allosterically activates the RyRs)
As the RyRs open, calcium is released from the SR into the local junctional space, which then diffuses into the bulk cytoplasm to cause a calcium spark. Note that the SR has a large calcium buffering capacity partially due to a calcium-binding protein called calsequestrin
The near synchronous activation of thousands of calcium sparks by the action potential causes a cell wide increase in calcium giving rise to the upstroke of the calcium transient.The sarco/endoplasmic reticulum calcium-ATPase (SERCA) actively pumps calcium back into the SR
As calcium declines back to resting levels, the force declines and relaxation occurs



a voltage-dependent calcium channel



a group of voltage-gated ion channels found in the membrane of excitable cells (e.g., muscle, glial cells, neurons, etc.) with a permeability to the calcium ion Ca2+. These channels are slightly permeable to sodium ions, so they are also called Ca2+-Na+ channels, but their permeability to calcium is about 1000-fold greater than to sodium under normal physiological conditions. At physiologic or resting membrane potential, VDCCs are normally closed. They are activated (i.e., opened) at depolarized membrane potentials and this is the source of the "voltage-dependent" epithet. The concentration of calcium (Ca2+ ions) is normally several thousand times higher outside of the cell than inside. Activation of particular VDCCs allows Ca2+ to rush into the cell, which, depending on the cell type, results in activation of calcium-sensitive potassium channels, muscular contraction, excitation of neurons, up-regulation of gene expression, or release of hormones or neurotransmitters.


Ryanodine receptors (RyRs)

Ryanodine receptors mediate the release of calcium ions from the sarcoplasmic reticulum, an essential step in muscle contraction. In skeletal muscle, it is thought that activation occurs via a physical coupling to the dihydropyridine receptor, whereas, in cardiac muscle, the primary mechanism is calcium-induced calcium release from the sarcoplasmic reticulum. It has been shown that calcium release from a number of ryanodine receptors in a ryanodine receptor cluster results in a spatiotemporally restricted rise in cytosolic calcium that can be visualised as a calcium spark.


Nuclear receptors

TF, activated by cell permeable steriod hormones, thyroid hormones, vitamin D, retinoic acid


PLC (phospholipase C)

a class of enzymes that cleave phospholipids just before the phosphate group. Receptors that activate this pathway are mainly G protein-coupled receptors coupled. PLC cleaves the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) into diacyl glycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG remains bound to the membrane, and IP3 is released as a soluble structure into the cytosol. IP3 then diffuses through the cytosol to bind to IP3 receptors, particularly calcium channels in the smooth endoplasmic reticulum (ER). This causes the cytosolic concentration of calcium to increase, causing a cascade of intracellular changes and activity. In addition, calcium and DAG together work to activate protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity.


adenylyl cyclases

an enzyme with key regulatory roles in essentially all cells. All classes of AC catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and pyrophosphate. Divalent cations (usually Mg) are generally required and appear to be closely involved in the enzymatic mechanism. The cAMP produced by AC then serves as a regulatory signal via specific cAMP-binding proteins, either transcription factors or other enzymes (e.g., cAMP-dependent kinases).


guanylyl cylcases

a lyase enzyme. Guanylate cyclase is part of the G protein signaling cascade that is activated by low intracellular calcium levels and inhibited by high intracellular calcium levels. In response to calcium levels, guanylyl cyclase synthesizes cGMP from GTP. cGMP keeps cGMP-gated channels open, allowing for the entry of calcium into the cell. cGMP is an important second messenger that internalizes the message carried by intercellular messengers such as peptide hormones and NO, and can also function as an autocrine signal. Depending on cell type, it can drive adaptive/developmental changes requiring protein synthesis. In smooth muscle, cGMP is the signal for relaxation, and is coupled to many homeostatic mechanisms including regulation of vascular and airway tone, insulin secretion, and peristalsis. Once formed, cGMP can be degraded by phosphodiesterases, which themselves are under different forms of regulation, depending on the tissue.


nitric oxide

an important cellular signaling molecule involved in many physiological and pathological processes. It is a powerful vasodilator with a short half-life of a few seconds in the blood. It was found that NO acts through the stimulation of the soluble guanylate cyclase, which is a heterodimeric enzyme with subsequent formation of cyclic-GMP. Cyclic-GMP activates protein kinase G, which causes reuptake of Ca2+ and the opening of calcium-activated potassium channels. The fall in concentration of Ca2+ ensures that the myosin light-chain kinase (MLCK) can no longer phosphorylate the myosin molecule, thereby stopping the crossbridge cycle and leading to relaxation of the smooth muscle cell.


GTP/GDP exchange

it is not a secondary messanger because the cell's response is not dependent on amount of GTP in cell


diacyl-glycerol (DAG)

In biochemical signaling, diacylglycerol functions as a second messenger signaling lipid, and is a product of the hydrolysis of the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) by the enzyme phospholipase C (PLC) (a membrane-bound enzyme) that, through the same reaction, produces inositol trisphosphate (IP3). Although inositol trisphosphate diffuses into the cytosol, diacylglycerol remains within the plasma membrane, due to its hydrophobic properties. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, whereas DAG is a physiological activator of protein kinase C (PKC). The production of DAG in the membrane facilitates translocation of PKC from the cytosol to the plasma membrane.



together with diacylglycerol (DAG), is a secondary messenger molecule used in signal transduction. Increases in the intracellular Ca2+ concentrations are often a result of IP3 activation. When a ligand binds to a G protein-coupled receptor (GPCR) that is coupled to a Gq heterotrimeric G protein, the α-subunit of Gq can bind to and induce activity in the PLC isozyme PLC-β, which results in the cleavage of PIP2 into IP3 and DAG. If a receptor tyrosine kinase (RTK) is involved in activating the pathway, the isozyme PLC-γ has tyrosine residues that can become phosphorylated upon activation of an RTK, and this will activate PLC-γ and allow it to cleave PIP2 into DAG and IP3. This occurs in cells that are capable of responding to growth factors such as insulin, because the growth factors are the ligands responsible for activating the RTK. IP3 (also abbreviated Ins3P) is a soluble molecule and is capable of diffusing through the cytoplasm to the ER, or the sarcoplasmic reticulum (SR) in the case of muscle cells, once it has been produced by the action of PLC. Once at the ER, IP3 is able to bind to the Ins3P receptor (Ins3PR) on a ligand-gated Ca2+ channel that is found on the surface of the ER. The binding of IP3 (the ligand in this case) to InsP3R triggers the opening of the Ca2+ channel, and thus release of Ca2+ into the cytoplasm. In heart muscle cells this increase in Ca2+ activates the ryanodine receptor-operated channel on the SR, results in further increases in Ca2+ through a process known as calcium-induced calcium release. IP3 may also activate Ca2+ channels on the cell membrane indirectly, by increasing the intracellular Ca2+ concentration.



an integral membrane protein that regulates the Ca2+ pump in cardiac muscle and skeletal muscle cells. This protein is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase (PKA) in cardiac muscle. The protein is an inhibitor of cardiac muscle sarcoplasmic reticulum Ca++-ATPase (SERCA) in the unphosphorylated state, but inhibition is relieved upon phosphorylation of the protein. The subsequent activation of the Ca++ pump leads to shorter intervals between contractions. When phospholamban is phosphorylated by PKA its ability to inhibit the sarcoplasmic reticulum calcium pump (SERCA) is lost.


Signal Termination

Extracellular Signaling Molecule: Diffusion; Inactivation; Uptake into Cells (by Transporters; can be important drug targets; for instance Dopamine Transporter). Receptor: Desensitization: Reduction of Binding or downstream signaling; Receptor internalization (often “plasticity” event affecting subsequent signals). 2nd messenger:Ca2+: ATP dependent pumps; out of cell or into stores. Others: metabolic modification, for example:cAMP or cGMP to AMP or GMP by PDEs (phosphodiesterases; drug targets; PDE5 for Viagra et al.). Phosphorylation -> dephosphorylation by Protein Phosphatases. Dephosphorylation -> rephosphorylation by Protein Kinases. Protein Binding/Targeting: Lack of the inducing stimulus; protein degradation. GTP binding proteins (2 classes: receptor linked, ras-like): are slow GTPases that break down GTP to GDP; GTPase activity can be enhanced by GAPs (GTPase Activating Proteins) [exchange of GDP for GTP for reactivation enhanced by GEFs (GDP/GTP Exchange Factors)]. Termination mediated by: Constitutively active “Terminators” (Ca2+ pumps; PDEs; Phosphatases; intrinsic GTPase). Signal induced “Terminators” (Phosphatases; GAP enhanced GTPase). Negative Feedback mechanism (Ca2+ pumps). most termination events can be at least modulated by signaling


Phosphodiesterase PDE5

catalyzes cleavage of cGMP to GMP. It has a catalytic site where cGMP binds but also has a non-catalytic binding site that also binds cGMP that increases both the catalytic site and the phorphorylation site. When phosphorylated, the other two sites activity is increased. NO (with viagra) activatesGC creating more cGMP which activates PKG which P PDE5.


pathways activated by RTKs

ras/raf/mapk, SRC, and P13K pathways



an adapter protein that consists of SH2 and SH3 protein interaction domains. an adaptor protein involved in signal transduction/cell communication. In humans, the GRB2 protein is encoded by the GRB2 gene. Grb2 is widely expressed and is essential for multiple cellular functions. Inhibition of Grb2 function impairs developmental processes in various organisms and blocks transformation and proliferation of various cell types, and so it is not surprising that a targeted gene disruption of Grb2 in mouse is lethal at an early embryonic stage. Grb2 is best known for its ability to link the epidermal growth factor receptor tyrosine kinase to the activation of Ras and its downstream kinases, ERK1,2. Grb2 is composed of an SH2 domain flanked on each side by an SH3 domain. Grb2 has two closely related proteins with similar domain organizations, Gads and Grap. Gads and Grap are expressed specifically in hematopoietic cells and function in the coordination of tyrosine kinase mediated signal transduction.



Sos is a Ras GEF, contains a Pro-rich region that binds to the Grb2 SH3 domain. Recruitment of Sos to the receptor brings Sos into close proximity with Ras, which is at the cell membrane. Activated by EGFR. Ras-GTPases act as molecular switches that bind to downstream effectors, such as the protein kinase c-Raf, and localise them to the membrane resulting in their activation. Ras-GTPases are considered inactive when bound to guanosine diphosphate (GDP), and active when bound to guanosine triphosphate (GTP). As the name implies, Ras-GTPases possess intrinsic enzymatic activity that hydrolyses GTP to GDP and phosphate. Thus, upon binding to GTP, the duration of Ras-GTPase activity depends on the rate of hydrolysis. SOS (and other guanine nucleotide exchange factors) act by binding Ras-GTPases and forcing them to release their bound nucleotide (usually GDP). Once released from SOS, the Ras-GTPase quickly binds fresh guanine nucleotide from the cytosol. Since GTP is roughly ten times more abundant than GDP in the cytosol, this usually results in Ras activation. The normal rate of Ras catalytic GTPase (GTP hydrolysis) activity can be increased by proteins of the RasGAP family, which bind to Ras and increase its catalytic rate by a factor of one thousand - in effect, increasing the rate at which Ras is inactivated.



SHC1 has been found to act in signaling information after epidermal growth factor(EGF) stimulation. Activated tyrosine kinase receptors, on the cell surface, use proteins such as SHC1 that contains phosphotyrosine binding domains. After the EGF stimulation SHC1 binds to groups of proteins that activate survival pathways. This activation is followed by a sub-network of proteins that bind to SHC1 and are involved cytoskeleton reorganization, trafficking and signal termination. It is also link activated receptor tyrosine kinase to the RAS pathway.The protein SHC1 also acts as a scaffold protein which is used in cell surface receptors



Multiple downstream pathways that promote cell growth, survival, motility etc. Ras proteins are membrane-bound switches that are regulated by GAPs (GTP activating proteins, thus activating ras) and GEFs (dephosphorylates GTP, deactivating Ras). Ras activation involves an adaptor (Grb2) and a GEF (Sos). It is the translocation of SOS to the plasma membrane that activates Ras, even in the absence of RTK stimulation.


SH3 domain

domains bind to Pro-containing peptides. It is a constitutivly bound unlike SH2 which is inducible


EGFR as a therapeutic target in cancer

Overexpressed in tumors: breast, lung, glioblastoma, head & neck, bladder, colorectal, ovarian, prostate. Mutated leading to constitutive activation in glioblastoma. Increased EGFR correlates with poorer clinical outcome in breast, lung, head & neck. Increased receptor associated with increased production of ligands- autocrine stimulatory pathway.



an epidermal growth factor receptor (EGFR) inhibitor used for the treatment of metastatic colorectal cancer, metastatic non-small cell lung cancer [1] and head and neck cancer. Cetuximab is a chimeric (mouse/human) monoclonal antibody given by intravenous infusion. Cetuximab binds to EGFR and turns off the uncontrolled growth in cancers with EGFR mutations preventing dimerization



Gefitinib inhibits EGFR tyrosine kinase by binding to the adenosine triphosphate (ATP)-binding site of the enzyme. Thus the function of the EGFR tyrosine kinase in activating the anti-apoptotic Ras signal transduction cascade is inhibited, and malignant cells are inhibited. Gefitinib blocks EGFR kinase activity and thus stops downstream signaling. Patients who respond have EGFR mutations. Mutant EGFR is more active and more potently inhibited by Gefitinib. One particular secondary mutation causes most of the resistanceClinical characteristics: usually never smokers, women, often Asian/Japanese decent. Secondary mutations in EGFR cause resistance to Gefitinib. One particular secondary mutation causes most of the resistance.


Describe mechanism of receptor tyrosine kinase activation.

Ligand binding drives dimerization, which activates catalytic activity of the kinase resulting in Tyrosine autophosphorylation at specific sites.


Explain molecular mechanism of stimulation of ras GTPase by RTKs

Tyrosine Phosphorylation of receptor causes binding by SH2-domain-containing proteins including the adaptor protein Grb2, which binds a Ras GEF called Sos. Proximity of Sos with membrane-bound Ras results in guanine nucleotide exchange.


Describe mechanism of action of two main classes of RTK-targeted anti-cancer agents (antibodies and TKI’s)

primary role of antibodies is to block ligand binding to the receptor. TKIs inhibit catalytic activity (usually) by binding in substrate-binding site of the kinase.


List tumor cell characteristics that predict clinical response to EGFR-targeted therapeutics

response to EGFR TKI correlated with receptor mutations that may “activate” the receptor, EGFR amplification or overexpression as determined by FISH or immunohistochemistry.


Describe mechanism of resistance to TKI’s.

Acquired resistance- second site mutations in EGFR arising or selected in patients who initially benefit from therapy but then acquire resistance and disease progression. These mutations block inhibitor binding to the kinase active site. May be able to design new inhibitors to avoid this problem. Activation of other receptors like Met or ErbB2. Combine inhibitors or make dual specificity inhibitors? Primary resistance- if the tumor has a Ras mutation inhibiting the receptor further up the pathway will not be effective


sarcoplasmic reticulum (SR)

smooth ER found in myocytes. The only structural difference between this organelle and the smooth endoplasmic reticulum is the medley of proteins they have, both bound to their membranes and drifting within the confines of their lumens. This fundamental difference is indicative of their functions: The endoplasmic reticulum synthesizes molecules, while the sarcoplasmic reticulum stores and pumps calcium ions. The sarcoplasmic reticulum contains large stores of calcium, which it sequesters and then releases when the muscle cell is stimulated.[12][13] It plays a major role in excitation-contraction coupling.