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In that case, we have to determine the rate law experimentally. But if we have a single step reaction, then we can use the coefficients to calculate the rate law. So in this particular case, going from A to B, a is the reactant and B is the product. And let's suppose the rate constant is k one and that means the rate law for this reaction is given by so the rate of the four reaction v forward is equal to k one multiplied by the concentration of A to the power of one, because the coefficient here is one. If this coefficient was two, then this exponent here would be two and so forth. Now, if we go in reverse, then the only thing that changes is this becomes the reactor, this becomes the product. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And let's suppose the rate constant is k one and that means the rate law for this reaction is given by so the rate of the four reaction v forward is equal to k one multiplied by the concentration of A to the power of one, because the coefficient here is one. If this coefficient was two, then this exponent here would be two and so forth. Now, if we go in reverse, then the only thing that changes is this becomes the reactor, this becomes the product. And so we replace the concentration A with concentration B and we replace k one with K minus one. And remember that if this reaction achieves equilibrium, then the rate of the forward will be equal to the rate of the reverse and these two quantities will be equal. Now notice, k one is not necessarily equal to K minus one. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so we replace the concentration A with concentration B and we replace k one with K minus one. And remember that if this reaction achieves equilibrium, then the rate of the forward will be equal to the rate of the reverse and these two quantities will be equal. Now notice, k one is not necessarily equal to K minus one. K one is only equal to K minus one if the concentration of A is equal to the concentration of b when equilibrium is actually achieved. So normally k one is not the same as k minus one. Now, what exactly is the meaning of k? | Effect of Enzymes on Rate Law and Rate Constant .txt |
K one is only equal to K minus one if the concentration of A is equal to the concentration of b when equilibrium is actually achieved. So normally k one is not the same as k minus one. Now, what exactly is the meaning of k? What exactly is the meaning of the rate constant? Well, the rate constant is given by the following equation known as the radius equation. And this Iranius equation describes what the rate constant actually symbolizes. | Effect of Enzymes on Rate Law and Rate Constant .txt |
What exactly is the meaning of the rate constant? Well, the rate constant is given by the following equation known as the radius equation. And this Iranius equation describes what the rate constant actually symbolizes. So the rate constant K is equal to the product of the frequency factor a and e to the power of negative EA divided by RT where r is the gas constant, t is the absolute temperature, EA is our activation energy. So right away, because the activation energy appears in this arrangeous equation, that means changing the activation energy changes the value of K. And so when an enzyme acts on a chemical reaction, it affects the k value. And that makes sense because we know that enzymes do not affect the concentrations of reactants or products. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So the rate constant K is equal to the product of the frequency factor a and e to the power of negative EA divided by RT where r is the gas constant, t is the absolute temperature, EA is our activation energy. So right away, because the activation energy appears in this arrangeous equation, that means changing the activation energy changes the value of K. And so when an enzyme acts on a chemical reaction, it affects the k value. And that makes sense because we know that enzymes do not affect the concentrations of reactants or products. And so if enzymes increase the rate of the reaction and they cannot increase the a value or b, that means they have to increase the k value, the rate constant. So if we look at the radius equation, we see that if we decrease the value of EA. So remember enzymes, they stabilize the energy of the transition state, decreasing the energy of the transition state and that decreases the free energy of activation. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so if enzymes increase the rate of the reaction and they cannot increase the a value or b, that means they have to increase the k value, the rate constant. So if we look at the radius equation, we see that if we decrease the value of EA. So remember enzymes, they stabilize the energy of the transition state, decreasing the energy of the transition state and that decreases the free energy of activation. And so when enzymes decrease the activation energy, EA, they essentially decrease this entire exponent. And since the exponent is negative, what that means is this entire quantity will increase. And so by decreasing the activation energy our enzyme increases the rate constant and that's precisely what increases the rate of that reaction. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so when enzymes decrease the activation energy, EA, they essentially decrease this entire exponent. And since the exponent is negative, what that means is this entire quantity will increase. And so by decreasing the activation energy our enzyme increases the rate constant and that's precisely what increases the rate of that reaction. So remember, inside our body the temperature remains constant. The core temperature is about 37 degrees Celsius. And that means all the reactions taking place inside our body take place at a constant temperature. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So remember, inside our body the temperature remains constant. The core temperature is about 37 degrees Celsius. And that means all the reactions taking place inside our body take place at a constant temperature. So the temperature remains constant. And what that means is the enzymes have to affect the EA to actually change the K to increase the rate of that particular reaction. Now? | Effect of Enzymes on Rate Law and Rate Constant .txt |
So the temperature remains constant. And what that means is the enzymes have to affect the EA to actually change the K to increase the rate of that particular reaction. Now? What about a Well, A is known as the frequency factor and this basically describes the frequency of collision between the reactants. Remember, according to the collision theory, for a reaction to actually take place those reactants have to collide with a great enough energy. Now this collision frequency is described by A. | Effect of Enzymes on Rate Law and Rate Constant .txt |
What about a Well, A is known as the frequency factor and this basically describes the frequency of collision between the reactants. Remember, according to the collision theory, for a reaction to actually take place those reactants have to collide with a great enough energy. Now this collision frequency is described by A. And we know if the collisions are more frequent then it's more likely that we're going to produce the products. And so if the frequency of collision increases, the A value increases and the K will also increase. Now, does the enzyme affect A? | Effect of Enzymes on Rate Law and Rate Constant .txt |
And we know if the collisions are more frequent then it's more likely that we're going to produce the products. And so if the frequency of collision increases, the A value increases and the K will also increase. Now, does the enzyme affect A? Well, remember, the enzyme places the substrate inside the active side and what that does is it creates a microenvironment and it basically decreases the space in which the reactants are colliding. And if the space is smaller, the collision between the reactants will be much more likely. And so enzymes can also actually increase A because they decrease the space in which the reactants are actually allowed to move. | Effect of Enzymes on Rate Law and Rate Constant .txt |
Well, remember, the enzyme places the substrate inside the active side and what that does is it creates a microenvironment and it basically decreases the space in which the reactants are colliding. And if the space is smaller, the collision between the reactants will be much more likely. And so enzymes can also actually increase A because they decrease the space in which the reactants are actually allowed to move. And so if the reactants basically collide more, the A value increases. So we see that enzymes predominantly affect the EA, but they can also affect A, they can decrease EA and increase A. And in both cases we basically increase the value of K. So enzymes affect the rate constant, they increase the rate constant. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so if the reactants basically collide more, the A value increases. So we see that enzymes predominantly affect the EA, but they can also affect A, they can decrease EA and increase A. And in both cases we basically increase the value of K. So enzymes affect the rate constant, they increase the rate constant. And so that in turn increases the rate of that reaction inside the rate law. So enzymes affect the rate constant and in turn affect the rate law. So if we take a look at the following elementary reaction in which we take A and produce B, where K is the rate constant, we see that this is our rate law. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so that in turn increases the rate of that reaction inside the rate law. So enzymes affect the rate constant and in turn affect the rate law. So if we take a look at the following elementary reaction in which we take A and produce B, where K is the rate constant, we see that this is our rate law. And when an enzyme is added into the mixture, the enzyme will increase K. It will not affect the concentration of A. And so to increase V the rate of that reaction, the enzyme must increase the value of K. Now what exactly is the order of the reaction? So earlier we said that the order of this reaction was one and the order of this reaction was also one. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And when an enzyme is added into the mixture, the enzyme will increase K. It will not affect the concentration of A. And so to increase V the rate of that reaction, the enzyme must increase the value of K. Now what exactly is the order of the reaction? So earlier we said that the order of this reaction was one and the order of this reaction was also one. And the same thing was true for this particular case. So we see that the order of the reaction basically describes the rate of the reaction and how it actually depends on the concentration of those reactants. So let's begin with the first order reaction that we basically described in this lecture. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And the same thing was true for this particular case. So we see that the order of the reaction basically describes the rate of the reaction and how it actually depends on the concentration of those reactants. So let's begin with the first order reaction that we basically described in this lecture. So when a reaction rate is directly proportional to the concentration of the reactant, it is set to be first order with respect to that reactant. So in this particular case, because the exponent is one, this is a first order reaction. And that means the rate law or the rate of that particular reaction depends directly, is directly proportional to the concentration. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So when a reaction rate is directly proportional to the concentration of the reactant, it is set to be first order with respect to that reactant. So in this particular case, because the exponent is one, this is a first order reaction. And that means the rate law or the rate of that particular reaction depends directly, is directly proportional to the concentration. So by doubling the concentration of A, we double the rate by quadrupling it, we quadruple the rate, by tripling it, we triple the rate and so forth. So if we have a direct correlation between the reactant concentration and the rate of the reaction, then that means that reactant is first order with respect to that particular reactant. Now to calculate the overall order of that particular reaction we have to sum up all the exponents in that particular chemical rate law. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So by doubling the concentration of A, we double the rate by quadrupling it, we quadruple the rate, by tripling it, we triple the rate and so forth. So if we have a direct correlation between the reactant concentration and the rate of the reaction, then that means that reactant is first order with respect to that particular reactant. Now to calculate the overall order of that particular reaction we have to sum up all the exponents in that particular chemical rate law. And so because in this particular case we only have one exponent, that means the rate, the order is first. And in this particular case the order is also first. But if we for example move on to a second order reaction, let's suppose we have A and B are the two reactants and they react to produce C. And this k value is basically the reaction constant, the rate constant. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so because in this particular case we only have one exponent, that means the rate, the order is first. And in this particular case the order is also first. But if we for example move on to a second order reaction, let's suppose we have A and B are the two reactants and they react to produce C. And this k value is basically the reaction constant, the rate constant. Now if A is first order and B is also first order, then this will be our rate law. So the rate of the reaction v is equal to k, that rate constant multiplied by the concentration of A to the power of one and the concentration of B to the power of one. And the overall order of this reaction is one plus one. | Effect of Enzymes on Rate Law and Rate Constant .txt |
Now if A is first order and B is also first order, then this will be our rate law. So the rate of the reaction v is equal to k, that rate constant multiplied by the concentration of A to the power of one and the concentration of B to the power of one. And the overall order of this reaction is one plus one. So we simply sum up the exponents and that gives us two. And what that means is by doubling A we double v as long as everything else remains constant. Likewise, if we double B while A and K is constant, v will also double. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So we simply sum up the exponents and that gives us two. And what that means is by doubling A we double v as long as everything else remains constant. Likewise, if we double B while A and K is constant, v will also double. But if we double A and B while K is constant, we quadruple that v value. And so that's what it means for reaction to actually be 1st 2nd order. Now we can also have a slightly different second order reaction. | Effect of Enzymes on Rate Law and Rate Constant .txt |
But if we double A and B while K is constant, we quadruple that v value. And so that's what it means for reaction to actually be 1st 2nd order. Now we can also have a slightly different second order reaction. So in this case we have two reactants. But what if we have a single reactant? So let's suppose we have A and A basically converts to form B. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So in this case we have two reactants. But what if we have a single reactant? So let's suppose we have A and A basically converts to form B. And let's suppose that we have two moles of A, produces 1 mol of B and this is an elementary reaction. So this is the k value, the rate constant. And so in this case, the rate law v is equal to k multiplied by the concentration of A. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And let's suppose that we have two moles of A, produces 1 mol of B and this is an elementary reaction. So this is the k value, the rate constant. And so in this case, the rate law v is equal to k multiplied by the concentration of A. But because this is an elementary reaction and the coefficient is two, what that means is we'll have a coefficient of two on top of that A. So this reaction is second order with respect to K and with respect to A. And the overall order is also second order. | Effect of Enzymes on Rate Law and Rate Constant .txt |
But because this is an elementary reaction and the coefficient is two, what that means is we'll have a coefficient of two on top of that A. So this reaction is second order with respect to K and with respect to A. And the overall order is also second order. So this reaction and this reaction, they are both second order. The only difference is we have a single reactant here but we have two reactants here. In this particular case if we double A, then we quadruple the velocity because two to the power of two gives us four. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So this reaction and this reaction, they are both second order. The only difference is we have a single reactant here but we have two reactants here. In this particular case if we double A, then we quadruple the velocity because two to the power of two gives us four. But in this case by doubling A we essentially double v if everything else is kept constant. But if we double A and B and we keep K constant then we quadruple the value of v and finally we can also have 0th order. And in the 0th order basically the concentration of the reactant has no effect on the rate of that reaction. | Effect of Enzymes on Rate Law and Rate Constant .txt |
But in this case by doubling A we essentially double v if everything else is kept constant. But if we double A and B and we keep K constant then we quadruple the value of v and finally we can also have 0th order. And in the 0th order basically the concentration of the reactant has no effect on the rate of that reaction. So if a reaction is 0th order with respect to some reactant then the rate is independent of that reactant's concentration. For instance, if we have A and A is transformed into B and K is the rate constant and we know that A is zero's order, what that basically means is the exponent will be zero. This will become one. | Effect of Enzymes on Rate Law and Rate Constant .txt |
So if a reaction is 0th order with respect to some reactant then the rate is independent of that reactant's concentration. For instance, if we have A and A is transformed into B and K is the rate constant and we know that A is zero's order, what that basically means is the exponent will be zero. This will become one. And so the rate law is v is equal to K. And notice that changing A, either increasing or decreasing will not affect the value of V. And some enzyme catalyze reactions inside our body are in fact 0th order. And what that means is by changing the concentration of A that will not affect that rate of the reaction. Now we can also have something known as a pseudo first order reaction. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And so the rate law is v is equal to K. And notice that changing A, either increasing or decreasing will not affect the value of V. And some enzyme catalyze reactions inside our body are in fact 0th order. And what that means is by changing the concentration of A that will not affect that rate of the reaction. Now we can also have something known as a pseudo first order reaction. And a pseudo first order reaction is actually a second order reaction that behaves like it's a first order reaction. Now what's one example of such a reaction? Well, let's suppose is we have a second order reaction as shown, but the concentration of A is very tiny but the concentration of B is very, very high. | Effect of Enzymes on Rate Law and Rate Constant .txt |
And that shape dictates what the function of that protein is. And so by changing the arrangement of our amino acids, we we can basically create a different protein with a different type of function. Now, in addition to increase the functionality and the diversity of the functionality of our proteins, we can basically modify the proteins by modifying the amino acids. And there are five common ways by which our cells modify amino acids, as we'll see in just a moment. Actually, there are many more ways, but we're going to focus on these five in this lecture. So we can modify amino acids by adding acetal groups, hydroxyl groups, carboxyl groups, sugar groups, phosphoryl groups, as well as many other different types of groups which we're going to discuss in future lectures. | Modification of Amino Acids .txt |
And there are five common ways by which our cells modify amino acids, as we'll see in just a moment. Actually, there are many more ways, but we're going to focus on these five in this lecture. So we can modify amino acids by adding acetal groups, hydroxyl groups, carboxyl groups, sugar groups, phosphoryl groups, as well as many other different types of groups which we're going to discuss in future lectures. So in this lecture, let's focus on these five. So let's begin with the first one. So the majority of the polypeptides and proteins inside our body are actually modified by the addition of acetyl groups. | Modification of Amino Acids .txt |
So in this lecture, let's focus on these five. So let's begin with the first one. So the majority of the polypeptides and proteins inside our body are actually modified by the addition of acetyl groups. And that's because what this does is it tells our cells not to break down and degrade those polypeptide. So many proteins are acetylated at the terminal amino groups to prevent degradation by our cells. So if we go to the beginning of our polypeptide, the nitrogen is basically modified by adding this acetal group. | Modification of Amino Acids .txt |
And that's because what this does is it tells our cells not to break down and degrade those polypeptide. So many proteins are acetylated at the terminal amino groups to prevent degradation by our cells. So if we go to the beginning of our polypeptide, the nitrogen is basically modified by adding this acetal group. And what that does is it prevents this polypeptide from being broken down. Now, another way by modifying proteins is by adding on hydroxyl groups. And one common example is Collagen. | Modification of Amino Acids .txt |
And what that does is it prevents this polypeptide from being broken down. Now, another way by modifying proteins is by adding on hydroxyl groups. And one common example is Collagen. So Collagen is by far the most abundant protein found in our body. It is found mostly in the extracellular tissue in our connective tissue, such as, for example, bone. And what Collagen does is it gives our tissue its strength. | Modification of Amino Acids .txt |
So Collagen is by far the most abundant protein found in our body. It is found mostly in the extracellular tissue in our connective tissue, such as, for example, bone. And what Collagen does is it gives our tissue its strength. So what is the structure of Collagen? Well, Collagen has a coronary structure, and one of the most abundant amino acids in Collagen is proline. Now, what Collagen does is it modifies the structure of proline by adding a hydroxyl group to produce hydroxyproline. | Modification of Amino Acids .txt |
So what is the structure of Collagen? Well, Collagen has a coronary structure, and one of the most abundant amino acids in Collagen is proline. Now, what Collagen does is it modifies the structure of proline by adding a hydroxyl group to produce hydroxyproline. And what that does is it increases the stability of the three dimensional structure of Collagen. So Collagen, the most abundant protein in our body, contains proline amino acids that contain hydroxyl groups. These hydroxyl groups, as shown in the following diagram, basically give the Collagen its stability. | Modification of Amino Acids .txt |
And what that does is it increases the stability of the three dimensional structure of Collagen. So Collagen, the most abundant protein in our body, contains proline amino acids that contain hydroxyl groups. These hydroxyl groups, as shown in the following diagram, basically give the Collagen its stability. Now, what happens if we can't produce these hydroxyproline groups? Well, basically, a condition in humans of a disease known as Scurvy is essentially this inability of Collagen to basically produce and modify its own proline molecules in the following way. So, in Scurvy, the body has a deficiency of vitamin C, and vitamin C is needed to basically modify and convert the proline molecules into hydroxyproline. | Modification of Amino Acids .txt |
Now, what happens if we can't produce these hydroxyproline groups? Well, basically, a condition in humans of a disease known as Scurvy is essentially this inability of Collagen to basically produce and modify its own proline molecules in the following way. So, in Scurvy, the body has a deficiency of vitamin C, and vitamin C is needed to basically modify and convert the proline molecules into hydroxyproline. And so, because we can't modify these amino acids in this way, the structure of collagen basically is destabilized. And what that means is it decreases the strength of our tissue. Now let's move on to carboxyl groups. | Modification of Amino Acids .txt |
And so, because we can't modify these amino acids in this way, the structure of collagen basically is destabilized. And what that means is it decreases the strength of our tissue. Now let's move on to carboxyl groups. So once again, many different types of proteins inside the body can be modified by the addition of carboxyl groups. And one particular example is a protein and enzyme in the blood clotting cascade we call prothrombin. So prothrombin is needed to basically stop bleeding. | Modification of Amino Acids .txt |
So once again, many different types of proteins inside the body can be modified by the addition of carboxyl groups. And one particular example is a protein and enzyme in the blood clotting cascade we call prothrombin. So prothrombin is needed to basically stop bleeding. And if prothrombin can't stop bleeding, then what that means is we're going to get a condition known as hemorrhage. Now, what happens is in some cases if, for example, our glutamate amino acid in prothrombin cannot be modified by this process of carboxylation, the addition of this carboxyl group, then our prothrombin will essentially not be as active, it will not be able to carry out its function correctly. And that can lead to the condition we call hemorrhage. | Modification of Amino Acids .txt |
And if prothrombin can't stop bleeding, then what that means is we're going to get a condition known as hemorrhage. Now, what happens is in some cases if, for example, our glutamate amino acid in prothrombin cannot be modified by this process of carboxylation, the addition of this carboxyl group, then our prothrombin will essentially not be as active, it will not be able to carry out its function correctly. And that can lead to the condition we call hemorrhage. Now, let's move on to addition of sugar group. So many, many proteins inside our body are modified by adding carbohydrate components. For example, the proteins that are destined to be in a cell membrane or outside the cell, they're modified in this way. | Modification of Amino Acids .txt |
Now, let's move on to addition of sugar group. So many, many proteins inside our body are modified by adding carbohydrate components. For example, the proteins that are destined to be in a cell membrane or outside the cell, they're modified in this way. And the reason we add carbohydrate components is to basically increase the polarity, increase the hydrophilic nature of those proteins, so that they can interact better with other proteins as well as with other hydrophilic molecules. So, for example, we can have asparagne, the amino acid asparagine be modified by the addition of the sugar component. And all these different hydroxyl groups basically increases the hydrophilic nature of that protein. | Modification of Amino Acids .txt |
And the reason we add carbohydrate components is to basically increase the polarity, increase the hydrophilic nature of those proteins, so that they can interact better with other proteins as well as with other hydrophilic molecules. So, for example, we can have asparagne, the amino acid asparagine be modified by the addition of the sugar component. And all these different hydroxyl groups basically increases the hydrophilic nature of that protein. Finally, we can also undergo the process of phosphorylation. We can add these phosphoryl groups onto our amino acids. In fact, many different types of cellular processes that take place inside our cells and inside our body use the phosphorylation as a way to turn on and off these different types of cell processes. | Modification of Amino Acids .txt |
Finally, we can also undergo the process of phosphorylation. We can add these phosphoryl groups onto our amino acids. In fact, many different types of cellular processes that take place inside our cells and inside our body use the phosphorylation as a way to turn on and off these different types of cell processes. For example, epinephrine, a hormone, and a newer transmitter can act on the serene and three anion amino acids by phosphorylating them. And that can turn on or off many different types of molecules and reactions of processes that exist inside our body. For example, insulin, which is a molecule that is used to regulate the amount of glucose found inside our body, inside our blood functions via this process. | Modification of Amino Acids .txt |
For example, epinephrine, a hormone, and a newer transmitter can act on the serene and three anion amino acids by phosphorylating them. And that can turn on or off many different types of molecules and reactions of processes that exist inside our body. For example, insulin, which is a molecule that is used to regulate the amount of glucose found inside our body, inside our blood functions via this process. So we can turn on or off insulin by using these phosphoryl groups. Now, finally, we can also not only modify the amino acids, but in some cases when we cleave peptides within the proteins, within our polypeptide that can activate or deactivate our protein. So many, many proteins inside our body are actually synthesized in their inactive form. | Modification of Amino Acids .txt |
So we can turn on or off insulin by using these phosphoryl groups. Now, finally, we can also not only modify the amino acids, but in some cases when we cleave peptides within the proteins, within our polypeptide that can activate or deactivate our protein. So many, many proteins inside our body are actually synthesized in their inactive form. And some examples include digestive enzymes, for example, chimotrypsin, we have blood clotting enzymes. Fibrin, we have hormones, for example, adrenal, corticotropic hormone, ACTH. All these different types of hormones in our body are synthesized initially in their inactive state and to activate them, some type of enzyme, some type of catalyst basically cleaves a peptide bond. | Modification of Amino Acids .txt |
Although our liver is responsible for the majority of the metabolism of amino acids that occurs inside our body, other organs and tissues can also break down amino acids and then use the carbon skeleton byproducts for energy. And one example of such a tissue is our muscle tissue. So if we're undergoing prolonged exercise or if we're fasting, our skeleton muscle tissue tissue can actually begin to break down branch chain amino acids such as valine, isolucine and leucine. And then we form carbon skeleton intermediates, and then those are used for energy purposes. But of course, every time we metabolize amino acids, we form nitrogen as a byproduct. More specifically, we form ammonium. | Glucose-alanine cycle .txt |
And then we form carbon skeleton intermediates, and then those are used for energy purposes. But of course, every time we metabolize amino acids, we form nitrogen as a byproduct. More specifically, we form ammonium. And as this process continually takes place, we build up the amount of ammonia that is present inside our skeleton muscle cells. Now, ammonium is toxic, and so what the skeleton muscle cells must do is they must be able to dispose of that ammonium. Now, unlike in the liver, and to a smaller extent in the kidney, where we have the urea cycle to basically dispose of that ammonium inside the skeleton muscle cells, we don't actually have a way to dispose of ammonium directly. | Glucose-alanine cycle .txt |
And as this process continually takes place, we build up the amount of ammonia that is present inside our skeleton muscle cells. Now, ammonium is toxic, and so what the skeleton muscle cells must do is they must be able to dispose of that ammonium. Now, unlike in the liver, and to a smaller extent in the kidney, where we have the urea cycle to basically dispose of that ammonium inside the skeleton muscle cells, we don't actually have a way to dispose of ammonium directly. And that's because the urea cycle does not take place inside the muscle. And so our body actually has two ways by which it can get rid of this ammonium from our skeletal muscle. But ultimately, what the skeleton muscle cell must do is it must be able to transport that ammonium back to the liver, where that ammonium can be fed into the urea cycle. | Glucose-alanine cycle .txt |
And that's because the urea cycle does not take place inside the muscle. And so our body actually has two ways by which it can get rid of this ammonium from our skeletal muscle. But ultimately, what the skeleton muscle cell must do is it must be able to transport that ammonium back to the liver, where that ammonium can be fed into the urea cycle. And one of these pathways is known as the glucose alanine cycle. And this will be the focus of this lecture. So let's suppose we are fasting. | Glucose-alanine cycle .txt |
And one of these pathways is known as the glucose alanine cycle. And this will be the focus of this lecture. So let's suppose we are fasting. Eventually, we begin to break down the branch chain amino acids into the carbon scale intermediates, and then we form ammonium as a byproduct. Now, ammonium must be transformed into some other molecules. So we must have some type of carrier molecule that ultimately transports through the blood to the liver. | Glucose-alanine cycle .txt |
Eventually, we begin to break down the branch chain amino acids into the carbon scale intermediates, and then we form ammonium as a byproduct. Now, ammonium must be transformed into some other molecules. So we must have some type of carrier molecule that ultimately transports through the blood to the liver. So ammonium must be combined with Pyruvate. Now, where do we get the Pyruvate from? Well, inside our muscle, we have glycogen storages. | Glucose-alanine cycle .txt |
So ammonium must be combined with Pyruvate. Now, where do we get the Pyruvate from? Well, inside our muscle, we have glycogen storages. We break down the glycogen to glucose, and we break down glucose into Pyruvate via glycolysis. So we generate ATP. That ATP can be used by the cell, and the Pyruvate can also be used to actually combine with ammonium to form glutamate, and then glutamate is transformed into aluminium. | Glucose-alanine cycle .txt |
We break down the glycogen to glucose, and we break down glucose into Pyruvate via glycolysis. So we generate ATP. That ATP can be used by the cell, and the Pyruvate can also be used to actually combine with ammonium to form glutamate, and then glutamate is transformed into aluminium. And actually, this is the reverse pathway that we discussed in the previous lecture. So previously we discussed how we can break down alanine into ammonium, but now we see how, under other conditions, we can actually do the reverse. We can take the ammonium combined with Pyruvate to ultimately form that alanine, and it's the alanine that is transported out of the cell into our bloodstream and that ultimately is absorbed by hepaticides, our liver cells. | Glucose-alanine cycle .txt |
And actually, this is the reverse pathway that we discussed in the previous lecture. So previously we discussed how we can break down alanine into ammonium, but now we see how, under other conditions, we can actually do the reverse. We can take the ammonium combined with Pyruvate to ultimately form that alanine, and it's the alanine that is transported out of the cell into our bloodstream and that ultimately is absorbed by hepaticides, our liver cells. Now, once the alanine moves into the liver, the alanine basically undergoes this pathway. But in reverse. So we begin with Alanine. | Glucose-alanine cycle .txt |
Now, once the alanine moves into the liver, the alanine basically undergoes this pathway. But in reverse. So we begin with Alanine. Alanine then is formed into glutamate, and then that breaks down into pyruvate and ammonium. So ultimately, what happened is the ammonium that we used here or that we formed here, eventually made its way to the liver. And it's the liver that uses the urea cycle to basically help our body dispose of this toxic substance. | Glucose-alanine cycle .txt |
Alanine then is formed into glutamate, and then that breaks down into pyruvate and ammonium. So ultimately, what happened is the ammonium that we used here or that we formed here, eventually made its way to the liver. And it's the liver that uses the urea cycle to basically help our body dispose of this toxic substance. Also notice, though, that we form pyruvate and it's in the liver that we undergo gluconeogenesis. It's in the liver where we undergo gluconeogenesis. And so pyruvate is used to form glucose. | Glucose-alanine cycle .txt |
Also notice, though, that we form pyruvate and it's in the liver that we undergo gluconeogenesis. It's in the liver where we undergo gluconeogenesis. And so pyruvate is used to form glucose. And the glucose that we essentially used here is then transported back into the skeleton muscle via the bloodstream. So ultimately, even though we used a glucose here to form that pyruvate, and we used that to essentially attach that ammonium and then transported via the bloodstream via Alanine, the glucose is ultimately returned back to the skeleton muscle tissue. So all that happened here is we ultimately transported this ammonium to our liver. | Glucose-alanine cycle .txt |
And the glucose that we essentially used here is then transported back into the skeleton muscle via the bloodstream. So ultimately, even though we used a glucose here to form that pyruvate, and we used that to essentially attach that ammonium and then transported via the bloodstream via Alanine, the glucose is ultimately returned back to the skeleton muscle tissue. So all that happened here is we ultimately transported this ammonium to our liver. Now, this is known as the glucose Allenine cycle. We call it glucose Allenine because we utilize a glucose here to form pyruvate, to use it to actually attach that ammonium and form that alanine. That's why we call it the glucose Alanine cycle. | Glucose-alanine cycle .txt |
Now, this is known as the glucose Allenine cycle. We call it glucose Allenine because we utilize a glucose here to form pyruvate, to use it to actually attach that ammonium and form that alanine. That's why we call it the glucose Alanine cycle. It cycles between glucose and Alanine, but it's also returned back to its source, the skeleton muscle cell. But the ammonium is transported into the skeletal, into the liver. It's not returned back to the skeleton muscle. | Glucose-alanine cycle .txt |
It cycles between glucose and Alanine, but it's also returned back to its source, the skeleton muscle cell. But the ammonium is transported into the skeletal, into the liver. It's not returned back to the skeleton muscle. Now, so the glucose Alanine cycle is one pathway by which we can transport the ammonium from our target tissue, our skeletal muscle tissue, to our liver. But there is another method and that utilizes an enzyme known as glutamine synthetase. So glutamine synthetase is an ATP driven enzyme. | Glucose-alanine cycle .txt |
Before we discuss the process of translation in which we synthesize our proteins from RNA molecules we have to discuss a concept known as the genetic code. Now, as we'll see in just a moment, the genetic code is basically a system that is used by the cells specifically by the ribosomes to translate the language used by the RNA molecules molecules the language that is used by our proteins. And we'll see what that means in just a moment. First, let's discuss several other important points. So the central dogma of molecular genetics is basically a concept that tells us that the flow of genetic information in any cell goes from the DNA molecule to the RNA molecule to the protein. Now, any given DNA molecule in any given organism consists of genes and genes are basically specific sequences of nucleotides that code for proteins. | The Genetic Code.txt |
First, let's discuss several other important points. So the central dogma of molecular genetics is basically a concept that tells us that the flow of genetic information in any cell goes from the DNA molecule to the RNA molecule to the protein. Now, any given DNA molecule in any given organism consists of genes and genes are basically specific sequences of nucleotides that code for proteins. Now, even though DNA molecules contain genes DNA molecules themselves are not directly used in protein synthesis. What happens is our DNA molecules, the genes in DNA molecules are transcribed into RNA molecules. So we basically transfer the genetic information from our DNA to our RNA and then those RNA molecules are used by ribosomes to basically form our proteins by using the genetic code as we'll see in just a moment. | The Genetic Code.txt |
Now, even though DNA molecules contain genes DNA molecules themselves are not directly used in protein synthesis. What happens is our DNA molecules, the genes in DNA molecules are transcribed into RNA molecules. So we basically transfer the genetic information from our DNA to our RNA and then those RNA molecules are used by ribosomes to basically form our proteins by using the genetic code as we'll see in just a moment. So it's not the DNA but it's the RNA molecules that is directly involved in the process of translation in the process of protein synthesis. Now, the entire sequence of DNA of any organism including the genes as well as the non coding regions of our DNA is known as the genome. And only a small percentage of the genome actually consists of the coding regions of the regions of nucleotides that code for proteins. | The Genetic Code.txt |
So it's not the DNA but it's the RNA molecules that is directly involved in the process of translation in the process of protein synthesis. Now, the entire sequence of DNA of any organism including the genes as well as the non coding regions of our DNA is known as the genome. And only a small percentage of the genome actually consists of the coding regions of the regions of nucleotides that code for proteins. And that's exactly why we have to use these RNA molecules because the DNA molecules consist predominantly of non coding regions. So one reason why we use the process of transcription is to basically only transcribe the genes into our RNA molecules so that we don't have to worry about the non coding regions about the non coding regions that basically do not code for any protein. Now let's recall what the process of transcription is. | The Genetic Code.txt |
And that's exactly why we have to use these RNA molecules because the DNA molecules consist predominantly of non coding regions. So one reason why we use the process of transcription is to basically only transcribe the genes into our RNA molecules so that we don't have to worry about the non coding regions about the non coding regions that basically do not code for any protein. Now let's recall what the process of transcription is. So as we mentioned earlier, the process of transcription is pretty simple and that's because both RNA and DNA molecules are polymers of the same exact units of the same exact molecule known as the nucleotide. The only difference between the nucleotides of RNA and DNA molecules is that in DNA the sugar is the deoxyribose and in RNA the sugar is the ribose and in RNA the thymine are replaced with the uracil nitrogenous bases. So let's take a look at the following diagram. | The Genetic Code.txt |
So as we mentioned earlier, the process of transcription is pretty simple and that's because both RNA and DNA molecules are polymers of the same exact units of the same exact molecule known as the nucleotide. The only difference between the nucleotides of RNA and DNA molecules is that in DNA the sugar is the deoxyribose and in RNA the sugar is the ribose and in RNA the thymine are replaced with the uracil nitrogenous bases. So let's take a look at the following diagram. So let's suppose we have the following DNA molecule that we want to use as the template for transcription. And this DNA molecule is commonly known as the antisense strand or the antisense strand. So basically the antisense strand consists of our adenine cytosine adenine and thymine nucleotides. | The Genetic Code.txt |
So let's suppose we have the following DNA molecule that we want to use as the template for transcription. And this DNA molecule is commonly known as the antisense strand or the antisense strand. So basically the antisense strand consists of our adenine cytosine adenine and thymine nucleotides. So when transcription takes place our cell transcribes beginning on the three end and ending at the five end, so that we transcribe the new RNA beginning at the five and ending at the three end. And the method by which we actually transcribe is pretty simple, because the language that is used by RNA and DNA is exactly the same. That is, both of these molecules use nucleotides. | The Genetic Code.txt |
So when transcription takes place our cell transcribes beginning on the three end and ending at the five end, so that we transcribe the new RNA beginning at the five and ending at the three end. And the method by which we actually transcribe is pretty simple, because the language that is used by RNA and DNA is exactly the same. That is, both of these molecules use nucleotides. So when transcribing from DNA to RNA, we synthesize RNA by using the nucleotides that are complementary to the nucleotides on the antisense DNA strands. So basically, if this is A, then we know this must be you. If this is cytositosine, this must be guanine. | The Genetic Code.txt |
So when transcribing from DNA to RNA, we synthesize RNA by using the nucleotides that are complementary to the nucleotides on the antisense DNA strands. So basically, if this is A, then we know this must be you. If this is cytositosine, this must be guanine. If this is adenine, this must be uracil. And if this is thymine, then this must be adenine, and so forth. So basically, when in the nucleus transcription takes place, the cell has no problem transcribing from our DNA to our RNA, because all it has to do is find the complementary nucleotide. | The Genetic Code.txt |
If this is adenine, this must be uracil. And if this is thymine, then this must be adenine, and so forth. So basically, when in the nucleus transcription takes place, the cell has no problem transcribing from our DNA to our RNA, because all it has to do is find the complementary nucleotide. But during the process of translation, when we synthesize our proteins from RNA molecules, things aren't that simple. And that's because our mRNA consists of nucleotides. So the language of RNA is the language of nucleotides, but proteins use the language of amino acids. | The Genetic Code.txt |
But during the process of translation, when we synthesize our proteins from RNA molecules, things aren't that simple. And that's because our mRNA consists of nucleotides. So the language of RNA is the language of nucleotides, but proteins use the language of amino acids. And as we know, nucleotides and amino acids are not the same type of molecules. So the question is, how exactly does the cell know what sequence of nucleotides corresponds to a sequence of amino acids? So once again, things become a bit more complicated when we synthesize proteins during the process of translation, which we'll discuss in much more detail in the next several lectures. | The Genetic Code.txt |
And as we know, nucleotides and amino acids are not the same type of molecules. So the question is, how exactly does the cell know what sequence of nucleotides corresponds to a sequence of amino acids? So once again, things become a bit more complicated when we synthesize proteins during the process of translation, which we'll discuss in much more detail in the next several lectures. So, in translation, the mRNA molecule, which itself is composed of nucleotides, is used as a template to synthesize our proteins that consist of amino acids. And here lies our problem. Nucleotides are different from amino acids, so we cannot use this complementary method. | The Genetic Code.txt |
So, in translation, the mRNA molecule, which itself is composed of nucleotides, is used as a template to synthesize our proteins that consist of amino acids. And here lies our problem. Nucleotides are different from amino acids, so we cannot use this complementary method. So how exactly does the cell know what sequence of nucleotides corresponds to what sequence of amino acids? So what the cell actually does is it translates the language of our nucleotides, our mRNA molecule, to the language of our proteins, our amino acids, by using a system known as the genetic code. So basically, the ribosomes of the cell use our RNA molecule, use our genetic code to translate the sequence of nucleotides in the mRNA molecule to the sequence of amino acids. | The Genetic Code.txt |
So how exactly does the cell know what sequence of nucleotides corresponds to what sequence of amino acids? So what the cell actually does is it translates the language of our nucleotides, our mRNA molecule, to the language of our proteins, our amino acids, by using a system known as the genetic code. So basically, the ribosomes of the cell use our RNA molecule, use our genetic code to translate the sequence of nucleotides in the mRNA molecule to the sequence of amino acids. So the genetic code basically is the link between the sequence of nucleotides and our sequence of amino acids. Now, what exactly does our genetic code actually consist of? Well, basically, the genetic code is a list of codons. | The Genetic Code.txt |
So the genetic code basically is the link between the sequence of nucleotides and our sequence of amino acids. Now, what exactly does our genetic code actually consist of? Well, basically, the genetic code is a list of codons. And a codon is basically a series of three consecutive nucleotides, where each codon corresponds to specific type of amino acids. So in the mRNA molecule, a series of three consecutive nucleotides, known as our codon, corresponds to some specific amino acid. For example, the sequence of nucleotides, our guanine, uracil. | The Genetic Code.txt |
And a codon is basically a series of three consecutive nucleotides, where each codon corresponds to specific type of amino acids. So in the mRNA molecule, a series of three consecutive nucleotides, known as our codon, corresponds to some specific amino acid. For example, the sequence of nucleotides, our guanine, uracil. Uracil, corresponds to a specific amino acid known as valine. So to see what we mean, let's take a look at the following diagram. So, let's suppose our ribosomes in the cell take the following mRNA. | The Genetic Code.txt |
Uracil, corresponds to a specific amino acid known as valine. So to see what we mean, let's take a look at the following diagram. So, let's suppose our ribosomes in the cell take the following mRNA. And what the ribosomes do is they use our genetic code to basically translate what these codons correspond to. So the codon guu, the sequence of Guamine uracil uracil, always corresponds to the amino acid valine, while the sequence CCU always corresponds to our amino acid proline. So we see that our genetic code links our mRNA molecule to our protein, and that's exactly how we synthesize or translate our proteins. | The Genetic Code.txt |
And what the ribosomes do is they use our genetic code to basically translate what these codons correspond to. So the codon guu, the sequence of Guamine uracil uracil, always corresponds to the amino acid valine, while the sequence CCU always corresponds to our amino acid proline. So we see that our genetic code links our mRNA molecule to our protein, and that's exactly how we synthesize or translate our proteins. Now, the question you might be wondering is, why is our codon exactly three nucleotides? Why isn't the sequence only two nucleotides? Well, to answer this question, we can use simple mathematics. | The Genetic Code.txt |
Now, the question you might be wondering is, why is our codon exactly three nucleotides? Why isn't the sequence only two nucleotides? Well, to answer this question, we can use simple mathematics. We can use simple combinatorics. So recall that proteins consist of 20 different amino acids. So we have 20 different amino acids that our body, as well as other organisms actually use. | The Genetic Code.txt |
We can use simple combinatorics. So recall that proteins consist of 20 different amino acids. So we have 20 different amino acids that our body, as well as other organisms actually use. So that means if the genetic code actually makes sense, then we better have 20 different unique codons that correspond to 20 different unique amino acids that appear in our body. But if we use simple math, we see that if we only have two different positions, two different nucleotides in our codon, then the maximum number of different types of codons is 16. And that's because we have four different possibilities for nucleotides. | The Genetic Code.txt |
So that means if the genetic code actually makes sense, then we better have 20 different unique codons that correspond to 20 different unique amino acids that appear in our body. But if we use simple math, we see that if we only have two different positions, two different nucleotides in our codon, then the maximum number of different types of codons is 16. And that's because we have four different possibilities for nucleotides. And four times four gives us 16. And 16 is not enough to actually correspond to the 20 different amino acids that exist in nature. And that's exactly why we have to add one more nucleotide so that we have three consecutive nucleotides in our codon sequence, because four times four times four gives us 64 possibilities. | The Genetic Code.txt |
And four times four gives us 16. And 16 is not enough to actually correspond to the 20 different amino acids that exist in nature. And that's exactly why we have to add one more nucleotide so that we have three consecutive nucleotides in our codon sequence, because four times four times four gives us 64 possibilities. And that is enough to basically describe the 20 different amino acids that exist in nature. Now, right away, you should notice that the genetic code contains 64 different codons in that particular genetic code. So 64 different variations of three letter sequences of nucleotides. | The Genetic Code.txt |
And that is enough to basically describe the 20 different amino acids that exist in nature. Now, right away, you should notice that the genetic code contains 64 different codons in that particular genetic code. So 64 different variations of three letter sequences of nucleotides. And since there are only 20 different amino acids that exist in nature, that implies that many of the three letter codons correspond to the same exact amino acid. And this phenomenon, the fact that two or more different codons can correspond to the same exact amino acid, makes our genetic code redundant or degenerate. So, basically, if we look at the following diagram, it describes what we just mentioned. | The Genetic Code.txt |
And since there are only 20 different amino acids that exist in nature, that implies that many of the three letter codons correspond to the same exact amino acid. And this phenomenon, the fact that two or more different codons can correspond to the same exact amino acid, makes our genetic code redundant or degenerate. So, basically, if we look at the following diagram, it describes what we just mentioned. So if we take our genetic code, we see that the sequence CC, you or cytosine cytosine yourself, and the sequence Cytosine cytosine cytosine or CCC, these two different sequences, both correspond to the same exact amino acid. They correspond to our amino acid proline. Now, I haven't actually listed all the codons that are found in the genetic code, but if you want to, you can look up our genetic code online or in a textbook. | The Genetic Code.txt |
So if we take our genetic code, we see that the sequence CC, you or cytosine cytosine yourself, and the sequence Cytosine cytosine cytosine or CCC, these two different sequences, both correspond to the same exact amino acid. They correspond to our amino acid proline. Now, I haven't actually listed all the codons that are found in the genetic code, but if you want to, you can look up our genetic code online or in a textbook. So, once again, as we'll see in the next several lectures, during the process of translation, when we synthesize our proteins from mRNA molecules, we have to have a way to translate the language used by the mRNA to the language that is used by the proteins. And what the ribosomes do is they use this system known as the genetic code, in which we basically have three letter sequences that are known as codons that correspond to specific amino acids. And the genetic code is set to be redundant or degenerate, which basically means that two or more different codons can correspond to the same exact amino acid. | The Genetic Code.txt |
The cells of our body depend on signal transduction pathways to carry out different types of cell processes at the right moments in time to basically produce physiological responses to certain types of external stimuli. Now, even though these signal transduction pathways are very, very important to the functionality of our cells, these signal transduction pathways must, must be closely maintained and regulated by ourselves. In fact, the inability of our cells to regulate and terminate these signal transduction pathways can actually lead to tumor growth and eventually cancer. And so in this lecture, what I'd like to focus on is discuss how different types of abnormalities in a signal transduction pathway can actually lead to cancer. Now, before we actually begin our discussion on the abnormality part, let's focus on how normal process takes place and how normally our cells terminate these signal transduction pathways. And to use an example, we're going to focus on the EGF signal transduction pathway where EGF stands for Epidermal growth factor. | Cancer and Termination of Signal Pathways .txt |
And so in this lecture, what I'd like to focus on is discuss how different types of abnormalities in a signal transduction pathway can actually lead to cancer. Now, before we actually begin our discussion on the abnormality part, let's focus on how normal process takes place and how normally our cells terminate these signal transduction pathways. And to use an example, we're going to focus on the EGF signal transduction pathway where EGF stands for Epidermal growth factor. Remember, this is the pathway used by the cells that ultimately stimulates the growth and division of epithelial and epidermal cells. So let's begin by focusing on how this pathway actually takes place, beginning with the binding of the EGF molecules onto their domains. So we have two EGF molecules bind onto each one of these domains shown in purple. | Cancer and Termination of Signal Pathways .txt |
Remember, this is the pathway used by the cells that ultimately stimulates the growth and division of epithelial and epidermal cells. So let's begin by focusing on how this pathway actually takes place, beginning with the binding of the EGF molecules onto their domains. So we have two EGF molecules bind onto each one of these domains shown in purple. And once the binding takes place, these two monomers associate with one another to form a dimer and that creates conformational changes in these two structures found in a cytoplasm. Now these two structures, and by the way, this is the EGF receptor these two structures actually contain tyrosine protein kinase domains. And once a conformational change takes place upon binding and the dimerization process, a cross phosphorylation takes place and the carboxyl terminal ends of this tail and this tail are phosphorylated by the active sides of these corresponding kinases. | Cancer and Termination of Signal Pathways .txt |
And once the binding takes place, these two monomers associate with one another to form a dimer and that creates conformational changes in these two structures found in a cytoplasm. Now these two structures, and by the way, this is the EGF receptor these two structures actually contain tyrosine protein kinase domains. And once a conformational change takes place upon binding and the dimerization process, a cross phosphorylation takes place and the carboxyl terminal ends of this tail and this tail are phosphorylated by the active sides of these corresponding kinases. And once we form these phosphorylated residues, we have an important adaptor protein known as GRB Two that binds onto this section and that calls upon another protein known as SOS. And what SOS does is it binds an inactive small G protein known as Ras. When Ras binds unto this structure, there's a conformational change that takes place in the Ras protein and the GDP Guanosine diphosphate is expelled and the GTP Guanosine triphosphate moves into that pocket. | Cancer and Termination of Signal Pathways .txt |
And once we form these phosphorylated residues, we have an important adaptor protein known as GRB Two that binds onto this section and that calls upon another protein known as SOS. And what SOS does is it binds an inactive small G protein known as Ras. When Ras binds unto this structure, there's a conformational change that takes place in the Ras protein and the GDP Guanosine diphosphate is expelled and the GTP Guanosine triphosphate moves into that pocket. And once GTP binds, that activates that G protein we call Ras. And once Ras is activated, it moves on and activates a protein kinase we call Raff. And once this protein kinase is activated, it goes on to form these to activate other protein kinases we call mex the Max. | Cancer and Termination of Signal Pathways .txt |
And once GTP binds, that activates that G protein we call Ras. And once Ras is activated, it moves on and activates a protein kinase we call Raff. And once this protein kinase is activated, it goes on to form these to activate other protein kinases we call mex the Max. Once activated, it goes on to activate other protein kinases we call Hercs. Now these Hercs can actually move into the nucleus of our cell. So we have this double phospholipid bilayer of the nucleus. | Cancer and Termination of Signal Pathways .txt |
Once activated, it goes on to activate other protein kinases we call Hercs. Now these Hercs can actually move into the nucleus of our cell. So we have this double phospholipid bilayer of the nucleus. These IRCS go into the cell nucleus and they activate transcription factors. These transcription factors then move on and express different types of genes that produce mRNA molecules which then exit the cell and they essentially are used by the ribosomes to produce proteins. The proteins are in turn used to basically build up the cytoplasm, build up the cytoskeleton which basically increases the size of the cell and that cell eventually is able to divide. | Cancer and Termination of Signal Pathways .txt |
These IRCS go into the cell nucleus and they activate transcription factors. These transcription factors then move on and express different types of genes that produce mRNA molecules which then exit the cell and they essentially are used by the ribosomes to produce proteins. The proteins are in turn used to basically build up the cytoplasm, build up the cytoskeleton which basically increases the size of the cell and that cell eventually is able to divide. And so in this process, the EGF signal transduction pathway stimulates cell differentiation, cell growth and cell proliferation of two types of cells, epidermal cells and epithelial cells. Now, once this pathway actually carries out its specific purpose, how exactly does a normal cell terminate this process? Well, there are three major methods. | Cancer and Termination of Signal Pathways .txt |
And so in this process, the EGF signal transduction pathway stimulates cell differentiation, cell growth and cell proliferation of two types of cells, epidermal cells and epithelial cells. Now, once this pathway actually carries out its specific purpose, how exactly does a normal cell terminate this process? Well, there are three major methods. Method number one is the fact that because we have a G protein involved and G proteins have Gtpa's activity, what that means is they have a built in clock that allows it to actually shut itself down following activation. So sometime after this has been activated into the GTP form, this green structure, the G protein, because it has Gtph activity, it is able to actually take a water molecule from the cytoplasm and hydrolyze the GTP back into GDP. And once it inactivates itself, this can no longer stimulate the rest of the process. | Cancer and Termination of Signal Pathways .txt |
Method number one is the fact that because we have a G protein involved and G proteins have Gtpa's activity, what that means is they have a built in clock that allows it to actually shut itself down following activation. So sometime after this has been activated into the GTP form, this green structure, the G protein, because it has Gtph activity, it is able to actually take a water molecule from the cytoplasm and hydrolyze the GTP back into GDP. And once it inactivates itself, this can no longer stimulate the rest of the process. And so this pathway essentially shuts down as a result. So cells can terminate the pathway by using Gtpa's activity of G proteins and that is built in into that molecule. Number two, these cells can also actually terminate the pathway by using a class of molecules we call phosphatases. | Cancer and Termination of Signal Pathways .txt |
And so this pathway essentially shuts down as a result. So cells can terminate the pathway by using Gtpa's activity of G proteins and that is built in into that molecule. Number two, these cells can also actually terminate the pathway by using a class of molecules we call phosphatases. So in fact, as soon as this pathway is activated, it also activates many different types of phosphatases. And what phosphatases do is they essentially remove us four groups that were attached by protein kinases. So for instance, we have the Rat, the Mechs, the Irks, and these two structures that act as protein kinases in this particular case. | Cancer and Termination of Signal Pathways .txt |
So in fact, as soon as this pathway is activated, it also activates many different types of phosphatases. And what phosphatases do is they essentially remove us four groups that were attached by protein kinases. So for instance, we have the Rat, the Mechs, the Irks, and these two structures that act as protein kinases in this particular case. And what the phosphatases do is they essentially move onto the target proteins and they remove those phosphoryl groups that were placed by all these different protein kinases. For instance, these phosphatases can remove these phosphoryl groups here and that essentially inactivates this part of the pathway and so it cannot continue and as a result it is shut down. And so anywhere I have an asterisk, that basically means we're dealing with a protein kinase. | Cancer and Termination of Signal Pathways .txt |
And what the phosphatases do is they essentially move onto the target proteins and they remove those phosphoryl groups that were placed by all these different protein kinases. For instance, these phosphatases can remove these phosphoryl groups here and that essentially inactivates this part of the pathway and so it cannot continue and as a result it is shut down. And so anywhere I have an asterisk, that basically means we're dealing with a protein kinase. And so these phosphatases can influence and shut down this protein, these proteins, these proteins and also these two structures here which are actually part of that EGF receptor. And finally we can terminate the pathway by inactivating that receptor of the pathway. And actually we already spoke about one way by which we can inactivate is by removing these phosphoryl groups. | Cancer and Termination of Signal Pathways .txt |