all right at this point we've talked about the function of the various proteins and the structure of proteins now we're going to talk about how we might be able to manipulate a protein's function like how well it's completing its function so a lot of proteins their activity level is contingent on them binding to another molecule which is called a ligand so we call these protein ligand interactions a ligand is just something that binds to a protein thus changing its activity level and ligands can be ions they can be molecules sometimes they can even be parts of other proteins and they always bind to a certain location on the protein and we call that locations they buy to bind to The Binding look The Binding site so for instance let's look at this example over here we'll be looking at the example of a sodium Channel a sodium channel is a transport protein and basically its function is simply to help bring sodium across the cell membrane sodium which is a charged ion can't cross the cell membrane on its own so if it's going to go into the cell or out it's got to go through one of these channels so in this picture this kind of greenish looking rectangle that is the that's the channel right and that is our protein in this situation the ligand is going to be the substance that binds to the sodium Channel and there are different kinds of ligands that you can have one type of ligand is something called acetylcholine okay so we can see that this ligand has a specific area on the protein that it's supposed to bind to it's binding site and when that ligand binds to that binding site what it does is it changes the folding of the channel and in essence it causes the channel to open which allows the ions in this case we're talking about sodium to enter now if the ligand releases so if it stops binding to that site then the folded pattern of the protein kind of resorts back to its original shape and that in essence closes the channel okay so really the activity of the protein is contingent on its interaction with the ligand it physically has to bind to the ligand in order for it to complete its function of transporting sodium now one thing I want to point out is that the ligands that can bind to a given protein are very specific it's not just any old ligand that will fit in a way proteins and ligands in this way are kind of analogous to Locks and keys if you have a lock then that lock has an area with a very specific shape this is kind of analogous to our binding spot on our protein and the lock in general is kind of analogous to the protein now as you know the the intention or the way that the Lock Works is by putting a key into the lock so the key in this case is analogous to our ligand and you're probably aware of the fact that not any old key will work in any lock if they did they wouldn't feel really good lock would it because it's supposed to restrict access to things rather there are only certain keys that will work for certain locks so you would say that there is specificity between the lock and the key right meaning there are specific keys to work with specific locks and there's also specificity between proteins and ligands only certain Pro only certain ligands will be able to bind to certain proteins which means that we can use some of these specific molecules to activate some proteins without activating others so really the ability of the protein and the ligand to interact with each other is going to be what manipulates how functional the protein is so some of the things that we can do to influence that interaction and therefore protein function is we can change the quantity of either the proteins or the ligands we can subject them to different environmental factors and then we'll talk about the influence of some different kinds of molecules that can affect how well proteins and ligands can interact with one another we're going to start first by talking about just simply manipulating the amount of proteins or ligands so I'm going to draw up here um our picture once again of a cell membrane and I'm going to kind of since it'll be hand drawn it's going to look a little different than the previous image but I'll try to stick to its format as much as possible okay so in my picture the double black lines this is the cell membrane and the little green boxes that I have these are my channel proteins for sodium and then I will use sort of this uh little well it was blue in the previous picture wasn't it let's try to stick with the colors so I'll use kind of the little teardrop shape to represent the ligands in the picture okay okay so currently the way that it's drawn we have three different sodium channels and if we have ligand to open those up so let's just say that we have a situation where every protein that we have a ligand that is able to bind to it and remember when it binds that's what opens the channels up and so we now have three channels available to bring in sodium what if we wanted to bring in more sodium the rate of sodium spilling in per channel is Pretty constant we can't really make it necessarily come in any faster so one thing we might do because we can only fit so many sodiums through at a time is what if we added more proteins as long as there were ligands available to bind with them adding more proteins would provide more passageways for sodium to come through right so you kind of Imagine That in terms of the rate of the protein function or the reaction that you get from it as you increase the number of proteins present you're going to be increasing ultimately the rate that that reaction occurs whatever that function is for that protein okay now that's not going to continue indefinitely you're going to eventually see this sort of start to Plateau for potentially one of two reasons one reason what if I keep adding in proteins but I don't add any more ligand right so if I reach a point where I've got more proteins than I have ligands and there's nothing for them to bind with then adding more proteins doesn't actually help me right if the channel is closed then having more channels doesn't help unless I have the keys to open them the other thing potentially is that you might eventually run out of reactants so in this case it's not really a chemical reaction we're facilitating rather we're trying to transport sodium but what if we reach a point where all of the sodium that's on this side that needs to travel through has traveled through Will adding more proteins speed up sodium transport will know because we don't have any sodium left to transport right so this Plateau could either be the result of you know if you run out of ligands more protein won't help or if you run out of reactants more proteins also won't be helpful okay so let's kind of reset our picture here for a second and let's close our channels back off and let's talk about what if we manipulated the amount of the ligand all right so all of our channels are closed currently we have none no sodium Transportation right because there's no ligand if we add a ligand and we open this channel then we're going to start to transport some sodium if we add more ligand and open more channels then we are going to transport even more sodium right so kind of like last time adding ligands is having a positive effect on the function that that protein completes but will adding light more and more ligands continue to give more and more benefit well up to a point adding those ligands open more channels so that was helpful but what if I keep adding okay now I'm adding more ligand but there's no protein for it to bind to so is that going to help give me any more function nope we're going to see a plateau just like we saw in the other graph right at this Plateau basically we've reached saturation we ran out of proteins we have more ligands than proteins there's nothing for it to bind to to even facilitate its function that's left so we can manipulate the overall activity of the protein by manipulating how many proteins and or ligands are available all right environmental factors proteins generally function best within certain environmental parameters one of which is temperature kind of what we find is that the rate of a reaction facilitated by a protein will increase as you increase temperature up to a point and then it will drop very dramatically so the reason why you have your rate increasing from here to here is because if you increase the temperature that the protein is in then you in end up increasing the kinetic energy which means that everything is moving faster so if we kind of think back to that example of our sodium Channel or ligand in here right if everything is moving quicker as we speed things up then the ligand is going to bind to the channel faster that means the channel will open and then the actually the individual sodium ions are going to move faster as well because they have more kinetic energy so the the function of transporting sodium will go faster if the temperature is warmer now clearly that only occurs up to a certain point because look at this steep drop off going forward the thing is is that if you get to too high of a temperature then proteins start to denature sorry that should be you denaturation means that proteins lose their three-dimensional shape and as a result they also lose their function so kind of imagine if we subjected this channel protein to a really really high temperature then that protein might start to lose its shape and kind of think of like a tunnel caving in if it loses that shape if that provides the passage is it going to be able to transport proteins sorry sodium ions across the channel well no it's not because you no longer have that pathway for it to move we can also have reduced function if we subject enzymes or other proteins to different PHS so generally proteins have specific PHS that they function well in and then if you become more basic or acidic beyond that point then you end up denaturing the enzyme it causes it to unfold it has to be within a certain range in order for it to have optimal functionality now most ends most proteins in your body will function best around a pH of seven but not all of them like for instance you have a you have some digestive enzymes in your stomach and they don't work best at a pH of seven because guess what your stomach is really really acidic and if that's the pH that they function best at then they probably really doing a very good job in your stomach so the enzyme the proteins that are in your stomach they tend to work best at more acidic PHS but even they have this range that they work optimally at and kind of likewise some proteins will have certain salinities that they work best in again kind of the general idea is that especially with higher salinities that might be a condition that would denature the protein and keep it from functioning so this kind of stands to show why our bodies spends so much energy trying to maintain homeostasis homeostasis is that State uh similar internal state that our body tries to maintain we spend a lot of energy trying to maintain our body temperature and trying to maintain our PH range and our kidneys are working hard to maintain our internal saline concentration why is it so important that those don't vary that much well it's really important because as you can see proteins tend to work best within a very specific range the range that our body is generally at and if we start to go too far in either direction in a lot of cases that means that the proteins start to denature they lose their function and then we've now lost whatever function that was providing and that can ultimately lead to death all right so the last thing that can influence a protein's function is the presence of certain types of molecules okay we have one group of molecules called Inhibitors and they decrease enzyme activity here's how they do that basically these types of molecules make it either harder or potentially impossible depending on the situation four proteins and their ligands to bind remember most of these proteins activity is contingent on them binding with their ligand so for making it either harder or impossible for the protein and the ligand to interact with each other I.E bind then you're not going to have a functional protein that's kind of why I put the off switch the Inhibitors are kind of turning the protein off activators are the opposite these are going to be molecules that make it easier for proteins to bind to their ligands and that's going to make them maintain their functionality right if they can do that binding that they're supposed to all right so within each one of these there are different kinds of Inhibitors in different kinds of activators and we're going to talk about the mechanisms through which they either make it harder or easier for the protein and the ligand to bind so for the for the Inhibitors let's start there here's going to be the image that we use as an illustration of what the binding is supposed to look like under normal conditions in this image this teal blue is our ligand purple is our protein and you can see that there is very clearly a three-dimensional indentation on our protein that is the right shape for our ligand that's our binding spot that the ligand is supposed to bind to and when it does that is kind of what activates the protein all right so one kind of inhibitor is called a competitive inhibitor and in our image that's this dark blue shape what competitive competitive Inhibitors do is they compete with the ligand for The Binding spot you can see that this inhibitor here is blocking the binding spot and that is making it impossible for the ligand to bind there like it should so they're competing with the ligands and specifically they're competing for The Binding spot and when they do they block The Binding spot from the actual ligand this is kind of analogous to putting chewing gum in a lock keys can turn locks to open doors right and they obviously fit those locks well now you can take a wad of chewing gum and shove it into the opening of the lock thus blocking the lock the gum doesn't open the door right you can't like use the gum to turn the lock to open but it does do a good job of preventing the key from going into the lock to do its job of opening the door and that's a sense essentially what these competitive Inhibitors do is that they are blocking the lock from being accessed by the key sometimes those Inhibitors are permanent fixtures meaning they bind there and then they never let go sometimes it's temporary they bind there for a while then they release and after they release then the lagging can come back it just kind of depends non-competitive Inhibitors are also called allosteric Inhibitors and they work a little differently so we can see that this orangish color thing right here that's the allosteric inhibitor and if you compare it to the competitive inhibitor you might notice that it's binding to somewhere other than the binding spot there's this other indentation on the opposite side of the protein which we call the allosteric site yellow steric inhibitor is called an allosteric inhibitor because it binds to that location and it's not competing with the ligand for The Binding spot it never binds to The Binding spot it binds to this other location and when it does it cause The Binding space to distort like you can see here the shape of The Binding site has changed this arm used to be more straightened and now when the non-competitive inhibitor bound to the allosteric site it caused the folding of the protein to change which distorted The Binding spot and now the binding spot isn't the correct shape to bind to the ligand so the end result is the same the ligand and the protein don't interact like they should but in this case it's not because the binding spot is blocked it's because the allosteric inhibitor distorted The Binding spot by binding somewhere else on the protein the allosteric site we also have activators that are going to make the connection between the ligand and protein better okay one of which is called a cofactor cofactors are sort of similar in a way to competitive Inhibitors in that they bind to The Binding spot so in our image this blue shape is the protein the purple shape is the cofactor and these two orangish shapes are our ligands the cofactor binds to The Binding site and provides the correct fit between the binding site and the ligands so the cofactor is producing a better fit for the ligands and that better fit is then allowing for the ligands to bind and activate the protein this is kind of analogous to if you've ever had a stripped Phillips screw the head of it a lot of times when you're trying to screw and unscrew a Phillips head the edges of the Little Star get worn down and then the tip of the screwdriver doesn't fit into the groove on the head of the screw as well one thing you can do in these cases when you strip the screw top is that you can put a rubber band over the edge of your screwdriver over the screw head and it basically acts as a cushion between the screwdriver and the head of the screw when you do that the screwdriver now has a better fit with the head of the screw and you're able to loosen it or tighten it allosteric activators are kind of similar to allosteric inhibitors the key is they bind to the allosteric site so in this picture the beiges beiges structure is the protein this purple circle is our ligand and our allosteric activator is this little purple square right here we can see that the activator is not bound to The Binding site it's bound to the allosteric site which is somewhere else on the surface of the protein that's the same thing that happens with an allosteric inhibitor it binds to the allosteric site but binding to the allosteric site for an activator has sort of an opposite action in the inhibitor binding to the allosteric site caused The Binding spot to be distorted with an allosteric activator binding to The Binding site reinforces the shape sorry binding to the allosteric site reinforces the shape of The Binding site and provides the correct shape for the protein to bind to its ligand so it's it's making sure that that binding site keeps the shape that it is supposed to now when you go through this material kind of the two things you want to make sure that you know for each of these or compared between them is where is the inhibitor or activator binding to The Binding site or to the allosteric site how is that allowing the ligand to bind or not okay if you kind of know roughly those two things about these four different types of molecules then you should be able to work your way through the types of questions that we would ask you concerning Inhibitors and cofact and activators regarding protein function