welcome in this video we're going to be focused on amino acids which are the monomers that make up the polymer proteins and we'll be looking at some of the functions of proteins specifically enzymes so what are the functions of proteins and what we find is that proteins function in a variety of locations inside of cells and outside of cells and they have a lot of function so you can see the list of functions there the first function of enzymes is they function as catalysts inside of cells they increase the rate of chemical reactions proteins that are catalysts are called enzymes the second function for proteins is they function in the defense mechanism and protection of cells the main one what i'm looking at here is antibodies so antibodies are proteins the third function of proteins is transport there are a number of proteins that are involving transport some proteins transport fats in our blood other proteins transport oxygen in our blood so we have a lot of diversity in function a lot of diversity in transporting different types of molecules number four is regulation some of the hormones that we have in our body are made of protein not all hormones are proteins but some are for example insulin is a protein the fifth function of proteins is structure so we see that some proteins make up the structural components of the cell so the extracellular matrix intracellular matrix we have actin myosin which are the structural makeup of muscles we have kinesins and dyneins that are functional inside of cells to move organelles from one to one side of the cell to the other so we see a number of them function in a structural capacity in addition to that we also have collagen alpha keratin these are both proteins that make up and are forming structures in various organisms the sixth one is contractile or movement so actin and myosin also fall into this category they are the main proteins in our striated muscles and finally the last function for proteins is storage so we have a number of proteins that are involved in storage storage of other molecules or storage of energy so what makes up proteins so proteins are polymers which means they are made up of many smaller individual units these individual small units are called amino acids they are the monomers so mono meaning one poly meaning many so proteins are polymers and they're composed of many amino acids or the monomers the amino acids themselves are composed of an amino group which is a nitrogen bonded covalently to hydrogens and in addition to that a carboxylic acid or a carboxyl group so that's a carbonyl carbon double bonded oxygen bonded to an oxygen and hydrogen so that is where the name amino acids comes from amino acids comes from the amine portion of the amino acid and the carboxylic acid portion of the amino acid there are 20 commonly incorporated amino acids into proteins and we will look at each of their structures shortly but if you look at the structure of the amino acid on the bottom of this slide you'll see that on the left there is the amino group on the right there is the carboxyl group and in addition to that we have a carbon that connects those two into that carbon we have an r group which we also called the side chain the black atoms or the black fonted atoms the nitrogen the carbon the carbonyl carbon and the oxygen would be considered the main chain atoms of an amino acid so each of these 20 different amino acids differ based on the consistency or composition of this r group which amino acid which atoms are found in this r group the other thing that you'll notice about this amino acid is that this nitrogen has accepted a proton and is positive and we know that nitrogens are basic and under the definition one of the definition of bases is they they are proton acceptors this was the bronsted-lowry definition and you can see that this amine has accepted a proton as become protonated and positively charged we also know that the carboxylic acid is an acid and is a proton donor based on the bronsted-lowry definition and you can see that this carboxylic acid has donated its proton and is now negatively charged and when we look at neutral phs which is what we find inside of cells and outside of the cells in our body the proton has been accepted by the nitrogen and has been donated by the oxygen of the carboxyl group and the nitrogen therefore is positively charged and the carboxyl group is therefore negatively charged if we look at all 20 of the amino acids we find that each of these 20 with the exception of one have a chiral carbon so 19 of the 20 amino acids have a chiral carbon and just as a reminder a chiral carbon is a carbon that is connected to four different groups so if you look at the structure of these two alanine molecules on the bottom the carbon the central carbon there is chiral the carbon is connected to one amine group one carboxyl group one hydrogen and one r group and assuming the r group is different than these other three groups we have four different groups connected to that carbon which makes it chiral as a result of a chiral carbon we can have two different stereoisomers and we label these stereoisomers l and d so the stereoisomer on the left is l-alanine and the stereoisomer on the right is d-alanine the way that we define l and d we place the carboxylic carbon at the top and we will draw down all of the carbons um in the r group and then we look at the position of the me the amine and the hydrogen that's connected to that central carbon is the amine to the left then it's l if the amine is to the right it's d if we look at the proteins that we find in life in all organisms plants animals fungi what we find is that all of these proteins are made up of just l amino acids and we have very few d amino acids in in our life or in the life of other organisms some organisms will have more than others but we really very rarely see any d amino acids in any proteins as we begin looking at these 20 amino acids they are going to be different based on their r group as we mentioned there are 20 that all have the amine the carbon and the carboxyl group and the different r groups will have different organic functional groups in them and as a result of those organic function groups we're going to place those into one of four different categories the first category is polar neutral these r groups contain alcohols or thials or amide functional groups the second group is acidic negative amino acids these r groups contain carboxylic acid functional groups the third functional group or the third r group or the three amino acid group is basic positive amino acids these r groups contain amine functional groups and finally the last category of amino acids is the non-polar amino acids and these r groups would contain either an alkyl group or an aryl group and just a reminder an alkyl group would be an alkane with one fewer hydrogen so that would be methyl ethyl propyl essentially hydrocarbons and then just as a reminder an arrow group would be benzene with one fewer hydrogen and in this particular case also just or almost solely hydrocarbons just carbons and hydrogens all right so we're going to look at each of these 20 amino acids and we're going to place them into one of these four categories you'll notice that in the definition of each of these categories there is a number in parentheses at the end of each definition that number represents how many of the 20 amino acids are found in that particular category in the polar neutral category of amino acids there are six of the 20. in the acidic negative there are two of the 20 in the basic positive there are three of the 20 and finally the non-polar category we would have 9 of the 20 amino acids and that as a result adds up to 20 6 2 3 and 9. all right so let's look at this first category polar neutral again these are amino acids that will contain an alcohol group which is an oh group a phyl group which is an sh group or an amide which is a carbonyl connected to a nitrogen here are the six polar neutral amino acids you can see on the top two serine and threonine both have a hydroxyl group or an alcohol functional group which makes them polar because that bond between the oxygen and hydrogen is polar the one on the top right is cysteine it has a sulfhydryl group it's a thiol it is also polar the bottom left amino acid is a tyrosine you can see that while it does have a benzene or aryl group it also has a hydroxyl group and that hydroxyl places it into the category of polar and finally the last two on the bottom right asparagine and glutamine also are polar neutral because they contain amide function groups a carbonyl connected to a nitrogen all right so what you're expected to know here is not how to draw each of the amino acids or for that matter even how to recognize them by name or to to see them and connect their name to their structure but what's important is to be able to put these six amino acids into the category of polar neutral so what does that mean well it means you need to be able to recognize the functional group and place that into one of these four categories so if you see a hydroxyl group or a sulfhydryl group or an amide on the r group then you would put it into the polar neutral category the important thing in addition to that is that the definition of the category polar and neutral only applies to the r group and the r groups on this particular slide are shown with a red font so you're not going to look at the the black fonted atoms in those molecules those black fonted atoms the molecules are the same for all 20 amino acids so you can't really categorize these amino acids into a category based on those black font amino acids because they are all the same we're only looking at the red fonted atoms which is the r group and we're again looking for in the case for polar neutral we are looking for an alcohol a thiol or an amide the second and third groups of amino acids are the acidic negative and basic positive amino acids so in the box on the left you'll see two amino acids that are acidic negative both of those have carboxylic acid groups and both of them also you can see are charged one of the things i forgot to mention is that at ph 7 we will see the nitrogen have accepted the proton the carboxylic acid will have donated the proton and in these two amino acids the r group carboxylic acid will have also donated its proton and be negatively charged and if we add up the positive negatives in these two amino acids aspartate and glutamate we'll find that both of them have a charge that is negative we have one positive and two negative charges and overall the the net charge of those two amino acids would be negative negative one if we look at the three amino acids on the right these are the basic positive amino acids each of these r groups contain an amine and you can see that each of these amines have accepted a proton and most of them have accepted a proton at ph 7 and so are positively charged again the main chain the black fonted atoms the positive on the nitrogen and the negative on the carboxyl group will will cancel out and give us a neutral charge so if we have a charge in the r group then that would give us the overall charge of the amino acid so you can see lysine arginine and histidine all have a positive charge in their r groups and therefore have a positive overall charge and therefore are placed in this category of positive again they're basic because they have amines and we already had mentioned in the last organic chapter that amines are basic they function as bases because they accept protons the final category is the non-polar amino acids and these are containing alcohol or aryl i'm sorry the alkyl groups or aryl groups so the alkyl groups and aryl groups are hydrocarbons almost entirely with just maybe two exceptions so you see glycine just has a hydrogen alanine a methyl group valine has a propyl group connected on the that middle carbon leucine and isoleucine have some branched hydrocarbons but the only thing that is there is carbon and hydrogen atoms methionine and tryptophan are a little unique in that they are they have r groups that don't just contain carbons and hydrogens methionine has a sulfur but the bond between the covalent bond between sulfur and carbon is categorized as nonpolar because their electronegativities are fairly similar in tryptophan the nitrogen and carbon bond there is fairly nonpolar as well and so we have that in addition to that we have lots of hydrocarbons lots of carbons and hydrogens which overwhelmingly cause that r group to be nonpolar phenylalanine you see is a benzene group and then finally proline is a little unique in that the r group will bend around and reconnect to the nitrogen on the main chain and form a ring type structure all right so again make sure you can recognize each of these and be able to put it into a category into one of these four categories the other thing that i want to mention on this slide is that glycine is the one out of the 20 that does not have a chiral carbon if you remember from our definition of chiral carbons the chiral carbon has to have four different groups connected to it and you can see with glycine that they have two of the same group we have two hydrogens connected to glycine and therefore that carbon is not chiral unlike the rest of the carbon in all the other amino acids now that we have an idea of the structure of each of the amino acids how do we begin connecting these amino acids together since they are the monomers that make up the polymers that are proteins so when we connect two amino acids together we form a peptide bond on the bottom left you'll see two amino acids on the left you'll see the amino acid alanine on the right you'll see the amino acid serine and we are going to connect those two amino acids together and when we connect those together we produce an amide bond so you see here the carbonyl connected to a nitrogen that is an amide functional group and that amide function group in the context of two amino acids connecting together is defined as a peptide bond how do we create the peptide bond well we're going to add the carboxyl group of one amino acid to the amine group of the other amino acid to form the peptide bond and what you'll notice is that some of the atoms have been pulled out of these two amino acids and are forming another molecule and that is water and so this particular reaction is called a condensation reaction because we're condensing two molecules together we're also condensing out the elements that make up water h2o we're removing two of the hydrogens from the nitrogen removing this oxygen from the carboxylic acid to make water this nitrogen will still have one of its hydrogens and you can see it's still connected to the nitrogen and this carbonyl group will be directly connected to the nitrogen you can see that covalent bond that's connected there that is the peptide bond or the amide bond that connects one amino acid to the next when we link amino acids together we can generally name them based on how many amino acids are connected together by placing a prefix in front of the word peptide so if we connect two amino acids together we get dipeptide if we connect three amino acids we get tripeptide tetrapeptide pentapeptide and so on as we add additional amino acids together these are generally named at least for the shorter amino acids or fewer amino acids that are connecting together but the important point with the prefixes ditri tetra it's based on the number of amino acids so again if we're connecting two amino acids together we get a dipeptide it's a little confusing because when we connect two amino acids together we only have one peptide bond so this dipeptide almost implies that we have two peptides because we're saying dipeptide but the dye indicates that we have two amino acids so don't get those confused all right as we begin looking at these amino acids that we're connecting together to form peptide bonds we're going to have an asymmetric molecule as a result when we're connecting the carboxyl group of one amino acid to the amine group of a neighboring amino acid and we form a dipeptide we'll actually have two distinct ends that dipeptide and if we keep adding amino acids we'll still have a unique end that is the amine and we'll have another end that is a carboxyl group and we have specific names for these ends of this polymer the end that has an amine group on the on one end is called the n terminal because it terminates in a nitrogen or the nitrogen of the amine on the other end you can see that the other end of this polymer that is a peptide or protein will end in a carboxyl group and that carboxyl end is called a c-terminal and or the c-terminal amino acid so in this particular dipeptide where we're bonding allene to serine we usually will name this starting from the n-terminal end this amino acid and going to the c-terminal end in this particular case there are only two but if we had three we would start naming from the n-terminal end and move our way to the c-terminal end and begin connecting amino acids together alanine connects to serine and we're forming a bond between there and that's the peptide bond there's our n-terminal end you can see it has a free nitrogen on that end and our c-terminal end has the carboxyl group on the other end in this polymer or dimer that is alanine covalently connected to serine now that we have an idea of how amino acids connect together by peptide bonds when we begin connecting many of them together together and we have a polymer that has a function we begin to call that polymer a protein and proteins in addition to having the structure that is connecting amino acids together and forming peptide bonds we have multiple layers of higher order structure and these layers of structure have been hierarchically ranked and labeled primary secondary tertiary quaternary the primary structure of amino acids is the amino acids connection from one amino acid to the next bipeptide bonds so if we have a protein that has 100 amino acids in it the primary structure would really be the sequence or order of amino acids that is bonded together in this polymer and is stabilized by peptide bonds all right so it's important that you know the definition so a primary structure consists of the sequence of amino acids and the stabilizing force that holds the primary structure together is a peptide bond it's an amide as we move from primary structure to secondary structure we will begin folding these amino acids that are connected together by peptide bonds into local arrangements of structure so secondary structure is defined as fixed arrangement of the polypeptide backbone or the main chain atoms not the r groups and the stabilizing force that holds a secondary structure together are hydrogen bonds as a reminder for hydrogen bond formation we need to have a hydrogen that's covalently bonded to fluorine nitrogen or oxygen and that hydrogen has to be connected to another fluorine nitrogen or oxygen as you noticed from all of the 20 amino acids that we don't have any fluorines but we do certainly have oxygens and nitrogens so we're really looking for a hydrogen that's covalently bonded to nitrogen oxygen that can donate that proton to another nitrogen or oxygen the two common secondary structures that we see in proteins are alpha helix and beta pleated sheet and so you can see the structures on the left and right of those two secondary structures in these two structures we've actually changed from showing these molecules with chemical symbols and lines representing covalent bonds to balls connected to sticks and you can see as we look through these balls and sticks the balls in these particular molecules that are black are carbons the balls that are blue are nitrogen the balls that are red are oxygen and these larger yellow balls are represent the r groups and so you can see this main chain would be the polypeptide connecting from one amino acid to the next and then this next one one amino acids the next one amino acids next and in beta pleated sheet we actually see hydrogen bonds the little dashed red lines here are hydrogen bonds that connect one sheet to the next in this particular beta sheet we don't see a connection between one of these strands to the next strand but what we would need is for this strand to go out and form a turn and then go down to this strand and then form a turn and go to this strand and form a turn and go this strand and in that way we would have a long polymer that would be bent up into a sheet-like structure where hydrogen bonds are going to be stabilizing one strand to the next and so you can see this network of hydrogen bonds that holds one beta sheet to the next beta our beta strand to the next beta strand and forms this sheet-like structure in the structure on the right you'll see that this polypeptide chain or main chain has been wound up into a helix almost like a spiral phone cord and what you'll notice is that we again have this network of hydrogen bonds and these hydrogen bonds are shown as three parallel lines or four parallel lines that are connecting the oxygen from one amino acid to the hydrogen of the nitrogen of a neighboring amino acid or at least neighboring in space not neighboring in terms of where it is in the sequence or primary structure and you can see this neighboring or this network of hydrogen bonds are stabilizing and holding this polymeric strand of amino acids in a very tightly wound coil or helix and you can see that we've represented these secondary structures with greek letters alpha helix and beta pleated sheet type structure those structures represent the main secondary structures that we see in many proteins in life as we move on to the next higher order structure of proteins we see we define this as tertiary structure this is the three-dimensional folding of these secondary structures so once we've connected these amino acids into alpha helices and beta strands or beta sheets we're going to fold all of these up into more of a glob-like structure or more spherical type structure and this gives us a three-dimensional fold of all of these secondary structures it also allows us to take these non-polar r groups and put them into the interior of the proton protein if you remember these proteins are moving around in the intracellular compartment called the cytoplasm or in the extracellular aqueous environment again both environments are aqueous and so these r groups that are nonpolar tend to be would tend to be hydrophobic they'd be water fearing so if we fold these proteins up into a glob what ends up happening is that these r groups that are nonpolar tend to be pushed into the interior of the protein and the hydrophilic groups those r groups that tend to have polar neutral or positively basic or negatively acidic charged r groups would be positioned on the exterior of the protein to make favorable contacts with water or the aqueous environment around the protein if we look at the interior of the protein we find that there are four stabilizing interactions that hold this three-dimensional structure this tertiary structure in more of a glob-like structure the first type of interaction we see is ionic bonds these are interactions between one acidic negative r group and one basic positive r group because we have a negative charge on one r group and a positive charge on the other r group these can form an electrostatic attraction opposites attract and form an ionic bond the second type of interaction is a hydrogen bond these hydrogen bonds interactions form between two polar neutral r groups so if we fold up these secondary structures and perhaps we have a alpha helix that is folded up into a glob near to either another alpha helix or a beta sheet and the r group from one r group for an alpha helix is sticking out and connecting with an r group from a beta pleated sheet if both of these are polar neutral r groups they can form hydrogen bonding interactions because they contain hydroxyl groups from the alcohol the amide functional group can also form hydrogen bonds we can form hydrogen bonding interaction that really will hold one secondary structure to another just like an ionic bond would the third type of interaction that we see stabilizing tertiary structure is a disulfide bond if you remember we form disulfide bonds between two thiol functional groups by oxidation reactions the thio function group that we saw in amino acids is just found in the amino acid cysteine so to form a disulfide bond we would have to have two cystine amino acids that are positioned near to each other in space once we fold up the secondary structures into a glob if we do see two cysteines near to each other as we fold them up these two cysteine r groups can oxidize and form a disulfide bond and stabilize that tertiary structure the last type of structure that or interaction that favors true stray structure is the london dispersion force interactions and these are primarily between the non-polar r groups so if we have a non-polar r group or non-polar amino acid and we have two of them positioned near to each other in space after we fold this up into a three-dimensional glob we can actually form stabilizing attractive forces called london dispersion force interactions so all four of these interactions stabilize tertiary structure the last type of protein structure is called quaternary structure quaternary structure is the association of multiple polypeptides so not all proteins have quaternary structure it would be only those proteins that require multiple polypeptides multiple protein chains to be functional and these protein chains would then have to come together and stick together and the ability to stick together or the interactions that stick them together are the same interactions that we just saw favoring tertiary structure but they would be between two polypeptides so these would be intermolecular ionic bonds inter molecular disulfide bonds intermolecular hydrogen bonds and intermolecular london spurgeon force interactions unlike the tertiary structure would be which would be intramolecular interactions if you look at the overview on the bottom you'll see each of these layers of protein structure on the right you'll see the primary structure which is the order of amino acids as you can see these amino acids are connected together by this line that line is indicating a peptide bond so peptide bonds hold amino acids together in the primary structure they are the force that stabilizes primary structure as we begin folding up those amino acids into secondary structures we can begin forming alpha helix or beta pleated sheet structures and the interactions that hold those together would be hydrogen bonds and in this particular case the hydrogen bonds are between main chain atoms and that's different than tertiary and quaternary structure where the hydrogen bonds or other interactions are holding together by r group r group interactions as we move and we begin folding up these secondary structures we can begin creating tertiary structure so you can see this alpha helix is just a small segment of the overall tertiary structure we could have alpha helix here or here or here and we begin folding these up into this glob and these r groups would begin sticking out away from the helix and we we could begin positioning our grip this direction and an argument from this maybe alpha helix could be sticking down here and we could form a favorable attraction between these two r groups in an intramolecular sense again they could be ionic hydrogen bond disulfide bond or london dispersion force interactions depending on the type of amino acids that we have and then as we move to this quaternary structure where we have multiple polypeptides you can see in this particular protein we have these two yellow or orangish type polypeptides and these two red or pinkish polypeptides in the background and these are all held together by r-group r group interactions the same type of interactions ionic attractions hydrogen bonds disulfide bonds or london dispersion force interactions and this is the structure on the one on the right is the structure of hemoglobin hemoglobin is formed from four different polypeptides and you can see this structure in here is representing the heme and this red sphere is representing the iron that is going to be bonding to the oxygen and carrying that oxygen through our blood now that we have an idea of protein structure we need to talk about a couple of chemical properties of the protein structure the first chemical property we want to talk about is protein denaturation proteins and polypeptides can be denatured or unfolded so those words can be used interchangeably denatured is another word for unfolded to denature a protein you need to disrupt the secondary tertiary and quaternary structure but you need to leave the primary structure intact which means we can't be breaking the peptide bonds or we would be doing more than protein denaturation denaturation is just unfolding it's not hydrolyzing the peptide bonds alright so in this particular case protein denature is denaturation is disruption of secondary tertiary quaternary structure when do we decide that it is denatured so if you look at this particular process you see a protein up in the top left of this image as folded protein and as we begin denaturing so this denature event represents the kind of this reaction arrow here into something that is unfolded we have a denatured protein so this would be native or natively folded natured prot naturally naturally found protein fold and then as we unfold it we get an unfolded or denatured protein and then in some cases that protein can be refolded or re renatured into a native form or structure of the protein that we might find in the body now the protein does not have to be completely unfolded like this the definition of denatured is a loss of structure that results in loss of the protein's function so it doesn't require a great deal of structural compromise as long as the protein's function is lost we define that as the protein is denatured one of the main mechanisms or one of the main ways that you might see or recognize protein denaturation is when you cook an egg so if you crack an egg instead of scrambling if you just crack an egg and you have that egg white you can see it's fairly clear translucent in many cases you can see right through it as you begin cooking that egg white which is very protein the protein begins to denature and begins to unfold and then as it unfolds the r groups on the interior which are nonpolar begin to stick to other proteins that have non-polar r groups that are on the interior and it begins to aggregate and precipitate and form a thicker white egg white that is cooked that's a denatured protein the last part of this chapter we're going to be focused on one of the main functions of proteins in our body and that is their ability to catalyze chemical reactions as enzymes enzymes are biological catalysts used to speed up the rate of reactions and in most cases catalysts inside of our body are usually proteins and therefore they're usually enzymes we do have some instances where rna functions in a catalytic mechanism to speed up reactions but the vast majority of catalysts that we find are proteins or enzymes the reactant of an enzyme so begin because the enzyme functions to speed up chemical reactions that means we're going to convert reactants to products in this particular case the reactant of an enzyme is defined as the substrate most human enzymes function optimally at 37 degrees celsius in ph 7 approximately so that's what the little tilde symbol is right before the 7 that means approximately 7 or right around seven this shouldn't be too surprising because most of these enzymes are in cellular environments that have a ph of seven and are at 37 degrees what's kind of interesting is that the enzymes have folded up and have been perhaps designed in terms of amino acids and their order and in their arrangement to create a protein that is optimally functional at those temperatures and ph as we move to other cellular environments we find that other enzymes like perhaps those in the stomach like pepsin proteins that are designed to begin breaking down proteins in our digestive tract have been optimized to function optimally at lower ph's which we would normally find in our stomach most enzymes have common suffix names and those are ase endings a's for example sucrase is an enzyme that breaks down the dietary molecule sucrose which is table sugar in the di track many of these enzymes names have are common names they're not iupac they're not systematic so they've been named based usually on the substrate or the product or the type of chemistry that is catalyzed inside of that reaction or inside of the enzyme most enzymes though have that suffix of ase if we look at the general reaction for an enzyme we see that enzymes will bind to substrates and the place of binding or the location that an enzyme binds the substrate is defined as the active site this is the place where the chemistry will be happening and the catalysis will be occurring when the enzyme binds the substrate at the active site we form what is called the enzyme substrate complex and you can see it listed there as es and when this happens the enzyme is changing its shape it's changing its conformation around the substrate this is called an induced fit model and this optimally arranges the r groups at the active site to form fabric interactions and attractions to the substrate typically this will align bonds align functional groups to form a bond or maybe put stress on bonds to break a bond or position groups for transfer or allow r groups to be positioned optimally to do acid-base catalysis so all these r groups of the amino acid are are important for all of those things optimal alignment bond for bronze breakage or for bond creation positioning functional groups for transfer positioning r groups for acid-base catalysis all of those again are facilitated by this conformational change when we look at the structure of an enzyme and we look at the active site without the substrate what we find is that it doesn't really look like kind of the whole of the substrate it doesn't look like a substrate would fit in there because the enzyme is actually changing the conformation to adapt to and fit to that substrate once that substrate has been converted to a product we'll typically have an enzyme product complex and then the product will be released the enzyme will be free to bind another substrate one of the definitions of a catalyst is that it can't be changed during the chemical reaction so in this particular case once the reaction has been completed and the product is released the enzyme has to return to the original form that had been found when it bind the substrate at the beginning if we look at enzyme activity we find that enzyme activity depends on four different properties one is enzyme concentration the second is substrate concentration the third is temperature and the last one is ph if we look at the enzymes activity as a function of enzyme concentration what you'll see if you look at the graph on the top left is that as we increase enzyme concentration the rate of the reaction continues to go up if we keep adding more and more enzyme we can keep converting substrate to product at a faster rate why is that well if i have one enzyme that is converting one substrate to one product per minute and if i put two in there then i can produce two products per minute if i put five in there then i can produce five products a minute so as long as i have enough substrate and i keep adding more and more enzyme i can create more and more product per given unit of time so the rate of reaction goes up in contrast if i hold the enzyme concentration fixed and i begin increasing the amount of substrate concentration what you see is that the rate of the reaction goes up to a point at which point the enzyme is saturated and we reach a point where we can't increase the rate of reaction any further and we've reached a maximum rate or velocity at which we can convert substrate to product all right so in this particular case the reaction is dependent on substrate concentration if we increase the substrate concentration we can increase the rate of reaction but only to the point of saturation once the enzyme has bound up all the enzyme that is there has bound up substrate then all the other substrates have to wait until that substrate has been converted to product in the enzyme and then released before that enzyme can bind up another substrate in this particular case once we've reached the point of saturation the enzyme is working as fast as it can and can no longer increase the rate any further it can just continue producing product at its normal amount at its normal rate and again other substrates would have to wait until that substrate is converted to product in the enzyme if you look at the bottom left what we find is that most enzymes have an optimal temperature at which they function and so what you'll see is more of a belt type shaped curve or a parabola and you can see that in this particular case this particular enzyme has a maximum rate of reaction or conversion of substrate to product at a temperature that's right around 37 degrees if we increase the temperature a little bit the rate of the reaction drops off if we increase it too much most of the drop off this rate of reaction is associated with protein denaturation if we decrease the temperature of the enzyme what we end up finding is that the enzyme and the molecules in the atoms tend to move a lot slower and as a result the rate of reaction is decreasing as well again most enzymes have an optimal temperature at which they maximize their rate in addition to temperature we see a similar relationship between ph and enzyme activity most enzymes have been optimized to work at a specific ph in this particular example you can see this enzyme has the highest activity at ph 8 and as we increase the ph and become more basic or decrease the ph and become more acidic we see that the enzyme activity drops off and begins to convert substrate to product more slowly the final thing that we want to talk about with enzymes is that in many cases these enzymes cannot function with just the amino acids in the protein themselves in some cases they require other things to help them catalyze their reaction one of the things that some enzymes require are cofactors cofactors are metal ions for example zinc two plus is a metal ion or iron three plus magnesium two plus in other cases some enzymes require a cofactor that is a small organic molecule we will talk more about nad plus but nad plus is a small organic molecule that is used by some enzymes for oxidation reduction reactions if you look at the structure down below this this protein structure is a protein structure of alcohol dehydrogenase you can see that we have alpha helices by the little spiraling amino acid sequence you can also see that we have beta strands kind of represented by these arrow structures and you can see that these flat arrow structures are aligning right next to each other to form a beta sheet type structure in addition to those you can see that this particular protein enzyme called alcohol dehydrogenase requires both metal ions and small organic molecules the metal ions are shown as these gray spheres you can see there are two gray spheres right here and right here and there's two gray spheres over here on this side these are zinc two plus so metal ions that are required for catalysis in addition you can see there's this green stick like structure this is an organic molecule small small organic molecule called nad plus you can see there's one there and one here and both of those are required by the enzyme to catalyze its reaction in this case the function of alcohol dehydrogenase is to break alcohol down to a different molecule an aldehyde all right these small organic molecules have another name they are called coenzymes they are functioning with the enzyme so co means with with the enzyme to mitigate or establish catalysis all of these coenzymes that we found to date are derived from water-soluble vitamins so water-soluble vitamins are converted by your body into coenzymes and those coenzymes then are converted to proteins your mother knew this when she told you to eat those costco gummy bears and your vitamins then would be incorporated into proteins and allow these proteins to be functional all right that's the last thing we're going to talk about in this particular chapter on amino acids proteins and enzymes