Enzymes and Enzymatic Processes

we're live hello everyone welcome back it is a gloomy gloomy evening a gloomy November evening it is cold it is gray but we're here and we're going to talk about chapter 2 in biochem enzymes and enzymatic processes right so when we talk about en also for the people watching back home make sure you check out the description for all the links to all of our lectures my notes which I'm uploading tonight and um everything else associated with this program so hope you enjoy when we talk about enzymes as parts of the body what do enzymes do what do enzymes do right so enzymes are what they're biological catalysts so instead of using catalysts like lead to speed up your reaction you're using proteins these are proteins that are specialized in catalyzing reactions right and when we talk about catalysts what is the main thing the catalysts do they lower what they lower the energy of activation of a reaction complex they don't affect Delta G they don't affect Delta H they don't affect Delta s they don't affect the the um equilibrium constant the one thing that they speed up is the rate of the reaction because the whole thing that we're getting at here is that if we have an uncatalyzed process and then we have a catalyze process you have a shorter Hill to climb right so that shorter Hill is climbed in a faster amount of time so this is the activation energy and this is the activation energy catalyzed and whenever we say catalyzed or catalytic it's parentheses c a right cat I went to a cat cafe today those cats were very cute enzymes are not so cute right so we have a couple classes of enzymes that we need to talk about right and the first class of enzymes we want to talk about are the oxido reductases or Oxo reductases right these catalyze what kinds of reactions yeah catalyze redo reactions and for each of these enzyme classes there's a specific group of names that we use for them so the names here include oxidase reductase and dehydrogenase for example when we talked about alcohol dehydrogenase we talked about how ethanol can be turned into an alahh right and we know that since we have more bonds to the oxygen that is a oxidation right so that's an oxidative process undertaken by the enzyme alcohol dehydrogenase which is a type of Oxo or oxido reductase enzyme right and a specific thing about this is that they usually have co-actors that help with the oxidations and reductions so what are those co-actors what in our bodies do we use for oxidations and reductions nad+ nadh fad fadh2 nadph or nadp plus and nadph let's copy that down one sec for all right so we have oxido reductases which we just talked about and now we're going to talk about other enzyme classes like transferases so what do you think transferases do yeah they'll transfer a group from one molecule to another so I'm just going to erase these co-actors get them out of the way and transferases take a group and transfer to another molecule I'm uh messaging my family because I'm supposed to meet them for dinner after this at a family friend's house but I forgot to text them because I was running late so if they blow up my phone the recording is going to stop that's what I'm worried about I usually put my phone on airplane mode but I forgot to and I don't want to restart the recording so we're going to gamble a little bit today all right so transferases usually have transfer in their name so stuff like imot transferase and K right so a ky why is a kise a type of transferase well what's the difference between a kise and a phosphor this is there you go right so the kinas a kinas is an enzyme that phosphorites using ATP or GTP or CTP or UTP or any of those triphosphates right so the reason it's a transferase is because you take the phosphate group and you transfer it from the ATP onto the target molecule right that's a kinas examples include hexokinase glucokinase etc etc eating Pringles hung you guys have gotten like more and more serious about this over time I've just like been in a downward spiral I'm like eating during the lecture so K is a type of transferase because it takes that phosphate group and transfer it onto another molecule a Target molecule right okay what's next hydroxylases right so these catalyze the breaking of a bond in a molecule via the addition of H2O breaks a bond with H2O right and the nomenclature depends on the substrate if you're breaking a phosphate it's a phosphatase if you're breaking a peptide bombed it's a peptidase if you're breaking a fat it's a lipase if you're breaking a sugar it's amas right I don't know and Elias is any en enzyme that Cleaves a substrate into multiple parts and if it catalyzes the reverse reaction which some enzymes do and they're named after the reverse reaction right it can also be called a synthes right lias and synthes lias are breaking synthes 4 bu exactly okay there's two more right let's erase some of these top ones so there's isomerases what are isomerases what do they do so these catalyze rearrangement of bonds within a molecule phosphoglucose isomerase turns glucose 6 phosphate into fructose 6 phosphate by moving around one of the bonds right because glucose right glucose and fructose are what isomers correct glucose and fructose are isomers just that thing moves and then if you put put a phosphate group on that sixth position right and then you put equilibrium arrows here and then you wrote p GI that's the function of phosphoglucose isomerase glucose 6 phosphate to fructose 6 phosphate and back this is what we call a reversible enzyme it it can catalyze the front and back reactions right they can go forward or backward and what determines whether it goes forwards or backwards well it depends on how much of each side you have right because there's obviously an equilibrium constant to that enzyme and if that equilibrium constant is thrown out of whack it'll go in One Direction or another and those are the basics of metabolism and equilibrium right that's a little zoom into the future right like we've been doing since the beginning and the last one they're called Li gases and I really like the way they describe this class these catalyze addition and synthesis reactions and the main thing they're trying to get at here is like DNA ligase right where you have the okazaki fragments in the um in the Strand that goes what's it called anti parallel or it's synthesizing the opposite dire something like that right so when you're synthesizing DNA you have to synthesize what in what direction what direction is DNA synthesis three prime to five Prime right or sorry isn't it five Prime to three prime I don't remember this 5 to three right 5 to three very basic biology I forget it all the time so you synthesize 5 to3 right but over here five is over here and three is over here and then your replication fork is here so when you make the okazaki fragments because you're going this way you need liase to fill in those spots so come and just fill in the little missing spots that's DNA and that's the addition or synthesis reaction they're talking about you guys remember that from like first year bio right stuff I forget all the time okay so they have a really really really funny dumb nemonic to remember the different classes of um enzymes Lil hot yeah it's like a rapper name right so it's liases isomerases liasis hydroxylases oxido reductases and transferases right right right right right right good okay let's talk about the two theories that we use to describe enzyme and substrate binding so basically the way that things happen is that you have a little enzyme and the enzyme bites down on a substrate right and then you get an enzyme substrate complex I know they don't look the same but they are hello guys pretend these two are the same right an enzyme substrate complex and then that's going to lead to enzyme and product so the enzyme is going to change the substrate somehow and turn it into the product in our case it's half shaded now instead of the full shading right so that's the product enzyme and product and notice that the enzyme is unchanged by the overall process and that is a characteristic that is common amongst catalysts they are unchanged they can be recovered from the end of the reaction there are two theories as to how this interaction happens number one is what I like to call the soulmate Theory but it's actually called the lock and key Theory why do I call it the soulmate Theory because they were built for one another right The Binding groove of the enzyme perfectly fits the substrate it is a perfect match when the enzyme is made when it's created and when it's cated for and when it folds that folding of the enzyme creates a perfect binding pocket for the substrate understood yeah um can someone please share the notes that we just took with them the classes of enzymes like whenever you guys get the chance when we take our break just make sure that they get it you didn't miss much you did miss me eating one Pringle I'm quite hungry today because I had brunch before and you guys did oh you missed the story my tire exploded on the highway here today that's why I was a little late then we have unfortunately I I would love to say that enzymes and substrates are soulmates but we have a more accepted Theory than this something that makes a little more sense does anyone know what that's called what's the name of that theory induced induced fit it's called the induced fit Theory right so the induced fit Theory implies that the enzyme substrate interaction causes The Binding Groove to change confirmation in a way I know that doesn't say confirmation hold on in a way that better binds the substrate the enzyme substrate interaction causes The Binding Groove to change confirmation in a way that better binds the substrate for okay is that good do you guys understand how that kind of works so let's say that this marker was the substrate right and my hand's kind of like this when the substrate this is the enzyme this is the substrate when the substrate comes near the enzyme it causes it to change confirmation in a way that is suitable for binding of the substrate so my hand closes in around the marker that's kind of how it works works right and how does that happen and why do we think this makes a little more sense well within the active site of the enzyme within the binding groove of the enzyme right we have intermolecular interactions that can take place that attract certain parts of the enzyme to certain parts of the substrate and attract certain parts of the substrate to certain parts of the enzyme and those intermolicular forces and interactions will obviously change the confirmation right will change the confirmation even the littlest bit so it's more believe this is a more believable Theory because of the fact that we know that intermolecular interactions play a very large part in enzyme activity right cool okay let's talk about co-actors so co-actors and co-enzymes are small molecules normally charged that bind the active site of the enzyme and when we say we they bind the active side are they the substrate no they're just helping out right they're helping out enzymes with their co-actor if they have one are called Hol enzymes and enzymes without their co-actor are called Appo enzymes so basically you have Appo enzyme and then you add a co-actor and now you have a Holo enzyme so co-actors and co-enzymes are small molecules which are normally charged that bind the active side of the enzyme right and important co-actors include like we talked about before nad+ nadh fad nadp+ stuff like that right but they also include vitamins vitamins are enzyme co-actors right right you'll find in many many many many places right like TPP is a really important co-actor to an enzyme but TPP is thamin pyrro phosphate what's thamin not thine but thamin what's thamin it's a vitamin B1 so vitamin B1 is basically the co-actor when you do TPP needam yeah we're about to go over it so since vitamins are enzyme co-actors what do we got to go over we got to go over vitamins right so we have fat soluble vitamins and the fat soluble vitamins everyone remembers this little acronym does anyone know it already anyone know the little pneumonic it's a deck a d e and K fat soluble vitamins and knowing that those are fat soluble brings up a really good point inside of uh medical knowledge the idea that if someone has a fat malabsorption problem right if they have a GI disorder which decreases their ability to absorb fats they may have a decrease in those vitamins because they're wasting them out of their body along with the fats right because when you ingest those vitamins they have to get uptaken with the fats because they're fat soluble so if you're not taking up the fats you're not taking up those vitamins either and then you get loss of those vitamins in your stool right you guys know the medical term for fatty stools it's like a Jeopardy word statera statera those are fat soluble vitamins why' I put them up there because that's pretty much all you got to know about them a d e and K those are fat soluble vitamins the water soluble vitamins we'll put a we'll put B over here on the right you got B and C so your vitamins that you need to know a b c d d e and K right we'll put B on the right side because I have more room but what I want you to do is take this and put it like to the right of your page so that you write B to the left and C to the right and you have a lot of space next to B because we're going to talk about all the different B vitamins all right I just didn't want to walk over okay so B vitamins are broken down into to different subsets or different types of B vitamins so we have B1 which we already said is thamin thamin thamin is really important in the formation of thamin pyrophosphate which is used in your body for if you know this fact it will score you a point on some MCAT some somewhere thond pyrophosphate is important for alpha decarbox alpha decarbox such as this is pyruvate in order to turn it into a settle COA you get rid of a CO2 and that CO2 is Alpha to a carboxilic acid group we saw in orgo how a beta decarbox works you just need the molecule for an alpha decarbox you need a catalyst so the enzyme pyruvate dehydrogenase has a TPP co-actor in order to help with that Alpha decarbox and the TPP co-actor is derived of vitamin B1 it also has an nad+ co-actor and that NAD plus co-actor we'll see is derived of vitamin B3 all right so thamin important for TPP do you need to know what they're important for probably not but it would help to recognize these terms when they come up B2 anyone know what it's called riboflavin what's that important to anyone know what fad stands for flaven adenine dinucleotide flaven ribo flaven this Celsius that I'm drinking it's got riboflavin nasin vitamin B6 vitam B12 penic acid and all of those are B vitamins oh and biotin but they don't write out the full names of some of the B vitamins because people would get scared like what's the full name of vitamin B6 pyxidatus fine all right B3 what is it anyone know anyone into skin care here anyone do a lot of skin care at home come on guys niin niin nasin which is an important part of nicotinamide which is an important part of nicotinamide addine dinucleotide nad+ is there a vitamin B4 there's not because it sounds too much like the word before B5 actually yeah D there's no vitamin B4 B5 anyone know Panic acid Panic acid how you going to remember that well pant sounds like pent and pent means five should you memorize these not necessarily will they help if you want to get like a 98 99 percentile score absolutely B6 pyxel phosphate you'll usually just see it written out as pyxine what's next is there a B7 yes there is B7 is good for your hair anyone know what it is biotin keratin a protein these are vitamins B9 really important for pregnant women H folic acid huh there's no B8 I don't know why I think it the way I think about it is that the eight looks too much like a b so it looks like BB folic acid and in the body it's not folic acid it's folate B12 has a 100 different names depending on where you look in the book it is five Prime deoxy adenos cobalamin five Prime deoxy adenos cobalamin but some people just call it cobalamin or cyano cobalamin if you ever see the word cobalamin you're good so you got thamin riboflavin nin Panic acid what would Panic acid be called if we were to refer to it as like the anion pant pantoate pyxine biotin folate and cobalamin vitamin B1 2 and three do pretty much everything vitamin B5 does everything vitamin B6 does literally everything B7 is good for hair um and it does a lot of stuff in the body as well B9 and b12 are really really really important for like protein metabolism and uh stuff like that and very important for pregnant women because B12 if you have a B12 deficiency while you're pregnant your baby's nervous system won't develop properly we don't know why that is but that's what happens and fetuses just love to eat up all of your folate that's what they do fetuses they just leech off of the mother's folate all right so those are your B vitamins okay good cool now it's time for the hard part of the chapter not only hard to learn but hard to teach who knows what we're talking about next huh enzyme kinetics you know it's bad when I clear the whole board and start up there so enzyme kinetics Des describe the effect of increases or decreases in the concentration of enzyme and the concentration of substrate on the velocity of the reaction enzyme kinetics describe the effects of increases or decreases in the concentration of enzyme and or the con concentration of substrate on the velocity of the reaction two things to remember number one an increase in the substrate concentration will increase velocity until until what until not equilibrium until VX Max is reached what is Vmax it's the maximum velocity as determined by every single enzyme is binding changing and spitting out product as quickly as possible right that whole process this whole process that whole process is just kicking just every single enzyme is saturated every single one is going you can't accommodate a single other substrate right so after that point at V Max it doesn't matter how much substrate you throw in there it's not going to be any faster right how many of us in this room today two four six eight 10 right there's 10 of us in the room right now not including me right I give each of you guys a Rubik's Cube and I'm like solve this solve this solve this solve this and let's say all of you guys can solve it in 3 minutes right if I take an 11th Rubik's Cube and throw it in the middle of the table are any of you guys going to pick it up no not until you've solved the ones you're already holding so it doesn't matter like how many solve Rubik cues do I want to throw out I'll only produce 10 every 3 minutes that's my maximum velocity right it can't get any quicker than that right but let's say that that three minutes is an average across everyone you can do it in four and you can do it in two right so if I throw you one and you do it in four the velocity the the thing is now one Rubik Cube every 4 minutes if I throw him one now it's average out to three but I'm getting two of them right so you guys see how this kind of works but it goes and goes and goes and goes until I get to the maximum velocity of 10 solved Rubik's Cubes every 3 minutes right that's the maximum veloc there's nothing I can do to change that unless I do what I start solving that because let's say that I can solve it in 2 minutes and 59 seconds just one second faster than the average so now if you were to average everything together it's just slightly faster than three minutes right the tiniest bit but it's faster right so that's the only way that you can increase Vmax so what are you guys if the Rubik cubes are substrates you guys are enzymes right and what am I when I come in and start doing the reaction I just added more enzyme I added more enzyme into the equation so the only way to increase V Max is to increase what the concentration of the enzyme do you guys understand that who knows what the curve looks like it's a sideways Parabola or I think this is like called hyperbolic I think it's called hyperbolic curve I don't know it's been a long time since I've taken mathematics H not like that it's more like I think it like starts a little steeper that's a little better so when that line flattens out on the velocity axis what is that velocity it's Vmax right Vmax so that guy is Vmax Vmax which would make this roughly here 12 of Vmax why is that important my biochm people what is one 12 Vmax or better yet what do we call the substrate concentration where we reach one half Vmax km km lowercase km km is defined very simply but it's a very difficult concept to understand this is the concentration of substrate at which half of all enzymes are bound therefore V equal V Max over two that is the quintessential definition of KM you guys got that yeah that is called the michis Menon constant right I believe I think if I'm not stupid stupid and there's a whole derivation of how to get there but we're not going to do that because I frankly even after Professor malitzky taught it for two hours I never understood it right but I also tried again and again and again but it's just not helpful for the MCAT I'll tell you everything you need to know know about km and that should be enough to go about your day right but before we do anything about why km how km how do I understand it let's understand some very basic fundamental details about what km tells us if I have an enzyme E1 and E2 right orgo people are quaking in their boots right now right E1 and E2 and E1 has a high km and E2 has a low km which enzyme is better at its job we got one vote for e22 two votes someone changed their vote we got two votes for E1 anyone KIRO Sarah E2 two votes for You2 three votes for You2 anyone three votes for E1 tied you guys want to know what I think it is I think it's E2 why why is a low km better because that means you need less substrate to get to an achievable Vmax right so let's think about this right I want to make rubber bands right and the people who are making me rubber bands are split into two groups one of them doesn't even know what a rubber band is right and the other group have been the pioneers of rubber band making technology for the past 7,000 years right I'm unbelievable at rubber band manufacturing right if I wanted to make 30 of them every minute right to get to half that velocity it's going to take the idiots 900 years to figure it out and it's going to take these guys two seconds right so the number of people they'll need to employ to do so so maybe one person out of that and 100 people from that group The the stupid group who don't know how to make rubber bands right so in order to get to half that maximum velocity how many people do we need and the less people we need the better because that means when we have a lot of people they're going to get to Vmax quick super quick stupid quick and if we get to Vmax quick the reaction's Done Quick and the substr are turned over quick and the prodcts are made quick so more substrate can be turned into more product in less amount of time yes good do do I have like eyes growing out of the back of my head you guys are looking at me like I'm crazy yeah it makes sense the km tells you nothing about the VMAX if km is KM tells you nothing about the Vmax why not I want you to answer me why doesn't the km tell you anything about the V-Max reread this really carefully if I just feed you everything you're never going to learn anyone anyone can answer the question km is the concentration of substrate at which half of all enzymes are bound therefore at the substrate concentration km V equals V Max over 2 why doesn't km tell you anything about Vmax based on subr conc exactly exactly and the Vmax is based on what the enzyme concentration km is based on the substrate and Vmax is based on the enzyme this is a this is a number a arbitrary term that says if we were to get to half of whatever the Vmax is whatever it is if we want to get to half that how much substrate do we need we don't know what it is the molecule is not smart enough to know what it is the molecule doesn't have a brain you do right you can look at the graph and figure out where one half Vmax is and figure out what the subst concentration blah blah you can you can do all that molecule doesn't know what the going on l that is absolutely correct that he said that low km is high Affinity also guys we are not meeting on Thursday it's Thanksgiving try your best to come on Tuesday I have a surprise for you you know what the surprise is it's a test it's a test pop quiz it's it's an entire MK okay guys wait but I do have on that note I do have like slightly bad news for you I would like all of you to take a diagnostic exam over your break and come back to me and tell you how tell me how you did yeah Diagnostics are like half half take a half length diagnostic not a full I don't I don't think you guys are like mentally prepared for a full yet I I wasn't you're not supposed to be are theree ones on yes there are yes there are they're all they're all equally even the full length all equally anything except for am is garbage people come to me they're like oh my God I got like a 498 blueprint I was like yo next week wake up take an AMC exam they get like 14 points higher I'm just like yeah like CU because here's the thing and let me go on my little rant and then we'll move on those testing uh programs how do they make money they make money if you do bad that's how they make money because if you do well you're not going to sign up and buy more of their so when you take their free exam and they tell you oh my god look you did by our program you're going to do it cuz you're like oh my God I did such but when the people who make the exam who make enough money by people signing up for the exam and paying $270 dollars every time they sign up and they're the people who control the USMLE and they're the people who control all the shelf exams and they're the people who control all the nbme and they're the people who control residency applications and medical school you think they give a about making a little bit of money off of you people no so they're genuinely going to tell you the truth because if they don't tell you the truth then it's going to Bar you from applying to medical school and that's where they make most of their money right so they give you the truth everyone else is lying to you they're going to tell you that you did worse than you actually did what's the highest I ever scored on a blueprint test 506 what did I get on my real MCAT a 521 I took two blueprint tests and then abandoned them that was dumb it was no all right so do you guys understand this do you want to run through it one more time yeah okay so basically what we're saying is that enzyme kinetics are the study of concentration of enzymes and concentration of substrate in a specific reaction vessel right the velocity of the equation of the reaction will increase as the substrate concentration increases up to a certain point that certain point is Vmax when all of the enzymes are saturated with substrate right and Vmax can only be increased by increasing the number of enzymes because then you have more enzymes doing more work which is more people solving more Rubik's cubes and more solved Rubik cubes are going out the back door right okay we have this little equation notice that the formation of I think I up before when I wrote this out for the first time the formation of product is a forward reaction right not always but in this case it's a forward reaction right when is it not like a forward reaction when you have reversible processes like a lot of the steps of glycolysis most of the steps of glycolysis are reversible processes anyone know the three steps of glycolysis that are not reversible processes hexokinase pfk1 and pyy and those are the steps you have to overcome when you do gluconeogenesis hexo we'll go over it but hexokinase pfk1 and pyy those are the irreversible enzymes of glycolysis all the rest of the enzymes of glycolysis catalyze the forward and reverse reactions right now we looked at this graph we looked at Vmax and went to one half of Vmax and we went to the substrate concentration at one half of Vmax which is now colloquially known as km it is the substrate concentration at which 1 half of all of the enzymes in the reaction vessel are bound and Performing the reaction action the lower the km the better the enzyme the better the Affinity right we want a low km High km is bad right okay let's talk about the michis Menon equation right we'll leave that definition up and we'll leave this graph up as well and we'll put some important facts over on the side there in my favorite color that a low km means higher Affinity if David had not said that I probably would have forgotten to put that on the board so thank you that's a very very good way of thinking about it and it's probably the way you should think about it the michaus men equation describes how the rate of a reaction velocity depends upon substrate concentration and enzyme concentration this is when it starts to get difficult all right so here's our little equation what is es it's the enzyme substrate complex right if you were to say the rate of these forward and backwards reactions this would be K1 little K right the rate am I illiterate K1 don't answer that K negative 1 and kkat K cat meaning the rate of catalysis catalyzing the formation of the product right if enzyme concentration is constant then V equals V Max s over km + S so K cat right there is defined as the number of substrate molecules turned over what do we mean by turned over catalized into the product right turned over per enzyme molecule per second number of substrate molecules turned over per enzyme molecule per second right so in one second how many substrate molecules are turned into product per enzyme so it's it's a zoom into one enzyme and one second and how many substrate molecules does it make you think not that many right because it's just one second but you have to remember these are very very very Lightning Fast processes right okay one more thing you have to know to go along with this is that Vmax equals the concentration of the enzyme time k cat cuz remember Vmax is dependent on the concentration of the enzyme how do people derive these I don't remember I learned at one point but I don't remember and if we have that and we have that then we can combine those two equations and write out a velocity equation and that velocity equation it's pretty important anyone see my red marker there it is I was uh rock climbing with a buddy yesterday and um we were we were at Cliffs at ganis and um he's I'm like a beginner so he's teaching me how to rock climb and I was like oh where do I start like over by the green he's like yeah by the red and I was like what and he he's like the red and I was like oh all right so V equals if we put this in for VMax we get K cat e s over km + S and can you guys imagine that if k m was way greater than the concentration of substrate right if it was far far greater than the concentration of substrate then this would happen V equals kkat over km * e * s that's the takeaway that the that the velocity when when the substrate concentration is low right when the substrate concentration is low because what is KM is the substr concentration at which half of all the enzymes are bound right what we're asking here is how do we increase that velocity how does it change so when we keep the subst concentration low the velocity is now contingent upon kcat over km which we're going to describe in one second the concentration of the enzyme and the concentration of the substrate what did we say enzyme kinetics were the effect of increases or decreases in the enzyme concentration substra concentration on velocity of the reaction that's your equation that's it km is basically the overall rate of this reaction right so along with being that it's also defined as a rate sorry all the way around I knew something was right there K cat plus K1 over K1 so what does that tell you look at this what are the things that increase km K cat going this way and K1 going that way things that move away from the enzyme substrate complex right and things that move towards the enzyme sub complex will decrease km so what does that tell you about km it kind of determines the amount of es that you have at any given time and that makes sense because half of all enzymes are bound not bound not not actively producing product but bound so if the enzyme is bound it makes the enzyme substrate complex so things that usher in more formation of the enzyme substrate complex will decrease there sorry increase the km things that get rid of the enzyme substrate complex will increase sorry yeah other way around I had right the first time see how confusing this is things that increase the amount of enzyme substrate complex will decrease the km things that decrease the amount of enzyme substr complex will increase the km it's a little reverse of what you would think right but that's going to become important when we talk about inhibition right and different types of inhibition and what they do to km because there's a km a true km and an apparent km right and we have talk about that a little bit later one more thing one more important thing that I need to fit somewhere on this board K cat over km which is seen right here is also known as the catalytic efficiency kkat over km is also known as the catalytic efficiency right and it's a way of judging how good an enzyme is at its job at its overall job right because what was Kat again Kat is the number of substrate molecules turned over per enzyme molecule per second and km is the Affinity right how much it wants to bind the substrate right or the tendency for it to fall apart both of those taken into consideration so when you do this divided by the km you'll get a general efficiency of the enzyme and that's how we rank enzymes in terms of how good they are at their job so there will be not just on one or two or three on possibly every single MCAT that you ever take practice or not real thing anything if you guys turn out to be tutors eventually which I hope some of you do right every single question every single bio and people who take practice exams already like when if you're testing in January let me know if this is true in every single biocham section you do there will be a question about km Kat and Catal efficiency every single one every single goddamn one this is the highest yield chapter in all of biocham in my opinion High K cat is good because it's more molecules turned over per enzyme per second low km is good because it's basically a representation of dissociation right which is why we want a lower representation of dissociation so sometimes biochemists will will teach you Professor malitzky taught me this because he is a biochemist right he has a masters in Biochemistry he taught me think of KM almost like KD dissociation dissociation constants right so imagine that a higher km more of is dissociating it's going away which makes sense because a higher km means higher K cat and higher K1 away from es this is what you want that's what you get do you guys follow what's on the board okay let's say that I gave you an hour to solve a couple math problems right and enough for you to do in an hour or maybe you solve one math problem an hour something like that right if you are one person one enzyme and I look at how many math problems you solved in one hour and there's 20 you solve 20 of them versus one of them isn't 20 better because you do more so if we zoom in on one enzyme and we look at that one enzyme for one second how many substrate molecules has it turned over if it turns 20 substrate molecules into product that's good if it only does one that's bad that's what Kat is you're zooming in you're looking how many substrate molecules do you turn over each second as one enzyme my imagine small good because as a fraction make it lar that's all you need to know okay that's it that's absolutely true and the fact that if km is low that means that you have a lower substrate concentration at which you reach half Vmax right we'll do the rest of the chapter in part two thank you for watching

we&#39;re live hello everyone welcome back it is a gloomy gloomy evening a gloomy November evening it is cold it is gray but we&#39;re here and we&#39;re going to talk about chapter 2 in biochem enzymes and enzymatic processes right so when we talk about en also for the people watching back home make sure you check out the description for all the links to all of our lectures my notes which I&#39;m uploading tonight and um everything else associated with this program so hope you enjoy when we talk about enzymes as parts of the body what do enzymes do what do enzymes do right so enzymes are what they&#39;re biological catalysts so instead of using catalysts like lead to speed up your reaction you&#39;re using proteins these are proteins that are specialized in catalyzing reactions right and when we talk about catalysts what is the main thing the catalysts do they lower what they lower the energy of activation of a reaction complex they don&#39;t affect Delta G they don&#39;t affect Delta H they don&#39;t affect Delta s they don&#39;t affect the the um equilibrium constant the one thing that they speed up is the rate of the reaction because the whole thing that we&#39;re getting at here is that if we have an uncatalyzed process and then we have a catalyze process you have a shorter Hill to climb right so that shorter Hill is climbed in a faster amount of time so this is the activation energy and this is the activation energy catalyzed and whenever we say catalyzed or catalytic it&#39;s parentheses c a right cat I went to a cat cafe today those cats were very cute enzymes are not so cute right so we have a couple classes of enzymes that we need to talk about right and the first class of enzymes we want to talk about are the oxido reductases or Oxo reductases right these catalyze what kinds of reactions yeah catalyze redo reactions and for each of these enzyme classes there&#39;s a specific group of names that we use for them so the names here include oxidase reductase and dehydrogenase for example when we talked about alcohol dehydrogenase we talked about how ethanol can be turned into an alahh right and we know that since we have more bonds to the oxygen that is a oxidation right so that&#39;s an oxidative process undertaken by the enzyme alcohol dehydrogenase which is a type of Oxo or oxido reductase enzyme right and a specific thing about this is that they usually have co-actors that help with the oxidations and reductions so what are those co-actors what in our bodies do we use for oxidations and reductions nad+ nadh fad fadh2 nadph or nadp plus and nadph let&#39;s copy that down one sec for all right so we have oxido reductases which we just talked about and now we&#39;re going to talk about other enzyme classes like transferases so what do you think transferases do yeah they&#39;ll transfer a group from one molecule to another so I&#39;m just going to erase these co-actors get them out of the way and transferases take a group and transfer to another molecule I&#39;m uh messaging my family because I&#39;m supposed to meet them for dinner after this at a family friend&#39;s house but I forgot to text them because I was running late so if they blow up my phone the recording is going to stop that&#39;s what I&#39;m worried about I usually put my phone on airplane mode but I forgot to and I don&#39;t want to restart the recording so we&#39;re going to gamble a little bit today all right so transferases usually have transfer in their name so stuff like imot transferase and K right so a ky why is a kise a type of transferase well what&#39;s the difference between a kise and a phosphor this is there you go right so the kinas a kinas is an enzyme that phosphorites using ATP or GTP or CTP or UTP or any of those triphosphates right so the reason it&#39;s a transferase is because you take the phosphate group and you transfer it from the ATP onto the target molecule right that&#39;s a kinas examples include hexokinase glucokinase etc etc eating Pringles hung you guys have gotten like more and more serious about this over time I&#39;ve just like been in a downward spiral I&#39;m like eating during the lecture so K is a type of transferase because it takes that phosphate group and transfer it onto another molecule a Target molecule right okay what&#39;s next hydroxylases right so these catalyze the breaking of a bond in a molecule via the addition of H2O breaks a bond with H2O right and the nomenclature depends on the substrate if you&#39;re breaking a phosphate it&#39;s a phosphatase if you&#39;re breaking a peptide bombed it&#39;s a peptidase if you&#39;re breaking a fat it&#39;s a lipase if you&#39;re breaking a sugar it&#39;s amas right I don&#39;t know and Elias is any en enzyme that Cleaves a substrate into multiple parts and if it catalyzes the reverse reaction which some enzymes do and they&#39;re named after the reverse reaction right it can also be called a synthes right lias and synthes lias are breaking synthes 4 bu exactly okay there&#39;s two more right let&#39;s erase some of these top ones so there&#39;s isomerases what are isomerases what do they do so these catalyze rearrangement of bonds within a molecule phosphoglucose isomerase turns glucose 6 phosphate into fructose 6 phosphate by moving around one of the bonds right because glucose right glucose and fructose are what isomers correct glucose and fructose are isomers just that thing moves and then if you put put a phosphate group on that sixth position right and then you put equilibrium arrows here and then you wrote p GI that&#39;s the function of phosphoglucose isomerase glucose 6 phosphate to fructose 6 phosphate and back this is what we call a reversible enzyme it it can catalyze the front and back reactions right they can go forward or backward and what determines whether it goes forwards or backwards well it depends on how much of each side you have right because there&#39;s obviously an equilibrium constant to that enzyme and if that equilibrium constant is thrown out of whack it&#39;ll go in One Direction or another and those are the basics of metabolism and equilibrium right that&#39;s a little zoom into the future right like we&#39;ve been doing since the beginning and the last one they&#39;re called Li gases and I really like the way they describe this class these catalyze addition and synthesis reactions and the main thing they&#39;re trying to get at here is like DNA ligase right where you have the okazaki fragments in the um in the Strand that goes what&#39;s it called anti parallel or it&#39;s synthesizing the opposite dire something like that right so when you&#39;re synthesizing DNA you have to synthesize what in what direction what direction is DNA synthesis three prime to five Prime right or sorry isn&#39;t it five Prime to three prime I don&#39;t remember this 5 to three right 5 to three very basic biology I forget it all the time so you synthesize 5 to3 right but over here five is over here and three is over here and then your replication fork is here so when you make the okazaki fragments because you&#39;re going this way you need liase to fill in those spots so come and just fill in the little missing spots that&#39;s DNA and that&#39;s the addition or synthesis reaction they&#39;re talking about you guys remember that from like first year bio right stuff I forget all the time okay so they have a really really really funny dumb nemonic to remember the different classes of um enzymes Lil hot yeah it&#39;s like a rapper name right so it&#39;s liases isomerases liasis hydroxylases oxido reductases and transferases right right right right right right good okay let&#39;s talk about the two theories that we use to describe enzyme and substrate binding so basically the way that things happen is that you have a little enzyme and the enzyme bites down on a substrate right and then you get an enzyme substrate complex I know they don&#39;t look the same but they are hello guys pretend these two are the same right an enzyme substrate complex and then that&#39;s going to lead to enzyme and product so the enzyme is going to change the substrate somehow and turn it into the product in our case it&#39;s half shaded now instead of the full shading right so that&#39;s the product enzyme and product and notice that the enzyme is unchanged by the overall process and that is a characteristic that is common amongst catalysts they are unchanged they can be recovered from the end of the reaction there are two theories as to how this interaction happens number one is what I like to call the soulmate Theory but it&#39;s actually called the lock and key Theory why do I call it the soulmate Theory because they were built for one another right The Binding groove of the enzyme perfectly fits the substrate it is a perfect match when the enzyme is made when it&#39;s created and when it&#39;s cated for and when it folds that folding of the enzyme creates a perfect binding pocket for the substrate understood yeah um can someone please share the notes that we just took with them the classes of enzymes like whenever you guys get the chance when we take our break just make sure that they get it you didn&#39;t miss much you did miss me eating one Pringle I&#39;m quite hungry today because I had brunch before and you guys did oh you missed the story my tire exploded on the highway here today that&#39;s why I was a little late then we have unfortunately I I would love to say that enzymes and substrates are soulmates but we have a more accepted Theory than this something that makes a little more sense does anyone know what that&#39;s called what&#39;s the name of that theory induced induced fit it&#39;s called the induced fit Theory right so the induced fit Theory implies that the enzyme substrate interaction causes The Binding Groove to change confirmation in a way I know that doesn&#39;t say confirmation hold on in a way that better binds the substrate the enzyme substrate interaction causes The Binding Groove to change confirmation in a way that better binds the substrate for okay is that good do you guys understand how that kind of works so let&#39;s say that this marker was the substrate right and my hand&#39;s kind of like this when the substrate this is the enzyme this is the substrate when the substrate comes near the enzyme it causes it to change confirmation in a way that is suitable for binding of the substrate so my hand closes in around the marker that&#39;s kind of how it works works right and how does that happen and why do we think this makes a little more sense well within the active site of the enzyme within the binding groove of the enzyme right we have intermolecular interactions that can take place that attract certain parts of the enzyme to certain parts of the substrate and attract certain parts of the substrate to certain parts of the enzyme and those intermolicular forces and interactions will obviously change the confirmation right will change the confirmation even the littlest bit so it&#39;s more believe this is a more believable Theory because of the fact that we know that intermolecular interactions play a very large part in enzyme activity right cool okay let&#39;s talk about co-actors so co-actors and co-enzymes are small molecules normally charged that bind the active site of the enzyme and when we say we they bind the active side are they the substrate no they&#39;re just helping out right they&#39;re helping out enzymes with their co-actor if they have one are called Hol enzymes and enzymes without their co-actor are called Appo enzymes so basically you have Appo enzyme and then you add a co-actor and now you have a Holo enzyme so co-actors and co-enzymes are small molecules which are normally charged that bind the active side of the enzyme right and important co-actors include like we talked about before nad+ nadh fad nadp+ stuff like that right but they also include vitamins vitamins are enzyme co-actors right right you&#39;ll find in many many many many places right like TPP is a really important co-actor to an enzyme but TPP is thamin pyrro phosphate what&#39;s thamin not thine but thamin what&#39;s thamin it&#39;s a vitamin B1 so vitamin B1 is basically the co-actor when you do TPP needam yeah we&#39;re about to go over it so since vitamins are enzyme co-actors what do we got to go over we got to go over vitamins right so we have fat soluble vitamins and the fat soluble vitamins everyone remembers this little acronym does anyone know it already anyone know the little pneumonic it&#39;s a deck a d e and K fat soluble vitamins and knowing that those are fat soluble brings up a really good point inside of uh medical knowledge the idea that if someone has a fat malabsorption problem right if they have a GI disorder which decreases their ability to absorb fats they may have a decrease in those vitamins because they&#39;re wasting them out of their body along with the fats right because when you ingest those vitamins they have to get uptaken with the fats because they&#39;re fat soluble so if you&#39;re not taking up the fats you&#39;re not taking up those vitamins either and then you get loss of those vitamins in your stool right you guys know the medical term for fatty stools it&#39;s like a Jeopardy word statera statera those are fat soluble vitamins why&#39; I put them up there because that&#39;s pretty much all you got to know about them a d e and K those are fat soluble vitamins the water soluble vitamins we&#39;ll put a we&#39;ll put B over here on the right you got B and C so your vitamins that you need to know a b c d d e and K right we&#39;ll put B on the right side because I have more room but what I want you to do is take this and put it like to the right of your page so that you write B to the left and C to the right and you have a lot of space next to B because we&#39;re going to talk about all the different B vitamins all right I just didn&#39;t want to walk over okay so B vitamins are broken down into to different subsets or different types of B vitamins so we have B1 which we already said is thamin thamin thamin is really important in the formation of thamin pyrophosphate which is used in your body for if you know this fact it will score you a point on some MCAT some somewhere thond pyrophosphate is important for alpha decarbox alpha decarbox such as this is pyruvate in order to turn it into a settle COA you get rid of a CO2 and that CO2 is Alpha to a carboxilic acid group we saw in orgo how a beta decarbox works you just need the molecule for an alpha decarbox you need a catalyst so the enzyme pyruvate dehydrogenase has a TPP co-actor in order to help with that Alpha decarbox and the TPP co-actor is derived of vitamin B1 it also has an nad+ co-actor and that NAD plus co-actor we&#39;ll see is derived of vitamin B3 all right so thamin important for TPP do you need to know what they&#39;re important for probably not but it would help to recognize these terms when they come up B2 anyone know what it&#39;s called riboflavin what&#39;s that important to anyone know what fad stands for flaven adenine dinucleotide flaven ribo flaven this Celsius that I&#39;m drinking it&#39;s got riboflavin nasin vitamin B6 vitam B12 penic acid and all of those are B vitamins oh and biotin but they don&#39;t write out the full names of some of the B vitamins because people would get scared like what&#39;s the full name of vitamin B6 pyxidatus fine all right B3 what is it anyone know anyone into skin care here anyone do a lot of skin care at home come on guys niin niin nasin which is an important part of nicotinamide which is an important part of nicotinamide addine dinucleotide nad+ is there a vitamin B4 there&#39;s not because it sounds too much like the word before B5 actually yeah D there&#39;s no vitamin B4 B5 anyone know Panic acid Panic acid how you going to remember that well pant sounds like pent and pent means five should you memorize these not necessarily will they help if you want to get like a 98 99 percentile score absolutely B6 pyxel phosphate you&#39;ll usually just see it written out as pyxine what&#39;s next is there a B7 yes there is B7 is good for your hair anyone know what it is biotin keratin a protein these are vitamins B9 really important for pregnant women H folic acid huh there&#39;s no B8 I don&#39;t know why I think it the way I think about it is that the eight looks too much like a b so it looks like BB folic acid and in the body it&#39;s not folic acid it&#39;s folate B12 has a 100 different names depending on where you look in the book it is five Prime deoxy adenos cobalamin five Prime deoxy adenos cobalamin but some people just call it cobalamin or cyano cobalamin if you ever see the word cobalamin you&#39;re good so you got thamin riboflavin nin Panic acid what would Panic acid be called if we were to refer to it as like the anion pant pantoate pyxine biotin folate and cobalamin vitamin B1 2 and three do pretty much everything vitamin B5 does everything vitamin B6 does literally everything B7 is good for hair um and it does a lot of stuff in the body as well B9 and b12 are really really really important for like protein metabolism and uh stuff like that and very important for pregnant women because B12 if you have a B12 deficiency while you&#39;re pregnant your baby&#39;s nervous system won&#39;t develop properly we don&#39;t know why that is but that&#39;s what happens and fetuses just love to eat up all of your folate that&#39;s what they do fetuses they just leech off of the mother&#39;s folate all right so those are your B vitamins okay good cool now it&#39;s time for the hard part of the chapter not only hard to learn but hard to teach who knows what we&#39;re talking about next huh enzyme kinetics you know it&#39;s bad when I clear the whole board and start up there so enzyme kinetics Des describe the effect of increases or decreases in the concentration of enzyme and the concentration of substrate on the velocity of the reaction enzyme kinetics describe the effects of increases or decreases in the concentration of enzyme and or the con concentration of substrate on the velocity of the reaction two things to remember number one an increase in the substrate concentration will increase velocity until until what until not equilibrium until VX Max is reached what is Vmax it&#39;s the maximum velocity as determined by every single enzyme is binding changing and spitting out product as quickly as possible right that whole process this whole process that whole process is just kicking just every single enzyme is saturated every single one is going you can&#39;t accommodate a single other substrate right so after that point at V Max it doesn&#39;t matter how much substrate you throw in there it&#39;s not going to be any faster right how many of us in this room today two four six eight 10 right there&#39;s 10 of us in the room right now not including me right I give each of you guys a Rubik&#39;s Cube and I&#39;m like solve this solve this solve this solve this and let&#39;s say all of you guys can solve it in 3 minutes right if I take an 11th Rubik&#39;s Cube and throw it in the middle of the table are any of you guys going to pick it up no not until you&#39;ve solved the ones you&#39;re already holding so it doesn&#39;t matter like how many solve Rubik cues do I want to throw out I&#39;ll only produce 10 every 3 minutes that&#39;s my maximum velocity right it can&#39;t get any quicker than that right but let&#39;s say that that three minutes is an average across everyone you can do it in four and you can do it in two right so if I throw you one and you do it in four the velocity the the thing is now one Rubik Cube every 4 minutes if I throw him one now it&#39;s average out to three but I&#39;m getting two of them right so you guys see how this kind of works but it goes and goes and goes and goes until I get to the maximum velocity of 10 solved Rubik&#39;s Cubes every 3 minutes right that&#39;s the maximum veloc there&#39;s nothing I can do to change that unless I do what I start solving that because let&#39;s say that I can solve it in 2 minutes and 59 seconds just one second faster than the average so now if you were to average everything together it&#39;s just slightly faster than three minutes right the tiniest bit but it&#39;s faster right so that&#39;s the only way that you can increase Vmax so what are you guys if the Rubik cubes are substrates you guys are enzymes right and what am I when I come in and start doing the reaction I just added more enzyme I added more enzyme into the equation so the only way to increase V Max is to increase what the concentration of the enzyme do you guys understand that who knows what the curve looks like it&#39;s a sideways Parabola or I think this is like called hyperbolic I think it&#39;s called hyperbolic curve I don&#39;t know it&#39;s been a long time since I&#39;ve taken mathematics H not like that it&#39;s more like I think it like starts a little steeper that&#39;s a little better so when that line flattens out on the velocity axis what is that velocity it&#39;s Vmax right Vmax so that guy is Vmax Vmax which would make this roughly here 12 of Vmax why is that important my biochm people what is one 12 Vmax or better yet what do we call the substrate concentration where we reach one half Vmax km km lowercase km km is defined very simply but it&#39;s a very difficult concept to understand this is the concentration of substrate at which half of all enzymes are bound therefore V equal V Max over two that is the quintessential definition of KM you guys got that yeah that is called the michis Menon constant right I believe I think if I&#39;m not stupid stupid and there&#39;s a whole derivation of how to get there but we&#39;re not going to do that because I frankly even after Professor malitzky taught it for two hours I never understood it right but I also tried again and again and again but it&#39;s just not helpful for the MCAT I&#39;ll tell you everything you need to know know about km and that should be enough to go about your day right but before we do anything about why km how km how do I understand it let&#39;s understand some very basic fundamental details about what km tells us if I have an enzyme E1 and E2 right orgo people are quaking in their boots right now right E1 and E2 and E1 has a high km and E2 has a low km which enzyme is better at its job we got one vote for e22 two votes someone changed their vote we got two votes for E1 anyone KIRO Sarah E2 two votes for You2 three votes for You2 anyone three votes for E1 tied you guys want to know what I think it is I think it&#39;s E2 why why is a low km better because that means you need less substrate to get to an achievable Vmax right so let&#39;s think about this right I want to make rubber bands right and the people who are making me rubber bands are split into two groups one of them doesn&#39;t even know what a rubber band is right and the other group have been the pioneers of rubber band making technology for the past 7,000 years right I&#39;m unbelievable at rubber band manufacturing right if I wanted to make 30 of them every minute right to get to half that velocity it&#39;s going to take the idiots 900 years to figure it out and it&#39;s going to take these guys two seconds right so the number of people they&#39;ll need to employ to do so so maybe one person out of that and 100 people from that group The the stupid group who don&#39;t know how to make rubber bands right so in order to get to half that maximum velocity how many people do we need and the less people we need the better because that means when we have a lot of people they&#39;re going to get to Vmax quick super quick stupid quick and if we get to Vmax quick the reaction&#39;s Done Quick and the substr are turned over quick and the prodcts are made quick so more substrate can be turned into more product in less amount of time yes good do do I have like eyes growing out of the back of my head you guys are looking at me like I&#39;m crazy yeah it makes sense the km tells you nothing about the VMAX if km is KM tells you nothing about the Vmax why not I want you to answer me why doesn&#39;t the km tell you anything about the V-Max reread this really carefully if I just feed you everything you&#39;re never going to learn anyone anyone can answer the question km is the concentration of substrate at which half of all enzymes are bound therefore at the substrate concentration km V equals V Max over 2 why doesn&#39;t km tell you anything about Vmax based on subr conc exactly exactly and the Vmax is based on what the enzyme concentration km is based on the substrate and Vmax is based on the enzyme this is a this is a number a arbitrary term that says if we were to get to half of whatever the Vmax is whatever it is if we want to get to half that how much substrate do we need we don&#39;t know what it is the molecule is not smart enough to know what it is the molecule doesn&#39;t have a brain you do right you can look at the graph and figure out where one half Vmax is and figure out what the subst concentration blah blah you can you can do all that molecule doesn&#39;t know what the going on l that is absolutely correct that he said that low km is high Affinity also guys we are not meeting on Thursday it&#39;s Thanksgiving try your best to come on Tuesday I have a surprise for you you know what the surprise is it&#39;s a test it&#39;s a test pop quiz it&#39;s it&#39;s an entire MK okay guys wait but I do have on that note I do have like slightly bad news for you I would like all of you to take a diagnostic exam over your break and come back to me and tell you how tell me how you did yeah Diagnostics are like half half take a half length diagnostic not a full I don&#39;t I don&#39;t think you guys are like mentally prepared for a full yet I I wasn&#39;t you&#39;re not supposed to be are theree ones on yes there are yes there are they&#39;re all  they&#39;re all equally  even the full length all equally  anything except for am is garbage people come to me they&#39;re like oh my God I got like a 498 blueprint I was like yo next week wake up take an AMC exam they get like 14 points higher I&#39;m just like yeah like CU because here&#39;s the thing and let me go on my little rant and then we&#39;ll move on those testing uh programs how do they make money they make money if you do bad that&#39;s how they make money because if you do well you&#39;re not going to sign up and buy more of their so when you take their free exam and they tell you oh my god look you did by our program you&#39;re going to do it cuz you&#39;re like oh my God I did such but when the people who make the exam who make enough money by people signing up for the exam and paying $270 dollars every time they sign up and they&#39;re the people who control the USMLE and they&#39;re the people who control all the shelf exams and they&#39;re the people who control all the nbme and they&#39;re the people who control residency applications and medical school you think they give a  about making a little bit of money off of you people no so they&#39;re genuinely going to tell you the truth because if they don&#39;t tell you the truth then it&#39;s going to Bar you from applying to medical school and that&#39;s where they make most of their money right so they give you the truth everyone else is lying to you they&#39;re going to tell you that you did worse than you actually did what&#39;s the highest I ever scored on a blueprint test 506 what did I get on my real MCAT a 521 I took two blueprint tests and then abandoned them that was dumb it was no all right so do you guys understand this do you want to run through it one more time yeah okay so basically what we&#39;re saying is that enzyme kinetics are the study of concentration of enzymes and concentration of substrate in a specific reaction vessel right the velocity of the equation of the reaction will increase as the substrate concentration increases up to a certain point that certain point is Vmax when all of the enzymes are saturated with substrate right and Vmax can only be increased by increasing the number of enzymes because then you have more enzymes doing more work which is more people solving more Rubik&#39;s cubes and more solved Rubik cubes are going out the back door right okay we have this little equation notice that the formation of I think I up before when I wrote this out for the first time the formation of product is a forward reaction right not always but in this case it&#39;s a forward reaction right when is it not like a forward reaction when you have reversible processes like a lot of the steps of glycolysis most of the steps of glycolysis are reversible processes anyone know the three steps of glycolysis that are not reversible processes hexokinase pfk1 and pyy and those are the steps you have to overcome when you do gluconeogenesis hexo we&#39;ll go over it but hexokinase pfk1 and pyy those are the irreversible enzymes of glycolysis all the rest of the enzymes of glycolysis catalyze the forward and reverse reactions right now we looked at this graph we looked at Vmax and went to one half of Vmax and we went to the substrate concentration at one half of Vmax which is now colloquially known as km it is the substrate concentration at which 1 half of all of the enzymes in the reaction vessel are bound and Performing the reaction action the lower the km the better the enzyme the better the Affinity right we want a low km High km is bad right okay let&#39;s talk about the michis Menon equation right we&#39;ll leave that definition up and we&#39;ll leave this graph up as well and we&#39;ll put some important facts over on the side there in my favorite color that a low km means higher Affinity if David had not said that I probably would have forgotten to put that on the board so thank you that&#39;s a very very good way of thinking about it and it&#39;s probably the way you should think about it the michaus men equation describes how the rate of a reaction velocity depends upon substrate concentration and enzyme concentration this is when it starts to get difficult all right so here&#39;s our little equation what is es it&#39;s the enzyme substrate complex right if you were to say the rate of these forward and backwards reactions this would be K1 little K right the rate am I illiterate K1 don&#39;t answer that K negative 1 and kkat K cat meaning the rate of catalysis catalyzing the formation of the product right if enzyme concentration is constant then V equals V Max s over km + S so K cat right there is defined as the number of substrate molecules turned over what do we mean by turned over catalized into the product right turned over per enzyme molecule per second number of substrate molecules turned over per enzyme molecule per second right so in one second how many substrate molecules are turned into product per enzyme so it&#39;s it&#39;s a zoom into one enzyme and one second and how many substrate molecules does it make you think not that many right because it&#39;s just one second but you have to remember these are very very very Lightning Fast processes right okay one more thing you have to know to go along with this is that Vmax equals the concentration of the enzyme time k cat cuz remember Vmax is dependent on the concentration of the enzyme how do people derive these I don&#39;t remember I learned at one point but I don&#39;t remember and if we have that and we have that then we can combine those two equations and write out a velocity equation and that velocity equation it&#39;s pretty important anyone see my red marker there it is I was uh rock climbing with a buddy yesterday and um we were we were at Cliffs at ganis and um he&#39;s I&#39;m like a beginner so he&#39;s teaching me how to rock climb and I was like oh where do I start like over by the green he&#39;s like yeah by the red and I was like what and he he&#39;s like the red and I was like oh all right so V equals if we put this in for VMax we get K cat e s over km + S and can you guys imagine that if k m was way greater than the concentration of substrate right if it was far far greater than the concentration of substrate then this would happen V equals kkat over km * e * s that&#39;s the takeaway that the that the velocity when when the substrate concentration is low right when the substrate concentration is low because what is KM is the substr concentration at which half of all the enzymes are bound right what we&#39;re asking here is how do we increase that velocity how does it change so when we keep the subst concentration low the velocity is now contingent upon kcat over km which we&#39;re going to describe in one second the concentration of the enzyme and the concentration of the substrate what did we say enzyme kinetics were the effect of increases or decreases in the enzyme concentration substra concentration on velocity of the reaction that&#39;s your equation that&#39;s it km is basically the overall rate of this reaction right so along with being that it&#39;s also defined as a rate sorry all the way around I knew something was right there K cat plus K1 over K1 so what does that tell you look at this what are the things that increase km K cat going this way and K1 going that way things that move away from the enzyme substrate complex right and things that move towards the enzyme sub complex will decrease km so what does that tell you about km it kind of determines the amount of es that you have at any given time and that makes sense because half of all enzymes are bound not bound not not actively producing product but bound so if the enzyme is bound it makes the enzyme substrate complex so things that usher in more formation of the enzyme substrate complex will decrease there sorry increase the km things that get rid of the enzyme substrate complex will increase sorry yeah other way around I had right the first time see how confusing this is things that increase the amount of enzyme substrate complex will decrease the km things that decrease the amount of enzyme substr complex will increase the km it&#39;s a little reverse of what you would think right but that&#39;s going to become important when we talk about inhibition right and different types of inhibition and what they do to km because there&#39;s a km a true km and an apparent km right and we have talk about that a little bit later one more thing one more important thing that I need to fit somewhere on this board K cat over km which is seen right here is also known as the catalytic efficiency kkat over km is also known as the catalytic efficiency right and it&#39;s a way of judging how good an enzyme is at its job at its overall job right because what was Kat again Kat is the number of substrate molecules turned over per enzyme molecule per second and km is the Affinity right how much it wants to bind the substrate right or the tendency for it to fall apart both of those taken into consideration so when you do this divided by the km you&#39;ll get a general efficiency of the enzyme and that&#39;s how we rank enzymes in terms of how good they are at their job so there will be not just on one or two or three on possibly every single MCAT that you ever take practice or not real thing anything if you guys turn out to be tutors eventually which I hope some of you do right every single question every single bio and people who take practice exams already like when if you&#39;re testing in January let me know if this is true in every single biocham section you do there will be a question about km Kat and Catal efficiency every single one every single goddamn one this is the highest yield chapter in all of biocham in my opinion High K cat is good because it&#39;s more molecules turned over per enzyme per second low km is good because it&#39;s basically a representation of dissociation right which is why we want a lower representation of dissociation so sometimes biochemists will will teach you Professor malitzky taught me this because he is a biochemist right he has a masters in Biochemistry he taught me think of KM almost like KD dissociation dissociation constants right so imagine that a higher km more of is dissociating it&#39;s going away which makes sense because a higher km means higher K cat and higher K1 away from es this is what you want that&#39;s what you get do you guys follow what&#39;s on the board okay let&#39;s say that I gave you an hour to solve a couple math problems right and enough for you to do in an hour or maybe you solve one math problem an hour something like that right if you are one person one enzyme and I look at how many math problems you solved in one hour and there&#39;s 20 you solve 20 of them versus one of them isn&#39;t 20 better because you do more so if we zoom in on one enzyme and we look at that one enzyme for one second how many substrate molecules has it turned over if it turns 20 substrate molecules into product that&#39;s good if it only does one that&#39;s bad that&#39;s what Kat is you&#39;re zooming in you&#39;re looking how many substrate molecules do you turn over each second as one enzyme my imagine small good because as a fraction make it lar that&#39;s all you need to know okay that&#39;s it that&#39;s absolutely true and the fact that if km is low that means that you have a lower substrate concentration at which you reach half Vmax right we&#39;ll do the rest of the chapter in part two thank you for watching

Transcript for:Enzymes and Enzymatic Processes

Transcript for:
Enzymes and Enzymatic Processes