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LECTURE #1 You have to understand the concept between structure and function. You have to understand the nature... that an enzyme is fundamentally selecting for function and that the evolution of the area is to understanding its secondary structure and tertiary structure and who are the people that developed the methods for secondary structure and tertiary structure, and that's who?... For tertiary and secondary and primary structure... who? At that stage you have to know Sanger. assay is in terms of function. the function biochemically. assay for fermentation? Sanger. You have to know what an What is it? It's a definition of And, who really developed the first Buchner. O.K., so you're getting the logic of what I'm expecting you to understand. Then what happened is you go from function to structure and then you evolve into where we are now. We can have alot of sequencing structure, but we don't know function. Now, what I gave you last time with the enzymology in terms of function, you had, there was a concept introduced and that's the transition state. transition state is an intermediate. And, the And you need that concept in order to understand how catalysis works, and that transition state 1 lowers the activation energy and allows the action to go forward at a faster rate. that doesn't exist?" The question is "How do you prove something Again you can make the analogy to love. Also, you have to understand what an equation is and how you create an equation... or you have a graph and from the graph, it's a pattern, how you create an equation for that graph that has an explanation. Now, I'll give it to you this way. what science is in general. some regularity. This is sort of You try to look for a patterns, for So, the idea is to find order in disorder, order in the universe, O.K.? Love sometimes gives you a sense of order. It may not be real, but it gives you a sense of purpose and order. Then you look for that pattern and you try to find an equation that fits that pattern. But so far, this is still numerology. You have a pattern and you have an equation. That's what happened to Mendel; he had a pattern of the distribution of genes, and he had an equation, which was the binary equation, ???a+b2 was the mendelian equation for genes, or you recognize it at A + small, dominant recessive. And you get homozygous dominant, heterozygous and homozygous recessive. That equation explained the pattern that Mendel found. The Michaelis-Menten equation explains a pattern for this graph. The graph is a pattern. quotes. You can find patterns on a gel, in stock Then you look for an equation. 2 At least then you can formalize it to the number of variables involved in that pattern. That's very useful, but that's not yet science. Then, you try to go from the equation to the explanation, or the cause or the mechanism, behind the equation; the mechanism, or the logic, that creates the equation. In population biology, there's a lot of scientists that give you equations that fit curves, and that's curve fitting. That's very nice, complicated and it looks like science; you have very equations, but they're not science in the real sense in that the equations themselves make no sense. the observation. equation, then They just fit the curve or When you have a mechanism that explains an you have science. And, the mechanism explains, or the logic behind this equation, was what?... that that the velocity is proportional to some enzyme substrate complex, that there's an intermediate, that doesn't exist. That's very important, that the logic, if you start with this logic, you can actually derive this equation, plus an equilibrium of the ES formed and the ES lost. But that's the logic behind this pattern. The logic behind the mendelian curve is "How do you generate a binary equation for genetics mechanistically?" When Mendel published this and he published his equation, it was called "The Golden Rule" because no one had any idea of what it meant. 3 It looked like a God-given rule. sure it was a God-given rule. weren't that sure. Since he was a priest, they were He wasn't promoted to pope, so they But, they were sure there was some rule that God gave to make this genetic rule. didn't understand it. mendelian genetics He had no mechanism; he It stayed dead for fifty years. was rediscovered in 1905. That's why It wasn't rediscovered because it wasn't true, because no one understood how he got this equation to explain the pattern of genetics. what's the explanation for this equation. You've seen this all your life and you don't know what the explanation is. garbled???????, that's correct. And, tape And there was a medical student who was sitting in class; premed (always the premed) named Sutton, and he saw something that everybody else saw. He saw slides of mitosis and meiosis, and he saw, basically, just that pattern of chromosomes lining up. And he made one assumption in his head. He said, "If this can move to the right half the time or this moves to left half the time, then it might postulate that this structure is carrying a gene, or the characteristic for a plant???, then half the time it'll move to this cell and half of the time it'll move to that cell". If that's the case, then I'd have a binomial distribution, then I've explained Mendel's genetics. But, the whole proof for Mendel's genetics, that if you look at the slide, it looks like the chromosome can go either to the right 4 or to the left. There's no evidence it does that. You don't know whether they all aren't going to go to this daughter chromosome. But the assumption is that they randomly go to the right or to the left. If they randomly go to the right or the left, then you explain this equation. So, the mechanism to explain this equation was independent and random assortment. Random, let's say random assortment to right or left of chromosome... Nobody's done that experiment, by the way... of putting a marker on a piece of DNA on chromosome and seeing if it goes 50% of the time to the daughter cells. And, it's doable now; it's never been doable, but now, you can actually physically check to see if a chromosome goes 50% of the time to one side or the other. genetics. Then, you have mendelian If it doesn't do that, it's not a mendelian gene. And because this explains this rule, he could say, very strongly, that genes are on the structures, that genes are on chromosomes. So, is a gene, in the mendelian sense, the gene's definition of a gene... a mendelian gene means it has to be on a chromosome and it has to sort 50-50 to the daughter cells and it has to pass a binomial distribution. It's a different assay. Is it the same gene as a DNA gene? No. The assay for a mendelian gene is this binomial distribution. What other gene did I mention before in the other lectures, will be on the exam? That's right, and who presented that? 5 Who was the guy who proposed the first gene? "I will sacrifice my life for one brother or two cousins or one sister." Remember that. I asked you whether you'd sacrifice your life for your brother or sister. Did I ask you that? Anybody here... who'd sacrifice their life for their brother or sister? You'd do that? that's nice, but how about for two cousins? Anybody else? interesting. O.K, That's Genetically, that's equivalent in the gene pool, not according to mendelian genetics, but according to a population biologist. gene. But that gene is a different gene than the mendelian It's population. a gene that just increases in frequency in the There's no evidence that gene's as popular as a mendelian gene. And, when they talk about genes involved in intelligence or mediocrity or any kind of behavior, no one's ever proved that those genes are mendelian genes. You can ask, "Do they have, do they sort independently and randomly?" That's a mendelian gene. Same with DNA... If you see a molecular biology gene, or they claim it's a gene, it's a sequence, you can ask, "Does it sort independently and randomly 50-50?" So, that's an important issue. So, those are three types of genes, but I really brought this up to say to you, that's why Mendel was unappreciated; not because he didn't get the equation for the pattern... are you still going to sacrifice for the cousins?... No? 6 He didn't have an assay. That's YOUR assay. you, "I think this is genetic. If someone says to I think exam taking is genetic, the ability to do well on exams." You have to say to them, "Well, what kind of gene?" and then they'll say, "I don't know what you mean." And, you'll say, "Well, is it a mendelian gene?, and they'll say, "I don't know what you mean." Then say, "Well, does that characteristic sort independently and randomly? If I tested for that characteristic in the next generation, would I get this distribution?" That's the assay for the mendelian gene." Or, will that characteristic just increase a certain proportion in the next generation? That would be a population biology gene, which is a little ????????????? as a concept. say that's the case, tell me what Or, even harder, if you the DNA piece is that corresponds to that. Let's do it in a medical sense. say what?... It means "Breast cancer is genetic." You That's right, you say, "What do you mean, genetic?" that my inherited in women. father Aha! Then had it...I'll have it? No, it's So, now, it has to be on the X chromosome, right? you say, "Does it sort? Is it a mendelian? Does it sort independently and randomly, or did you just find a piece of DNA on a gel that correlates to the disease?" Do you see what I'm saying? And what happens if that piece of DNA shows up in a male? 7 Then, they'll say to you, "Well, keep an eye on him; he might get breast cancer." STUDENT QUESTION... this rule. It can or can't be, as long as they follow But, I just told you, no one's ever actually watched a piece of DNA to see, a piece of DNA on a chromosome to see if it moves independently and randomly. look at the phenotype. It's an assumption, because you But, no one's checked the mechanism. This guy, Sutton, did this when he was a premed student in 1910 or something like that. And, then he went to medical school, never heard of again. Who was the other medical student that was never heard of again? Lesch-Nyhan, I told you, discovered that HGPRT for monoclonal antibody. I'm just giving you good stories about premeds that were brilliant before they went to medical school, and then how medical school ground them into mediocrity. memorize a lot of material. Well, you have to This is very creative thinking, but the point here is that the mechanism explains the equation. It took 50 years before someone saw that and explained the equation. So, Mendel is credited with being such a genius, but really, he found an observation and an equation. He didn't have a mechanism. That's also ???Harvey Weinberg??? actually, but this is also mendelian different. genetics. Well, ???Harvey Weinberg's a little It's one minus...square... It's an equilibrium of two 8 genes in a population, a similar situation. But, it isn't clear what creates that mechanism. But, you can see that this, if it turned out that chromosomes move to one daughter cell two times as frequently as another daughter cell, than this equation would be different, right? phenotypes would look different. And the It just happens that they claim there's an equal mobility on either side. And, it's interesting, because you could also argue the big chromosomes should move slower than the small chromosomes, right? move at the same speed. things. this That puts a kind of a constraint on I won't go into it. rule. You think But they all seem to it But it has a certain consequence, should leave behind the smaller chromosomes when they're having division, that it should be faster and the bigger one should be laggard. Anyway, the point here is, this guy understood that he could explain the pattern of the equation by an assumption. I told you before, that Planck said that the frequency was proportional to ?H-nu??, the energid<<<?? sign. That the energy was proportional to the frequency of the radiation. And he came up, arbitrarily, with a constant to make an equation. an equation. also on the You have to know how to make Remember what I said about equations, ???, that's exam. There are proportionality to an equation. two parts, one, to How do you do that? 9 convert a And what's the difference proportional? between inverse proportional You have to know what that is. and directly Which is directly proportional, Michaelis-Menten or Bragg's diffraction equation? Which is inverse space? the next one. You don't have that yet; you'll get it in What's the other part of that equation? To find out if you've got the right equation, what would be the constant dimensions in the equation, dimensionality, is a good way, and that way you can write your own equation, and we'll check how you do. There's a constant, John's constant... What's John's constant? That can't show up on the Scarlet notes, can it? dimensions of John's constant? grades per hour slept. go. What are the What is it?... That's right; Who was here for John's? O.K., there you That's a very ?????? exam question, but that's a kind of exam questions I do. Last year, I gave Michael's constant, that was another constant. But, you get the point, O.K. You can make up your own equation that is just as valid. But this is the logic of science. giving insight. you a very understand this. big years to I had a pattern of nucleotide sequences. I analyzed nucleotide sequences. nucleotide sequences. rules of harmony ???? It took me many I'm I was looking for the logic of You can say they're random or they're like And you look for a pattern. 10 I found a pattern. I could actually predict equations. I could predict different sequences, but I didn't have a logic yet of why they were there. And, that logic took many years. And when I had the logic to figure out what the equations were for the pattern, then it became science. And then it was stolen by Crick, Brennar and Klug, my colleagues and we all published together. British way. And that's the Until you solve the whole thing, they won't steal it from you, because it's not science. In America, they'll sell it as long as they can sell it along the way; it doesn't matter. Anyway, that's the logic. Sutton, in a sense, discovered the logic of mendelian genetics. It's very important. And here, the logic is the transition state. This is a very powerful concept. Haldane, the same guy that gave you the population gene, also gave you the energetic that enzymes interact by weak bonds. state. Then, Pauling gave you the transition And, I'm going to take this concept of the transition state a little further into this lipid lecture. And it's not in Lenninger, but it kind of fell out as I was restudying it to lecture to you, some interesting aspects of how this concept of a transition state... Now, the transition state as a concept for catalysis was very good and it held and the only evidence was the Michaelis-Menten structural equation evidence for as the a kinetic transition building a transition state analogue. 11 argument. state Right? was The first getting and Anyone?... Two things, with enzymes, what did he do?... population genetics?... Remember that? life for a sister or two cousins? Would you sacrifice your Population gene... Would you? The cousins you couldn't care about, huh? their cousins. O.K. and in terms of Most people don't know Some people dont' even know their sisters. You find out later in life...aha... that... what happened? Anyway, I will give a lecture on how to look at the world from a DNA point of view as opposed to the phenotype. a very funny country. The concept of America looks like genes, you have to understand, in terms of, not genes and genetics, in terms of an assay. That's what you were asking about. What's the assay? An assay can be like a Buchner funnel, a physical assay, but it can be a concept like a mendelian gene, a binary distribution. You can say, "Does it fit that rule and therefore, I can call it that type of a gene?" a functional function. An assay is, basically, a way of describing, in sense... Now, It's with this actually the transition manifestation state, there of the was a consequence to the concept that if it existed and you could get a structural representation of the transition state, you could make a complimentary surface to that transition state, and that complimentary surface would then act as an enzyme for the initial non-stable version of this state, or the transition state itself. Is that clear?... For some. If this is love, and love is pure and it's noble (I shouldn't make judgments here too) and you call 12 the transition state analogue transitory, and it's temporal. the stable of love is But you can have a permanent state of love, which is sort of a ???brothel. state analogue. version That's the transition So if you make a complimentary surface to that, and then go back to love, the analogue, it should be a catalyst on that. Now, I'll make this a little classier. Cleopatra had to take training before she married Cesar, because she was a virgin. So, she had to go make a transition state analogue before she went to the transition state with Cesar ????? Cesarea. historical consequence. Notes either. So, it also has an Anyway, that may not show up on Scarlet But I was trying to figure out the transition state analogue, is the compliment to the transition state analogue, does not cleave the transition state analogue. misunderstand. That's what people It cleaves the transition state. compliment to the phosphone. If you make a It'll cleave the ester linkage. And, the nature of the transition state, chemically, is that it's usually one valence higher than the previous one. carbon, you end up with a phosphate. So, if it's You have something coming in, let's say it's a hydroxyl group, you end up with a phosphate. And if it's a nitrogen, it can be carbon. it can be nitrogen. 13 And if it's an oxygen, So these are the analogues to the transition state substrates. And that's important, because with monoclonal antibodies, if you can make a complimentary surface to the analogue, you can make an enzyme for any, ANY, ANY function; not just take the enzymes that exist in nature or any function that exists in nature. If you take an antibody which is complimentary to a particular analogue structure, it will act as an enzyme on the original substrate. And, these are called catalytic antibodies... And I'm going to show you this,in terms of lipids now, it's not in Lenninger, but you'll see it now, how clearly, what's happening, by looking at the structure of lipids. Lipids, in themselves, used to be not interesting, and I figured out that they're probably much more interesting than one would have thought. If one looks at them, not as simple substrates, but one looks at them as transition state analogues. But they're also energy sources and they're also involved in structure. They're also involved in what we call combinatorial chemistry. So, historically, also, there's another set that you'll have to know. The difference between what we did historically is function giving structure, going to rational drug design. rational drug design? pharmaceutical setting? And what's Rational drug design... Anyone work in a Yes, go ahead... No, rational drug design means that you're designing the drug to fit the shape of the receptor. Again, not dissimilar to the transition logic, but you 14 know the structure of your receptor, three-dimensional structure, and you design your drug to be something small that fits exactly the shape of whatever interacts there. And, if you can inhibit that interaction or enhance that interaction, then you have a drug that you can sell. And, ideally, you want a drug that doesn't kill the patient, doesn't ?????help?>? the patient very much, but that he has to take it every week. flow. And this gives you a cash And that's rational drug design. Now, that's changed, because there you had to know the structure and you had to know the function and you had to know something about what you were working on. What's the new chemistry now? It's perfect for students that don't want to study, don't want to know anything. If you don't want to know anything about chemistry, you don't want to study structure of chemistry, you don't want to study how to put them together and you don't want to know anything about how to make them, what do you do? everything. chemistry. If you make everything, that's You make combinatorial And, that's what they're doing now, make everything... And this guy knows everything and he's been sleeping through this class, that's right, that's subliminal, and that's what you should do now. Everybody, take a nap, because obviously, you're doing very well. material. Everyone, sleep...sleep...relax. Don't be anxious. 15 You will learn this Combinatorial chemistry means, you make everything first and then select afterwards. And, that's what physicians do, right? You go into the emergency room, you get a new intern, he knows nothing. What does he do? What are the four things a doctor can do? told you... in medical school. is he going to do? You go in with chest pains. What are the four things. I What I told you already, what? Lasix, cortisone, probably have an inflammation around the heart, right, and it's not going to hurt you, and you're in pain, what does he give you? Pain medication? right away...go ahead... what else? you get an infection from the IV. He gives you morphine And some antibiotics in case Right, that's it, he gives you all four. Go ahead...no, you were in the bathroom when this happened, no... O.K. What? Lasix...you should stay in your class, peaceful, Oh, I'm sorry about that, I shouldn't joke, O.K. Lasix, this is all the medicine. It's a diuretic. What does Lasix do, anybody? It's the only thing that works when you're filling up your lungs, when you're going into pulmonary failure. Obviously you're having...and you're fortunate enough not to know. But, usually, when you get to a certain age, somebody in your family has a heart condition, and it's the only thing that works. And, it's dramatic. You're filling up with water in your lungs and that's how you die. And unless you get Lasix into the patient immediately, and that what the paramedics do... It will drain you out, it's a diuretic and it's dramatic, and all of a sudden, you can breathe again. O.K., so that works. 16 And then you have pain, so that's only pain medication, right? And antibiotics, right and cortisone for any skin disease or inflammation. Everything else has so many side effects, it's not worth trying. Plus, there's a thing called the "placebo effect". The placebo effect What's is what? What's the percentage? effectiveness of most rational drug design? 30%. Not 80%, 80? on! Seventy, 60-70% if you're lucky, on THEIR numbers, O.K.? usually 50%, O.K.? their drugs. the Come It's And, it doesn't affect the whole population, It only affects a small proportion. That's what they're all looking for, the genetics of the receptor, to find out how to experiment. Anyway, that's also what you call combinatorial medicine. You give the patient everything and if they survive, you're a goddamn genius! Okay? That's the doctor, that's your usual intern. people know this is true. Most There's a good movie by George C. Scott: A guy comes in completely healthy and ends up in a coma. What do you do for AIDS? Nothing! What are you going to do for AIDS? You sell them a cash-flow of drugs, okay, $15,000 a year and you come in and put them on a morphine drip. mean, what are you going to do? 17 Anything else, I Cancer: What can you do?. STUDENT COMMENT ..for what for AIDS, yes, I'll tell you about it. They use it for antibodies... You're big on that issue... We'll discuss that. discuss it. I'm not going to Well, I'll tell you, actually, people have used it historically also for antigens for vaccines, because it's sterile and there's a whole history. It doesn't work, okay? That doesn't work; this doesn't work. That's combinatorial medicine. So, you can do everything first and see what happens afterwards, okay? If it's limited. And so you have to know the logic of that, that combinatorial chemistry. All of science before was apriori. Aposteriori, okay...after the fact. theory. It's blind. And this chemistry now, what?... This is like evolutionary You do all the random changes and then you see what the environment selects as being adaptive. in is it's easier, faster everything and then see what happens. and It turns out, cheaper to make You can make it in two ways, systematically or randomly, you can get everything. People are sequencing randomly, and later, we'll go into the logic of the nuances of making this kind of chemistry. So that's the overview of what we were looking at with the enzymology and the receptor sites, and the combinatorial chemistry will fit in a little bit here with lipids, I'll give you more on 18 that. What else did I cover? Is there anything YOU want on the exam? Well, I gave you the questions and the answers. You want the ???Innua story?? You want What...go ahead. me to write mythological story and then you write the equation for it? could do that and you write the... Is that too complicated? a I I'll write up sort of a love poem, and then you write the equation that corresponds to it? Or one of these... I was thinking of doing that one... What is this... English Literature, Milton's "Paradise Lost"? But you can see the analogies. If you think at a certain level, there is a logic to things. Now, lipids come... Yes, that's the transition state. monoclonal antibodies, Mitchell, yes. that's phosphone. Oh, Martha Yeah, but no one ever heard of Martha Mitchell. Did anyone look her up on the WEB. Tells me how old I am. his name. Yes... That's the Did anyone look up Watergate? John Mitchell was her husband. He was the Attorney General for Nixon. I forgot He was the guy in charge of prosecuting all the crimes in the United States. And he was perpetuating the biggest crime, which was Watergate. Not only was he perpetuating it, but he was covering it up. Not only did he cover it up when his wife went to the newspapers to tell 19 the truth, Martha Mitchell, he went out of his way, I believe, to have her killed. Okay? And the proof lies in whether her immunoglobulin is the same as any other immunoglobulin in the database. She died of a myeloma at Sloan Kettering. And the directors of Sloan Kettering, at that time, were Halderman and Erlichman. Okay? Who were they?... They went to jail for Watergate. So, chances are, they had access to this material. And when you see the latest CIA, where they pushed the guy to the Penn Station Building, you know, the Penn Hotel outside of Penn Station, where they tested LSD randomly on New Yorkers... did you see it on TV recently? were random... There Oh, there's a whole program where they they go with combinatorial LSD. They randomly tested LSD on anybody in the bars, in the subways in New York City to see the effects. Huh?... It was on A&E, you know. No, no, it was random. Not only not aware... let's try it out. they're on... it was completely, But with New Yorkers, you can't tell whether It doesn't matter. controlled experiment, you see. Alright, that's not a It's probably just increased the dose a slight bit. Lipids, okay. So you don't know. So with Martha, see, she's a hero, a heroine, I should say, and since you don't know her, I bring her up again because there will be another heroine. Okay, who's the other heroine for enzyme competitive inhibitors and... Huh? No! Some amoral class here. 20 You got it wrong; that's wrong... ????????????? (CHUCKLING). I can see where coming from. That's an unsung hero, too; there you go. you get older. Poor kids. You'll respect your wife. Okay, now, lipids have three characteristics. for energy. They are a storage And this is normally a very boring topic, lipids, because they're just hydrocarbons. carbon. Wait till But, if you think They're just long chains of about world wars and all relationships, it's really about these long-chain carbons. the And isolating and identifying oil is all part of geopolitics...... In fact, the whole Bush campaign is related to this. So, we'll discuss a that. Also, lipids can be looked at as natural combinatorial chemistry because they come in, let's say, multiple associations where you can have A, B and C, where A, B and C can be 10 or 11 different types of compounds and they all hook up to a common backbone. So complex lipids have combinations of chains attached to a backbone. So, there is a combinatorial chemistry aspect to lipids, and that has never been pointed out except in this class. So it may be true, it may not be true and I'll show you patterns, and we'll actually derive an equation. Now, they also have another aspect. there are... which is They are storage, ????? and interesting. They're involved in information transfer, in a very minor way, where you have various hormones, and they're involved 21 in structures, more complex structures in terms of membranes and something novel, in terms of cholesterol, which is what I call "fluidity buffering" or "density buffering". And then there's one new thing, which is that they may be involved, and I don't know how to give it a name yet, but they seem to have patterns of transition states. So what I'm saying to you, I think, is I've found a pattern, and I'm going to try to get an equation and you try to find a mechanism, maybe in five to ten years, to explain this pattern that we're observing. So lipids, even though they started off and in the chapter they're given, considered kind of boring, they may turn out to be quite interesting. Now, the first part of lipids is the global aspect of lipids... END OF LECTURE #1 22 23