| [{"text": "[SQUEAKING]", "start": 0.0, "duration": 1.936}, {"text": "[RUSTLING]", "start": 1.936, "duration": 2.42}, {"text": "[CLICKING]", "start": 4.356, "duration": 0.968}, {"text": "MATTHEW VANDER HEIDEN:\nHello, everybody.", "start": 10.66, "duration": 1.71}, {"text": "Last time, I introduced\nthe idea of the TCA cycle,", "start": 12.37, "duration": 5.01}, {"text": "tricarboxylic acid cycle.", "start": 17.38, "duration": 2.2}, {"text": "Also known as the citric acid\ncycle, because citric acid", "start": 19.58, "duration": 2.99}, {"text": "is a tricarboxylic acid,\nas you'll see later today.", "start": 22.57, "duration": 3.12}, {"text": "Also known as the\nKrebs cycle, named", "start": 25.69, "duration": 2.01}, {"text": "after Hans Krebs,\nwho discovered it", "start": 27.7, "duration": 4.11}, {"text": "in the early part\nof the last century.", "start": 31.81, "duration": 3.73}, {"text": "The TCA cycle is the\nseries of reactions", "start": 35.54, "duration": 2.79}, {"text": "that occurs in the\nmitochondrial matrix", "start": 38.33, "duration": 2.1}, {"text": "and it allows the complete\noxidation of two carbon", "start": 40.43, "duration": 3.12}, {"text": "units, derived from many things,\nincluding pyruvate, derived", "start": 43.55, "duration": 3.54}, {"text": "from glucose and glycolysis and\nenables the complete oxidation", "start": 47.09, "duration": 5.82}, {"text": "of that carbon to CO2.", "start": 52.91, "duration": 2.61}, {"text": "Now, it's a cycle\nbecause those two carbon", "start": 55.52, "duration": 2.55}, {"text": "units from pyruvate or other\nsources enter the cycle,", "start": 58.07, "duration": 4.98}, {"text": "combine with 4-carbon\noxaloacetate,", "start": 63.05, "duration": 2.88}, {"text": "and combine to make\n6-carbon citrate.", "start": 65.93, "duration": 2.31}, {"text": "Hence the citric\nacid cycle, or TCA", "start": 68.24, "duration": 3.3}, {"text": "cycle, that is then oxidized\nback to 4 carbon units,", "start": 71.54, "duration": 4.26}, {"text": "forming a cycle\nthat allows cells", "start": 75.8, "duration": 5.76}, {"text": "to release lots of energy.", "start": 81.56, "duration": 1.71}, {"text": "Complete oxygen\nenables, ultimately,", "start": 83.27, "duration": 2.1}, {"text": "complete oxidation\nof glucose to CO2.", "start": 85.37, "duration": 2.64}, {"text": "We've talked many times\nhow this releases energy.", "start": 88.01, "duration": 2.55}, {"text": "And it also generates\nlots of intermediates", "start": 90.56, "duration": 2.19}, {"text": "for the cell that can be\nused to make other stuff.", "start": 92.75, "duration": 3.51}, {"text": "Last time, I alluded to the\nfact that citrate can be", "start": 96.26, "duration": 3.03}, {"text": "used, say, to make fatty acids.", "start": 99.29, "duration": 3.09}, {"text": "Today, what I want to\ndo is I want to dive", "start": 102.38, "duration": 1.98}, {"text": "into the details of how\nthis TCA cycle occurs", "start": 104.36, "duration": 4.65}, {"text": "and the consequences\nof the way it works,", "start": 109.01, "duration": 2.97}, {"text": "and how that affects other\naspects of metabolism.", "start": 111.98, "duration": 3.66}, {"text": "You'll see that it\nactually affects", "start": 115.64, "duration": 2.28}, {"text": "the ability of\ndifferent organisms,", "start": 117.92, "duration": 3.52}, {"text": "whether or not they\ncan make things", "start": 121.44, "duration": 1.61}, {"text": "from intermediates\nin this cycle,", "start": 123.05, "duration": 2.88}, {"text": "because of how the cycle works.", "start": 125.93, "duration": 1.735}, {"text": "Now, to start.", "start": 137.75, "duration": 0.645}, {"text": "Of course, if we're going\nto start from pyruvate.", "start": 141.15, "duration": 3.83}, {"text": "Pyruvate, of course,\nhas three carbons.", "start": 147.87, "duration": 3.34}, {"text": "And so if we're going to\ngenerate a two-carbon acetate", "start": 151.21, "duration": 4.55}, {"text": "group, we have to lose CO2.", "start": 155.76, "duration": 2.13}, {"text": "And as I described a\ncouple lectures ago,", "start": 164.22, "duration": 3.06}, {"text": "acetate is also\nthe thing that we", "start": 167.28, "duration": 2.46}, {"text": "can derive from\nmetabolism of ethanol,", "start": 169.74, "duration": 2.97}, {"text": "showing us two things--", "start": 172.71, "duration": 2.01}, {"text": "metabolized glucose to\npyruvate or ethanol itself--", "start": 174.72, "duration": 3.03}, {"text": "can both be turned into acetate.", "start": 177.75, "duration": 2.07}, {"text": "But really, the donor is\nthis molecule, acetyl-CoA.", "start": 179.82, "duration": 6.12}, {"text": "Which is basically also a\ncarboxylic acid, but rather", "start": 185.94, "duration": 3.3}, {"text": "than being a carboxylic\nacid, instead makes this", "start": 189.24, "duration": 2.94}, {"text": "a thioester bond, which\nactivates this carbon", "start": 192.18, "duration": 3.7}, {"text": "as a leaving group, such that it\ncan combine with oxaloacetate,", "start": 195.88, "duration": 19.88}, {"text": "which you'll remember\nfrom gluconeogenesis,", "start": 215.76, "duration": 5.37}, {"text": "releasing that S-CoA molecule\nto generate six-carbon citric.", "start": 221.13, "duration": 11.63}, {"text": "So, this is citric.", "start": 255.73, "duration": 0.96}, {"text": "You can see that we've made\na bond from this carbon", "start": 256.69, "duration": 3.42}, {"text": "on the acetate, losing this\nS-CoA group to this carbon", "start": 260.11, "duration": 5.59}, {"text": "oxaloacetate to make this\nsix-carbon citrate molecule,", "start": 265.7, "duration": 4.59}, {"text": "which is a one, two, three--", "start": 270.29, "duration": 1.88}, {"text": "three-carboxylic acid,\nor tricarboxylic acid.", "start": 272.17, "duration": 4.29}, {"text": "Hence the name\ncitric acid cycle,", "start": 276.46, "duration": 2.82}, {"text": "tricarboxylic acid cycle.", "start": 279.28, "duration": 2.17}, {"text": "Now, these six\ncarbons can then--", "start": 281.45, "duration": 3.14}, {"text": "or this six-carbon\ncitrate molecule", "start": 284.59, "duration": 2.31}, {"text": "can then be oxidized, generating\ntwo CO2 molecules that", "start": 286.9, "duration": 6.84}, {"text": "are released, and\nultimately reforming", "start": 293.74, "duration": 2.66}, {"text": "oxaloacetate that can pick up\nanother two-carbon acetyl-CoA", "start": 296.4, "duration": 5.38}, {"text": "to generate another citrate,\nand around and around the cycle", "start": 301.78, "duration": 3.33}, {"text": "goes, allowing in\nthe end the net entry", "start": 305.11, "duration": 4.92}, {"text": "of two carbons,\neffectively from acetate,", "start": 310.03, "duration": 3.81}, {"text": "and release of two\ncarbons as CO2.", "start": 313.84, "duration": 4.8}, {"text": "Now, as I alluded to, this\ncan come from pyruvate.", "start": 318.64, "duration": 5.55}, {"text": "It can come from\nacetate itself, vinegar.", "start": 324.19, "duration": 3.48}, {"text": "It can come from alcohol.", "start": 327.67, "duration": 1.53}, {"text": "It turns out that when\nyou break down fat,", "start": 329.2, "duration": 1.8}, {"text": "you also break it\ninto two carbon units.", "start": 331.0, "duration": 4.18}, {"text": "And so this cycle becomes\nvery useful for cells,", "start": 335.18, "duration": 3.5}, {"text": "because it allows the oxidation\nof many different molecules", "start": 338.68, "duration": 4.92}, {"text": "to completely turn\nthat carbon into CO2.", "start": 343.6, "duration": 5.2}, {"text": "Now, if we're going to\ndo this from glucose,", "start": 348.8, "duration": 4.57}, {"text": "however, you'll remember that\npyruvate has three carbons.", "start": 353.37, "duration": 12.38}, {"text": "And so if we're going\nto turn pyruvate", "start": 365.75, "duration": 1.94}, {"text": "into acetate, or acetyl-CoA, we\nhave to lose a carbon of CO2.", "start": 367.69, "duration": 6.75}, {"text": "We have to lose\nthis carbon as CO2.", "start": 374.44, "duration": 3.49}, {"text": "Now, we saw this before,\nthat we can do this via--", "start": 377.93, "duration": 3.77}, {"text": "this is exactly how\nwe generated ethanol", "start": 381.7, "duration": 5.1}, {"text": "when we did fermentation\nof pyruvate to ethanol,", "start": 386.8, "duration": 6.03}, {"text": "but that molecule\ndidn't generate acetate,", "start": 392.83, "duration": 3.3}, {"text": "It generated acetaldehyde.", "start": 396.13, "duration": 2.4}, {"text": "The difference, of course, being\nwhether or not this carbon gets", "start": 398.53, "duration": 3.66}, {"text": "oxidized in the case\nof acetate to the acid,", "start": 402.19, "duration": 2.64}, {"text": "or in acetaldehyde in\nethanol metabolism,", "start": 404.83, "duration": 2.37}, {"text": "where it remains an aldehyde.", "start": 407.2, "duration": 2.37}, {"text": "Now obviously, you can\nmake ethanol and then", "start": 409.57, "duration": 2.76}, {"text": "turn that ethanol into acetate.", "start": 412.33, "duration": 2.25}, {"text": "And that's a pathway that I\nguess certainly would work.", "start": 414.58, "duration": 3.22}, {"text": "However, that's not the way\nit happens in most organisms.", "start": 417.8, "duration": 3.62}, {"text": "Most organisms actually\ndirectly produce", "start": 421.42, "duration": 5.76}, {"text": "acetate, or more correctly,\nacetyl-CoA from pyruvate.", "start": 427.18, "duration": 4.69}, {"text": "So let's take a look\nat that reaction.", "start": 431.87, "duration": 2.33}, {"text": "So here once again is pyruvate.", "start": 438.5, "duration": 1.87}, {"text": "And if we turn\nthat pyruvate into", "start": 444.49, "duration": 3.42}, {"text": "this two-carbon\nacetyl-CoA, let's", "start": 447.91, "duration": 6.68}, {"text": "look here what has to happen.", "start": 454.59, "duration": 2.8}, {"text": "Well, the first\nthing is that we have", "start": 457.39, "duration": 4.67}, {"text": "to decarboxylate this molecule.", "start": 462.06, "duration": 5.99}, {"text": "And so that generates a CO2.", "start": 468.05, "duration": 3.56}, {"text": "We have to lose that one carbon.", "start": 471.61, "duration": 3.81}, {"text": "Also, as I pointed\nout, if we do this", "start": 475.42, "duration": 4.59}, {"text": "as if we did it in\nethanol metabolism,", "start": 480.01, "duration": 2.31}, {"text": "we'd be left with an aldehyde.", "start": 482.32, "duration": 2.38}, {"text": "But this is an acid, and so this\ncarbon also has to be oxidized.", "start": 484.7, "duration": 6.23}, {"text": "We know how to do that.", "start": 490.93, "duration": 1.11}, {"text": "We can donate those electrons\nto something like NAD,", "start": 492.04, "duration": 7.2}, {"text": "so the NAD is reduced to NADH.", "start": 499.24, "duration": 3.81}, {"text": "And we had to add this\nS-CoA molecule, which", "start": 503.05, "duration": 7.72}, {"text": "I'll come to in a minute.", "start": 510.77, "duration": 2.68}, {"text": "And so each of\nthese steps ends up", "start": 513.45, "duration": 6.28}, {"text": "making a fairly\ncomplicated reaction.", "start": 519.73, "duration": 3.99}, {"text": "Obviously, several co-factors\nare going to be involved.", "start": 523.72, "duration": 3.078}, {"text": "You should be able to guess\nthat just by looking at it.", "start": 526.798, "duration": 2.292}, {"text": "Obviously, I already\ndrew up there NAD.", "start": 529.09, "duration": 2.31}, {"text": "If we're going to\ndecarboxylate, remember", "start": 531.4, "duration": 3.06}, {"text": "this is a alpha\ncarboxylic, an alpha", "start": 534.46, "duration": 9.29}, {"text": "ketoacid-- the ketone group is\nalpha to the carboxylic acid.", "start": 543.75, "duration": 4.42}, {"text": "And so if we're doing\nalpha decarboxylation,", "start": 548.17, "duration": 3.02}, {"text": "as you might guess,\nwe need a co-factor.", "start": 551.19, "duration": 2.31}, {"text": "That co-factor, as\nI told you before,", "start": 553.5, "duration": 1.71}, {"text": "is the co-factor factor\nthiamine pyrophosphate.", "start": 555.21, "duration": 2.64}, {"text": "And finally, there's\nthis S-CoA group.", "start": 557.85, "duration": 4.09}, {"text": "We need to describe\nwhat that is.", "start": 561.94, "duration": 3.38}, {"text": "However, before delving\ninto those, and there's", "start": 565.32, "duration": 3.87}, {"text": "actually a couple other factors\nthat are needed as well,", "start": 569.19, "duration": 2.97}, {"text": "I want to mention\none other issue", "start": 572.16, "duration": 3.99}, {"text": "about this reaction, in\nthat this reaction happens", "start": 576.15, "duration": 4.83}, {"text": "in the mitochondria,\nbecause that's also", "start": 580.98, "duration": 3.84}, {"text": "where the TCA cycle happens.", "start": 584.82, "duration": 1.95}, {"text": "So, recall that if we divide\nthe cell into two compartments", "start": 586.77, "duration": 4.05}, {"text": "like an eukaryotic cell,\nhere we have the cytosol", "start": 590.82, "duration": 3.06}, {"text": "and the mitochondria\nin a eukaryotic cell.", "start": 593.88, "duration": 2.76}, {"text": "As we've already talked about,\nhaving different compartments", "start": 596.64, "duration": 3.0}, {"text": "helps facilitate different\nmetabolic reactions,", "start": 599.64, "duration": 2.753}, {"text": "because you can have different\nconditions in the two", "start": 602.393, "duration": 2.167}, {"text": "compartments.", "start": 604.56, "duration": 1.3}, {"text": "And so as we said, glycolysis\noccurs in the cytosol.", "start": 605.86, "duration": 9.38}, {"text": "Glucose to pyruvate.", "start": 615.24, "duration": 1.85}, {"text": "And last time I\nmentioned, the TCA cycle", "start": 617.09, "duration": 9.63}, {"text": "occurs in the mitochondria.", "start": 626.72, "duration": 4.62}, {"text": "And so that means if we're\ngoing to fully oxidize", "start": 631.34, "duration": 3.36}, {"text": "the pyruvate carbon\nto CO2 using the TCA", "start": 634.7, "duration": 4.2}, {"text": "cycle in the mitochondria,\nthat pyruvate", "start": 638.9, "duration": 2.61}, {"text": "has to get from the cytosol to\nthe mitochondria, or at least", "start": 641.51, "duration": 3.33}, {"text": "carbons from the pyruvate\nhave to get there.", "start": 644.84, "duration": 2.568}, {"text": "It turns out, you'll\nsee in a minute,", "start": 647.408, "duration": 1.542}, {"text": "acetyl-CoA is a\nvery large group.", "start": 648.95, "duration": 1.92}, {"text": "And so pyruvate\nitself is transported", "start": 650.87, "duration": 2.88}, {"text": "into the mitochondria.", "start": 653.75, "duration": 1.89}, {"text": "And that's where\nthe reaction occurs", "start": 655.64, "duration": 1.62}, {"text": "to turn it into acetyl-CoA that\ncan then enter the TCA cycle", "start": 657.26, "duration": 3.36}, {"text": "and oxidize.", "start": 660.62, "duration": 1.92}, {"text": "However, what this means is\nthat a transporter is actually", "start": 662.54, "duration": 4.83}, {"text": "needed to get this across\nthe mitochondrial membranes", "start": 667.37, "duration": 3.24}, {"text": "and into the matrix of the\nmitochondria where the TCA", "start": 670.61, "duration": 2.61}, {"text": "cycle happens.", "start": 673.22, "duration": 1.942}, {"text": "And I like to mention\nthis because it turns out", "start": 675.162, "duration": 1.958}, {"text": "the pyruvate carrier--", "start": 677.12, "duration": 1.17}, {"text": "that is, the\ntransporter-- the way", "start": 678.29, "duration": 1.5}, {"text": "that it actually gets that\npyruvate from the cytosol", "start": 679.79, "duration": 3.03}, {"text": "into the mitochondria\nactually was", "start": 682.82, "duration": 2.4}, {"text": "an unknown thing\nabout metabolism", "start": 685.22, "duration": 1.83}, {"text": "until 2012, so\nnot that long ago.", "start": 687.05, "duration": 3.33}, {"text": "Sometimes one can be\nleft with the feeling,", "start": 690.38, "duration": 4.77}, {"text": "listening to these metabolism\nclasses or reading a textbook,", "start": 695.15, "duration": 3.54}, {"text": "that everything about metabolism\nhas been known forever,", "start": 698.69, "duration": 3.66}, {"text": "but it's actually not true.", "start": 702.35, "duration": 1.59}, {"text": "Here's a very key, central\npart of the pathway that", "start": 703.94, "duration": 3.57}, {"text": "was actually just\ndiscovered, at least", "start": 707.51, "duration": 2.25}, {"text": "at the time of this lecture,\nless than 10 years ago.", "start": 709.76, "duration": 2.46}, {"text": "It also illustrates that not\nall metabolism is completely", "start": 715.04, "duration": 4.3}, {"text": "understood.", "start": 719.34, "duration": 3.17}, {"text": "Now, let's get back to this\nreaction, how you turn pyruvate", "start": 722.51, "duration": 4.47}, {"text": "into acetyl-CoA.", "start": 726.98, "duration": 2.61}, {"text": "And I want to go through\nnow and point out", "start": 729.59, "duration": 2.31}, {"text": "that several\nco-factors are needed.", "start": 731.9, "duration": 3.1}, {"text": "And so I already mentioned\none of them, S-CoA,", "start": 735.0, "duration": 4.46}, {"text": "which is shorthand\nfor coenzyme A. So,", "start": 739.46, "duration": 7.03}, {"text": "I need to tell you what that is.", "start": 746.49, "duration": 3.38}, {"text": "You hopefully are already\nfamiliar with TPP plus,", "start": 749.87, "duration": 4.98}, {"text": "thiamine pyrophosphate.", "start": 754.85, "duration": 1.32}, {"text": "We talked about\nthat when we talked", "start": 756.17, "duration": 3.12}, {"text": "about how you do alpha\ndecarboxylation to generate", "start": 759.29, "duration": 3.6}, {"text": "ethanol from pyruvate,\nalso used here", "start": 762.89, "duration": 2.55}, {"text": "for the alpha\ndecarboxylation reaction.", "start": 765.44, "duration": 3.18}, {"text": "Redox reaction\nhappens, and so we", "start": 768.62, "duration": 2.58}, {"text": "needed NAD plus to get\nconverted into NADH.", "start": 771.2, "duration": 6.56}, {"text": "We talked a lot about how that\nserves as an electron carrier,", "start": 777.76, "duration": 3.36}, {"text": "but it turns out that there's\ntwo additional electron", "start": 781.12, "duration": 3.0}, {"text": "carriers that are\ninvolved in this reaction.", "start": 784.12, "duration": 3.27}, {"text": "One of them is called\nFAD and the other one", "start": 787.39, "duration": 4.56}, {"text": "is called lipoic acid.", "start": 791.95, "duration": 2.205}, {"text": "Now you might say,\nwhy do we need", "start": 798.12, "duration": 1.58}, {"text": "all these electron carriers?", "start": 799.7, "duration": 2.37}, {"text": "Well, these are just\ndifferent molecules", "start": 802.07, "duration": 2.19}, {"text": "that can carry two\nelectrons, similar to NADH.", "start": 804.26, "duration": 6.34}, {"text": "And effectively, what these can\ndo by having multiple electron", "start": 810.6, "duration": 3.83}, {"text": "carriers--", "start": 814.43, "duration": 1.05}, {"text": "one can build chains of\noxidation and reduction", "start": 815.48, "duration": 4.2}, {"text": "reactions.", "start": 819.68, "duration": 1.26}, {"text": "And it turns out these chains\nof oxidation reduction reactions", "start": 820.94, "duration": 3.18}, {"text": "really become central to\nenergy transfers in biology,", "start": 824.12, "duration": 4.08}, {"text": "because building\nthese chains allows", "start": 828.2, "duration": 2.49}, {"text": "more easy stepwise\nrelease of energy", "start": 830.69, "duration": 3.33}, {"text": "as one moves across these\noxidation reduction reactions.", "start": 834.02, "duration": 3.64}, {"text": "Which remember, as I\nalluded to earlier, really", "start": 837.66, "duration": 2.51}, {"text": "are at the core of bioenergetics\nand a lot of what allows energy", "start": 840.17, "duration": 6.72}, {"text": "release from these pathways.", "start": 846.89, "duration": 3.09}, {"text": "What I mean by this\nwill be more explicit", "start": 849.98, "duration": 3.51}, {"text": "as we go through what some of\nthese co-factors look like.", "start": 853.49, "duration": 4.86}, {"text": "So, I'm not going to draw TPP\nplus or NAD again, but let's", "start": 858.35, "duration": 7.2}, {"text": "define what some of these\nother cofactors look like.", "start": 865.55, "duration": 4.54}, {"text": "So, let's start with coenzyme\nA. So, coenzyme A, it turns out,", "start": 870.09, "duration": 9.32}, {"text": "is useful.", "start": 879.41, "duration": 1.8}, {"text": "It's actually involved in\nlots of acylation reactions.", "start": 881.21, "duration": 5.15}, {"text": "What's an acylation reaction?", "start": 886.36, "duration": 1.71}, {"text": "Well, that's basically if you're\nmaking a carbon-carbon bond", "start": 888.07, "duration": 4.68}, {"text": "by adding a molecule of greater\nthan one carbon, so two carbons", "start": 892.75, "duration": 3.45}, {"text": "or greater, to something else.", "start": 896.2, "duration": 1.83}, {"text": "That's an acylation\nreaction, as we", "start": 898.03, "duration": 2.04}, {"text": "did with adding the two-carbon\nacetate to oxaloacetate", "start": 900.07, "duration": 4.74}, {"text": "to make citrate.", "start": 904.81, "duration": 1.65}, {"text": "And you'll actually see\ncoenzyme A will come up", "start": 906.46, "duration": 2.22}, {"text": "in this in many, many\nlectures throughout the rest", "start": 908.68, "duration": 2.43}, {"text": "of the course.", "start": 911.11, "duration": 1.29}, {"text": "Why this becomes useful\nis because it activates", "start": 912.4, "duration": 4.35}, {"text": "this basically carbon to\nthe left of, in this case,", "start": 916.75, "duration": 8.78}, {"text": "the ketone.", "start": 925.53, "duration": 0.92}, {"text": "Because, by having\nthat thioester there,", "start": 926.45, "duration": 2.88}, {"text": "ends up activating that carbon\nand allows it to carry out", "start": 929.33, "duration": 4.29}, {"text": "these acylation reactions.", "start": 933.62, "duration": 3.45}, {"text": "Coenzyme A itself is\nderived from a vitamin", "start": 937.07, "duration": 3.93}, {"text": "called pantothenic acid.", "start": 941.0, "duration": 3.285}, {"text": "And as a vitamin,\nthis is something", "start": 948.67, "duration": 4.05}, {"text": "that you have to\nget from the diet.", "start": 952.72, "duration": 2.65}, {"text": "Now, when we\nabbreviate coenzyme A,", "start": 955.37, "duration": 3.32}, {"text": "which is often\nabbreviated S-CoA,", "start": 958.69, "duration": 3.75}, {"text": "you get the sense that it's\nthis little tiny molecule", "start": 962.44, "duration": 2.52}, {"text": "that's just stuck on sulfur--", "start": 964.96, "duration": 1.74}, {"text": "stuck on to the end to\nmake this thioester bond.", "start": 966.7, "duration": 2.91}, {"text": "But it turns out coenzyme A is\nactually a giant molecule, one", "start": 969.61, "duration": 3.12}, {"text": "of the reasons why you\nactually synthesize acetyl-CoA", "start": 972.73, "duration": 6.66}, {"text": "in the mitochondria,\nbecause it's", "start": 979.39, "duration": 1.41}, {"text": "hard to transport\nthis giant molecule.", "start": 980.8, "duration": 3.37}, {"text": "And so this is what\npantothenic acid looks like.", "start": 984.17, "duration": 4.82}, {"text": "So, if I put an acid group here\nand a hydroxyl group there,", "start": 1007.92, "duration": 5.48}, {"text": "that would be pantothenic\nacid, the thing", "start": 1013.4, "duration": 2.13}, {"text": "that's in your cereal, on\nthe side of your cereal box.", "start": 1015.53, "duration": 4.545}, {"text": "Then there's these\nadditional pieces.", "start": 1025.47, "duration": 2.22}, {"text": "This is the active\nend of the molecule,", "start": 1027.69, "duration": 9.69}, {"text": "that's that sulfur\nfrom the S-CoA,", "start": 1037.38, "duration": 2.459}, {"text": "and then this side of the\nmolecule is esterified to two", "start": 1039.839, "duration": 5.341}, {"text": "phosphates, which\nare esterified to--", "start": 1045.18, "duration": 3.63}, {"text": "I'm not going to\ndraw it out, but this", "start": 1051.477, "duration": 1.583}, {"text": "would have an adenine base\nand a phosphate there.", "start": 1053.06, "duration": 6.14}, {"text": "So basically, this is\nADP, with a phosphate", "start": 1059.2, "duration": 8.34}, {"text": "added to the 3 prime\nposition of the ADP molecule,", "start": 1067.54, "duration": 4.2}, {"text": "added to pantothenic acid,\nadded to this short chain", "start": 1071.74, "duration": 4.26}, {"text": "with the sulfur on the end.", "start": 1076.0, "duration": 1.56}, {"text": "And this whole molecule\ntogether is coenzyme A.", "start": 1077.56, "duration": 3.99}, {"text": "And so when we say\nacetyl-CoA, it's", "start": 1081.55, "duration": 1.98}, {"text": "this giant molecule,\nS-thioester to the carbonyl,", "start": 1083.53, "duration": 9.1}, {"text": "the acid on acetate, to CH3.", "start": 1092.63, "duration": 4.32}, {"text": "And so that would be,\nbasically, acetyl-CoA.", "start": 1096.95, "duration": 3.73}, {"text": "And so one convenient\nthing about this", "start": 1100.68, "duration": 3.35}, {"text": "is it's much easier than\ndrawing that big molecule,", "start": 1104.03, "duration": 2.58}, {"text": "but it is a little bit\nmisleading in terms", "start": 1106.61, "duration": 4.32}, {"text": "of its size.", "start": 1110.93, "duration": 1.74}, {"text": "So, that's coenzyme A.", "start": 1112.67, "duration": 3.3}, {"text": "Next one I want to\ntalk about is FAD", "start": 1115.97, "duration": 6.27}, {"text": "which stands for flavin\nadenine dinucleotide.", "start": 1122.24, "duration": 8.88}, {"text": "So, flavin adenine dinucleotide\nis an electron carrier,", "start": 1134.6, "duration": 3.51}, {"text": "just like NAD plus.", "start": 1138.11, "duration": 1.725}, {"text": "And it's derived from\nthe vitamin riboflavin,", "start": 1145.33, "duration": 6.15}, {"text": "also referred to as vitamin B2.", "start": 1151.48, "duration": 3.0}, {"text": "Another thing from the side of\nyour cereal box, and basically", "start": 1157.24, "duration": 4.17}, {"text": "looks like this.", "start": 1161.41, "duration": 2.03}, {"text": "So, like NAD, it's\na dinucleotide.", "start": 1163.44, "duration": 8.23}, {"text": "And so here's ADP, just\nlike we do for CoA, or just", "start": 1180.14, "duration": 5.13}, {"text": "like one end of NAD.", "start": 1185.27, "duration": 2.16}, {"text": "One difference is that the\nother nucleotide down here", "start": 1187.43, "duration": 3.9}, {"text": "actually isn't\ntechnically a sugar.", "start": 1191.33, "duration": 2.68}, {"text": "It's ribitol instead of ribose.", "start": 1194.01, "duration": 3.23}, {"text": "What does that mean?", "start": 1197.24, "duration": 1.0}, {"text": "It doesn't have an aldehyde.", "start": 1198.24, "duration": 1.7}, {"text": "Instead, it is just\na five-carbon chain", "start": 1199.94, "duration": 4.77}, {"text": "where all of the\ncarbons are alcohols.", "start": 1204.71, "duration": 3.3}, {"text": "And so since\nthere's no aldehyde,", "start": 1214.45, "duration": 1.8}, {"text": "it doesn't form a ring.", "start": 1216.25, "duration": 1.95}, {"text": "And the base on this\nend, as a nicotinamide,", "start": 1245.15, "duration": 4.53}, {"text": "is this flavin group,\nwhich looks like this.", "start": 1249.68, "duration": 17.5}, {"text": "And so this is FAD, which\nis in the oxidized form.", "start": 1267.18, "duration": 8.56}, {"text": "Turns out, in the\noxidized form, FAD", "start": 1275.74, "duration": 3.51}, {"text": "is yellow, hence riboflavin--\n\"flavin\", yellow.", "start": 1279.25, "duration": 6.27}, {"text": "And the reason it's\nyellow-- you see", "start": 1285.52, "duration": 1.89}, {"text": "there's a conjugated double\nbond here across this part.", "start": 1287.41, "duration": 3.36}, {"text": "It turns out this is the\nactive part of the molecule,", "start": 1290.77, "duration": 3.69}, {"text": "and it works as follows.", "start": 1294.46, "duration": 1.44}, {"text": "And so if you have\na hydride ion,", "start": 1295.9, "duration": 2.64}, {"text": "remember the way we can\ntransfer two electrons.", "start": 1298.54, "duration": 3.06}, {"text": "Can transfer the two\nelectrons that way,", "start": 1306.39, "duration": 2.88}, {"text": "and that allows it to generate.", "start": 1309.27, "duration": 1.65}, {"text": "And I'll just draw\nthe middle, here.", "start": 1310.92, "duration": 2.7}, {"text": "Active part of the molecule.", "start": 1313.62, "duration": 2.7}, {"text": "So, that would be\nthese two nitrogens.", "start": 1331.18, "duration": 2.33}, {"text": "We've added two electrons to it.", "start": 1333.51, "duration": 1.84}, {"text": "And so this is\nabbreviated FADH2,", "start": 1335.35, "duration": 5.24}, {"text": "or the reduced form of FAD.", "start": 1340.59, "duration": 4.11}, {"text": "And it is colorless,\nbecause now you no longer", "start": 1344.7, "duration": 4.36}, {"text": "have that conjugated double\nbond system, loses its color.", "start": 1349.06, "duration": 3.75}, {"text": "And so you can follow whether\nFAD is oxidized or reduced", "start": 1352.81, "duration": 3.78}, {"text": "by just looking at color change.", "start": 1356.59, "duration": 3.96}, {"text": "So, that's FAD.", "start": 1360.55, "duration": 1.95}, {"text": "It's an electron carrier,\ncarries electrons", "start": 1362.5, "duration": 3.39}, {"text": "by a hydride transfer,\nvery similarly", "start": 1365.89, "duration": 3.24}, {"text": "to what we described\nfor NAD, but obviously", "start": 1369.13, "duration": 3.24}, {"text": "a different molecule.", "start": 1372.37, "duration": 2.52}, {"text": "And the last molecule,\nthe last co-factor", "start": 1374.89, "duration": 4.11}, {"text": "that we need for this\nreaction, is lipoic acid.", "start": 1379.0, "duration": 6.91}, {"text": "Which, unlike most\nthings in metabolism,", "start": 1385.91, "duration": 2.31}, {"text": "doesn't have an abbreviation\nand also functions", "start": 1388.22, "duration": 4.62}, {"text": "as an electron carrier.", "start": 1392.84, "duration": 1.86}, {"text": "And so lipoic acid\nlooks like this.", "start": 1394.7, "duration": 2.34}, {"text": "So, that is lipoic acid.", "start": 1417.57, "duration": 3.24}, {"text": "This is in the oxidized form.", "start": 1420.81, "duration": 4.38}, {"text": "And so where it's\noxidized is here", "start": 1425.19, "duration": 2.91}, {"text": "at this sulfur-sulfur bond.", "start": 1428.1, "duration": 1.56}, {"text": "So, you can think of this as\nthe same as a disulfide bond", "start": 1429.66, "duration": 3.72}, {"text": "that you learned about from\nProfessor Yaffe in proteins.", "start": 1433.38, "duration": 3.73}, {"text": "And so this is the oxidized\nform of the disulfide bond.", "start": 1437.11, "duration": 4.28}, {"text": "If I take this hydride, transfer\ntwo electrons across that bond,", "start": 1441.39, "duration": 7.84}, {"text": "then it goes to-- and I'll\njust draw here the active end.", "start": 1449.23, "duration": 4.445}, {"text": "Then we go here to the\nreduced form of lipoic acid,", "start": 1459.37, "duration": 5.74}, {"text": "and there's no\nabbreviation for oxidized", "start": 1465.11, "duration": 2.91}, {"text": "or reduced lipoic acid.", "start": 1468.02, "duration": 1.68}, {"text": "It's just lipoic acid,\noxidized lipoic acid, reduced.", "start": 1469.7, "duration": 4.26}, {"text": "And how they're\noxidized and reduced", "start": 1473.96, "duration": 2.25}, {"text": "is basically very similar\nto the disulfide bonds", "start": 1476.21, "duration": 5.34}, {"text": "that you saw in proteins being\noxidized, disulfide bond being", "start": 1481.55, "duration": 5.22}, {"text": "oxidized, or it can be reduced\nto not be a disulfide bond.", "start": 1486.77, "duration": 5.58}, {"text": "Now, it turns out that these\ncofactors, our TPP, FAD,", "start": 1492.35, "duration": 10.41}, {"text": "and lipoic acid, are\nall stably associated", "start": 1502.76, "duration": 4.92}, {"text": "with different subunits\nof a multi-protein complex", "start": 1507.68, "duration": 6.38}, {"text": "that assembles to catalyze that\nreaction to convert pyruvate", "start": 1514.06, "duration": 6.24}, {"text": "to acetyl-CoA.", "start": 1520.3, "duration": 3.03}, {"text": "The enzyme or\nenzyme complex that", "start": 1523.33, "duration": 2.28}, {"text": "carries this out is\nreferred to as PDH,", "start": 1525.61, "duration": 3.6}, {"text": "sometimes abbreviated\nPDC, which stands", "start": 1529.21, "duration": 3.42}, {"text": "for the pyruvate\ndehydrogenase complex.", "start": 1532.63, "duration": 13.48}, {"text": "So, pyruvate dehydrogenase, PDH,\npyruvate dehydrogenase complex,", "start": 1546.11, "duration": 4.08}, {"text": "PDC.", "start": 1550.19, "duration": 1.6}, {"text": "This complex is basically\nthree different polypeptides", "start": 1551.79, "duration": 4.67}, {"text": "that come together\nto form a complex", "start": 1556.46, "duration": 2.19}, {"text": "and catalyze that reaction.", "start": 1558.65, "duration": 2.31}, {"text": "Now, where this complex sits--", "start": 1560.96, "duration": 2.65}, {"text": "so, this is the mitochondria.", "start": 1563.61, "duration": 2.03}, {"text": "This is the matrix.", "start": 1565.64, "duration": 2.13}, {"text": "That's where this pyruvate\ndehydrogenase reaction occurs.", "start": 1567.77, "duration": 2.76}, {"text": "That's where the\nTCA cycle occurs.", "start": 1570.53, "duration": 2.64}, {"text": "And this PDH\ncomplex is basically", "start": 1573.17, "duration": 2.46}, {"text": "sitting here at the\nmembrane on the matrix side", "start": 1575.63, "duration": 3.96}, {"text": "of the membrane.", "start": 1579.59, "duration": 2.86}, {"text": "Now, the three\ndifferent polypeptides", "start": 1582.45, "duration": 2.27}, {"text": "that come together\nto form this complex", "start": 1584.72, "duration": 2.25}, {"text": "are creatively named\nE1, E2, and E3, four.", "start": 1586.97, "duration": 8.04}, {"text": "Enzyme one, two, and three.", "start": 1595.01, "duration": 2.67}, {"text": "And each of these,\nas I alluded to,", "start": 1597.68, "duration": 3.33}, {"text": "is associated with a\ndifferent co-factor.", "start": 1601.01, "duration": 3.557}, {"text": "And so E1 is associated\nwith thymine pyrophosphate.", "start": 1609.71, "duration": 7.05}, {"text": "E2 is associated\nwith lipoic acid.", "start": 1616.76, "duration": 10.75}, {"text": "And E3 is associated with FAD.", "start": 1627.51, "duration": 5.165}, {"text": "Now, let's go\nthrough the mechanism", "start": 1637.09, "duration": 3.03}, {"text": "for how this pyruvate\ndehydrogenase reaction works.", "start": 1640.12, "duration": 5.225}, {"text": "So remember, this is the\nactive part of TBP plus.", "start": 1702.47, "duration": 5.48}, {"text": "It is bound in the\nactive site of E1.", "start": 1707.95, "duration": 4.5}, {"text": "And it reacts with pyruvate to\ncatalyze alpha decarboxylation,", "start": 1712.45, "duration": 11.15}, {"text": "just like we described\nfor conversion of pyruvate", "start": 1723.6, "duration": 4.95}, {"text": "to alcohol.", "start": 1728.55, "duration": 1.56}, {"text": "So, you're going to see\nexactly the same mechanism", "start": 1730.11, "duration": 3.69}, {"text": "that we drew before.", "start": 1733.8, "duration": 2.69}, {"text": "So, that decarboxylates\nthe alpha-keto acid,", "start": 1755.98, "duration": 4.47}, {"text": "just like we saw to\ngenerate acetaldehyde.", "start": 1760.45, "duration": 6.99}, {"text": "The difference is rather\nthan resolve this such", "start": 1773.39, "duration": 3.9}, {"text": "that this carbon has\nthe same oxidation state", "start": 1777.29, "duration": 2.49}, {"text": "and make acetaldehyde, instead\nthe next step of this reaction", "start": 1779.78, "duration": 4.74}, {"text": "is going to be oxidized\nby reducing lipoic acid.", "start": 1784.52, "duration": 11.71}, {"text": "So, the active\npart of lipoic acid", "start": 1796.23, "duration": 2.81}, {"text": "that is in the active\nsite of the E2 subunit.", "start": 1799.04, "duration": 5.49}, {"text": "So this will now regenerate\nE1, but what we're left with,", "start": 1880.75, "duration": 6.42}, {"text": "then, is this.", "start": 1887.17, "duration": 3.65}, {"text": "Now, this intermediate\nbound to E2.", "start": 1890.82, "duration": 3.99}, {"text": "Here's where coenzyme\nA can come in, which", "start": 1905.13, "duration": 9.04}, {"text": "will then generate acetyl-CoA.", "start": 1914.17, "duration": 10.09}, {"text": "But now we are left with\nE2 in the reduced state,", "start": 1927.65, "duration": 12.24}, {"text": "rather than being in\nthe oxidized state.", "start": 1939.89, "duration": 3.06}, {"text": "So E2 has to be re-oxidized\nin order for this complex", "start": 1942.95, "duration": 5.04}, {"text": "to carry out the next\ncatalytic cycle, and the way", "start": 1947.99, "duration": 4.83}, {"text": "that works is as follows.", "start": 1952.82, "duration": 2.31}, {"text": "So you have FAD bound on E3.", "start": 1955.13, "duration": 6.0}, {"text": "And so you have a hydride\nion from the oxidation of E3", "start": 1961.13, "duration": 13.42}, {"text": "that can be transferred to FAD.", "start": 1974.55, "duration": 3.57}, {"text": "That will generate FAD from the\noxidized to the reduced form.", "start": 1978.12, "duration": 9.38}, {"text": "So re-oxidize lipoic acid\non E2, reduce FAD to FADH2,", "start": 1987.5, "duration": 8.7}, {"text": "and then that FADH2\ncan be re-oxidized back", "start": 1996.2, "duration": 3.81}, {"text": "to FAD via transferring\nthose electrons to NAD", "start": 2000.01, "duration": 6.41}, {"text": "plus to generate NADH.", "start": 2006.42, "duration": 5.3}, {"text": "So in this case, FADH2\nre-oxidized the FAD, NAD", "start": 2011.72, "duration": 5.46}, {"text": "plus reduced to NADH.", "start": 2017.18, "duration": 3.9}, {"text": "And so, effectively,\nwhat this happens", "start": 2021.08, "duration": 3.33}, {"text": "is that enzyme E1\nand E2 cooperate", "start": 2024.41, "duration": 4.68}, {"text": "to call what's referred to as\noxidative alpha decarboxylation", "start": 2029.09, "duration": 13.74}, {"text": "of pyruvate, while\nadding -CoA, so that's", "start": 2042.83, "duration": 4.26}, {"text": "where you get acetyl-CoA, with\nreduction of lipoic acid in E2,", "start": 2047.09, "duration": 8.0}, {"text": "and then E3 re-oxidizes\nthe lipoic acid in E2", "start": 2055.09, "duration": 5.28}, {"text": "while generating NADH.", "start": 2060.37, "duration": 4.039}, {"text": "This NADH, once it's\ngenerated, of course", "start": 2064.409, "duration": 2.268}, {"text": "those electrons have\nto go somewhere,", "start": 2066.677, "duration": 1.542}, {"text": "so they, like in glycolysis--", "start": 2068.219, "duration": 2.19}, {"text": "it also needs to regenerate\nto NAD at some point.", "start": 2070.409, "duration": 3.48}, {"text": "This is ultimately the\nelectrons that end up on oxygen,", "start": 2073.889, "duration": 4.231}, {"text": "and it's really this series\nof electron transfers,", "start": 2078.12, "duration": 4.47}, {"text": "with oxygen being a good\nelectron acceptor, that", "start": 2082.59, "duration": 2.91}, {"text": "ultimately allows controlled\nenergy release during carbon", "start": 2085.5, "duration": 5.07}, {"text": "oxidation.", "start": 2090.57, "duration": 1.169}, {"text": "And cells, you'll see, can\nuse that to make ATP or do", "start": 2091.739, "duration": 3.331}, {"text": "other kinds of work.", "start": 2095.07, "duration": 3.87}, {"text": "So, the net reaction\nand/or another way", "start": 2098.94, "duration": 3.78}, {"text": "to draw the pyruvate\ndehydrogenase reaction", "start": 2102.72, "duration": 4.44}, {"text": "would be as follows, and that's\ntaking pyruvate to acetyl-CoA.", "start": 2107.16, "duration": 8.23}, {"text": "And so we're going to take\ncoenzyme A and release CO2.", "start": 2118.89, "duration": 9.09}, {"text": "This is done by TPP\nplus, as part of E1.", "start": 2127.98, "duration": 14.52}, {"text": "That involves converting\nthe lipoic acid in E2", "start": 2142.5, "duration": 10.16}, {"text": "from the oxidized to\nthe reduced state.", "start": 2152.66, "duration": 3.42}, {"text": "That lipoic acid then\nhas to be re-oxidized.", "start": 2156.08, "duration": 4.05}, {"text": "If something's\noxidized, something else", "start": 2160.13, "duration": 2.13}, {"text": "has to be reduced.", "start": 2162.26, "duration": 1.53}, {"text": "That's FAD on E3,\nwhich also then cycles", "start": 2163.79, "duration": 6.3}, {"text": "between the oxidized\nand reduce state.", "start": 2170.09, "duration": 3.93}, {"text": "And ultimately, those\nelectrons ended up", "start": 2174.02, "duration": 3.42}, {"text": "being transferred to NAD\nplus to generate NADH.", "start": 2177.44, "duration": 6.57}, {"text": "And so the PDH complex\nis basically a chain", "start": 2184.01, "duration": 8.37}, {"text": "of electron transfer reactions.", "start": 2192.38, "duration": 8.63}, {"text": "And it's the first example of\na chain of electron transfer", "start": 2201.01, "duration": 4.68}, {"text": "reactions.", "start": 2205.69, "duration": 0.54}, {"text": "We're going to see that there\nis the electron transport", "start": 2206.23, "duration": 2.4}, {"text": "chain in the mitochondria,\neffectively does", "start": 2208.63, "duration": 3.27}, {"text": "the same thing.", "start": 2211.9, "duration": 0.97}, {"text": "And by coupling oxidation\nand reduction reactions", "start": 2212.87, "duration": 3.53}, {"text": "across chains of molecules like\nthis, effectively as a preview,", "start": 2216.4, "duration": 4.08}, {"text": "allows the stepwise energy\nrelease of these oxidation", "start": 2220.48, "duration": 3.45}, {"text": "reactions to occur.", "start": 2223.93, "duration": 4.24}, {"text": "So remember, if we burn glucose,\ncompletely oxidize it in one", "start": 2228.17, "duration": 3.38}, {"text": "step, where those electrons\nare directly transferred", "start": 2231.55, "duration": 2.2}, {"text": "to oxygen in combustion.", "start": 2233.75, "duration": 1.76}, {"text": "Lots of energy released,\nbut all in one step.", "start": 2235.51, "duration": 3.21}, {"text": "By doing these stepwise\nelectron transfers,", "start": 2238.72, "duration": 2.49}, {"text": "we can then basically break\nup that energy release", "start": 2241.21, "duration": 3.9}, {"text": "in a way that can be\ncaptured by cells to do work.", "start": 2245.11, "duration": 4.08}, {"text": "Here, the way\nenergy is captured,", "start": 2249.19, "duration": 1.86}, {"text": "it's not so obvious in this\nelectron transport reaction.", "start": 2251.05, "duration": 3.81}, {"text": "But effectively,\nyou're using oxidation", "start": 2254.86, "duration": 3.72}, {"text": "of the ketone on pyruvate, with\ndecarboxylation to the acid", "start": 2258.58, "duration": 8.19}, {"text": "to generate, rather than just\nthe acid, a thioester bond.", "start": 2266.77, "duration": 3.63}, {"text": "And that's that thioester bond--", "start": 2270.4, "duration": 2.07}, {"text": "as well as NADH, that's\nenergy as well-- but it's", "start": 2272.47, "duration": 2.64}, {"text": "really that thioester bond that\nthen can be recaptured later", "start": 2275.11, "duration": 3.51}, {"text": "to drive synthesis of\ncitrate in the TCA cycle.", "start": 2278.62, "duration": 4.8}, {"text": "Now, next what I want to do is\nI want to discuss the TCA cycle", "start": 2286.48, "duration": 5.49}, {"text": "reactions.", "start": 2291.97, "duration": 0.63}, {"text": "Now that you see how you\ncan get acetyl-CoA, at least", "start": 2292.6, "duration": 2.82}, {"text": "from pyruvate, I want to\ndiscuss how you can now", "start": 2295.42, "duration": 3.03}, {"text": "use that acetyl-CoA and\noxidize it back to combine it", "start": 2298.45, "duration": 5.46}, {"text": "with oxaloacetate,\nand oxidize it back", "start": 2303.91, "duration": 4.05}, {"text": "to make citrate, and then\noxidize it back to oxaloacetate", "start": 2307.96, "duration": 3.39}, {"text": "to run the TCA cycle.", "start": 2311.35, "duration": 4.14}, {"text": "OK, great.", "start": 2315.49, "duration": 2.47}, {"text": "So, the first reaction\nof the TCA cycle.", "start": 2317.96, "duration": 16.16}, {"text": "Here's acetyl-CoA.", "start": 2334.12, "duration": 5.97}, {"text": "It will combine\nwith oxaloacetate.", "start": 2340.09, "duration": 13.44}, {"text": "This reaction is catalyzed by an\nenzyme called citrate synthase,", "start": 2366.42, "duration": 31.71}, {"text": "and generates the six-carbon\ntricarboxylic acid citrate.", "start": 2398.13, "duration": 7.35}, {"text": "So, how does this reaction work?", "start": 2405.48, "duration": 3.86}, {"text": "Here's drawing acetyl-CoA\nin a slightly different way.", "start": 2447.99, "duration": 4.93}, {"text": "If I redraw this\nas the enol, this", "start": 2452.92, "duration": 32.7}, {"text": "will generate citrate via,\neffectively, that mechanism.", "start": 2485.62, "duration": 60.72}, {"text": "Next, citrate is\nconverted by adding water", "start": 2549.61, "duration": 12.99}, {"text": "across this carbon-carbon,\nor by removing water", "start": 2562.6, "duration": 5.85}, {"text": "across this carbon-carbon\nbond, to generate", "start": 2568.45, "duration": 8.34}, {"text": "this intermediate\ncalled cis-aconitate.", "start": 2576.79, "duration": 2.47}, {"text": "So this intermediate is\ncalled cis-aconitate.", "start": 2611.989, "duration": 2.671}, {"text": "so all I did was\ndehydrate across that bond", "start": 2618.26, "duration": 3.18}, {"text": "so there's a double bond there.", "start": 2621.44, "duration": 1.9}, {"text": "And then if I re-add\nwater across that bond,", "start": 2623.34, "duration": 12.84}, {"text": "I generate this molecule\ncalled isocitrate.", "start": 2636.18, "duration": 23.46}, {"text": "So effectively, to convert\ncitrate to isocitrate,", "start": 2662.24, "duration": 4.26}, {"text": "I'm moving the hydroxyl\ngroup from that carbon", "start": 2666.5, "duration": 3.48}, {"text": "to this carbon.", "start": 2669.98, "duration": 1.65}, {"text": "To do that, I basically\ndehydrate, make a double bond,", "start": 2671.63, "duration": 4.13}, {"text": "remove water, re-add\nwater across that bond", "start": 2675.76, "duration": 2.95}, {"text": "in the opposite direction\nto generate this molecule,", "start": 2678.71, "duration": 3.24}, {"text": "isocitrate.", "start": 2681.95, "duration": 1.6}, {"text": "This reaction is carried out\nby an enzyme called aconitase,", "start": 2683.55, "duration": 16.66}, {"text": "and converts citrate\nto isocitrate.", "start": 2700.21, "duration": 5.3}, {"text": "I think it's a little\neasier to see this reaction", "start": 2705.51, "duration": 5.31}, {"text": "if I draw it a\nslightly different way.", "start": 2710.82, "duration": 2.27}, {"text": "So, this here is\njust drawing citrate", "start": 2772.59, "duration": 2.3}, {"text": "by just slightly rotating the\nmolecule to look like that.", "start": 2774.89, "duration": 6.67}, {"text": "And so I'm basically\nremoving water here.", "start": 2781.56, "duration": 2.93}, {"text": "And then I'm now just\nadding water back", "start": 2811.04, "duration": 6.06}, {"text": "in the opposite orientation\nto generate isocitrate.", "start": 2817.1, "duration": 23.75}, {"text": "Now, you'll notice\nwhen I drew this--", "start": 2848.83, "duration": 4.47}, {"text": "if you look at citrate, this\nis actually a symmetrical", "start": 2853.3, "duration": 3.6}, {"text": "molecule, so the top half and\nthe bottom half of citrate", "start": 2856.9, "duration": 6.48}, {"text": "are identical.", "start": 2863.38, "duration": 2.32}, {"text": "And so what's interesting\nabout nature is", "start": 2865.7, "duration": 3.71}, {"text": "that it treats these carbons--", "start": 2869.41, "duration": 2.1}, {"text": "the green carbons that\ncame from acetyl-CoA--", "start": 2871.51, "duration": 2.55}, {"text": "different from the side\nof the molecule that", "start": 2874.06, "duration": 3.21}, {"text": "comes from oxaloacetate.", "start": 2877.27, "duration": 2.94}, {"text": "And effectively, nature always\nmoves the hydroxyl group", "start": 2880.21, "duration": 5.16}, {"text": "to this carbon that\ncame from oxaloacetate,", "start": 2885.37, "duration": 3.45}, {"text": "and never moves\nit to this carbon", "start": 2888.82, "duration": 2.85}, {"text": "that came from acetyl-CoA.", "start": 2891.67, "duration": 3.6}, {"text": "This is an example\nwhere enzymes--", "start": 2895.27, "duration": 2.97}, {"text": "nature treats a symmetrical\nmolecule like citrate", "start": 2898.24, "duration": 4.71}, {"text": "in an asymmetrical way.", "start": 2902.95, "duration": 2.13}, {"text": "And this has consequences for\nhow carbon is actually traced", "start": 2905.08, "duration": 4.83}, {"text": "through the entire TCA cycle.", "start": 2909.91, "duration": 2.49}, {"text": "Because even though you\nmight think things could get", "start": 2912.4, "duration": 2.19}, {"text": "scrambled at citrate,\nthey never do.", "start": 2914.59, "duration": 2.64}, {"text": "Meaning an isocitrate-- it's\nalways these green carbons", "start": 2917.23, "duration": 4.35}, {"text": "that came from acetyl-CoA.", "start": 2921.58, "duration": 1.74}, {"text": "You never get\nthose green carbons", "start": 2923.32, "duration": 1.86}, {"text": "on the other side of isocitrate.", "start": 2925.18, "duration": 3.78}, {"text": "And so when we go\nthrough the TCA cycle,", "start": 2928.96, "duration": 2.01}, {"text": "I'll keep these carbons\ngreen until the point where", "start": 2930.97, "duration": 3.06}, {"text": "you can no longer distinguish\nwhich carbon came from", "start": 2934.03, "duration": 4.26}, {"text": "came from which reaction.", "start": 2938.29, "duration": 1.295}, {"text": "The next reaction is\nwe're going to oxidize", "start": 2942.16, "duration": 5.58}, {"text": "this carbon of isocitrate.", "start": 2947.74, "duration": 4.29}, {"text": "So if we're going to\noxidize that carbon,", "start": 2952.03, "duration": 2.52}, {"text": "those electrons have\nto go somewhere.", "start": 2954.55, "duration": 2.82}, {"text": "And so if we oxidize\nthe carbon, we", "start": 2976.31, "duration": 3.84}, {"text": "can use NAD plus as an electron\nacceptor, reduce it to NADH.", "start": 2980.15, "duration": 9.09}, {"text": "That generates\nthis intermediate.", "start": 2989.24, "duration": 9.01}, {"text": "So hopefully this is clear\nto everybody at this point,", "start": 3020.46, "duration": 3.48}, {"text": "but just in case.", "start": 3023.94, "duration": 2.21}, {"text": "So, this carbon\nhere and isocitrate.", "start": 3029.23, "duration": 5.33}, {"text": "If I oxidize that\nalcohol to the ketone,", "start": 3034.56, "duration": 15.01}, {"text": "now I generate a hydride ion.", "start": 3049.57, "duration": 2.04}, {"text": "Those two electrons and the\nhydrogen can go to NAD plus", "start": 3051.61, "duration": 2.67}, {"text": "and reduce it to NADH.", "start": 3054.28, "duration": 2.79}, {"text": "That generates\nthis intermediate.", "start": 3057.07, "duration": 2.52}, {"text": "It's called oxalosuccinate.", "start": 3062.43, "duration": 3.79}, {"text": "Which then, if you\nnotice, the oxalosuccinate", "start": 3066.22, "duration": 5.64}, {"text": "is now a beta keto acid.", "start": 3071.86, "duration": 4.56}, {"text": "So alpha, beta.", "start": 3076.42, "duration": 6.0}, {"text": "The acid group is\nbeta to the ketone,", "start": 3082.42, "duration": 3.31}, {"text": "so it's a beta keto acid.", "start": 3085.73, "duration": 1.95}, {"text": "Remember, beta\ndecarboxylation is favorable,", "start": 3087.68, "duration": 4.59}, {"text": "and so I can lose that CO2.", "start": 3092.27, "duration": 3.59}, {"text": "And what I'm left with\nis this molecule, which", "start": 3095.86, "duration": 19.31}, {"text": "is called alpha keto glutarate.", "start": 3115.17, "duration": 10.93}, {"text": "So this whole reaction\nhere, the oxidation", "start": 3126.1, "duration": 8.27}, {"text": "of the alcohol to\nthe ketone, followed", "start": 3134.37, "duration": 2.22}, {"text": "by beta decarboxylation\nof oxalosuccinate", "start": 3136.59, "duration": 3.42}, {"text": "to alpha ketoglutarate,\nis carried out", "start": 3140.01, "duration": 2.55}, {"text": "by an enzyme called\nisocitrate dehydrogenase.", "start": 3142.56, "duration": 6.12}, {"text": "And of course,\njust to remind you,", "start": 3154.31, "duration": 16.352}, {"text": "here's that beta keto\nacid in oxalosuccinate.", "start": 3170.662, "duration": 7.998}, {"text": "And so that can decarboxylate,\nleading this enol.", "start": 3184.51, "duration": 16.06}, {"text": "Which can, of course, rearrange\nback to the ketone that we see,", "start": 3200.57, "duration": 15.23}, {"text": "an alpha ketoglutarate.", "start": 3215.8, "duration": 6.45}, {"text": "Now, if you look at\nalpha ketoglutarate,", "start": 3222.25, "duration": 7.46}, {"text": "you'll notice that-- and\nI will redraw over here.", "start": 3229.71, "duration": 7.155}, {"text": "So, this here is just me\nredrawing alpha ketoglutarate,", "start": 3251.94, "duration": 6.69}, {"text": "which is often\nabbreviated alpha kG.", "start": 3258.63, "duration": 5.33}, {"text": "Just drew it as a straight line.", "start": 3263.96, "duration": 2.41}, {"text": "Now, if you'll notice,\nalpha keto glutarate", "start": 3266.37, "duration": 2.93}, {"text": "is a alpha ketoacid.", "start": 3269.3, "duration": 3.45}, {"text": "And so here the acid group\nis alpha to the ketone.", "start": 3272.75, "duration": 4.87}, {"text": "So, an alpha keto acid.", "start": 3277.62, "duration": 2.0}, {"text": "It's effectively\njust like pyruvate,", "start": 3279.62, "duration": 2.55}, {"text": "but has this additional\npieces on it.", "start": 3282.17, "duration": 2.94}, {"text": "And it turns out the next\nstep in the TCA cycle", "start": 3285.11, "duration": 3.63}, {"text": "is the exact\nreaction that we saw", "start": 3288.74, "duration": 4.08}, {"text": "with pyruvate dehydrogenase.", "start": 3292.82, "duration": 3.42}, {"text": "It's alpha decarboxylation,\noxidative alpha", "start": 3296.24, "duration": 5.01}, {"text": "keto acid decarboxylation,\nas follows.", "start": 3301.25, "duration": 21.03}, {"text": "So, we carry out.", "start": 3322.28, "duration": 2.81}, {"text": "This is a molecule\ncalled succinyl-CoA.", "start": 3357.15, "duration": 7.56}, {"text": "And so, you'll see what happened\nthere is decarboxylated here,", "start": 3364.71, "duration": 6.12}, {"text": "this carbon, while oxidizing\nthis ketone to the acid", "start": 3370.83, "duration": 7.2}, {"text": "and adding -CoA.", "start": 3378.03, "duration": 1.77}, {"text": "That's a redox reaction.", "start": 3379.8, "duration": 1.6}, {"text": "So NAD, NADH, it turns out this\nis exactly the same mechanism--", "start": 3381.4, "duration": 7.43}, {"text": "so I don't need\nto draw it again--", "start": 3388.83, "duration": 1.53}, {"text": "that I just showed you for\npyruvate dehydrogenase.", "start": 3390.36, "duration": 4.38}, {"text": "So it needs all the\nsame cofactors--", "start": 3394.74, "duration": 1.98}, {"text": "TPP plus, lipoic acid, FAD.", "start": 3396.72, "duration": 4.05}, {"text": "And in fact, it even shares some\nof the same enzyme complexes,", "start": 3400.77, "duration": 6.24}, {"text": "subunits, as pyruvate\ndehydrogenase.", "start": 3407.01, "duration": 4.71}, {"text": "And so this is a reaction\nthat's catalyzed by alpha", "start": 3411.72, "duration": 5.61}, {"text": "ketoglutarate dehydrogenase.", "start": 3417.33, "duration": 2.13}, {"text": "Like pyruvate dehydrogenase,\nthis is a complex,", "start": 3422.52, "duration": 3.69}, {"text": "and so it has a unique\nE1, which makes sense.", "start": 3426.21, "duration": 3.44}, {"text": "Remember, E1 of\npyruvate dehydrogenase", "start": 3429.65, "duration": 2.35}, {"text": "was actually the subunit\nthat bound the pyruvate.", "start": 3432.0, "duration": 3.03}, {"text": "E1 of alpha ketoglutarate\ndehydrogenase is unique.", "start": 3435.03, "duration": 2.79}, {"text": "It binds alpha ketoglutarate\ninstead of pyruvate.", "start": 3437.82, "duration": 2.58}, {"text": "However, they share\nthe same E2 and E3s,", "start": 3440.4, "duration": 4.35}, {"text": "and so the E2s and\nE3s would carry out", "start": 3444.75, "duration": 3.39}, {"text": "exactly the same reaction\nand play the same part", "start": 3448.14, "duration": 4.2}, {"text": "in the mechanism of how you\ndo this alpha oxidative alpha", "start": 3452.34, "duration": 6.06}, {"text": "decarboxylation to turn\nalpha ketoglutarate", "start": 3458.4, "duration": 2.7}, {"text": "into succinyl-CoA.", "start": 3461.1, "duration": 4.23}, {"text": "Now, remember in\npyruvate dehydrogenase,", "start": 3465.33, "duration": 2.01}, {"text": "once we got that\nacetyl-CoA, we then", "start": 3467.34, "duration": 1.77}, {"text": "use this CoA group to drive\ncondensation with citrate.", "start": 3469.11, "duration": 3.57}, {"text": "Well, in this case,\nwhat happens is", "start": 3472.68, "duration": 1.86}, {"text": "you don't want to combine\ncondensation here.", "start": 3474.54, "duration": 3.57}, {"text": "Instead, what is\ngoing to happen is", "start": 3478.11, "duration": 2.58}, {"text": "you want to use this CoA\ngroup to now generate ATP.", "start": 3480.69, "duration": 7.47}, {"text": "And so this is going to\ncouple release of the CoA", "start": 3488.16, "duration": 7.05}, {"text": "to generate an ATP equivalent.", "start": 3495.21, "duration": 2.22}, {"text": "It's actually GTP that's\ngenerated by the TCA cycle.", "start": 3497.43, "duration": 5.32}, {"text": "And so, this is\ngoing to generate", "start": 3502.75, "duration": 11.88}, {"text": "this molecule, succinate.", "start": 3514.63, "duration": 4.86}, {"text": "And the enzyme that does this\nis called succinic bio-kinase.", "start": 3519.49, "duration": 8.3}, {"text": "So, let's go through over\nhere how this enzyme works.", "start": 3536.93, "duration": 4.275}, {"text": "So here's succinyl-CoA,\nbasically using favorable loss", "start": 3552.8, "duration": 12.15}, {"text": "of the CoA breaking the\nthioester bond to generate", "start": 3564.95, "duration": 15.97}, {"text": "this acid anhydride.", "start": 3580.92, "duration": 1.83}, {"text": "We saw an acid anhydride\nbefore in glycolysis.", "start": 3582.75, "duration": 5.4}, {"text": "Remember, we made\n1-3-bisphosphoglycerate,", "start": 3588.15, "duration": 2.91}, {"text": "so that's a good\nphosphate donor.", "start": 3591.06, "duration": 3.12}, {"text": "And then that can be used\nto generate succinate,", "start": 3594.18, "duration": 4.93}, {"text": "and transferring that\nphosphate to GDP to make GTP,", "start": 3599.11, "duration": 6.45}, {"text": "just like\n1-3-bisphosphoglycerate,", "start": 3605.56, "duration": 3.06}, {"text": "was able to transfer\nthe phosphate", "start": 3608.62, "duration": 1.8}, {"text": "from the acid anhydride to\nADP to make ATP in glycolysis.", "start": 3610.42, "duration": 7.95}, {"text": "So, the next step is to\noxidize this carbon-carbon bond", "start": 3620.95, "duration": 13.54}, {"text": "in succinate.", "start": 3634.49, "duration": 2.91}, {"text": "So if we're going to oxidize\na carbon-carbon bond,", "start": 3637.4, "duration": 4.29}, {"text": "those electrons have\nto go somewhere.", "start": 3641.69, "duration": 2.4}, {"text": "So there's our\ncarbon-carbon bond.", "start": 3650.67, "duration": 3.12}, {"text": "And so if we\ngenerate hydride ion", "start": 3661.67, "duration": 11.53}, {"text": "just like we did in other\noxidation reactions,", "start": 3673.2, "duration": 5.07}, {"text": "but this hydride ion is\ntransferred not to NAD,", "start": 3678.27, "duration": 5.61}, {"text": "but instead to FAD, a\ndifferent electron carrier,", "start": 3683.88, "duration": 6.63}, {"text": "to generate if FADH2.", "start": 3690.51, "duration": 4.17}, {"text": "Now, I should point out\nsuccinate, like citrate, is", "start": 3694.68, "duration": 3.69}, {"text": "a symmetrical molecule.", "start": 3698.37, "duration": 1.68}, {"text": "But at this point, nature\ndoesn't tell the difference.", "start": 3700.05, "duration": 3.63}, {"text": "Once it generates\nsuccinate, this molecule", "start": 3703.68, "duration": 3.76}, {"text": "now gets scrambled.", "start": 3707.44, "duration": 1.31}, {"text": "And so everything\ndownstream of succinate,", "start": 3708.75, "duration": 2.58}, {"text": "you no longer know which\ncarbons came from acetyl-CoA.", "start": 3711.33, "duration": 3.42}, {"text": "This generates this\nmolecule called fumarate,", "start": 3725.77, "duration": 4.77}, {"text": "and this reaction is carried\nout by an enzyme called", "start": 3730.54, "duration": 8.48}, {"text": "succinate dehydrogenase,\noften abbreviated SDH", "start": 3739.02, "duration": 13.0}, {"text": "for succinate dehydrogenase.", "start": 3752.02, "duration": 2.55}, {"text": "Now, the next reaction\nis, we're going", "start": 3757.85, "duration": 7.05}, {"text": "to add water across this\ndouble bond of fumarate.", "start": 3764.9, "duration": 5.62}, {"text": "And that generates this\nintermediate, malate.", "start": 3808.27, "duration": 5.425}, {"text": "This reaction is\ncarried out by an enzyme", "start": 3817.95, "duration": 4.68}, {"text": "called fumarate hydratase.", "start": 3822.63, "duration": 9.3}, {"text": "And it's simply adding\na water molecule", "start": 3831.93, "duration": 3.39}, {"text": "across that double bond.", "start": 3835.32, "duration": 3.15}, {"text": "Once we have malate,\nif you look what's", "start": 3838.47, "duration": 3.24}, {"text": "the difference between\nmalate and oxaloacetate,", "start": 3841.71, "duration": 4.74}, {"text": "the difference is that in\noxaloacetate, this carbon", "start": 3846.45, "duration": 5.1}, {"text": "is a ketone.", "start": 3851.55, "duration": 1.41}, {"text": "Whereas in malate,\nit's an alcohol.", "start": 3852.96, "duration": 2.43}, {"text": "And so if we want to turn\nthis carbon from the alcohol", "start": 3855.39, "duration": 2.76}, {"text": "into the ketone, that is, of\ncourse, a oxidation reaction,", "start": 3858.15, "duration": 6.34}, {"text": "and so those electrons\nhave to go somewhere.", "start": 3864.49, "duration": 7.98}, {"text": "Don't need to draw\nthe mechanism again.", "start": 3872.47, "duration": 4.32}, {"text": "It's basically just\nthe hydride transfer", "start": 3876.79, "duration": 4.29}, {"text": "to oxidize this to an\nalcohol, to the ketone.", "start": 3881.08, "duration": 4.64}, {"text": "That oxidation couples to a\nreduction of NAD plus to NADH.", "start": 3885.72, "duration": 5.46}, {"text": "This is carried out by an enzyme\ncalled malate dehydrogenase.", "start": 3891.18, "duration": 6.913}, {"text": "And doing this\ncompletes the TCA cycle,", "start": 3907.19, "duration": 5.79}, {"text": "regenerating oxaloacetate,\nthat can then", "start": 3912.98, "duration": 3.18}, {"text": "recombine with\nanother acetyl-CoA", "start": 3916.16, "duration": 2.52}, {"text": "to go through another\nround of the cycle.", "start": 3918.68, "duration": 5.52}, {"text": "You'll notice that going\nthrough this cycle,", "start": 3924.2, "duration": 4.5}, {"text": "there's two CO2s lost.", "start": 3928.7, "duration": 3.39}, {"text": "One of them is lost here\nat the isocitrate to alpha", "start": 3932.09, "duration": 6.93}, {"text": "ketoglutarate reaction.", "start": 3939.02, "duration": 1.84}, {"text": "So, this decarboxylation\nfrom oxaloacetate", "start": 3940.86, "duration": 4.555}, {"text": "to alpha ketoglutarate.", "start": 3945.415, "duration": 1.255}, {"text": "That beta decarboxylation,\nthat's the first CO2.", "start": 3946.67, "duration": 3.33}, {"text": "The other one is lost here\nat the alpha ketoglutarate.", "start": 3950.0, "duration": 3.405}, {"text": "The alpha ketoglutarate\ndehydrogenase step,", "start": 3957.37, "duration": 2.73}, {"text": "where you have this\nalpha decarboxylation", "start": 3960.1, "duration": 3.87}, {"text": "to take alpha ketoglutarate\nto succinyl-CoA", "start": 3963.97, "duration": 3.57}, {"text": "oxidative alpha decarboxylation.", "start": 3967.54, "duration": 4.74}, {"text": "Now, what's cool about\nthis, as you noticed,", "start": 3972.28, "duration": 3.39}, {"text": "we just discussed all the\nreactions of the TCA cycle.", "start": 3975.67, "duration": 5.1}, {"text": "And I showed you, reminded\nyou, of some chemistry", "start": 3980.77, "duration": 2.69}, {"text": "that you've already\nseen, but unless you", "start": 3983.46, "duration": 2.55}, {"text": "count the chemistry we showed\nyou earlier for how the PDH", "start": 3986.01, "duration": 3.465}, {"text": "and alpha ketoglutarate\ndehydrogenase", "start": 3989.475, "duration": 1.875}, {"text": "reactions work with E1, E2\nand E3, with lipoic acid, FAD.", "start": 3991.35, "duration": 4.26}, {"text": "That was obviously\nnew for today.", "start": 3995.61, "duration": 1.69}, {"text": "But other than that,\neverything else", "start": 3997.3, "duration": 2.3}, {"text": "was chemistry that\nyou've already seen.", "start": 3999.6, "duration": 2.64}, {"text": "And this really\npoints out the point", "start": 4002.24, "duration": 1.65}, {"text": "that I made earlier, that\nmetabolism is really variations", "start": 4003.89, "duration": 3.57}, {"text": "on relatively few reactions.", "start": 4007.46, "duration": 1.77}, {"text": "We've just repurposed some of\nthe same tricks, if you will,", "start": 4009.23, "duration": 3.4}, {"text": "that we're used in\nglycolysis, and allowed", "start": 4012.63, "duration": 3.07}, {"text": "it to now do an entire different\npathway, the TCA cycle.", "start": 4015.7, "duration": 4.39}, {"text": "It also points out how Hans\nKrebs was-- well, is still--", "start": 4020.09, "duration": 2.78}, {"text": "remarkable, able to figure\nout from chemistry alone,", "start": 4022.87, "duration": 3.66}, {"text": "because there's actually quite\na bit of logic to the way", "start": 4026.53, "duration": 2.88}, {"text": "metabolism works.", "start": 4029.41, "duration": 2.62}, {"text": "Now, I want to say this again.", "start": 4032.03, "duration": 1.25}, {"text": "Note there were two carbons\nthat entered acetyl-CoA,", "start": 4033.28, "duration": 3.0}, {"text": "and two carbons that\nwere lost to CO2.", "start": 4036.28, "duration": 3.77}, {"text": "But if you look,\nthe green carbons", "start": 4040.05, "duration": 2.64}, {"text": "remain in the same places\nuntil they get to succinate.", "start": 4042.69, "duration": 4.5}, {"text": "and so the two\ncarbons that enter", "start": 4047.19, "duration": 2.13}, {"text": "are not lost on the\nfirst turn of the cycle.", "start": 4049.32, "duration": 3.03}, {"text": "It's actually two carbons\nthat came from oxaloacetate", "start": 4052.35, "duration": 5.46}, {"text": "that are converted to CO2\nas that acetyl-CoA goes", "start": 4057.81, "duration": 4.41}, {"text": "through the cycle.", "start": 4062.22, "duration": 1.12}, {"text": "And so to oxidize the exact\ncarbons from acetyl-CoA to CO2", "start": 4063.34, "duration": 4.58}, {"text": "requires more than\none turn of the cycle.", "start": 4067.92, "duration": 5.3}, {"text": "You'll also notice that\nthe cycle is oxidation.", "start": 4073.22, "duration": 4.44}, {"text": "And so oxidation reactions,\nof course, release energy.", "start": 4077.66, "duration": 4.01}, {"text": "We've talked about that.", "start": 4081.67, "duration": 1.0}, {"text": "And so it's favorable.", "start": 4082.67, "duration": 2.4}, {"text": "And the products, if you will,\nare three NADH molecules.", "start": 4085.07, "duration": 6.965}, {"text": "You can say plus one more NADH\nif we're going all the way", "start": 4092.035, "duration": 4.465}, {"text": "from glucose or from pyruvate.", "start": 4096.5, "duration": 4.529}, {"text": "Glucose derived pyruvate because\nthe pyruvate dehydrogenase", "start": 4101.029, "duration": 3.091}, {"text": "reaction also generates an\nNADH to make that a acetyl-CoA.", "start": 4104.12, "duration": 5.529}, {"text": "One FADH2, as well\nas one GTP molecule.", "start": 4109.649, "duration": 8.71}, {"text": "And so lots of\noxidation going on here.", "start": 4118.359, "duration": 3.21}, {"text": "We completely oxidized\ntwo carbons to CO2,", "start": 4121.569, "duration": 2.781}, {"text": "so that's energy release.", "start": 4124.35, "duration": 2.879}, {"text": "But you notice you only get\none GTP from the molecule.", "start": 4127.229, "duration": 5.05}, {"text": "Now, this GTP, of\ncourse-- that reaction,", "start": 4132.279, "duration": 3.231}, {"text": "the succinic\nthiokinase reaction,", "start": 4135.51, "duration": 2.429}, {"text": "like the reactions\nwe saw on glycolysis,", "start": 4137.939, "duration": 2.071}, {"text": "is such that it can generate\nGTP at a high DGP-GDP", "start": 4140.01, "duration": 4.53}, {"text": "ratio, or ATP-ADP ratio.", "start": 4144.54, "duration": 1.678}, {"text": "Remember, those are equivalent.", "start": 4146.218, "duration": 1.292}, {"text": "Those energy charge are similar,\nand so that makes sense.", "start": 4147.51, "duration": 3.389}, {"text": "But most of the energy\nreleased is actually", "start": 4150.899, "duration": 4.351}, {"text": "reducing NAD and FAD\nto NADH and FADH2.", "start": 4155.25, "duration": 4.71}, {"text": "And of course, these need\nto transfer their electrons", "start": 4159.96, "duration": 5.34}, {"text": "somewhere else, and\nthat's the role of oxygen.", "start": 4165.3, "duration": 3.12}, {"text": "Oxygen, remember, is a\nvery good electron donor,", "start": 4168.42, "duration": 2.83}, {"text": "and so it's the ultimate\ntransfer of those electrons", "start": 4171.25, "duration": 3.229}, {"text": "from these molecules to oxygen\nthat also provide energy", "start": 4174.479, "duration": 6.271}, {"text": "that the cell can use to do\nwork, but it does so, in a way,", "start": 4180.75, "duration": 3.99}, {"text": "by charging up different\nratios in the cell.", "start": 4184.74, "duration": 5.17}, {"text": "So the NAD-NADH or\nthe FADH2-FAD ratios.", "start": 4189.91, "duration": 6.92}, {"text": "And just like we talked about,\nthe ratio or the energy of ATP", "start": 4196.83, "duration": 5.19}, {"text": "is in the interconversion\nbetween ATP and ADP.", "start": 4202.02, "duration": 3.15}, {"text": "It's the ratio that drives\nthe free energy change.", "start": 4205.17, "duration": 4.02}, {"text": "The same thing exists for an\nNADH and NAD, FADH2 and FAD.", "start": 4209.19, "duration": 4.59}, {"text": "And so charging up these ratios\nwhile passing through the TCA", "start": 4213.78, "duration": 3.21}, {"text": "cycle, and the ultimate\ndownstream transfer", "start": 4216.99, "duration": 2.82}, {"text": "of those electrons\nto oxygen, really", "start": 4219.81, "duration": 2.73}, {"text": "is where most of the energy\nis captured as carbon", "start": 4222.54, "duration": 4.11}, {"text": "is oxidized through\nthe TCA cycle.", "start": 4226.65, "duration": 3.57}, {"text": "And exactly how that works and\nhow it can be related to ATP", "start": 4230.22, "duration": 4.86}, {"text": "will be something that'll be\nmore explicit in the coming", "start": 4235.08, "duration": 2.67}, {"text": "lectures.", "start": 4237.75, "duration": 1.55}, {"text": "Now, I want to point out\napart from the oxidation,", "start": 4239.3, "duration": 3.9}, {"text": "there's actually lots of\nintermediates made here.", "start": 4243.2, "duration": 3.16}, {"text": "And it turns out, a bunch\nof these intermediates", "start": 4246.36, "duration": 2.09}, {"text": "are useful for\ncells to make stuff.", "start": 4248.45, "duration": 3.16}, {"text": "So we talked about\ngluconeogenesis.", "start": 4251.61, "duration": 1.64}, {"text": "Gluconeogenesis needs\nelectron balance.", "start": 4253.25, "duration": 1.92}, {"text": "We get NADH from the\nTCA cycle, and so you", "start": 4255.17, "duration": 2.97}, {"text": "can think of gluconeogenesis\nas an alternative", "start": 4258.14, "duration": 3.15}, {"text": "to fermentation to\ndispose of electrons.", "start": 4261.29, "duration": 2.15}, {"text": "Well, you can use the\nNADH from the TCA cycle", "start": 4263.44, "duration": 2.56}, {"text": "to run gluconeogenesis as well.", "start": 4266.0, "duration": 2.98}, {"text": "But beyond the cofactors,\nthe carbon itself.", "start": 4268.98, "duration": 2.64}, {"text": "So citrate, I've alluded\nto now a few times,", "start": 4271.62, "duration": 2.84}, {"text": "is important as a\nprecursor to make fat.", "start": 4274.46, "duration": 2.67}, {"text": "We'll discuss that in\nlater lectures, too.", "start": 4277.13, "duration": 2.49}, {"text": "But other intermediates\nin this pathway", "start": 4279.62, "duration": 3.09}, {"text": "are useful for various amino\nacids and nucleic acids.", "start": 4282.71, "duration": 4.0}, {"text": "And so there's\nlots of things that", "start": 4286.71, "duration": 2.63}, {"text": "can come from the\nTCA cycle that cells", "start": 4289.34, "duration": 3.15}, {"text": "can find useful to do,\nnot just catabolism,", "start": 4292.49, "duration": 5.35}, {"text": "but also anabolic processes.", "start": 4297.84, "duration": 4.04}, {"text": "Now, the way the TCA\ncycle works, though,", "start": 4301.88, "duration": 4.21}, {"text": "is that there's\nactually an issue", "start": 4306.09, "duration": 2.57}, {"text": "if you want to use the\nintermediates from the TCA", "start": 4308.66, "duration": 3.48}, {"text": "cycle to make stuff.", "start": 4312.14, "duration": 2.98}, {"text": "And so what is that issue?", "start": 4315.12, "duration": 4.77}, {"text": "Well, the TCA cycle functions\nat a site as a cycle.", "start": 4319.89, "duration": 5.528}, {"text": "And so, if we're going to\ntake things in and out of it,", "start": 4325.418, "duration": 2.292}, {"text": "that has consequences\nfor how the cycle runs.", "start": 4327.71, "duration": 4.02}, {"text": "Now there's a couple\nwords for this", "start": 4331.73, "duration": 3.01}, {"text": "that I want to just\nintroduce to you.", "start": 4334.74, "duration": 2.46}, {"text": "The first one is cataplerosis\nand the second one", "start": 4337.2, "duration": 3.17}, {"text": "is anaplerosis.", "start": 4340.37, "duration": 2.83}, {"text": "And so cataplerosis is\nthe act of removing stuff", "start": 4343.2, "duration": 9.48}, {"text": "from a metabolic cycle.", "start": 4352.68, "duration": 1.545}, {"text": "So, we're going\nto remove citrate", "start": 4358.03, "duration": 1.65}, {"text": "from the cycle to make fat.", "start": 4359.68, "duration": 1.44}, {"text": "That's cataplerosis.", "start": 4361.12, "duration": 1.74}, {"text": "And anaplerosis is adding\nstuff back to a metabolic cycle", "start": 4362.86, "duration": 14.68}, {"text": "so it can continue to function.", "start": 4377.54, "duration": 3.84}, {"text": "Viewing this is really evident\nif you think of the TCA cycle", "start": 4381.38, "duration": 3.75}, {"text": "as a chicken and egg problem.", "start": 4385.13, "duration": 2.2}, {"text": "So, the very first\ntime acetyl-CoA", "start": 4387.33, "duration": 2.34}, {"text": "was generated, how\ndo you start the TCA", "start": 4389.67, "duration": 3.05}, {"text": "cycle in the first place?", "start": 4392.72, "duration": 1.77}, {"text": "You can't add it\nto the TCA cycle", "start": 4394.49, "duration": 2.31}, {"text": "unless you have\noxaloacetate to combine", "start": 4396.8, "duration": 3.12}, {"text": "with the acetyl-CoA,\nwhich can then", "start": 4399.92, "duration": 2.13}, {"text": "generate another oxaloacetate.", "start": 4402.05, "duration": 3.12}, {"text": "So where does the first\noxaloacetate come from?", "start": 4405.17, "duration": 4.33}, {"text": "Well, we already talked\nabout one reaction.", "start": 4409.5, "duration": 2.06}, {"text": "We talked about it in the\ncontext of gluconeogenesis.", "start": 4411.56, "duration": 3.48}, {"text": "That can solve this problem.", "start": 4415.04, "duration": 1.36}, {"text": "And so we have pyruvate.", "start": 4416.4, "duration": 1.82}, {"text": "And so we talked\nearlier today how", "start": 4418.22, "duration": 2.16}, {"text": "we can do oxidative\ndecarboxylation of pyruvate", "start": 4420.38, "duration": 5.34}, {"text": "to give acetyl-CoA.", "start": 4425.72, "duration": 2.73}, {"text": "But we talked to in\nthe gluconeogenesis", "start": 4428.45, "duration": 1.71}, {"text": "lecture how we can add a\nCO2 pyruvate to generate", "start": 4430.16, "duration": 5.31}, {"text": "oxaloacetate.", "start": 4435.47, "duration": 1.8}, {"text": "So if I do those\ntwo reactions, now I", "start": 4437.27, "duration": 2.64}, {"text": "have all the carbon I\nneed to generate a citrate", "start": 4439.91, "duration": 6.49}, {"text": "and start off the TCA cycle.", "start": 4446.4, "duration": 4.79}, {"text": "Now obviously, if\nI do cataplerosis", "start": 4451.19, "duration": 4.94}, {"text": "and I remove that citrate\nI made to make fat,", "start": 4456.13, "duration": 3.09}, {"text": "well, now I need\ntwo pyruvate again", "start": 4459.22, "duration": 1.98}, {"text": "to generate the next citrate\nif I'm using this pathway,", "start": 4461.2, "duration": 4.74}, {"text": "because every time I bring\nan acetyl-CoA into the cycle,", "start": 4465.94, "duration": 3.48}, {"text": "I need an oxaloacetate\nto combine it with.", "start": 4469.42, "duration": 3.24}, {"text": "And so if I remove something,\nI have to add something back.", "start": 4472.66, "duration": 3.18}, {"text": "And so pyruvate to oxaloacetate,\nthe pyruvate carboxylase", "start": 4475.84, "duration": 3.9}, {"text": "reaction is an example of\nan anaplerotic reaction.", "start": 4479.74, "duration": 6.11}, {"text": "Now what this means,\nthough, is that in order", "start": 4485.85, "duration": 4.05}, {"text": "to do an anaplerosis,\nyou have to be", "start": 4489.9, "duration": 2.7}, {"text": "able to generate\nfour-carbon oxaloacetate,", "start": 4492.6, "duration": 4.35}, {"text": "or a four-carbon molecule.", "start": 4496.95, "duration": 2.83}, {"text": "Now, pyruvate carboxylase,\npyruvate to oxaloacetate,", "start": 4499.78, "duration": 2.81}, {"text": "allows you to do that.", "start": 4502.59, "duration": 1.212}, {"text": "We can take a\nthree-carbon molecule", "start": 4503.802, "duration": 1.458}, {"text": "and generate four-carbon\noxaloacetate.", "start": 4505.26, "duration": 2.82}, {"text": "However, if we start from\na two-carbon molecule", "start": 4508.08, "duration": 4.86}, {"text": "like acetate or acetyl-CoA\nthat enters the cycle,", "start": 4512.94, "duration": 7.27}, {"text": "it's actually not so simple to\ntake that two-carbon molecule", "start": 4520.21, "duration": 4.2}, {"text": "and turn it into\nfour-carbon oxaloacetate.", "start": 4524.41, "duration": 2.94}, {"text": "And in fact, humans\nlack any enzymes", "start": 4527.35, "duration": 3.72}, {"text": "that allow them to\ntake a two-carbon unit,", "start": 4531.07, "duration": 2.37}, {"text": "to take acetate or\nacetyl-CoA, and turn it", "start": 4533.44, "duration": 3.24}, {"text": "into anything that's\nlonger than net-- turn", "start": 4536.68, "duration": 4.32}, {"text": "it into anything that's\nlonger than two carbons.", "start": 4541.0, "duration": 3.27}, {"text": "And this has\nimportant implications", "start": 4544.27, "duration": 1.83}, {"text": "for human physiology,\nbecause what it says", "start": 4546.1, "duration": 2.97}, {"text": "is that we can't make\nglucose from anything", "start": 4549.07, "duration": 3.3}, {"text": "that starts with something\nless than three carbons long.", "start": 4552.37, "duration": 4.21}, {"text": "So if you drink alcohol and\nyou metabolize that alcohol", "start": 4556.58, "duration": 3.17}, {"text": "to acetate, it turns\nout you take fat", "start": 4559.75, "duration": 2.76}, {"text": "and you break down fat\nalso to acetyl-CoA,", "start": 4562.51, "duration": 2.82}, {"text": "to acetate two carbons long.", "start": 4565.33, "duration": 2.19}, {"text": "There is no way to turn\nthose molecules into glucose,", "start": 4567.52, "duration": 5.94}, {"text": "because you cannot generate\nthe oxaloacetate to do", "start": 4573.46, "duration": 3.15}, {"text": "the anaplerosis that's\nnecessary to get it there.", "start": 4576.61, "duration": 4.87}, {"text": "What this means is\nthat our body can only", "start": 4584.23, "duration": 5.79}, {"text": "store calories that come\nfrom two carbon units,", "start": 4590.02, "duration": 3.18}, {"text": "fat or alcohol, as fat.", "start": 4593.2, "duration": 2.4}, {"text": "We can never turn them back\ninto glucose or make glycogen.", "start": 4595.6, "duration": 5.602}, {"text": "And this is very relevant\nfor those of you that", "start": 4601.202, "duration": 1.958}, {"text": "go to medical\nschool, because it's", "start": 4603.16, "duration": 1.417}, {"text": "relevant to our physiology.", "start": 4604.577, "duration": 2.093}, {"text": "And that is, when\nour bodies exhaust", "start": 4606.67, "duration": 2.04}, {"text": "all of our stores of\nglucose, what happens?", "start": 4608.71, "duration": 2.61}, {"text": "Our liver can no longer\ndo gluconeogenesis.", "start": 4611.32, "duration": 2.82}, {"text": "And so what happens?", "start": 4614.14, "duration": 0.99}, {"text": "Now it has to switch over\nto doing something else.", "start": 4615.13, "duration": 2.32}, {"text": "It has to work with\ntwo carbon units.", "start": 4617.45, "duration": 1.92}, {"text": "And ultimately, this is\nketone metabolism, which we'll", "start": 4619.37, "duration": 2.78}, {"text": "talk about in a few lectures.", "start": 4622.15, "duration": 3.45}, {"text": "It also said that the body--", "start": 4625.6, "duration": 2.055}, {"text": "that this is also the basis\nof a very old adage that's", "start": 4631.31, "duration": 3.75}, {"text": "out there that some of\nyou may have heard--", "start": 4635.06, "duration": 2.22}, {"text": "that you need to have\nsome other fuel if you're", "start": 4637.28, "duration": 2.94}, {"text": "going to burn fat.", "start": 4640.22, "duration": 2.04}, {"text": "The basis for that is that\nfat is turned into two carbon", "start": 4642.26, "duration": 3.48}, {"text": "units, acetyl-CoA units.", "start": 4645.74, "duration": 2.1}, {"text": "And so if you're going to\ntake those acetyl-CoA units", "start": 4647.84, "duration": 2.34}, {"text": "and ultimately burn them\naway, turn them into CO2,", "start": 4650.18, "duration": 2.91}, {"text": "you need a source\nof oxaloacetate,", "start": 4653.09, "duration": 2.1}, {"text": "or your TCA cycle won't work.", "start": 4655.19, "duration": 2.4}, {"text": "And you don't need a lot of\nsomething, but it is true.", "start": 4657.59, "duration": 2.7}, {"text": "You can't start just with\nacetyl-CoA as a human and turn", "start": 4660.29, "duration": 4.71}, {"text": "it into CO2, so you need some--", "start": 4665.0, "duration": 1.86}, {"text": "at least a little\nbit of oxaloacetate", "start": 4666.86, "duration": 2.34}, {"text": "to get your TCA cycle started.", "start": 4669.2, "duration": 3.21}, {"text": "Now, that's a problem that we as\nhumans and other mammals face,", "start": 4672.41, "duration": 4.925}, {"text": "but it turns out there's\nlots of microbes out there", "start": 4677.335, "duration": 2.125}, {"text": "that grow just fine on\nacetate or on alcohol,", "start": 4679.46, "duration": 3.42}, {"text": "even if it's only carbon source.", "start": 4682.88, "duration": 2.1}, {"text": "And so those organisms\nmust have some way", "start": 4684.98, "duration": 3.57}, {"text": "to build stuff from\ntwo carbon units.", "start": 4688.55, "duration": 2.28}, {"text": "That is a way to use two carbon\nunits and do an anaplerosis.", "start": 4690.83, "duration": 4.45}, {"text": "And it turns out the way\nthey do this is via something", "start": 4695.28, "duration": 2.33}, {"text": "called the glyoxylate cycle.", "start": 4697.61, "duration": 2.8}, {"text": "And so the glyoxylate cycle\nis an alternative version", "start": 4703.05, "duration": 3.17}, {"text": "of the TCA cycle that\neffectively uses two enzymes", "start": 4706.22, "duration": 3.39}, {"text": "that we lack as mammals.", "start": 4709.61, "duration": 2.4}, {"text": "And so I'll quickly\ntell you about it here.", "start": 4712.01, "duration": 2.22}, {"text": "So, this is isocitrate\nfrom the TCA cycle.", "start": 4727.92, "duration": 9.5}, {"text": "And some microbes have an\nenzyme called isocitrate lyase.", "start": 4737.42, "duration": 10.85}, {"text": "And what isocitrate lyase does\nis basically splits citrate", "start": 4748.27, "duration": 10.16}, {"text": "in half, such that the top\nportion of the molecule", "start": 4758.43, "duration": 4.83}, {"text": "is another TCA cycle\nintermediate, succinate.", "start": 4763.26, "duration": 6.93}, {"text": "And the bottom\nportion of a molecule", "start": 4770.19, "duration": 3.96}, {"text": "is this two carbon\naldehyde called glyoxylate.", "start": 4774.15, "duration": 8.7}, {"text": "Glyoxylate can react with\nacetyl-CoA by another enzyme", "start": 4782.85, "duration": 18.04}, {"text": "that we lack as humans\ncalled malate synthase.", "start": 4800.89, "duration": 7.5}, {"text": "And I don't have time to\nshow the mechanism again,", "start": 4811.03, "duration": 3.85}, {"text": "but malate synthase basically\nadds the two carbons", "start": 4814.88, "duration": 4.28}, {"text": "from acetyl-CoA to the\naldehyde, the carbonyl,", "start": 4819.16, "duration": 7.02}, {"text": "the aldehyde carbonyl of\nglyoxylate in a reaction that", "start": 4826.18, "duration": 3.72}, {"text": "is, for all intents and\npurposes, exactly what happens", "start": 4829.9, "duration": 3.72}, {"text": "in citrate synthase.", "start": 4833.62, "duration": 2.43}, {"text": "That will generate this\nmolecule, which is malate, also", "start": 4836.05, "duration": 15.88}, {"text": "in the TCA cycle.", "start": 4851.93, "duration": 2.44}, {"text": "And so having these two extra\nreactions, isocitrate lyase", "start": 4854.37, "duration": 3.62}, {"text": "and malate synthase,\ngives microbes", "start": 4857.99, "duration": 3.93}, {"text": "the ability to have\nacetyl-CoA be anaplerotic.", "start": 4861.92, "duration": 6.12}, {"text": "And so how does that work?", "start": 4868.04, "duration": 1.41}, {"text": "Well, that's because if we start\nwith one oxaloacetate, four", "start": 4869.45, "duration": 6.39}, {"text": "carbons, and acetyl-CoA, two\ncarbons, can run the TCA cycle", "start": 4875.84, "duration": 10.56}, {"text": "and make citrate, six carbons.", "start": 4886.4, "duration": 4.71}, {"text": "Turn that citrate\ninto isocitrate.", "start": 4891.11, "duration": 2.774}, {"text": "Use isocitrate lyase to generate\nglyoxylate, two carbons.", "start": 4897.95, "duration": 11.14}, {"text": "Plus succinate.", "start": 4909.09, "duration": 2.46}, {"text": "That succinate can run through\nsuccinate dehydrogenase", "start": 4915.31, "duration": 6.76}, {"text": "to generate malate,\nwhich you can", "start": 4922.07, "duration": 1.98}, {"text": "go through malate dehydrogenase\nto generate oxaloacetate.", "start": 4924.05, "duration": 4.14}, {"text": "This glyoxylate can start\nwith a second acetyl-CoA.", "start": 4928.19, "duration": 7.74}, {"text": "Two carbons come\ntogether, generate malate.", "start": 4935.93, "duration": 3.96}, {"text": "That generates a\nsecond malate molecule,", "start": 4939.89, "duration": 2.88}, {"text": "which can then exit the cycle\nas malate or oxaloacetate", "start": 4942.77, "duration": 7.41}, {"text": "or whatever you want.", "start": 4950.18, "duration": 1.95}, {"text": "And so basically, it allows\ntwo acetyl-CoAs to net", "start": 4952.13, "duration": 4.29}, {"text": "generate an oxaloacetate,\nand so net generates a way", "start": 4956.42, "duration": 4.62}, {"text": "to do an anaplerosis\nfrom two carbon units", "start": 4961.04, "duration": 4.05}, {"text": "by having this malate\nsynthase reaction", "start": 4965.09, "duration": 6.07}, {"text": "and this isocitrate\nlyase reaction", "start": 4971.16, "duration": 6.2}, {"text": "and run this alternative\nversion of the TCA cycle,", "start": 4977.36, "duration": 3.57}, {"text": "called the glyoxylate cycle.", "start": 4980.93, "duration": 3.06}, {"text": "And it's a nice way how life--\nagain, no new chemistry here,", "start": 4983.99, "duration": 4.11}, {"text": "just variations on what\nwe've already shown--", "start": 4988.1, "duration": 2.64}, {"text": "repurposed the\nsimilar chemistries", "start": 4990.74, "duration": 1.95}, {"text": "that it's already using\nas a way to live off", "start": 4992.69, "duration": 3.93}, {"text": "of carbon sources that contain\nonly two carbons, like ethanol", "start": 4996.62, "duration": 7.92}, {"text": "or acetate.", "start": 5004.54, "duration": 2.81}, {"text": "So in closing today,\nthe last thing", "start": 5007.35, "duration": 4.05}, {"text": "I want to talk\nabout, very briefly,", "start": 5011.4, "duration": 3.03}, {"text": "is how the TCA\ncycle is regulated.", "start": 5014.43, "duration": 6.18}, {"text": "And we don't need to\nspend a ton of time", "start": 5020.61, "duration": 2.01}, {"text": "on this, because it really\nfollows principles that", "start": 5022.62, "duration": 6.09}, {"text": "make sense, particularly when\nwe think about things that we've", "start": 5028.71, "duration": 5.63}, {"text": "already talk about.", "start": 5034.34, "duration": 1.48}, {"text": "And so, regulation of the TCA\ncycles is of course important,", "start": 5035.82, "duration": 3.98}, {"text": "and it's really a critical hub,\nboth for anabolic and catabolic", "start": 5039.8, "duration": 3.63}, {"text": "pathways.", "start": 5043.43, "duration": 0.52}, {"text": "So, you needed to get energy\nto fully oxidize carbon,", "start": 5043.95, "duration": 2.99}, {"text": "but it's also a useful\nplace to get stuff.", "start": 5046.94, "duration": 3.312}, {"text": "And before I talk\nabout regulation,", "start": 5050.252, "duration": 1.458}, {"text": "I just want to point out that\nmany of the enzymes in the TCA", "start": 5051.71, "duration": 2.88}, {"text": "cycle, even though we talk\nabout it in the mitochondria", "start": 5054.59, "duration": 3.06}, {"text": "and we're about to talk\nabout regulation in terms", "start": 5057.65, "duration": 2.34}, {"text": "of catabolism--\nthat is oxidation,", "start": 5059.99, "duration": 2.67}, {"text": "ways to release energy--", "start": 5062.66, "duration": 2.4}, {"text": "many of these enzymes are\nalso in other locations", "start": 5065.06, "duration": 2.64}, {"text": "in the cell, because there's\nfunctions for them in making", "start": 5067.7, "duration": 4.47}, {"text": "stuff that is very different\nthan what goes on in the TCA", "start": 5072.17, "duration": 2.85}, {"text": "cycle.", "start": 5075.02, "duration": 0.99}, {"text": "And the regulation that\nI'll tell you about,", "start": 5076.01, "duration": 3.45}, {"text": "and that comes up on\nMCAT exams and stuff", "start": 5079.46, "duration": 2.82}, {"text": "like that, usually\ntalks about this pathway", "start": 5082.28, "duration": 3.18}, {"text": "as a catabolic pathway, as a\nway to make CO2, to make ATP.", "start": 5085.46, "duration": 4.48}, {"text": "However, recognize\nthat there's also", "start": 5089.94, "duration": 3.44}, {"text": "variations on this pathway that\ncan use in anabolic things,", "start": 5093.38, "duration": 4.23}, {"text": "making stuff.", "start": 5097.61, "duration": 1.11}, {"text": "And that regulation is something\nthat really is not necessarily", "start": 5098.72, "duration": 4.98}, {"text": "what we're going\nto talk about here", "start": 5103.7, "duration": 1.89}, {"text": "and is a little bit\nless well-understood.", "start": 5105.59, "duration": 4.2}, {"text": "But at least the\nregulation, in terms", "start": 5109.79, "duration": 1.74}, {"text": "of catabolism, if we put it in\ncontext of glucose metabolism--", "start": 5111.53, "duration": 7.39}, {"text": "so here's glycolysis, turning\nglucose into pyruvate.", "start": 5118.92, "duration": 6.97}, {"text": "And then that\npyruvate can operate", "start": 5132.34, "duration": 3.21}, {"text": "through the pyruvate\ndehydrogenase reaction", "start": 5135.55, "duration": 4.74}, {"text": "to generate acetyl-CoA.", "start": 5140.29, "duration": 4.14}, {"text": "That acetyl-CoA can\ncombine with oxaloacetate", "start": 5144.43, "duration": 5.76}, {"text": "to generate citrate.", "start": 5150.19, "duration": 3.592}, {"text": "That citrate, of course,\ncan be used to generate fat,", "start": 5153.782, "duration": 3.748}, {"text": "as we've talked about.", "start": 5157.53, "duration": 2.87}, {"text": "That can go to isocitrate.", "start": 5160.4, "duration": 1.68}, {"text": "Isocitrate to alpha\nketoglutarate.", "start": 5164.94, "duration": 4.33}, {"text": "That's catalyzed by\nisocitrate dehydrogenase,", "start": 5169.27, "duration": 4.23}, {"text": "which I will abbreviate IDH.", "start": 5173.5, "duration": 2.13}, {"text": "Alpha ketoglutarate\nto succinate.", "start": 5175.63, "duration": 4.12}, {"text": "More correctly, to succinyl-CoA\nby alpha ketoglutarate", "start": 5179.75, "duration": 11.08}, {"text": "dehydrogenase, Alpha KGDH.", "start": 5190.83, "duration": 4.41}, {"text": "And then this back\nto oxaloacetate.", "start": 5195.24, "duration": 2.91}, {"text": "And so the main enzymes\nthat are typically", "start": 5198.15, "duration": 3.06}, {"text": "discussed as being regulated\nare alpha ketoglutarate", "start": 5201.21, "duration": 3.92}, {"text": "dehydrogenase,\nisocitrate dehydrogenase,", "start": 5205.13, "duration": 2.98}, {"text": "and pyruvate dehydrogenase.", "start": 5208.11, "duration": 2.07}, {"text": "I also drew glycolysis.", "start": 5210.18, "duration": 3.01}, {"text": "And I'll just write over\nhere, gluconeogenesis up here,", "start": 5213.19, "duration": 5.07}, {"text": "because we can now see\nmore fully how this plays", "start": 5218.26, "duration": 6.31}, {"text": "in with citrate acting\nas a positive regulator", "start": 5224.57, "duration": 5.19}, {"text": "with gluconeogenesis and\nan inhibitor of glycolysis.", "start": 5229.76, "duration": 6.07}, {"text": "Again, we're full in citrate,\nstop running glycolysis,", "start": 5235.83, "duration": 5.58}, {"text": "start running gluconeogenesis.", "start": 5241.41, "duration": 3.54}, {"text": "Now, the other regulation.", "start": 5244.95, "duration": 1.74}, {"text": "If you have a lot of\nacetyl-CoA, stop making it", "start": 5246.69, "duration": 3.39}, {"text": "from pyruvate. acetyl-CoA is\na negative regulator of PDH.", "start": 5250.08, "duration": 4.74}, {"text": "This is carbon oxidation.", "start": 5254.82, "duration": 2.73}, {"text": "Releases a lot of energy,\ngenerates a lot of ATP,", "start": 5257.55, "duration": 3.48}, {"text": "generates a lot of NADH.", "start": 5261.03, "duration": 3.12}, {"text": "If you have lots\nof those things,", "start": 5264.15, "duration": 1.86}, {"text": "no reason to keep\nsending carbon into", "start": 5266.01, "duration": 3.38}, {"text": "acetyl-CoA to go\ninto the TCA cycle.", "start": 5269.39, "duration": 3.57}, {"text": "Ultimately, we have to send\nthose electrons somewhere.", "start": 5272.96, "duration": 3.773}, {"text": "So if there's\nnowhere to put them,", "start": 5276.733, "duration": 1.417}, {"text": "low oxygen also inhibits\npyruvate dehydrogenase.", "start": 5278.15, "duration": 4.35}, {"text": "And of course, if you need\nmore energy, if ADP is high,", "start": 5282.5, "duration": 4.17}, {"text": "that activates\npyruvate dehydrogenase.", "start": 5286.67, "duration": 3.33}, {"text": "So at least in terms of glucose,\ncomplete glucose oxidation,", "start": 5290.0, "duration": 4.32}, {"text": "a lot of regulation happens\nat pyruvate dehydrogenase.", "start": 5294.32, "duration": 3.96}, {"text": "And a lot of it\nreally makes sense.", "start": 5298.28, "duration": 3.77}, {"text": "High levels of ATP,\nhigh levels of NADH,", "start": 5302.05, "duration": 5.4}, {"text": "also inhibit isocitrate\ndehydrogenase and alpha", "start": 5307.45, "duration": 6.72}, {"text": "ketoglutarate dehydrogenase.", "start": 5314.17, "duration": 4.52}, {"text": "Makes sense.", "start": 5318.69, "duration": 1.15}, {"text": "Succinol-CoA high, inhibit alpha\nketoglutarate dehydrogenase.", "start": 5319.84, "duration": 5.15}, {"text": "High levels of ADP, need\nto release more energy,", "start": 5324.99, "duration": 7.23}, {"text": "activate alpha\nketoglutarate dehydrogenase.", "start": 5332.22, "duration": 4.08}, {"text": "Again, these are the feedbacks\nthat people talk about", "start": 5339.18, "duration": 2.85}, {"text": "on board exams.", "start": 5342.03, "duration": 1.56}, {"text": "Good to know, but you can\nalmost guess what they", "start": 5343.59, "duration": 2.64}, {"text": "would be from first principles.", "start": 5346.23, "duration": 1.98}, {"text": "Because remember,\nthis is a pathway", "start": 5348.21, "duration": 1.59}, {"text": "that releases a lot of energy.", "start": 5349.8, "duration": 1.86}, {"text": "High energy high\nATP, high NADH--", "start": 5351.66, "duration": 3.21}, {"text": "don't run the cycle, don't\nenter carbon in the cycle.", "start": 5354.87, "duration": 3.3}, {"text": "Low energy, high ADP,\nput carbon in the cycle,", "start": 5358.17, "duration": 5.73}, {"text": "run the cycle faster.", "start": 5363.9, "duration": 1.86}, {"text": "Makes sense.", "start": 5365.76, "duration": 1.14}, {"text": "Also makes sense of the\nreciprocal regulation", "start": 5366.9, "duration": 2.58}, {"text": "of glycolysis and\ngluconeogenesis.", "start": 5369.48, "duration": 3.58}, {"text": "Great.", "start": 5373.06, "duration": 0.5}, {"text": "Next time, we will\ntalk more about", "start": 5373.56, "duration": 4.56}, {"text": "how we can oxidize fatty acids,\nfat, by accessing acetyl-CoA", "start": 5378.12, "duration": 8.64}, {"text": "and entering it into the cycle.", "start": 5386.76, "duration": 1.62}, {"text": "Thanks.", "start": 5388.38, "duration": 1.55}] |