The MCAT Basics Podcast continues its series on Metabolism, and in today’s episode, Alex Starks talks about the Krebs cycle, also known as the TCA cycle and Citric Acid cycle. This episode examines the chemistry, biochemistry, and biology of pyruvate metabolism and details how this high-yield MCAT topic will be tested on the AAMC MCAT Exam.
- [01:30] Aerobic fate of Pyruvate
- [03:45] Acetyl-coa in the mitochondrial matrix
- [04:22] Visualizing the molecules and structure
- [06:10] The Krebs Cycle
- [23:56] ATP and The Electron Transport Chain
- [26:07] Quiz and Important Takeaways
Oxygen Present or Aerobic Fate of Pyruvate
The first thing that happens is that the pyruvate enters the mitochondria because glycolysis occurs in the cytosol. Pyruvate’s entrance into the mitochondria is mediated by a complex of enzymes called the pyruvate dehydrogenase complex (PDC). The PDC is a three-enzyme complex that converts cytosolic pyruvate into mitochondrial acetyl-COA. Not only are we moving from the cytosol into the mitochondria, we’re also chemically modifying our substrate, and this involves a decarboxylation of pyruvate which generates carbon dioxide and also a generation of NADH, which then deposits electrons into the electron transport chain. There are some co-factors that are involved, one of which is called a lipoate, a conjugate base of a fatty acid lipoic acid. Lipoate helps to move the substrate from one complex to another. Pyruvate goes into a factory called the PDC and out pops acetyl-COA, ready to join the Krebs Cycle.
Acetyl-COA in the Mitochondrial Matrix
Now that the acetyl-COA is in the mitochondrial matrix, we can subject it to further oxidation and can strip away even more electrons to power the mitochondria using NAD+ and FAD as the shovels to move the electrons from the substrate into the electron transport chain.
The Krebs Cycle
Step 1: Acetyl-coa is added to oxaloacetate to make citrate. We’re adding the acetyl group, the two-carbon group that used to be a pyruvate, to the substrate formed in the previous cycle.
Step 2: Citrate becomes isocitrate. Our catabolic machinery doesn’t like the shape of citrate, particularly the presence of a hydroxyl group on carbon 3. The cell rearranges this by using an enzyme called aconitase that first removes the hydroxyl group from carbon 3 and that hydroxyl group loses water and adds it back in at carbon 4.
Step 3: Isocitrate becomes alpha-ketoglutarate. This is an oxidated decarboxylation step and occurs in two different reactions: oxidation then decarboxylation and are both carried out by an enzyme called isocitrate-dehydrogenase.
Step 4: Alpha-ketoglutarate becomes succinyl-COA. Alpha-ketoglutarate is oxidized, gives its electrons to NAD+ to become NADH and gets rid of any carbon dioxide amount. Acetyl-COA is added to alpha-ketoglutarate and becomes succinyl-COA. This is the step where we lose our second carbon.
Step 5: Succinyl-COA becomes succinate. The COA bond is cleaved from succinyl, and that energy is used to take a GDP and attach a phosphate to it, making GTP. There are no phosphate groups in succinyl-COA and we must add a free, inorganic phosphate to make GDP. It’s important to note that a synthetase creating this GDP is not a synthase.
Step 6: Succinate becomes fumarate. Succinate-dehydrogenase takes succinate and FAD and produces FADH2 and fumarate. The enzyme pulls hydrogen atoms with electrons off Carbons 2 and 3 of succinate, creating fumarate which has a double bond between those two carbons. This step occurs inside of a complex of enzymes called Complex 2 of the electron transport chain and FAD is covalently attached to the succinate-dehydrogenase.
Step 7: Fumarate becomes malate. That fumarate molecule has a carboxylic acid on carbon 1 and carbon 4 and a double bond between carbon 2 and 3. The enzyme recognizes that there’s an opportunity to create more a electronically-dense molecule and adds water across the double bond.
Step 8: Malate becomes oxaloacetate. In the final step, we regenerate oxaloacetate by squeezing in one more redox reaction. We use a molecule called malate-dehydrogenase and produce NADH. This is an intersection of multiple metabolic pathways.