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[SQUEAKING] [RUSTLING] [CLICKING] MATTHEW VANDER HEIDEN: So today I want to continue our discussion of amino acid metabolism. And before we do that, I just want to come back for a few minutes and revisit the urea cycle and the Krebs bicycle that we discussed at the very end of the last lecture. I only want to do that because it-- a lot going on with this cycle. It can appear on the surface to be confusing, the molecules are hard to draw. And so I just wanted to draw it neatly here for you one last time and go through it again. And so remember, if we start from the amino acid arginine, arginine can be converted into the non-proteinogenic amino acid ornithine, and in the process, release urea. That ornithine can then be in the mitochondria converted to citrulline, another non-proteinogenic amino acid. By picking up a carbon and a nitrogen from this molecule, carbamoyl phosphate, which is generated from CO2/bicarbonate, as well as ammonia and to phosphorylations with ATP to ...

[SQUEAKING] [RUSTLING] [CLICKING] MATTHEW VANDER HEIDEN: OK, hello. So last time, we discussed the pentose phosphate pathway, which can serve as this shunt from glycolysis where glucose can be converted to five-carbon ribulose 1, 5-bisphosphate generating NADPH and ribose. And this shunt from glycolysis can work with the non-oxidative pathway, where those five-carbon units can then be used by the non-oxidative pathway to re-enter glycolysis, giving cells and ability to generate NADPH. Now, we described that this non-oxidative pathway can also operate in the reverse direction, such that cells can take products of glycolysis and instead use them to generate ribose for nucleotides and avoid the production of NADPH, really giving cells the flexibility to either make NADPH when they need it, make ribose when they need it, with the ability to either operate in this direction as a shunt and allow NADPH to be produced and material to re-enter glycolysis for further oxidation, or ...

[SQUEAKING] [RUSTLING] [CLICKING] MATTHEW VANDER HEIDEN: So today we're going to begin by going over the Calvin cycle, which I know I went quite quickly on just to introduce it at the end of the last lecture. And so we'll spend a little time there first. And then we'll move on to discuss the main topic of today, which is the pentose phosphate pathway. But before we get there, I just want to remind you about the Calvin cycle, which you'll recall happened in three phases. So there was the fixation, reduction, and regeneration phases. And so remember, fixation was this special reaction that occurs only in photosynthetic organisms catalyzed by rubisco ribulose-1,5-bisphosphate carboxylase/oxygenase, where a ribulose-1,5-bisphosphate molecule combines with CO2, and then is split to produce 2,3-phosphoglycerates. This was the reaction that Calvin described as the dark reaction, that now bears the name of this as the Calvin cycle. Once you get those 2,3-phosphogl...