Citric Acid Cycle I
The following is a summary of my lecture. I provide it (and subsequent ones) for your information and not as a mechanism of dumping more information on you. Use them if they help you to recall the material. Otherwise, don't bother.
1. Both oxidative decarboxylation (in higher cells) and non-oxidative decarboxylation (in yeast) use an enzymatic activity called the pyryvate dehydrogenase complex to convert pyruvate from glycolysis into acetyl-Coa for the citric acid cycle. This enzyme complex is in the mitochondrion and requires that pyruvate from the cytoplasm be transported to the mitochondrion. This complex includes the following:
Pyruvate decarboxylase (your book calls it "Pyruvate Dehydrogenase Component" (E1)
Dihyrolipoamide transacetylase (E2)
Dihyrolipoamide dehydrogenase (E3)
It also uses the coenzymes, Thiamine Pyrophosphate (TPP), Lipoamide, NAD, FAD, and Coenzyme A (also called CoASH or CoA).
2. The mechanism of the reaction catalyzed by the complex is very similar to that catalyzed by the alpha-keto-glutarate dehydrogenase complex of the Citric Acid Cycle. Both involve oxidation of alpha-keto acids.
3. In aerobic higher organisms, the reaction mechanism involves binding of pyruvate by an ionized TPP, decarboxylation, transfer to the lipoamide molecules, linkage of the acetyl group to CoASH to form acetyl-CoA, transfer of the electrons from the oxidation to FAD (forming FADH2) and transfer of electrons from FADH2 to NAD+ to form NADH.
4. In yeast fermentation, the reaction that occurs stops at the decarboxylation step with resolution to form acetealdehyde without loss/gain of electrons (no oxidation/reduction). Thus, enzyme activities E2 and E3 above are not needed in yeast fermentation. Acetaldehye in yeast fermentation is converted to ethanol. Note that when oxygen is present, fermentation in yeast does not occur and activities E2 and E3 catalyze reactions just like animal cells, producing acetyl-CoA.
5. Mitochondria are the "power plants" of the cell and are the places where much oxidation occurs.
6. The citric acid cycle occurs in the mitochondrial matrix (inner portion of mitochondrion) and is found in almost every cell. In the cycle, two carbons are added from acetyl-CoA and two carbons are released as carbon dioxide.
7. Biological oxidations in the citric acid cycle involve NAD+ (reduced to NADH) and FAD (reduced to FADH2). In the citric acid cycle, three NADH and one FADH2 are produced, along with one high energy phosphate (GTP in animals, ATP in plants and bacteria) per acetyl-CoA that enters the cycle (Remember that one molecule of glucose yields two acetyl-CoAs for the cycle).
8. The citric acid cycle consists of two main parts - release of CO2 (first part) and conversion to oxaloacetate (second part). You are NOT responsible for the structures of molecules in the citric acid cycle, but you need to know the names of the intermediates, the number of carbons they contain and the names of the enzymes.
9. In the "first" reaction of the citric acid cycle, citrate synthase catalyzes the joining of the acetyl group from acetyl-CoA to oxaloacetate to make citrate. This reaction is VERY energetically favorable, due to breaking of the thioester bond in acetyl-CoA. The energetically favorable reaction helps to "pull" the relatively unfavorable reaction preceding it.
10. Aconitase catalyzes the rearrangement of citrate to isocitrate. For your information - Aconitase is inhibited by fluorocitrate. Fluoroacetate is a poison that can be used by citrate synthase to make fluorocitrate.
11. The first decarboxylation of the citric acid cycle is catalyzed by isocitrate dehydrogenase and the reaction is strongly favored to the right. The products of this reaction are NADH and alpha ketoglutarate.
12. Alpha ketoglutarate is an important intermediate for its involvement in anaplerotic reactions related to transamination (we'll talk about these later). The mechanism of the enzyme acting on alpha ketoglutarate (alpha ketoglutarate dehydrogenase complex) is virtually identical to the mechanism of action of the pyruvate dehydrogenase complex and involves all of the same coenzymes. The products of this reaction are succinyl-CoA and NADH