Some catabolic pathways do indeed make citric acid cycle intermediates; for example, plants and bacteria use phospoenolpyruvate carboxylase to create oxaloacetate from phosphoenolypyruvate. Anaplerotic reactions refill the citric acid cycle with intermediates, rather than remove them. Some archaea have a complete citric acid cycle; it is the bacteria that mostly do not have a complete cycle. In eukaryotes, citrate cleavage does indeed take place in the cytosol; that citrate is transported to the cytosol from mitochondria, and the acetyl-CoA can be used for fatty acid synthesis.

The citric acid cycle is a series of reactions that occur within the matrix of the mitochondria. With every turn of the cycle, one acetyl-CoA molecule enters, and a variety of molecules leave. These leaving molecules include , , , and ATP. The acetyl-CoA that enters the cycle is derived from other cellular pathways, such as beta-oxidation and glycolysis. In this way, the citric acid cycle serves as a conduit by which metabolites from other pathways can be broken down to ultimately provide energy for the cell.

Since the citric acid cycle occurs in mitochondria, only eukaryotes are capable of performing this process. Also, the citric acid cycle is not responsible for the production of urea from ammonia. Rather, it is the urea cycle that performs this role. It is worth noting, however, that the citric acid cycle and the urea cycle are energetically linked by the aspartate-argininosuccinate shunt. This is because these two cycle share a few common intermediates, and the citric acid cycle can help to offset the demanding energy requirements of the urea cycle.

When glycogen phosphorylase reaches a branching point in glycogen, the bonds switch from being alpha-1,4-glycosidic bonds to alpha-1,6-glycosidic bonds.  It is unable to cleave these bonds, and so other enzymes (a transferase and a glucosidase) must come into play.

Glycogen is first debranched and broken down from its non-reducing end by glycogen phosphorylase to give the product G1P, which is then converted into G6P by phosphoglutomutase. Glycogen synthase, glycogen branching enzyme, and UDP-glucose pyrophosphorylase are required for glycogen synthesis.

Glycogen phosphorylase, the rate-limiting enzyme of glycogenolysis  does not breaks alpha 1,6 glycosidic bonds. It releases glucose from glycogen by hydrolyzing alpha 1,4 glycosidic bonds until it reaches a branch point in the glycogen molecule. At this time, another enzyme, a debranching alpha 1,6 glycosidase hydrolyzes the alpha 1,6 glycosidic bonds. Glycogen phosphorylase is under regulation by many hormones, including insulin and glucagon, as well as epinephrine.

In order to break down glycogen into individual glucose-6-phosphate units, all of the above enzymes are required. Each plays a specific role in one of the following activities: degradation of glycogen initially, remodeling of the glycogen so that it can be acted upon by the enzymes, and conversion of glucose-1-phosphate to glucose 6-phosphate.

Glycogen is mostly stored in the liver and skeletal muscle. When it is broken down in the liver, the last enzyme, a phosphatase, removes the last phosphate group to release plain glucose into the bloodstream. In the muscle, there is no need to release the glucose, so glycogen is only broken down as far as glucose-6-phosphate. Skeletal muscle cells lack the last phosphatase required to remove the phosphate from carbon 6. This isn't an obstacle, however, because the glucose-6-phosphate is already on to the second stage of glycolysis.

Insulin is released in response to high blood glucose. It causes a signaling cascade that, in addition to other things, stops glycogenolysis. This is done by converting glycogen phosphorylase from it's active "a" form to its inactive "b" configuration. The "R" state is the active state, so the presence of glucose would not trigger the breakdown of glycogen. 5' AMP would not inhibit an inactive form of an enzyme. High AMP would mean a demand for ATP, so it would convert the enzyme to its "a" form.

Oxaloacetate is the four-carbon molecule that is regenerated by the enzyme malate dehydrogenase in order to continue the cycle to form citrate with acetyl-CoA in the first step of the Krebs cycle. The other answer choices are intermediates of the citric acid cycle, but only oxaloacetate is regenerated, making it a true cycle.

Phosphorylation of glycogen phosphorylase activates it, converting it from its inactive B-form to its active A-form.