Alternative Pathways - Biochemistry

Answering this question requires knowledge of the pathway of gluconeogenesis. In this pathway, non-carbohydrate carbon substrates such as lactate, pyruvate, and certain amino acids are used to generate glucose as the final product. Much of this pathway utilizes the same enzymes used in glycolysis, which is essentially the reverse of gluconeogenesis. However, it is critical to note that there are 3 reactions in glycolysis that are irreversible. Therefore, gluconeogenesis is not an exact reverse of glycolysis, and instead there are a few different enzymes in gluconeogenesis that bypass these irreversible reactions. One of the irreversible steps in glycolysis is the formation of pyruvate from phosphoenolpyruvate (PEP), catalyzed by the glycolytic enzyme pyruvate kinase. To bypass this irreversible reaction, gluconeogenesis makes use of two enzymes. First, the enzyme pyruvate carboxylase converts pyruvate into oxaloacetate, which requires the input of one molecule of ATP per molecule of pyruvate used. Next, the gluconeogenic enzyme PEP carboxykinase converts oxaloacetate into PEP, using one molecule of GTP per molecule of oxaloacetate used. The other step that requires an investment of energy is by a reaction that is reversible. The conversion of 3-phosphoglycerate into 1,3-bisphosphoglycerate (1,3-BPG) by the enzyme phosphoglycerate kinase utilizes one molecule of ATP per molecule of 1,3-BPG generated. This is a reversible reaction. Now, we can add up the energy requirements. Since each of these reactions need to occur twice in order to generate a single molecule of glucose, we'll need to multiply the energy investment by two in each step. Thus, we have two molecules of ATP from the reaction catalyzed by pyruvate carboxylase. We also have two molecules of GTP from the reaction catalyzed by PEP carboxykinase. And lastly, we have two molecules of ATP used from the reaction catalyzed by phosphoglycerate kinase. Adding all of these up, we have a total of four molecules of ATP and two molecules of GTP.

In the first step of gluconeogenesis, pyruvate carboxylase (with ATP and bicarbonate) converts pyruvate to oxaloacetate. Then phosphoenolpyruvate carboxykinase (PEPCK) (with GTP) releases carbon dioxide to give phosphoenolpyruvate.

GTP and ATP are used to drive the reactions that make pyruvate into PEP. Specifically, ATP catalyzes PEP carboxylase and GTP catalyzes PEP carboxykinase. A mutase moves phosphate groups already on a molecule, so it cannot be used to introduce one. The citric acid cycle can make pyruvate into any of the citric acid intermediates, but PEP isn't one of them. Pyruvate kinase is the enzyme that makes pyruvate into PEP, which is only favorable in the forward direction.

Futile cycling occurs when two metabolic processes occur in opposite directions, and thus result in no net change. This is very wasteful, and not ideal. The only example of the answer choices of metabolic processes occurring in opposite directions is glycolysis and gluconeogenesis occurring simultaneously. Other possible examples could include: glycogenesis and glycogenolysis, beta-oxidation and fatty acid synthesis, etc.

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.

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.

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 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.

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.

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

Phosphorolysis is the name given to the addition of phosphate across a bond. Remember that in glycogenolysis, glycogen phosphorylase adds a phosphate across the a-1,4-glycosidic bonds between the glucose units of glycogen. The result is that glucose leaves as glucose-1-phosphate. If hydrolysis were performed instead of phosphorolysis, free glucose would be severed from glycogen and would be able to leave the cell.

AMP is an activator of GP, whereas ATP is an inhibitor of GP. GP cleaves the alpha 1-4 glycosidic bond between a terminal glucose molecule and the rest of the glycogen straight chain, yielding glucose-1-phosphate during glycogenolysis.

In the absence of oxygen, oxidative phosphorylation cannot be used to produce ATP, so glycolysis becomes the primary source of ATP for the cell. The importance of lactic acid fermentation is that it replenishes cellular for the glyceraldehyde-3-phosphate dehydrogenase reaction, which precedes the ATP-producing steps. Without lactic acid fermentation, concentrations would become too low for the glyceraldehyde-3-phosphate dehydrogenase reaction to occur, and the ATP-producing steps would not continue to be reached.

When glucose is fermented, it forms the product lactate. Lactate can then continue on to be fermented to acetate. However, the other answer choices do not represent the correct direction from reactant to product in fermentation. In some organisms, ethanol and carbon dioxide may be produced via fermentation, but carbon dioxide is a byproduct, not a major product in these organisms.

NADH is, under aerobic conditions, returned to when it has its electrons taken in the electron transport chain. However, anaerobic conditions disallow this from occurring, and so NADH will build up in the cell. Fermentation is a pathway that allows pyruvate to be converted to either ethanol or lactic acid (depending on the organism) in order to regenerate the supply of .

Fermentation take place when there is a lack of oxygen in a cell. Without oxygen, the only process that can create ATP from glucose is glycolysis. However, NADH is created during glycolysis, and must be turned back to in order to continue metabolizing glucose with glycolysis. Fermentation, therefore, has the main responsibility of regenerating .

As alluded to in the question stem, an abundance of oxygen allows aerobic respiration to proceed. This allows glucose to be oxidized completely to yield a high amount of energy. In contrast, when oxygen is scarce, cells revert to an alternative method of producing energy, but one that is far less efficient. This is known as anaerobic respiration.

Though there are different types of anaerobic respiration, the one relevant to this question is lactic acid fermentation. In this process, the pyruvate coming from glycolysis is converted into lactic acid. When this happens, NADH is also oxidized back into its non-reduced form. This is the reason why fermentation occurs. If all of the cell's NAD were to be in its reduced form, then there's no way that glycolysis could proceed. Since glycolysis doesn't rely on oxygen, this is the only pathway to provide a stable energy source during oxygen deprivation. So in order to regenerate the needed for glycolysis to continue, it needs to donate its electrons onto pyruvate, which produces lactic acid.