MCAT Biochemistry Review
Chapter 10: Carbohydrate Metabolism II: Aerobic Respiration
Have you ever heard that eating peach pits is deadly? Before you start panicking about the snack you had during your study break, you should know that the accuracy of such a statement is debatable. While it is true that digesting peach pits can result in the formation of trace amounts of cyanide, the concentration is far too low to be clinically worrisome. Cyanide is a poison that binds irreversibly to cytochrome a/a3, a protein located in the electron transport chain of the mitochondria. Why can this be deadly? Blocking the electron transport chain (ETC) inhibits aerobic respiration from yielding the ATP the body requires to function properly. Cyanide poisoning leaves cells unable to utilize oxygen for aerobic respiration because it blocks oxygen from binding to the ETC. Therefore, symptoms resemble those of tissue hypoxia: perceived difficulty breathing, general weakness, and, in higher doses, cardiac arrest followed by death within minutes.
But what about the metabolic pathways described in Chapter 9 of MCAT Biochemistry Review—don't they produce energy without oxygen? While glycolysis does not depend on oxygen, it only yields a net 2 ATP per molecule of glucose, which is not nearly enough to maintain the body's energy requirements. This brings us to two of the most tested topics on the MCAT: the citric acid cycle and oxidative phosphorylation.
In this chapter, we'll take a close look at what's gained when the products of glycolysis and other derivatives of metabolic pathways enter the citric acid cycle. We'll also look at how this process is regulated with regard to the substrates, products, and reactions involved. Lastly, we'll observe what happens when this cycle's products undergo oxidative phosphorylation, with particular emphasis on how the electron transport chain facilitates the process and the ATP that is yielded.
The citric acid cycle, also called the Krebs cycle or the tricarboxylic acid (TCA) cycle, occurs in the mitochondria. The main function of this cycle is the oxidation of acetyl-CoA to CO2 and H2O. In addition, the cycle produces the high-energy electron-carrying molecules NADH and FADH2. Acetyl-CoA can be obtained from the metabolism of carbohydrates, fatty acids, and amino acids, making it a key molecule in the crossroads of many metabolic pathways and a highly testable one.
METHODS OF FORMING ACETYL-CoA
Recall from Chapter 9 of MCAT Biochemistry Review that after glucose undergoes glycolysis, its product, pyruvate, enters the mitochondrion via active transport and is oxidized and decarboxylated. These reactions are catalyzed by a multienzyme complex called the pyruvate dehydrogenase complex, which is located in the mitochondrial matrix. As we take a deeper look at the enzymes that make up this complex, as well as the substrates and products of their reactions, it is helpful to follow the carbons in the molecules. For example, the three-carbon pyruvate is cleaved into a two-carbon acetyl group and carbon dioxide. This reaction is irreversible, which explains why glucose cannot be formed directly from acetyl-CoA. In mammals, pyruvate dehydrogenase complex is made up of five enzymes: pyruvate dehydrogenase (PDH), dihydropropyl transacetylase, dihydrolipoyl dehydrogenase, pyruvate dehydrogenase kinase, and pyruvate dehydrogenase phosphatase. While the first three work in concert to convert pyruvate to acetyl-CoA, the latter two regulate the actions of PDH. Figure 10.1 shows the overall reaction for the conversion of pyruvate to acetyl-CoA. The reaction is exergonic The complex is inhibited by an accumulation of acetyl-CoA and NADH that can occur if the electron transport chain is not properly functioning or is inhibited.
Figure 10.1. Overall Reaction of Pyruvate Dehydrogenase Complex
Similar to the gluco–/glyco– terminology in Chapter 9 of MCAT Biochemistry Review, it is critical to keep straight the various enzymes containing pyruvate: pyruvate dehydrogenase (PDH), its two regulators (PDH kinase and PDH phosphatase), and pyruvate carboxylase, an enzyme in gluconeogenesis.
Note that coenzyme A (CoA) is written as CoA–SH in the reaction above. This is because CoA is a thiol, containing an –SH group. When acetyl-CoA forms, it does so via covalent attachment of the acetyl group to the –SH group, resulting in the formation of a thioester, which contains sulfur instead of the typical oxygen ester –OR. The formation of a thioester rather than a typical ester is worth noting because of the high-energy properties of thioesters. That is to say, when a thioester undergoes a reaction such as hydrolysis, a significant amount of energy will be released. This can be enough to drive other reactions forward, like the citric acid cycle. The pyruvate dehydrogenase complex enzymes needed to catalyze acetyl-CoA formation are listed below in sequential order, and the mechanism is shown in Figure 10.2.
· Pyruvate dehydrogenase (PDH): pyruvate is oxidized, yielding CO2, while the remaining two-carbon molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP). TPP is a coenzyme held by noncovalent interactions to PDH. Mg2+ is also required.
· Dihydropropyl transacetylase: the two-carbon molecule bonded to TPP is oxidized and transferred to lipoic acid, a coenzyme that is covalently bonded to the enzyme. Lipoic acid's disulfide group acts as an oxidizing agent, creating the acetyl group. The acetyl group is now bonded to lipoic acid via thioester linkage. After this, dihydropropyl transacetylase catalyzes the CoA–SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA. Lipoic acid is left in its reduced form.
· Dihydrolipoyl dehydrogenase: flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions. As lipoic acid is reoxidized, FAD is reduced to FADH2. In subsequent reactions, this FADH2 is reoxidized to FAD, while NAD+ is reduced to NADH.
Figure 10.2. Mechanism of Pyruvate Dehydrogenase
In studies of pathologies that affect the central cholinergic system such as Alzheimer's disease, Huntington's disease, and even alcoholism, a decrease in glucose metabolism and oxidative phosphorylation has been observed in the brain. Ongoing research will hopefully determine if the resulting lack of acetyl-CoA could be a cause of the disease or a result of the disease. With decreased amounts of acetyl-CoA, not only is energy production a concern, but also the production of the neurotransmitter acetylcholine.
While glycolysis is a heavily reviewed and heavily tested contributor to the production of acetyl-CoA, other pathways are capable of forming acetyl-CoA. These pathways act on fatty acids, ketogenic amino acids, ketone bodies, and alcohol. Descriptions of these pathways are provided below. The ultimate production of acetyl-CoA allows all of these pathways to culminate in the final common pathway of the citric acid cycle.
· Fatty acid oxidation (β-oxidation): in the intermembrane space, a process called activation causes a thioester bond to form between carboxyl groups of fatty acids and CoA. Activated fatty acyl-CoA is then transported to the intermembrane space of the mitochondrion. Because fatty acyl-CoA cannot cross the inner mitochondrial membrane, the fatty acyl group is transferred to carnitine via a transesterification reaction, as shown in Figure 10.3. Carnitine is a molecule that can cross the inner membrane with a fatty acyl group in tow. One acyl-carnitine crosses the inner membrane; it transfers the fatty acyl group to a mitochondrial CoA–SH via another transesterification reaction. In other words, carnitine's function is merely to carry the acyl group from a cytosolic CoA–SH to a mitochondrial CoA–SH. Once acyl-CoA is formed in the matrix, β-oxidation can occur, which removes two-carbon fragments from the carboxyl end.
Figure 10.3. Fatty Acid Activation and Transport
· Amino acid catabolism: certain amino acids can be used to form acetyl-CoA. These amino acids must lose their amino group via transamination; their carbon skeletons can then form ketone bodies. These amino acids are termed ketogenic for that reason. The conversion of ketone bodies to acetyl-CoA is mentioned below.
· Ketones: although acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, the reverse reaction can occur as well. The actual enzymes for this process are outside the scope of the MCAT.
· Alcohol: when alcohol is consumed in moderate amounts, the enzymes alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA. However, this reaction is accompanied by NADH buildup, which inhibits the Krebs cycle. Therefore, the acetyl-CoA formed through this process is used primarily to synthesize fatty acids.
Once formed, mitochondrial acyl-CoA can undergo β-oxidation. This process is discussed in Chapter 11 of MCAT Biochemistry Review.
While the brain normally uses glucose for energy, under conditions such as starvation, ketone bodies can become the brain's major source of energy.
MCAT Concept Check 10.1:
Before you move on, assess your understanding of the material with these questions.
1. What is the overall reaction of the pyruvate dehydrogenase complex?
2. What other molecules can be used to make acetyl-CoA, and how does the body perform this conversion for each?
Mechanism of Converstion to Acetyl-CoA