Question

If at this point the student is still unconvinced as to the importance of organic chemistry in daily life, let one consider glycolysis, the process whereby glucose is broken down into \(\mathrm{CO}_{2}, \mathrm{ATP}\), and \(\mathrm{H}_{2} \mathrm{O}\) by the same nebulous mechanisms that the beginning organic student has been trying to master for two semesters. (a) Consider the initial step of the Krebs Cycle; the reaction of oxaloacetate with acetyl CoA, in the presence of base and water to yield citric acid and CoASH. What would be the mechanism of this reaction if it occurs as written below: (b) Vitamin \(\mathrm{B}_{1}\) (Thiamine) also plays an important role in the Krebs cycle, catalyzing several important glycolysis reactions. One reaction it catalyzes in particular is the decarboxylation of \(\alpha\) -ketoglutaric acid to succinic acid. Given the following reactions, propose a mechanism for the decarboxylation of \(\alpha\) -ketoglutaric acid to succinic acid.

Short answer

In part (a), the formation of citric acid from oxaloacetate and acetyl CoA involves the following steps: (1) base-mediated deprotonation of oxaloacetate, (2) nucleophilic attack of the resulting alkoxide ion on the carbonyl carbon of Acetyl CoA, (3) protonation of the carbonyl oxygen, and (4) cleavage of the thioester bond to form CoASH. In part (b), the decarboxylation of α-ketoglutaric acid catalyzed by Vitamin B1 (Thiamine) proceeds through the following steps: (1) formation of thiamine ylide, (2) nucleophilic attack of the ylide carbon on the carbonyl group of α-ketoglutaric acid, (3) carbanion formation in the α-position, (4) expulsion of carbon dioxide (CO2), (5) generation of an enol intermediate, and (6) tautomerization to produce succinic acid.

Step-by-step solution

Part (a): Reaction mechanism of the formation of citric acid

First, let's write the overall balanced equation for this reaction: Oxaloacetate + Acetyl CoA + Base + H2O → Citric Acid + CoASH Now we need to propose a mechanism for this reaction. Following are the steps: 1. The base abstracts a proton from alcohol group of oxaloacetate to form an alkoxide ion. 2. The alkoxide ion attacks the carbonyl carbon of the Acetyl CoA, forming a new carbon-carbon bond. 3. The carbonyl oxygen is protonated by the water molecule. 4. A CoASH molecule is formed by cleavage of the thioester bond. Now we have the mechanism for the formation of citric acid from oxaloacetate and acetyl CoA.

Part (b): Propose a mechanism for the decarboxylation of α-ketoglutaric acid

Given the reactions described in the exercise, we need to propose a mechanism for the decarboxylation of α-ketoglutaric acid catalyzed by Vitamin B1 (Thiamine). Following are the steps for this mechanism: 1. Thiamine converts to thiamine ylide by the abstraction of a proton from the amino group and deprotonation on the sulfur-containing ring. This results in a nucleophilic carbon on the five-membered ring. 2. The nucleophilic carbon attacks the carbonyl group of the α-ketoglutaric acid, resulting in a new carbon-carbon bond. 3. A carbanion is formed inα-position due to the movement of electrons in the negatively charged carbon towards the carbonyl carbon atom. 4. The carbanion pushes out carbon dioxide (CO2) from the molecule through the cleavage of the carbon-carbon bond. 5. The electron pair moves back to the carbonyl carbon generating an enol intermediate. 6. The enol intermediate tautomerizes to generate succinic acid. Now we have the mechanism for the decarboxylation of α-ketoglutaric acid catalyzed by Vitamin B1.

Key concepts

Glycolysis

Glycolysis is a crucial metabolic pathway where glucose, a six-carbon sugar, is split into two molecules of pyruvate, each with three carbons. This process occurs in the cytoplasm of cells and serves as the foundation for both aerobic and anaerobic respiration.

During glycolysis, which translates to 'splitting sugars', a single glucose molecule undergoes a series of enzyme-catalyzed reactions. These reactions are divided into two phases: the energy investment phase and the energy payoff phase. Initially, two molecules of ATP are used to phosphorylate glucose and its isomer, fructose-6-phosphate, which prepares the six-carbon sugar molecule for cleavage into two three-carbon molecules. These molecules are then converted through a sequence of steps into pyruvate while generating a net gain of two ATP molecules and two NADH molecules.

Glycolysis is a prime example of enzyme catalysis in action - each step is facilitated by a specific enzyme which dramatically increases the reaction rate and ensures cellular efficiency in energy production.

Krebs Cycle

The Krebs cycle, also known as the citric acid cycle or the tricarboxylic acid (TCA) cycle, is a series of chemical reactions used by aerobic organisms to generate energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins into carbon dioxide and chemical energy. It occurs in the mitochondria following glycolysis if oxygen is present.

The Krebs cycle begins with the combination of acetyl-CoA and oxaloacetate to form citrate, as the provided exercise suggests. This eight-step process continues to oxidize the acetyl group, reducing NAD+ to NADH and FAD to FADH2, while releasing carbon dioxide. These electron carriers then shift to the electron transport chain where a significant amount of ATP is produced. The Krebs cycle is a pivotal mechanism in cellular respiration, not just for its production of energy carriers, but also for providing precursor metabolites for various biosynthetic pathways.

Enzyme Catalysis

Enzymes are biological catalysts that speed up chemical reactions in organisms. They function by lowering the activation energy of reactions, thereby accelerating the rate at which reactants are converted into products. Enzyme catalysis is highly specific, meaning individual enzymes will typically act on a single substrate or a group of closely related substrates.

Enzymes bind to substrates at their active site, forming an enzyme-substrate complex. This induces a fit that changes the shape of the enzyme and helps the chemical reaction to occur. Enzymes are not consumed or permanently altered during this process, so they can be used repeatedly. Factors such as temperature, pH, and substrate concentration can influence enzyme activity. This exquisite control over reaction pathways is paramount in processes like glycolysis and the Krebs cycle, where multiple enzymes work in concert to ensure cells can efficiently produce the energy they require.

Carboxylation and Decarboxylation Reactions

Carboxylation and decarboxylation are two opposing types of reactions that play vital roles in biological systems, particularly in metabolic processes like photosynthesis and cellular respiration. Carboxylation is the addition of a carboxyl group (-COOH) to a substrate, whereas decarboxylation is the removal of this group as carbon dioxide (CO2).

Enzymes such as carboxylases and decarboxylases catalyze these types of reactions. In the Krebs cycle, decarboxylation reactions occur multiple times and involve the release of CO2 as part of the oxidation of organic molecules. One specific instance, as noted in the student exercise, involves the decarboxylation of α-ketoglutaric acid to form succinic acid, which is catalyzed by an enzyme that uses thiamine pyrophosphate (vitamin B1) as a cofactor. These processes are crucial for the regulation of metabolic pathways and the generation of energy-rich molecules like ATP.