Citric Acid Cycle, Redox Reactions, and Lipid Biosynthesis in Eukaryotic Cells

Where does the citric acid cycle take place in eukaryotic cells?

The mitochondrial matrix

What advantages do eukaryotic cells gain from performing the TCA in mitochondria rather than the cytoplasm?

Highly efficient energy production, precise regulation of metabolic intermediates, and a compartmentalized environment for signaling and biosynthesis.

Why are the terms TCA cycle and Krebs cycle appropriate for the citric acid cycle?

TCA Cycle highlights the tricarboxylic acid structure of citric acid; Krebs Cycle honors the biochemist who elucidated its functions.

What are redox reactions?

The transfer of electrons between chemical species, causing a change in their oxidation states.

How do redox reactions play a role in the citric acid cycle?

They transfer high-energy electrons from fuel sources to electron carriers, primarily NADH and FADH2.

What are the major products of the citric acid cycle?

3 molecules of NADH, 1 FADH2, 1 nucleoside triphosphate (ATP or GTP).

Why is the citric acid cycle referred to as a 'cycle'?

The final product, oxaloacetate, is also used to start the first step of the cycle.

What is the primary input into the citric acid cycle?

Acetyl-CoA.-

How many carbons are in oxaloacetate, the acetyl group, and the resulting citrate?

Oxaloacetate has 4 carbons, the acetyl group has 2 carbons, and citrate has 6 carbons.

What provides the energy to render the condensation of acetate with oxaloacetate exergonic?

The hydrolysis of the thioester in the intermediate.

Why is it necessary to isomerize citrate to isocitrate?

To position the hydroxyl for oxidation to a carbonyl group, enabling beta-decarboxylation.

What are the products generated when isocitrate is converted to alpha-ketoglutarate?

NADH and CO2.

What is the fate of the carboxyl group removed from alpha-ketoglutarate?

It is released as CO2.

What roles do CoA-SH, NAD+, TPP, lipoate, and FAD play in the α-ketoglutarate dehydrogenase complex?

CoA-SH is a carrier; NAD+ is the final electron acceptor; TPP is a cofactor; lipoate is an acyl and electron carrier; FAD is an electron carrier.

What are some key similarities between α-ketoglutarate dehydrogenase complex and pyruvate dehydrogenase complex?

Both catalyze oxidative decarboxylation of an alpha keto acid, produce CO2, NADH, and acyl-CoA, and consist of three core enzymes.

What are the main differences between α-ketoglutarate dehydrogenase complex and pyruvate dehydrogenase complex?

PDH uses pyruvate (3C) as a substrate; α-KGDH uses alpha-ketoglutarate (5C).

How many steps are in each phase of the citric acid cycle and what is their purpose?

Steps 1-4: Oxidative decarboxylation phase to extract high energy electrons; Steps 5-8: Regeneration phase to regenerate oxaloacetate.

What drives the formation of GTP in step 5 of the citric acid cycle?

The strongly negative standard free energy of hydrolysis.

What does substrate-level phosphorylation mean in the context of the citric acid cycle?

The direct transfer of a phosphate group from a high-energy substrate molecule to GDP, forming GTP.

In which steps of the citric acid cycle are electrons removed and stored in FADH2 or NADH?

Steps 1 & 3.

What are the types of reactions that occur in the last three steps of the citric acid cycle?

Oxidation → Hydration → Oxidation.

Do the two carbons from acetyl-CoA that enter the citric acid cycle leave as CO₂ in the same cycle turn? Why or why not?

No, they do not leave in the same cycle turn.

What happens to the carbons from acetyl-CoA in the citric acid cycle?

They are incorporated into the cycle's intermediates and released after multiple turns.

What effect do high levels of NADH have on the citric acid cycle?

They inhibit isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.

What is an amphibolic pathway?

A metabolic pathway used in both catabolism and anabolism.

Which key metabolic intermediates serve as precursors for biosynthesis?

Pyruvate, Acetyl-CoA, Citrate, α-Ketoglutarate, Oxaloacetate.

What are anaplerotic reactions?

Reactions that replenish citric acid cycle intermediates withdrawn for biosynthesis.

How does the Malate-Aspartate Shuttle function?

It transports reducing equivalents of NADH from the cytosol into the mitochondria.

In which state do organisms synthesize and store lipids?

In the fed state.

What is the source of metabolic energy for fatty acid synthesis?

ATP.

What is the source of reducing power for fatty acid synthesis?

NADPH.

What are the two enzymes required for fatty acid biosynthesis?

1. Acetyl-CoA carboxylase 2. Fatty acid synthetase (FAS).

What is the product of acetyl-CoA carboxylase?

Malonyl-CoA.

Why is ATP required for acetyl-CoA carboxylase?

To provide energy for the carboxylation of acetyl-CoA to malonyl-CoA.

What is the role of the biotin carrier protein domain in acetyl-CoA carboxylase?

It carries a carboxyl group between domains of the enzyme.

What happens to the fifth carbon during the first round of reactions in fatty acid synthesis?

It is released as a molecule of CO2.

Where is Acetyl-CoA attached in the FAS I Complex?

To the terminal thiol of the Acyl Carrier Protein (ACP) domain.

What is the order of the next three reactions after the initial condensation reaction in fatty acid synthesis?

Reduction → Dehydration → Reduction.

What are the requirements for activated carrier molecules in each elongation cycle of fatty acid synthesis?

1 ATP for malonyl-CoA synthesis and 2 NADPH for reduction reactions.

What is the typical product formed by the FAS I Complex?

Palmitate.

How does cellular compartmentalization affect fatty acid synthesis regulation?

It separates anabolic and catabolic pathways into different environments.

How does energy availability regulate fatty acid synthesis?

Fatty acid synthesis requires significant amounts of ATP and NADPH.

Which hormone stimulates fatty acid synthesis?

Insulin.

Which hormone inhibits fatty acid synthesis?

Palmitate.

Why is acetyl-CoA carboxylase (ACC) a target for regulation of fatty acid synthesis?

It catalyzes the first committed and rate-limiting step of fatty acid synthesis.

What are the two precursors required for the biosynthesis of glycerophospholipids in animal cells?

Fatty acids and L-glycerol 3-phosphate.

Why is esterification of fatty acids using acetyl-CoA necessary for glycerophospholipid formation?

It activates fatty acids for incorporation into glycerophospholipids.

What is the general structure of a triacylglycerol molecule?

A triacylglycerol molecule has a glycerol backbone with three fatty acid tails attached via ester bonds.

What molecule serves as a precursor of both triacylglycerols and glycerophospholipids?

Phosphatidic acid is the precursor for both triacylglycerols and glycerophospholipids.

What effect does insulin have on triacylglycerol levels?

Insulin promotes the synthesis of fatty acids and increases lipid storage in the form of triglycerol in adipose tissues.

What effect do glucagon and epinephrine have on triacylglycerol levels?

They stimulate the mobilization of free fatty acids from triglycerol stored in adipose tissue.

What functions does cholesterol have?

Cholesterol production is regulated by intercellular cholesterol concentration, ATP supply, and hormones.

What is the primary precursor molecule for the biosynthesis of cholesterol?

Acetyl-CoA.

What are the four stages of cholesterol biosynthesis?

1. Acetate → Mevalonate via HMG-CoA reductase. 2. Mevalonate → Activated isoprene units. 3. Isoprene units → Squalene. 4. Squalene → Cholesterol.

Why is HMG-CoA reductase the limiting enzyme of cholesterol biosynthesis?

It catalyzes the conversion of HMG-CoA to mevalonate, a critical checkpoint in the pathway.

What effects do insulin and glucagon have on the activity of HMG-CoA?

Insulin increases activity by promoting the active form and increasing mRNA and protein levels, while glucagon decreases activity by favoring the inactive form.

Is HMG-CoA regulated by feedback inhibition?

Yes, HMG-CoA reductase is regulated by feedback inhibition.

What is the name for the class of drugs that inhibit HMG-CoA?

Statins, which competitively inhibit HMG-CoA reductase.

What are some examples of the fates of cholesterol?

Cholesterol is exported as bile acids, biliary cholesterol, or cholesteryl esters, and converted into steroid hormones or vitamin D.

What is a lipoprotein?

Lipoproteins transport lipids in the bloodstream, including chylomicrons, VLDL, LDL, and HDL.

What role do apolipoproteins play?

They help regulate which cells take up lipoprotein particles.

What can defects in apolipoproteins lead to?

Disorders like familial hypercholesterolemia.

What is the role of glucagon and epinephrine in fatty acid release?

They stimulate the release of free fatty acids from triacylglycerol molecules in adipocytes.

What is the first step of preparing fatty acids for entry into the β-oxidation pathway?

Dehydrogenation of the fatty acyl-CoA produces a double bond, yielding trans-Δ2-enoyl-CoA + FADH2.

What is the function of carnitine palmitoyltransferase 1 in the β-oxidation pathway?

It catalyzes the conversion of long-chain fatty acyl-CoAs into acylcarnitines.

What is the function of carnitine palmitoyltransferase 2 in the β-oxidation pathway?

It reconverts fatty acid-carnitine molecules back into fatty acyl-CoA esters.

Where does the β-oxidation pathway occur in eukaryotic cells?

In the mitochondria.

What is the final product of the β-oxidation pathway?

Acetyl-CoA and, for fatty acids with an odd number of carbons, propionyl-CoA.

Which activated carrier molecules are produced during the β-oxidation pathway?

NADH and FADH₂.

What is the role of thiolase in β-oxidation?

Thiolase catalyzes the final step by cleaving a two-carbon unit from a fatty acyl-CoA molecule.

What happens to energy production from fatty acids if L-β-hydroxyacyl-CoA is formed?

Energy production would be severely impaired, stopping after L-β-hydroxyacyl-CoA and preventing acetyl-CoA generation.

What is the fate of Acetyl-CoA generated by the β-oxidation pathway?

It primarily enters the citric acid cycle to produce ATP through oxidative phosphorylation.

What is the role of Acetyl-CoA Carboxylase in fatty acid metabolism?

It regulates the balance between fatty acid synthesis and oxidation by controlling malonyl-CoA levels.

How does increased malonyl-CoA affect fatty acid β-oxidation?

It inhibits fatty acid β-oxidation by blocking fatty acids' entry into the mitochondria.

What effect does insulin have on Acetyl-CoA Carboxylase activity?

Insulin activates Acetyl-CoA Carboxylase by promoting its dephosphorylation, increasing fatty acid synthesis.

What effect does glucagon have on Acetyl-CoA Carboxylase activity?

It inactivates Acetyl-CoA Carboxylase, halting fatty acid synthesis.

What metabolic condition triggers ketosis?

A lack of sufficient glucose leads the body to break down stored fat for fuel.

Which organ is primarily responsible for ketone body synthesis?

Liver

Which of the following is NOT a ketone body?

Pyruvate

Why doesn't the liver use ketone bodies as a fuel source?

Lack of succinyl-CoA transferase (thiophorase).

Why is biologically available nitrogen limiting despite high atmospheric N2 levels?

Atmospheric N2 is relatively inert and must be converted to ammonia or nitrate for biological use.

What type of organisms can perform nitrogen fixation?

Bacteria and cyanobacteria.

What is nitrification?

The process of converting ammonia (NH3) to nitric oxide (NO), nitrite (NO2⁻), and nitrate (NO3⁻).

What is denitrification?

The process of reducing NO3⁻ and NO2⁻ to maintain atmospheric N2 levels under anaerobic conditions.

What is anammox?

The process of producing nitrogen gas (N2) through the oxidation of ammonium (NH₄⁺) using nitrite (NO₂⁻) as the electron acceptor.

What is nitrogen assimilation?

The biological process by which inorganic nitrogen is incorporated into amino acids.

Why does nitrogen reduction require a large input of energy?

The nitrogen triple bond is very stable, requiring high activation energy to break.

What is the nitrogenase complex responsible for?

The fixation of nitrogen, with key enzymes being dinitrogenase reductase and dinitrogenase.

What is the symbiotic relationship between plants and nitrogen-fixing bacteria?

Bacteria in root nodules are protected from oxygen by leghemoglobin, allowing nitrogen fixation.

Why are extreme conditions required in the Haber-Bosch process?

To balance the reaction rate and equilibrium yield for ammonia production.

What is the role of glutamine synthetase?

It catalyzes the reaction of glutamate with ammonia to form glutamine.

Why does the synthesis of glutamine from glutamate require ATP hydrolysis?

ATP hydrolysis activates glutamate for nucleophilic attack by ammonia.

What role does pyridoxal phosphate play in transamination?

It serves as a transient amino group carrier essential for aminotransferases.

Why is ammonia toxic in most cells?

Excess ammonia can cause serious neurological damage.

How do glutamate and glutamine detoxify ammonia?

They convert into each other to bind and neutralize toxic ammonia.

What is the overall purpose of the Urea cycle?

To convert ammonia into a non-toxic form for mammals.

Which molecules are required to generate carbamoyl phosphate?

Ammonia and bicarbonate (HCO3⁻).

Which steps of the urea cycle occur in the mitochondria?

the enzyme carbamoyl phosphate

synthetase I combines the ammonia generated by

glutaminase and glutamate dehydrogenase with CO2 (as

HCO3⁻) produced by mitochondrial respiration, to form

carbamoyl phosphate

Step 1: Ornithine transcarbamoylase catalyzes the donation of

the carbamoyl group of carbamoyl phosphate to ornithine to form

citrulline.

Which steps of the urea cycle require ATP?

A and B: When considered in isolation, the urea cycle appears to require multiple high-energy phosphate groups: two ATP molecules for carbamoyl phosphate, and one ATP for argininosuccinate

Which step requires 2 ATP in the urea cycle?

Step C for carbamoyl phosphate.