The roles of ATP in living cells and the mechanisms of production of ATP

Question 1

What is anabolism?

Answer 1

Anabolism refers to synthetic reactions in which pathways end in ‘genesis,’ such as glycogenesis (synthesis of glycogen from glucose).

Question 2

What is catabolism?

Answer 2

Catabolism refers to breakdown reactions in which pathways end in ‘lysis,’ such as glycolysis (breakdown of glucose to pyruvate).

Question 3

What is metabolism?

Answer 3

Metabolism encompasses both anabolism and catabolism. It involves the continuous synthesis and breakdown of small molecules, macromolecules, and supramolecular complexes, resulting in a constant flux of mass and energy.

Question 4

What is the role of ATP in metabolism?

Answer 4

Energy released via catabolic reactions is ‘captured’ as adenosine triphosphate (ATP) and stored for later use in anabolic reactions.

Question 5

Why is metabolism important?

Answer 5

Metabolism is crucial for living cells and organisms as it provides the necessary energy for various processes, including motion (muscle contraction), transport of ions/molecules across membranes, biosynthesis of essential metabolites, growth, replacement of damaged cells, and thermoregulation.

Question 6

How do cells acquire free energy?

Answer 6

Cells acquire free energy from nutrient molecules through processes like cellular respiration. For example, the equation C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + Energy represents the breakdown of glucose (sugar) and oxygen to produce carbon dioxide, water, and energy.

Question 7

What happens when a cell can no longer obtain energy?

Answer 7

When a cell can no longer obtain energy, it dies and begins to decay. Constant investment in energy is required to maintain life.

Question 8

What are the three important thermodynamic quantities related to energy?

Answer 8

Enthalpy (H) - the heat content of the reacting system.
Entropy (S) - the randomness or disorder in a system.
Gibbs free energy (G) - the energy capable of doing work at constant temperature and pressure.

Question 9

What does ΔH represent in thermodynamics?

Answer 9

ΔH reflects the types and quantities of chemical bonds broken and formed during a reaction. It is positive (+ve) when energy is absorbed by the reaction, indicating an endothermic process.

Question 10

What does ΔS describe in thermodynamics?

Answer 10

ΔS describes the change in randomness or disorder in a system. It can be positive (+ve) when the randomness increases, such as when large complex molecules are broken down into smaller molecules or vice versa, as in DNA formation or protein formation.

Question 11

What is the equation for Gibbs free energy (ΔG)?

Answer 11

The equation is ΔG = ΔH - TΔS, where ΔG represents the Gibbs free energy, ΔH is the change in enthalpy, T is the temperature, and ΔS is the change in entropy.

Question 12

What is the condition for a spontaneous reaction to occur?

Answer 12

For a reaction to occur spontaneously, ΔG must be negative (-ve), indicating that energy is released by the reaction.

Question 13

How does the free energy of products compare to that of reactants?

Answer 13

The products have less free energy than the reactants, making them more stable. The formation of products is considered “downhill” or spontaneous in terms of energy.

Question 14

What type of reactions are involved in catabolism?

Answer 14

Catabolism involves exergonic reactions, which release free energy (in kJ/mol) during the breakdown of molecules.

Question 15

How does the free energy of products compare to that of reactants in an endergonic reaction?

Answer 15

In an endergonic reaction, the products have more free energy than the reactants, making them less stable. The formation of products is considered “uphill” in terms of energy.

Question 16

What is the concept of coupling reactions?

Answer 16

An endergonic reaction can be driven in the forward direction by coupling it to an exergonic reaction, where the exergonic reaction provides the necessary energy to drive the endergonic reaction.

Question 17

Can you provide an example of coupled reactions?

Answer 17

Glucose + Pi (inorganic phosphate) can react with ATP (adenosine triphosphate) to form glucose-6-phosphate + H2O. The ΔG° (standard Gibbs free energy change) for this reaction is 13.8 kJ/mol. Simultaneously, ATP can undergo hydrolysis to form ADP + Pi with a ΔG° of -30.5 kJ/mol. By coupling these reactions, the overall reaction becomes ATP + glucose → ADP + glucose-6-phosphate with a ΔG° of -16.7 kJ/mol.

Question 18

How does the hydrolysis of ATP contribute to driving an unfavorable reaction?

Answer 18

The hydrolysis of ATP provides the energy required to drive an unfavorable reaction forward. ATP releases a phosphate group (Pi) and converts to ADP, releasing energy that can be utilized to overcome the energy barrier of the unfavorable reaction.

Question 19

What is the role of ATP in providing free energy?

Answer 19

ATP provides most of the free energy required for cellular processes. It acts as the “energy currency” of the cell, storing and releasing energy as needed.

Question 20

How is ATP generated in the cell?

Answer 20

ATP is generated through the process of substrate-level phosphorylation (SLP). This involves the transfer of a phosphate group from a substrate to ADP, resulting in the formation of ATP.

Question 21

What is the difference between substrate-level phosphorylation (SLP) and respiration-linked phosphorylation?

Answer 21

Substrate-level phosphorylation (SLP) refers to the formation of ATP through the transfer of a phosphoryl group from a substrate to ADP. It occurs with soluble enzymes and chemical intermediates. Respiration-linked phosphorylation, on the other hand, involves membrane-bound enzymes and transmembrane gradients of protons. It requires oxygen and occurs during cellular respiration.

Question 22

What distinguishes SLP from respiration-linked phosphorylation?

Answer 22

Substrate-level phosphorylation (SLP) is distinguished from respiration-linked phosphorylation by the involvement of soluble enzymes, chemical intermediates, and the absence of reliance on oxygen.

Question 23

What are enzymes?

Answer 23

Enzymes are biological catalysts that accelerate the rate of chemical reactions in living organisms. They achieve this by creating a new pathway for the reaction, one with a lower activation energy.

Question 24

How do enzymes influence the reaction?

Answer 24

Enzymes do not influence the ΔG (Gibbs free energy) of the reaction. Instead, they lower the activation energy required for the reaction to occur, making it easier and faster for the reaction to proceed.

Question 25

What are cofactors and coenzymes?

Answer 25

Cofactors and coenzymes are molecules that assist enzymes in their catalytic activity.

Cofactors are non-protein molecules, such as metal ions, that bind to enzymes and are necessary for their function.
Coenzymes, on the other hand, are organic molecules derived from vitamins. They participate in enzymatic reactions and often function as carriers of specific atoms or functional groups.

Question 26

What are prosthetic groups?

Answer 26

Prosthetic groups are specific types of coenzymes that have a tight and permanent association with their respective enzymes. They do not diffuse freely and remain bound to the enzyme throughout the reaction.

Question 27

How do coenzymes participate in enzymatic reactions?

Answer 27

Coenzymes have a loose association with their enzymes and can diffuse between different enzymes. They often carry electrons or specific functional groups, cycling between their oxidized and reduced forms during the reaction.

Question 28

What are prosthetic groups?

Answer 28

Prosthetic groups are non-protein cofactors that are covalently bound to the enzyme. They are not released as part of the reaction and act as a temporary store for electrons or reaction intermediates.

Question 29

What are some examples of coenzymes derived from vitamins?

Answer 29

Vitamin B1 (Thiamine) gives rise to thiamine pyrophosphate (TPP), which acts as a prosthetic group.
Vitamin B2 (Riboflavin) can form flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN), which act as prosthetic groups.
Vitamin B5 (Pantothenate) contributes to the formation of coenzyme A, which functions as a co-substrate.
Vitamin B6 (Pyridoxalphosphate) leads to the formation of pyridoxal phosphate (PLP), which acts as a prosthetic group.
Vitamin B12 (Cobalamin) can form 5-deoxyadenosylcobalamin, which acts as a prosthetic group.
Niacin gives rise to NAD+ (nicotinamide adenine dinucleotide), which functions as a co-substrate.
Folic acid contributes to the formation of tetrahydrofolate, which acts as a prosthetic group.
Biotin gives rise to biotin, which acts as a prosthetic group.

Question 30

What is the role of major coenzymes/prosthetic groups involved in energy transduction?

Answer 30

Major coenzymes/prosthetic groups involved in energy transduction include NAD+ (nicotinamide adenine dinucleotide), FAD (flavin adenine dinucleotide), and FMN (flavin mononucleotide). These molecules are involved in the transfer of electrons and hydrogen, reducing the cofactor in the process.

Question 31

What is the role of Nicotinamide Adenine Dinucleotide (NAD+)?

Answer 31

NAD+ and its phosphorylated form, NADP+, function as electron carriers. They accept pairs of electrons to form NADH or NADPH.
NADH is utilized for ATP synthesis.
NADPH is used in reductive biosyntheses.

Question 32

What is the functional part of NAD+?

Answer 32

The functional part of NAD+ is the nicotinamide moiety. It is responsible for accepting and donating electrons during redox reactions.

Question 33

How are NADH and FADH2 re-oxidized?

Answer 33

NADH and FADH2 are recycled through the respiratory chain in the mitochondria. This process is coupled to ATP synthesis and is known as oxidative phosphorylation.

Question 34

How many molecules of ATP can be synthesized by re-oxidizing NADH and FADH2?

Answer 34

Approximately 2.5 molecules of ATP can be synthesized for every NADH molecule re-oxidized. For every FADH2 molecule re-oxidized, about 1.5 molecules of ATP can be synthesized.

Question 35

Where does glycolysis occur?

Answer 35

Glycolysis occurs in the cell cytoplasm.

Question 36

What are the priming stages of glycolysis?

Answer 36

The priming stages of glycolysis involve the following reactions:

Glucose is converted to glucose-6-phosphate (G-6-P) by the enzyme hexokinase.
G-6-P is converted to fructose-6-phosphate (F-6-P).
F-6-P is further converted to fructose-1,6-bisphosphate (FBP) by the enzyme phosphofructokinase-1 (PFK-1), which is the committed step of glycolysis.

Question 37

What happens in the payoff reactions of glycolysis?

Answer 37

1,3-bisphosphoglycerate (1,3 BPG) is converted to 3-phosphoglycerate.
3-phosphoglycerate is converted to 2-phosphoglycerate.
2-phosphoglycerate is converted to phosphoenolpyruvate (PEP).
PEP is further converted to pyruvate.

Question 38

What is the role of glyceraldehyde-3-phosphate (GAP) in glycolysis?

Answer 38

GAP continues through glycolysis and is involved in subsequent reactions.

Question 39

How many times does each reaction occur for every glucose molecule metabolized in glycolysis?

Answer 39

Each reaction in glycolysis occurs twice for every glucose molecule metabolized.

Question 40

What are the enzymes involved in glycolysis?

Answer 40

Some of the enzymes involved in glycolysis are hexokinase, phosphofructokinase-1 (PFK-1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), enolase, and pyruvate kinase.

Question 41

What are the two possible fates of pyruvate?

Answer 41

Under aerobic conditions (with sufficient oxygen availability), it undergoes oxidation and complete degradation.
In hypoxic (low oxygen) conditions, it can be reduced to lactate.

Question 42

Why has the system of lactate production evolved?

Answer 42

The system of lactate production has evolved as a way to regenerate NAD+ under hypoxic conditions. By reducing pyruvate to lactate, cells can regenerate NAD+ for continued glycolysis to produce ATP, even when oxygen is limited.

Question 43

How does pyruvate enter the mitochondria under aerobic conditions?

Answer 43

Under aerobic conditions, pyruvate transport occurs via a specific carrier protein embedded in the mitochondrial membrane.

Question 44

What happens to pyruvate inside the mitochondrion?

Answer 44

Inside the mitochondrion, pyruvate undergoes oxidative decarboxylation by the pyruvate dehydrogenase complex. This reaction produces acetyl CoA, CO2, NADH, and H+.
Pyruvate + CoA + NAD+ -> Acetyl CoA + CO2 + NADH + H+

Question 45

What is the significance of the pyruvate dehydrogenase complex reaction?

Answer 45

The reaction catalyzed by the pyruvate dehydrogenase complex is irreversible and serves as the link between glycolysis and the citric acid cycle (also known as the Krebs cycle or TCA cycle).

Question 46

How is the structure of mitochondria related to pyruvate transport?

Answer 46

The structure of mitochondria includes a specific carrier protein in the mitochondrial membrane that allows for the transport of pyruvate into the mitochondrial matrix.

Question 47

What is the enzyme responsible for the conversion of Succinyl CoA to Succinate?

Answer 47

Succinyl-CoA synthetase is the enzyme responsible for the conversion of Succinyl CoA to Succinate.

Question 48

What is the enzyme responsible for the dehydrogenation of Succinate to Fumarate?

Answer 48

Succinate dehydrogenase is the enzyme responsible for the dehydrogenation of Succinate to Fumarate.

Question 49

What is the enzyme responsible for the hydration of Fumarate to Malate?

Answer 49

Fumarase is the enzyme responsible for the hydration of Fumarate to Malate.

Question 50

What is the enzyme responsible for the dehydrogenation of Malate to Oxaloacetate?

Answer 50

Malate dehydrogenase is the enzyme responsible for the dehydrogenation of Malate to Oxaloacetate.

Question 51

What is the enzyme responsible for the formation of Acetyl CoA from Oxaloacetate?

Answer 51

Citrate synthase is the enzyme responsible for the formation of Acetyl CoA from Oxaloacetate, which marks the start of the TCA cycle again.

Question 52

What are the products of one turn of the TCA cycle starting with Acetyl CoA?

Answer 52

2 carbons enter (from Acetyl CoA)
2 carbons leave (as CO2)
3 NADH molecules are produced (2 NADH per turn x 1 turn)
1 GTP (or ATP) molecule is produced (1 GTP or ATP per turn x 1 turn)
1 FADH2 molecule is produced (1 FADH2 per turn x 1 turn)

Question 53

What are the two levels of tight regulation in the TCA cycle?

Answer 53

The flow of carbon atoms from pyruvate into and through the TCA cycle is tightly regulated at two levels:

Conversion of pyruvate to acetyl-CoA (in the PDH reaction).
Entry of acetyl-CoA into the TCA cycle (in the citrate synthase reaction).

Question 54

Which reactions in the TCA cycle are main regulatory points?

Answer 54

The main regulatory points in the TCA cycle are the irreversible reactions, including the conversion of pyruvate to acetyl-CoA (PDH reaction), the entry of acetyl-CoA into the TCA cycle (citrate synthase reaction), and the reactions catalyzed by isocitrate dehydrogenase and α-ketoglutarate dehydrogenase.

Question 55

How are NADH and FADH2 re-oxidized in the electron transport chain?

Answer 55

NADH and FADH2 are re-oxidized using electron transport proteins in the electron transport chain, also known as the respiratory chain.

Question 56

What occurs in the electron transport chain?

Answer 56

In the electron transport chain, a series of coupled oxidation and reduction reactions occur. Electrons are passed along a series of carriers, leading to the reduction of oxygen (O2) to water (H2O). This process helps generate ATP through oxidative phosphorylation.

Question 57

How is ATP synthesis in oxidative phosphorylation accomplished?

Answer 57

ATP synthesis in oxidative phosphorylation utilizes electrical energy and chemical potential energy, which are generated by the difference in H+ concentration between the intermembrane space and the mitochondrial matrix. This difference is created by the transfer of H+ (proton pumping) from the matrix to the intermembrane space by complexes I, III, and IV in the electron transport chain.

Question 58

What drives the synthesis of ATP using ATP synthase?

Answer 58

The proton (H+) motive force, which is the separation of charge between the intermembrane space and the mitochondrial matrix, drives the synthesis of ATP using ATP synthase.

Question 59

What are the components of ATP synthase?

Answer 59

F0: This portion of ATP synthase resides in the inner membrane of the mitochondria and forms a channel for the flow of protons (H+).
F1: This portion of ATP synthase projects into the matrix of the mitochondria and is responsible for the actual synthesis of ATP.

Question 60

How does ATP synthase function to produce ATP?

Answer 60

As H+ flows through the membrane, the cylinder within the F0 portion and the g-shaft rotate. The rotation of the g-shaft causes conformational changes in each of the β subunits of the F1 portion. These conformational changes facilitate the formation of ATP from ADP and Pi (inorganic phosphate).