Unit 6 - Practice Quiz

The First Law of Thermodynamics, also known as the law of conservation of energy, states that energy cannot be created or destroyed, only converted from one form to another, such as light energy being converted to chemical energy in photosynthesis.

Entropy is a fundamental concept in thermodynamics that quantifies the amount of randomness or disorder within a system. According to the Second Law of Thermodynamics, the entropy of an isolated system always tends to increase.

An open system can exchange both energy (like heat and work) and matter (like food and waste) with its environment. Living organisms constantly do this to maintain their structure and function.

The prefix 'exo-' means 'out'. Exothermic reactions release energy, usually in the form of heat, causing the temperature of the surroundings to rise.

The prefix 'endo-' means 'in'. An endothermic reaction absorbs heat from its surroundings to proceed. This absorption of heat makes the container feel cold.

Exergonic reactions release free energy, meaning the products have less free energy than the reactants. This results in a negative value for the change in Gibbs Free Energy () and indicates the reaction can occur spontaneously.

Endergonic reactions are non-spontaneous and require an input of free energy from the surroundings to occur. They have a positive change in Gibbs Free Energy ().

The hydrolysis of ATP is a highly exergonic reaction, releasing a significant amount of free energy. Cells couple this reaction to endergonic reactions to power cellular work.

Chloroplasts are the specialized organelles within plant and algal cells that contain chlorophyll and are the site of photosynthesis.

Photosynthesis uses energy from sunlight to convert carbon dioxide () and water () into glucose (a sugar) and oxygen.

Chlorophyll is the green pigment found in chloroplasts that absorbs light energy, primarily in the blue and red parts of the spectrum, which drives the photosynthetic process.

During the light-dependent reactions of photosynthesis, water molecules are split, which releases oxygen gas () as a byproduct.

Glycolysis is the initial stage of cellular respiration and it takes place in the cytoplasm of virtually all cells, both prokaryotic and eukaryotic.

The term glycolysis comes from 'glyco' (sugar) and 'lysis' (splitting). It is the metabolic pathway that breaks down one molecule of glucose (a 6-carbon sugar) into two molecules of pyruvate (a 3-carbon compound).

Although 4 ATP molecules are produced during glycolysis, 2 ATP are consumed in the initial investment phase, resulting in a net gain of 2 ATP.

Glycolysis breaks a six-carbon glucose molecule into two three-carbon molecules of pyruvate. Pyruvate is a key crossroads molecule in metabolism.

The Krebs cycle is a central part of cellular respiration and occurs in the mitochondrial matrix, the innermost compartment of the mitochondria.

Cellular respiration is the process of breaking down glucose to produce ATP. It consists of three main stages: glycolysis, the Krebs cycle, and the electron transport chain.

Pyruvate from glycolysis is transported into the mitochondria and undergoes oxidative decarboxylation to form Acetyl-CoA, which is the molecule that actually enters the Krebs cycle.

A primary function of the Krebs cycle is to harvest high-energy electrons from carbon compounds. These electrons are transferred to the electron carriers NAD+ and FAD to form NADH and FADH₂, which then donate the electrons to the next stage of respiration.

Cells are open systems. To maintain their internal order (low entropy), they take in energy and release waste products and heat into the environment. This release of heat increases the entropy of the surroundings more than the cell's internal entropy decreases, ensuring the total entropy of the universe increases, thus satisfying the Second Law.

By coupling the endergonic synthesis of X (+15.0 kJ/mol) with the exergonic hydrolysis of ATP (-30.5 kJ/mol), the overall coupled reaction has a net of -15.5 kJ/mol. A negative indicates the overall process is spontaneous and can proceed.

In the light-dependent reactions, Photosystem II (PSII) contributes to the proton gradient for ATP synthesis, while Photosystem I (PSI) is primarily responsible for reducing NADP+ to NADPH. If PSI is inhibited, the final step of linear electron flow is blocked, halting NADPH production. However, electrons from PSII can still contribute to the proton gradient, allowing some ATP synthesis to continue.

Adding phosphate groups makes the sugars negatively charged, preventing them from diffusing back across the nonpolar cell membrane. This phosphorylation also 'activates' the sugars, making them less stable and more reactive for the later steps of glycolysis, such as the cleavage of fructose-1,6-bisphosphate.

The Krebs cycle begins when the 2-carbon acetyl-CoA combines with the 4-carbon molecule oxaloacetate to form the 6-carbon molecule citrate. Through a series of reactions, two carbons are lost as CO2, and oxaloacetate is regenerated, allowing the cycle to continue with the next molecule of acetyl-CoA.

For a reaction to be spontaneous, its Gibbs free energy change () must be negative. In the equation , if the reaction is endothermic ( is positive), the only way for to be negative is if the entropy change () is positive and large enough, so that the term is a large negative number that outweighs the positive .

Cellular respiration breaks down glucose through a long series of enzyme-catalyzed reactions. This stepwise oxidation allows the energy to be released gradually. A significant portion of this energy is captured in the high-energy phosphate bonds of ATP molecules, with the rest released as heat, which prevents cell damage.

During the light-dependent reactions, water molecules are split in a process called photolysis to provide electrons for the electron transport chain. This process releases electrons, protons (H+), and molecular oxygen. Therefore, the oxygen atoms from the water molecule (HO) are the ones that form the gaseous oxygen (O) released.

PFK-1 catalyzes an early, committed step in glycolysis. High levels of ATP signal that the cell has an abundance of energy. To prevent the wasteful breakdown of glucose when energy is not needed, ATP binds to an allosteric site on PFK-1, inhibiting its activity and slowing down the entire glycolytic pathway. Conversely, high levels of ADP or AMP would activate it.

Glycolysis breaks one molecule of glucose (6 carbons) into two molecules of pyruvate (3 carbons). Each pyruvate is converted to one molecule of acetyl-CoA, which then enters the Krebs cycle. Therefore, one molecule of glucose leads to two 'turns' of the Krebs cycle. Since each turn produces one molecule of FADH, two turns produce two molecules of FADH.

A positive signifies an endergonic reaction. The equilibrium constant K_eq is related to by . A positive means K_eq is less than 1. Since K_eq = [B]/[A], a K_eq < 1 indicates that at equilibrium, the concentration of the reactant [A] will be greater than the concentration of the product [B].

In hot, dry conditions, plants close their stomata, which reduces CO intake and favors photorespiration in C3 plants. C4 plants have a spatial separation of processes. They initially fix CO into a 4-carbon acid in mesophyll cells, then transport this acid to bundle-sheath cells where CO is released at a high concentration, favoring the Calvin cycle over photorespiration.

While its primary role is catabolic (breaking down acetyl-CoA), the Krebs cycle's intermediates are also starting points for biosynthetic (anabolic) pathways. For example, -ketoglutarate can be converted to the amino acid glutamate, and oxaloacetate can be converted to aspartate. This dual function makes the cycle amphibolic.

Glycolysis requires a constant supply of NAD to act as an electron acceptor. During anaerobic fermentation, the electron transport chain is unavailable to re-oxidize NADH. The reduction of pyruvate to lactate oxidizes NADH back to NAD, providing the necessary coenzyme for glycolysis to continue producing a small amount of ATP.

Enzymes do not alter the thermodynamics (the initial and final energy states) of a reaction; the overall remains the same. Instead, they provide an alternative reaction pathway with a lower activation energy barrier. By lowering the energy required to reach the transition state, they significantly speed up the rate at which the reaction reaches equilibrium.

'Spontaneous' means the reaction is exergonic (). The observation that the test tube gets cold means the reaction is absorbing heat from its surroundings, which is the definition of an endothermic reaction (). This is possible if the reaction causes a large increase in entropy (), making the term in the Gibbs equation large and negative enough to overcome the positive .

Substrate-level phosphorylation is a direct method of ATP synthesis where an enzyme transfers a phosphate group from a phosphorylated substrate molecule (like 1,3-bisphosphoglycerate or phosphoenolpyruvate) directly to an ADP molecule. This is distinct from oxidative phosphorylation, which involves a proton gradient and ATP synthase.

Pyruvate, the end product of glycolysis, is transported into the mitochondrial matrix. There, the enzyme complex pyruvate dehydrogenase catalyzes its conversion into acetyl-CoA. This reaction also produces NADH and CO. Acetyl-CoA is the molecule that then enters the Krebs cycle.

The Calvin cycle constitutes the 'synthesis' part of photosynthesis. It uses the chemical energy (ATP) and reducing power (NADPH) produced during the light-dependent reactions to fix atmospheric carbon dioxide into organic molecules, ultimately producing glyceraldehyde-3-phosphate (G3P), a 3-carbon sugar.

While many steps in a pathway may be near equilibrium, a few key reactions have a large negative . These steps are essentially irreversible under cellular conditions. They act as regulatory points and ensure that the entire pathway proceeds in one direction, preventing a futile cycle.

Living systems are not at equilibrium and do not violate the Second Law. They maintain order by taking in energy-rich molecules (like glucose) and breaking them down, releasing heat and simple, low-energy molecules (like CO₂ and H₂O) into the environment. This process drastically increases the entropy of the surroundings, more than compensating for the decrease in entropy within the organism itself. Thus, the total entropy of the universe increases.

A reaction becomes spontaneous when the Gibbs free energy () is negative. The equation is . For to be zero (the transition point), . First, convert units to be consistent: . Then, solve for T: . Since the entropy term () is negative, increasing the temperature above 200 K will make increasingly negative, driving the reaction to be spontaneous.

The methyl carbon of acetyl-CoA becomes C4 of citrate. Through the initial steps, it becomes the C4 of isocitrate and then the C3 of -ketoglutarate. The two carbons lost as CO₂ in the first turn originate from the oxaloacetate that started the cycle. After conversion to the symmetric succinate molecule, the label is randomized. By the time oxaloacetate is regenerated, the C label is distributed within its carbon skeleton, not released as CO₂ until subsequent turns.

This is a classic example of Le Châtelier's principle in biochemistry. While the standard free energy change () is positive, the actual free energy change () inside the cell is near zero or slightly negative. This is because the next enzymes in the pathway, triose phosphate isomerase and G3P dehydrogenase, immediately use up the products (DHAP and G3P). This keeps the product concentration far below equilibrium, which, according to the equation , makes the actual favorable for the forward reaction.

The conditions described (low CO₂, high O₂) strongly favor photorespiration in C3 plants, where RuBisCO inefficiently binds O₂ instead of CO₂. C4 plants have a mechanism (the C4 pathway using PEP carboxylase) to concentrate CO₂ in bundle sheath cells where the Calvin cycle occurs. This effectively outcompetes O₂ for RuBisCO's active site, suppressing photorespiration and allowing the C4 plant to maintain a much higher rate of net photosynthesis under these specific stress conditions.

Inhibiting isocitrate dehydrogenase creates a bottleneck in the Krebs cycle. The substrates for this enzyme, isocitrate and its precursor citrate, will accumulate. Since this is a major NAD⁺-reducing step, its inhibition will lead to less NADH being produced by the cycle. This will decrease the overall cellular NADH/NAD⁺ ratio, signaling a lower energy state to other pathways.

The actual free energy change () is dependent on the reaction quotient, Q, as shown by the equation . In a living cell, the concentration of ATP is kept very high relative to the concentrations of its products, ADP and Pi. This makes the ratio Q = [ADP][Pi]/[ATP] very small, causing the term to be large and negative, thus making the actual much more negative (more exergonic) than the standard .

ATP synthesis in chloroplasts is driven by chemiosmosis, which requires a proton gradient across the thylakoid membrane. DNP eliminates this gradient, so ATP synthase can no longer function, halting ATP production. However, NADPH production is the result of the linear electron transport chain where electrons from Photosystem I are passed to NADP⁺. This process is not directly dependent on the proton gradient (though the gradient is formed by it), so it can continue as long as there is light and an electron source.

In normal glycolysis, the reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase is followed by the phosphoglycerate kinase step, which generates 2 ATP (one for each 3-carbon unit) via substrate-level phosphorylation. Arsenate uncouples these two steps. By forming an unstable arseno-intermediate that hydrolyzes, it bypasses the substrate-level phosphorylation step. Therefore, the 2 ATP that would have been generated at this stage are lost. Since 2 ATP are invested at the beginning of glycolysis and the final substrate-level phosphorylation step (pyruvate kinase) still produces 2 ATP, the net yield becomes 2 - 2 = 0 ATP.

For a process to be spontaneous, the change in Gibbs free energy () must be negative. The relationship is . If the process is endothermic ( is positive), the only way for to be negative is if the entropy term, , is large and negative. This requires that the change in entropy, , must be large and positive. In this case, the dissolution of the solid crystal into ions in solution represents a massive increase in disorder (entropy), which overcomes the positive enthalpy change.

Glutamate and glutamine are synthesized from the Krebs cycle intermediate -ketoglutarate. If the cell is rapidly siphoning off -ketoglutarate for amino acid synthesis, the cycle will be depleted of its intermediates. Pyruvate carboxylase catalyzes the most important anaplerotic reaction, converting pyruvate directly into oxaloacetate. This replenishes the cycle's carbon skeleton, allowing it to continue functioning despite the removal of intermediates for biosynthesis.

Normally, high levels of ATP and citrate (which signals that the Krebs cycle is saturated) allosterically inhibit PFK-1, slowing down glycolysis. In cancer cells exhibiting the Warburg effect, glycolysis runs unchecked. A mutation that makes PFK-1 insensitive to its inhibitors (like ATP or citrate) would cause the enzyme to remain active even when cellular energy is high, leading to a constitutively high glycolytic rate. Decreasing its affinity for citrate would remove a key negative feedback signal.

The Calvin cycle requires more ATP (3 per CO₂) than NADPH (2 per CO₂). Linear electron flow produces ATP and NADPH in roughly equal amounts. Cyclic photophosphorylation provides a mechanism to produce only ATP. By cycling electrons from PSI back through the cytochrome complex, more protons are pumped into the thylakoid lumen, driving ATP synthase without involving PSII or producing NADPH. This allows the cell to adjust the ATP/NADPH output to meet the specific demands of carbon fixation.

The overall standard free energy change for a pathway is the sum of the changes for the individual steps: kJ/mol. Since the total is negative, the overall pathway is exergonic and spontaneous under standard conditions. The highly exergonic second step (B C) is thermodynamically 'coupled' to the other steps by keeping the concentration of its reactant (B) low and its product (C) high relative to their equilibrium values, effectively pulling the first reaction forward and pushing the third one.

The standard reduction potential of the FAD/FADH₂ couple is higher than that of NAD⁺/NADH. The energy released by oxidizing succinate is not sufficient to reduce NAD⁺. Instead, FAD is used as the electron acceptor. Since FADH₂ donates its electrons to Complex II, bypassing Complex I (the first proton pump), its electrons contribute less to the proton gradient than electrons from NADH. Consequently, FADH₂ oxidation yields approximately 1.5 ATP, whereas NADH yields about 2.5 ATP.

Glycolysis requires a continuous supply of NAD⁺ to act as an electron acceptor in the glyceraldehyde-3-phosphate dehydrogenase reaction. In aerobic conditions, NADH is re-oxidized to NAD⁺ by the electron transport chain. In anaerobic conditions, this is not possible. Lactic acid fermentation solves this problem by using NADH to reduce pyruvate to lactate, thereby regenerating the NAD⁺ needed to keep glycolysis running and producing a small but rapid supply of ATP.

The cell couples the endergonic glutamine synthesis to the highly exergonic hydrolysis of ATP ( to -50 kJ/mol). The overall coupled reaction proceeds in two steps, often involving a phosphorylated intermediate. The large negative free energy change from ATP hydrolysis is harnessed to drive the unfavorable synthesis reaction, resulting in a net negative for the combined process, making it spontaneous.

The addition of CO₂ to RuBP is a highly exergonic step ( kJ/mol), which commits the carbon to the Calvin cycle. In contrast, the oxygenase activity initiates the photorespiratory pathway, a salvage pathway that consumes O₂ and produces CO₂. This salvage pathway requires the expenditure of both ATP and NADPH to convert the products back into a usable form (3-PGA), representing a net energy loss for the cell.

A defective E3 component cripples both the conversion of pyruvate to acetyl-CoA and the conversion of -ketoglutarate to succinyl-CoA. This effectively shuts down ATP production from glucose, lactate, and amino acids like alanine (which convert to pyruvate). However, fatty acid beta-oxidation produces acetyl-CoA directly, which can enter the Krebs cycle. While the cycle itself is impaired at the -ketoglutarate step, the acetyl-CoA can still be oxidized to citrate and isocitrate, generating some NADH. More importantly, the FADH₂ and NADH generated during beta-oxidation itself can feed into the electron transport chain, providing a significant source of ATP independent of the defective enzymes.

A system at equilibrium has no net fluxes and thus produces no entropy (). A living system, being in a non-equilibrium steady state, constantly undergoes irreversible processes (like metabolism) and thus has a positive rate of entropy production (). According to the principles of non-equilibrium thermodynamics (as proposed by Prigogine), for stable steady states near equilibrium, the system will arrange itself to have the minimum possible rate of entropy production for the given constraints.