AP Biology Unit 3: Cellular Energetics

Comprehensive practice flashcards for AP Biology Unit 3: Cellular Energetics, covering enzyme kinetics, thermodynamics, cellular respiration, and photosynthesis.

How do enzymes affect the rate and activation energy of biological reactions?

Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy required for the reaction to occur, without being consumed in the process.

What is the induced fit model of enzyme catalysis?

A model describing how an enzyme undergoes a mild conformational shift in shape upon substrate binding at the active site to maximize catalytic alignment and efficiency.

In the provided 3D model of an enzyme's active site, what are the distinct roles of the binding sites (blue) and the catalytic site (red)?

The binding sites bind and properly orient the substrate(s), while the catalytic site reduces the chemical activation energy of the reaction.

What are four specific ways an enzyme can lower activation energy?

1. Positioning two substrates so they align perfectly for the reaction.
2. Providing an optimal microenvironment (e.g., acidic or polar) within the active site.
3. Contorting or stressing substrate bonds to make them less stable.
4. Temporarily reacting chemically with the substrate to make it less stable.

Why does the rate of an enzyme-mediated reaction plateau as substrate concentration increases?

All active sites of the available enzyme molecules become saturated with substrate, causing the enzyme concentration to become the limiting factor.

How do temperatures below versus above the optimal range affect enzyme function?

Temperatures below the optimum reduce kinetic energy, leading to fewer collisions and decreased activity (often reversible). Temperatures above the optimum disrupt intermolecular interactions (such as hydrogen bonds), causing the enzyme to denature and lose its active site shape (often irreversible).

Why does a change in environmental pH alter enzyme efficiency?

Altering $[H^+]$ changes the charges and ionization of amino acid R-groups throughout the protein and at the active site, disrupting hydrogen and ionic bonds necessary to maintain tertiary structure and substrate binding.

Based on this graph, how do competitive and noncompetitive inhibitors differ in their impact on the maximum reaction rate?

Competitive inhibitors slow the initial reaction rate but do not reduce the maximal rate (it can still be reached at high substrate concentrations). Noncompetitive inhibitors reduce the maximal rate regardless of substrate concentration.

According to the diagram, what is the operational difference between allosteric activators and allosteric inhibitors?

Allosteric inhibitors bind to a regulatory site and stabilize the enzyme in its inactive form with non-functional active sites, whereas allosteric activators bind to stabilize the active form with functional active sites.

What is the structural difference between enzyme cofactors and coenzymes?

Cofactors are inorganic ions (such as $Fe^{2+}$, $Mg^{2+}$, and $Zn^{2+}$), whereas coenzymes are organic non-protein helper molecules (such as ATP, $NAD^+$, and dietary vitamins).

How do statin drugs lower blood cholesterol levels?

Statins act as enzyme inhibitors that block HMG-CoA reductase, the enzyme responsible for synthesizing cholesterol from lipids in the body.

What is feedback inhibition in a metabolic pathway?

A regulatory mechanism in which the accumulated end product of a metabolic pathway allosterically binds to and inhibits an upstream enzyme, halting further pathway activity.

What is the difference between anabolic and catabolic pathways?

Anabolic pathways synthesize large molecules from smaller ones and require energy ($\Delta G > 0$), whereas catabolic pathways break down large molecules into smaller ones and release energy ($\Delta G < 0$).

What thermodynamic condition defines an exergonic reaction?

A negative change in Gibbs free energy ($\Delta G < 0$), meaning energy is released and the reaction can occur spontaneously without external energy input.

Based on this structural diagram of ATP, what are the names of the three phosphate groups ordered from closest to furthest relative to the ribose sugar?

The alpha phosphate group (closest), the beta phosphate group (middle), and the gamma phosphate group (furthest).

What is energy coupling, and what is a cellular example involving an active transport protein?

Energy coupling is the linking of an exergonic process to drive an endergonic process. An example is the sodium-potassium pump, which uses energy from exergonic ATP hydrolysis to pump 3 $Na^+$ ions out of the cell and 2 $K^+$ ions in.

What is substrate-level phosphorylation, and in which specific steps of glycolysis does it occur?

Substrate-level phosphorylation is the direct enzymatic transfer of a phosphate group from a phosphorylated metabolic intermediate to ADP to form ATP. It occurs at step 7 (1,3-bisphosphoglycerate $\rightarrow$ 3-phosphoglycerate) and step 10 (PEP $\rightarrow$ pyruvate).

What are the net inputs and net outputs of glycolysis per molecule of glucose?

Net inputs: 1 glucose, 2 $NAD^+$, and 2 ADP + 2 $P_i$. Net outputs: 2 pyruvate, 2 NADH, and 2 ATP (net gain from 4 formed minus 2 used).

What chemical changes occur during the oxidation of each pyruvate molecule entering the mitochondrial matrix?

One carboxyl group is removed and released as $CO_2$, the remaining two-carbon fragment is oxidized to transfer electrons to $NAD^+$ (forming NADH), and Coenzyme A attaches to form acetyl CoA.

What are the products of two complete turns of the citric acid (Krebs) cycle per glucose molecule?

6 NADH, 2 $FADH_2$, 2 ATP (or GTP), and 4 $CO_2$.

Based on this diagram of the mitochondrial membrane during electron transport, how do proton concentration and pH compare between the intermembrane space and the matrix?

The intermembrane space has a high $H^+$ concentration and low (acidic) pH, while the mitochondrial matrix has a low $H^+$ concentration and high (basic) pH.

What is the final electron acceptor in the mitochondrial electron transport chain?

Oxygen ($O_2$), which is reduced at complex IV and combines with protons ($H^+$) to form water ($H_2O$).

How does the decoupling of oxidative phosphorylation from electron transport benefit endothermic animals?

Decoupling allows protons to flow back into the matrix without passing through ATP synthase, dissipating the energy of the electrochemical gradient as heat to regulate body temperature (e.g., in brown adipose tissue).

What is the primary physiological purpose of fermentation when oxygen is unavailable?

Fermentation oxidizes NADH back to $NAD^+$ so that glycolysis can continue to produce ATP via substrate-level phosphorylation in the absence of oxygen.

What role did prokaryotic cyanobacteria play in the evolution of life on Earth?

Cyanobacterial photosynthesis produced the oxygen that formed Earth's oxygenated atmosphere and established the metabolic foundation for eukaryotic photosynthesis.

Based on the absorption spectra shown, which wavelengths of light are primarily absorbed by chlorophyll a and chlorophyll b?

They absorb blue-violet wavelengths (approximately $400\text{--}480\,nm$) and red wavelengths (approximately $640\text{--}680\,nm$), while reflecting and transmitting green wavelengths.

How are electrons replaced in photosystem II during the light reactions of photosynthesis?

Electrons are replenished by the photolysis (splitting) of water molecules ($H_2O$), which releases protons ($H^+$) and molecular oxygen ($O_2$) as a byproduct.

According to this diagram of the Calvin cycle, what are the three main phases and what is the net carbohydrate output for every 3 molecules of $CO_2$ fixed?

Phase 1: Carbon Fixation (catalyzed by RuBisCO); Phase 2: Reduction (using ATP and NADPH); Phase 3: Regeneration of RuBP. The net output is 1 molecule of glyceraldehyde-3-phosphate (G3P).

What are the specific locations within the chloroplast for the light-dependent reactions and the Calvin cycle?

The light-dependent reactions take place across the thylakoid membranes (organized in grana), while the Calvin cycle occurs in the stroma.

What is photorespiration, and what property of RuBisCO causes it to occur?

Photorespiration is a non-productive metabolic pathway where RuBisCO binds oxygen ($O_2$) instead of carbon dioxide ($CO_2$) due to its dual oxygenase and carboxylase capabilities, preventing sugar production.