Chapter 6 – How Cells Utilize Energy

Comprehensive practice flashcards covering thermodynamics, enzyme kinetics, metabolic pathways, cellular respiration (glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation), and anaerobic pathways based on Chapter 6 lecture notes.

What is energy, and how do kinetic energy and potential energy differ?

Energy is the ability to promote change or do work. Kinetic energy is energy associated with movement, whereas potential energy is energy due to structure or location (such as chemical potential energy stored in covalent bonds).

What do the first and second laws of thermodynamics state regarding biological energy transformations?

The first law of thermodynamics states that energy cannot be created or destroyed, but can be transferred and transformed. The second law of thermodynamics states that every transfer or transformation of energy increases the entropy (degree of disorder) of a system, meaning less usable energy remains available to promote change.

How does free-energy change ($\Delta G$) distinguish exergonic reactions from endergonic reactions?

In an exergonic reaction, products have less free energy than reactants, $\Delta G$ is negative ($\Delta G < 0$), energy is released, and the reaction is spontaneous. In an endergonic reaction, products have more free energy than reactants, $\Delta G$ is positive ($\Delta G > 0$), energy must be supplied, and the reaction is non-spontaneous.

How do cells use ATP hydrolysis to drive endergonic reactions?

ATP hydrolysis is a highly exergonic reaction ($\Delta G = -7.3\,\text{kcal/mol}$). Cells couple ATP hydrolysis to an endergonic reaction; the coupled processes proceed spontaneously as long as the net overall free-energy change ($\Delta G$) is negative.

What is activation energy ($E_A$), and how do enzymes alter it?

Activation energy ($E_A$) is the initial input of energy required to stretch bonds to their limit and allow reactants to achieve the transition state. Enzymes act as catalysts that increase reaction rates by lowering this activation energy barrier (for example, by straining bonds and positioning reactants close together).

What occurs when an enzyme binds its substrate to form an enzyme-substrate complex via induced fit?

Substrates bind with high specificity to the enzyme's active site. Upon binding, the enzyme undergoes conformational changes (induced fit) that bind the substrates more tightly, straining bonds within the substrates and/or bringing them closer together.

Based on the Michaelis-Menten plot shown below, what do $V_{\max}$ and $K_M$ represent in enzyme kinetics?

$V_{\max}$ is the maximal rate or velocity of an enzymatic reaction when active sites are saturated with substrate. $K_M$ is the substrate concentration at which the reaction velocity is half of its maximal velocity ($\frac{V_{\max}}{2}$), inversely reflecting the enzyme's affinity for the substrate.

Based on the graphs below, how do competitive inhibitors and noncompetitive inhibitors differ in their binding mechanisms and kinetic effects?

Competitive inhibitors bind noncovalently to the active site, increasing the apparent $K_M$ (more substrate is required to achieve the same velocity) without altering $V_{\max}$. Noncompetitive inhibitors bind to a separate allosteric site, altering enzyme conformation to lower $V_{\max}$ without affecting $K_M$.

What are the distinctions among prosthetic groups, cofactors, and coenzymes?

A prosthetic group is a small molecule permanently attached to an enzyme (e.g., heme in hemoglobin). A cofactor is an inorganic ion that temporarily binds to an enzyme (e.g., $Fe^{3+}$, $Zn^{2+}$). A coenzyme is an organic molecule that participates directly in the reaction but is left unchanged afterward (e.g., $NAD^+/NADH$).

Based on the graph below, what is the optimal temperature for a typical human enzyme, and what occurs at temperatures above this point?

The optimal temperature for a typical human enzyme is $37^\circ\text{C}$ (approximately $98.6^\circ\text{F}$). At excessively high temperatures, the enzyme may be denatured, causing a sharp drop in reaction rate.

What is the primary difference between catabolic and anabolic pathways?

Catabolic reactions break down larger molecules into smaller ones, are typically exergonic, release energy to synthesize energy intermediates (such as ATP or NADH), and recycle organic building blocks. Anabolic reactions synthesize larger molecules from smaller ones, are typically endergonic, and must be coupled to exergonic reactions.

Based on the diagram below, what occurs during the reduction of $NAD^+$ to NADH?

Reduction is the addition of electrons. During the reduction of nicotinamide adenine dinucleotide ($NAD^+$) to NADH, two electrons ($2e^-$) and one proton ($H^+$) are added to the nicotinamide ring (reducing its double bonds from 3 to 2), storing energy in its chemical bonds.

How does feedback inhibition regulate metabolic pathways as illustrated below?

In feedback inhibition, when the concentration of the pathway's final product becomes elevated, it binds to an allosteric site on an initial enzyme (e.g., Enzyme 1), causing a conformational change that inhibits its activity and shuts down further conversion of the initial substrate.

What are the four metabolic pathways of cellular respiration in chronological order, and what are their overall ATP yields per glucose molecule?

1. Glycolysis ($+2\,\text{ATP}$ via substrate-level phosphorylation), 2. Breakdown of pyruvate (pyruvate oxidation), 3. Citric acid cycle ($+2\,\text{ATP}$ via substrate-level phosphorylation), and 4. Oxidative phosphorylation ($+30\text{--}34\,\text{ATP}$ via chemiosmosis).

Where in eukaryotic cells does glycolysis take place, and what are its three distinct phases?

Glycolysis takes place in the cytosol. Its 10 enzymatic reactions are divided into three phases: the energy investment phase (steps 1–3), the cleavage phase (steps 4–5), and the energy liberation phase (steps 6–10).

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

One molecule of glucose ($6\,\text{carbons}$) yields a net output of $2\,\text{molecules of pyruvate}$ ($3\,\text{carbons each}$), $2\,\text{NADH}$, and a net gain of $2\,\text{ATP}$ produced via substrate-level phosphorylation.

Based on the diagram below, describe the events and products of pyruvate breakdown per molecule of glucose.

Pyruvate enters the mitochondrial matrix via an $H^+/\text{pyruvate symporter}$. Pyruvate dehydrogenase oxidizes each pyruvate: one $CO_2$ is removed, the remaining acetyl group is attached to coenzyme A (CoA) to make acetyl CoA, and $1\,\text{NADH}$ is produced. Per glucose ($2\,\text{pyruvates}$), outputs are $2\,\text{acetyl CoA}$, $2\,\text{CO}_2$, and $2\,\text{NADH}$.

How does an acetyl group enter the citric acid cycle, and what are the yields for two turns of the cycle (per glucose)?

A $2\text{-carbon}$ acetyl group is transferred from acetyl CoA to $4\text{-carbon}$ oxaloacetate to form $6\text{-carbon}$ citrate. Per glucose molecule (two turns of the cycle), processing yields $4\,\text{CO}_2$, $6\,\text{NADH}$, $2\,\text{FADH}_2$, and $2\,\text{ATP}$ (synthesized via GTP).

How does the electron transport chain (ETC) establish an electrochemical gradient during oxidative phosphorylation?

Protein complexes in the inner mitochondrial membrane transfer electrons from NADH and $FADH_2$ through a series of redox reactions to components of increasing electronegativity, ending with $O_2$ as the final electron acceptor (forming $H_2O$). The free energy released pumps $H^+$ from the matrix into the intermembrane space.

Based on the diagram below, what are the membrane-embedded and nonmembrane-embedded subunit components of ATP synthase?

The membrane-embedded portion consists of a ring of $9\text{--}12\,c$ subunits, $1\,a$ subunit, and $2\,b$ subunits. The nonmembrane-embedded catalytic portion consists of $1\,\varepsilon$, $1\,\gamma$, $1\,\delta$, $3\,\alpha$, and $3\,\beta$ subunits.

As illustrated below, what are the three conformational states that the $\beta$ subunit of ATP synthase cycles through as the $\gamma$ subunit rotates?

As the $\gamma$ subunit turns in $120^\circ$ increments, each $\beta$ subunit transitions through: Conformation 1 (ADP and $P_i$ bind with good affinity), Conformation 2 (ADP and $P_i$ bind very tightly, straining bonds so ATP is synthesized), and Conformation 3 (ATP binds very weakly and is released).

Why is the actual amount of ATP synthesized per glucose in oxidative phosphorylation (~25 ATP) lower than the theoretical maximum (30–34 ATP)?

Cells rarely achieve the maximal yield because some NADH is shuttled into anabolic pathways, and part of the $H^+$ electrochemical gradient is diverted to other cellular processes rather than exclusively driving ATP synthase.

According to the metabolic pathway map below, where do catabolized proteins and fats enter cellular respiration?

Proteins are broken down into amino acids, which can enter at glycolysis, acetyl CoA, or the citric acid cycle. Fats are broken down into glycerol (which enters glycolysis as glyceraldehyde-3-phosphate) and fatty acids (which enter as acetyl CoA).

Based on the diagram below, how does anaerobic respiration in Escherichia coli generate ATP without oxygen?

Under anaerobic conditions, E. coli uses nitrate reductase in its plasma membrane, which uses nitrate ($NO_3^-$) instead of $O_2$ as the final electron acceptor (reducing it to $NO_2^- + H_2O$). This electron transport generates an $H^+$ electrochemical gradient that powers ATP synthase.

Based on the diagram below, what is the biochemical role of fermentation in muscle and yeast cells, and what are their respective products?

Fermentation regenerates $NAD^+$ from NADH without net oxidation, allowing glycolysis to continue producing ATP via substrate-level phosphorylation under anaerobic conditions. In human muscle cells, pyruvate is reduced to lactate; in yeast, pyruvate is decarboxylated to acetaldehyde, which is reduced to ethanol.