The Use of Energy by Cells Practice Flashcards

Flashcards covering the use of energy by cells, metabolism, thermodynamics, activated carriers, and the processes of glycolysis, the citric acid cycle, and oxidative phosphorylation.

Metabolism

The sum total of all catabolic and anabolic pathways within a cell.

Catabolic pathways

Metabolic pathways that break down food molecules into smaller molecules, generating both a useful form of energy and heat.

Anabolic pathways

Metabolic pathways that use the energy harnessed by catabolism to drive the synthesis of many molecules that form the cell.

Photosynthetic organisms

Organisms that use sunlight to synthesize organic molecules such as sugars from $CO_2$.

Oxidation

The removal of electrons from an atom, often occurring when covalently bonded hydrogen atoms are replaced by oxygen atoms.

Reduction

The gain of electrons by an atom, occurring when an atom ends up with a greater share of electrons in a polar covalent bond.

Enzymes

Highly effective catalysts that reduce the activation energy needed to initiate spontaneous reactions while remaining unchanged themselves.

Activation Energy

The energy required to boost a reactant over an energy barrier to get a reaction started.

Free-energy change ($\Delta G$)

The difference in free energy between the products and reactants; it determines whether a reaction can occur spontaneously.

Energetically favorable reaction

A reaction with a negative $\Delta G$ ($\Delta G < 0$) that occurs spontaneously, increasing the disorder of the universe.

Energetically unfavorable reaction

A reaction with a positive $\Delta G$ ($\Delta G > 0$) that can only occur if it is coupled to a second, energetically favorable reaction.

Reaction Coupling

The process by which an energetically unfavorable reaction is powered by an energetically favorable reaction to yield a net negative $\Delta G$.

Activated carrier

A molecule that stores and transfers energy in a form cells can use, such as ATP, NADH, or NADPH.

ATP (Adenosine 5'-triphosphate)

The most widely used activated carrier in cells, storing energy in high-energy phosphoanhydride bonds.

Phosphoanhydride bonds

The two outermost high-energy phosphate bonds in ATP that release a large amount of free energy when hydrolyzed.

NADH

An activated carrier of electrons used primarily as an intermediate in the catabolic system of reactions that generate ATP through oxidation of food molecules.

NADPH

An activated carrier of electrons that operates chiefly with enzymes that catalyze anabolic reactions, supplying high-energy electrons for biosynthesis.

Hydride ion

A structure consisting of two electrons and one proton ($H^-$) that is transferred to $NADP^+$ to form NADPH.

Acetyl CoA

An activated carrier that carries an acetyl group linked by a high-energy thioester bond, used to add carbon units to various molecules.

Thioester bond

The high-energy linkage between the sulfur atom of coenzyme A and an acetate group that releases a large amount of free energy upon hydrolysis.

Carboxylated biotin

An activated carrier responsible for transferring a carboxyl group ($-COO^-$) during biosynthesis.

S-adenosylmethionine

An activated carrier used to transfer a methyl group ($-CH_3$) to other molecules.

Uridine diphosphate glucose

An activated carrier used to transfer glucose molecules during the synthesis of biological polymers.

Glycolysis

A process occurring in the cytoplasm that converts one molecule of glucose into two molecules of pyruvate, generating a net of $2$ ATP and $2$ NADH.

Substrate-level phosphorylation

A method of ATP generation that occurs by the direct transfer of a phosphate group from a substrate molecule to ADP.

Fermentation

An anaerobic process that allows cells to regenerate $NAD^+$ from NADH in the absence of oxygen to keep glycolysis moving.

Warburg effect

The observation by Otto Warburg that cancer cells often shift from oxidative phosphorylation to aerobic glycolysis (fermentation) even when oxygen is present.

Citric Acid Cycle

A series of reactions in the mitochondrial matrix that oxidizes the acetyl group of acetyl CoA to $CO_2$, producing NADH, $FADH_2$, and GTP.

FADH2

An activated carrier produced during the citric acid cycle and fatty acid oxidation that carries high-energy electrons to the electron-transport chain.

Outer mitochondrial membrane

The membrane containing pores made of porin that allow passive diffusion of molecules up to $500\text{ kDa}$.

Inner mitochondrial membrane

The site of the electron-transport chain and ATP synthase; it is impermeable to most ions and small molecules.

Mitochondrial matrix

The internal compartment of the mitochondrion containing the citric acid cycle enzymes, mitochondrial DNA, and ribosomes.

Cristae

Sheetlike and tubelike invaginations of the inner mitochondrial membrane that extend into the center of the mitochondrion.

Crista junctions

Sharp bends that connect the boundary membrane of the inner mitochondrial membrane to the cristae.

Malate-Aspartate shuttle

A mechanism that transfers electrons from cytosolic NADH across the inner mitochondrial membrane to maintain cytosolic and matrix $NAD^+$ concentrations.

Mitochondrial Pyruvate Carrier (MPC)

A hetero-dimer protein (MPC1/MPC2) that co-transports pyruvate and a proton into the mitochondrial matrix.

Electron-transport chain (ETC)

A series of four major multiprotein complexes (I–IV) in the inner mitochondrial membrane that transfer electrons to oxygen to pump protons.

Coenzyme Q (Ubiquinone)

A lipid-soluble electron carrier that shuttles electrons between Complex I or II and Complex III in the mitochondrial electron-transport chain.

Cytochrome c

A water-soluble electron carrier that shuttles electrons from Complex III to Complex IV in the electron-transport chain.

Complex I (NADH dehydrogenase)

The first complex in the ETC that accepts electrons from NADH and pumps four protons across the inner membrane.

Complex III (Cytochrome c reductase)

The ETC complex that receives electrons from Coenzyme Q and transfers them to cytochrome c, pumping protons via the Q cycle.

Complex IV (Cytochrome c oxidase)

The final protein complex of the ETC that transfers electrons to molecular oxygen ($O_2$) to form water ($H_2O$).

Reduction potential ($E^{\circ \prime}$)

A measure of the affinity of a molecule for electrons; it increases from NADH ($-320\text{ mV}$) to $O_2$ ($+860\text{ mV}$) along the ETC.

Q cycle

An evolutionarily conserved mechanism in Complex III that optimizes proton pumping by transferring four protons for every pair of electrons processed.

Chemiosmosis

The process by which a proton-motive force generated by electron transport powers the synthesis of ATP.

Proton-motive force

The steep electrochemical proton gradient across the inner mitochondrial membrane used to drive ATP synthesis.

ATP synthase ($F_0F_1$ complex)

A reversible coupling device that uses the energy of the electrochemical proton gradient to produce ATP from ADP and $P_i$.

$F_0$ portion

The rotating part of ATP synthase embedded in the inner mitochondrial membrane that acts as a proton channel.

$F_1$ ATPase

The stationary head of ATP synthase that projects into the mitochondrial matrix and contains the catalytic sites for ATP synthesis.

$O$ (open) state

A conformation of the F1 ATPase subunit that binds ATP very poorly and ADP and $P_i$ weakly.

$L$ (loose) state

A conformation of the F1 ATPase subunit that binds ADP and $P_i$ more strongly but cannot bind ATP.

$T$ (tight) state

A conformation of the F1 ATPase subunit that binds ADP and $P_i$ tightly enough to spontaneously form ATP.

Binding-change mechanism

The process where proton movement through $F_0$ drives the rotation of the $\gamma$ subunit, changing the states of $\beta$ subunits to synthesize ATP.

Membrane potential ($\Delta V$)

The voltage difference across a membrane, which is a major component of the electrochemical $H^+$ gradient in mitochondria.

H+ concentration gradient ($\Delta pH$)

The difference in pH across the inner mitochondrial membrane, contributing to the proton-motive force.

Uncoupling Proteins (UCPs)

Proteins that allow protons to flow down their gradient without passing through ATP synthase, dissipating energy as heat instead of ATP.

2,4-dinitrophenol (DNP)

A dangerous chemical uncoupling agent that dissipates the proton gradient, resulting in heat production and potential death.

Total ATP yield per glucose

Approximately $30$ ATP molecules are produced from the complete aerobic oxidation of one glucose molecule.

Pyruvate oxidation yield

The oxidation of two pyruvates into two acetyl CoA molecules yields $2$ NADH and $2\,CO_2$.

Citric Acid Cycle yield (per glucose)

The oxidation of two acetyl groups yields $6$ NADH, $2\,FADH_2$, and $2$ GTP (or ATP).

Free energy ($G$)

The measure of a molecule's potential to do useful work at a constant temperature in a living cell, expressed in $kJ/mole$.

Standard free-energy change ($\Delta G^{\circ}$)

The gain or loss of free energy as one mole of reactant is converted to one mole of product under standard conditions ($1\text{ M}$, pH $7.0$).

Equilibrium constant ($K$)

The ratio of concentrations of products to reactants when the forward and backward reaction rates are equal ($\Delta G = 0$).

Biosynthesis

The enzyme-catalyzed process in cells where complex molecules are formed from simpler ones, often requiring ATP or NADPH.

Phosphorylation of sugar

An example of reaction coupling where ATP hydrolysis powers the addition of a phosphate to a sugar substrate.

Stroma

The compartment in chloroplasts containing enzymes that catalyze $CO_2$ fixation and starch synthesis, analogous to the mitochondrial matrix.

Thylakoid membrane

The site of light absorption, ATP synthesis, and NADPH production in chloroplasts.

Aerobic oxidation

The process in the cytoplasm and mitochondria where sugars and fatty acids are oxidized to $CO_2$, yielding NADH and ATP.

Stepwise oxidation

The process of burning organic molecules in small steps to ensure that energy is captured in activated carriers rather than just lost as heat.

$$1\text{ Joule}$$

A unit of energy where $1\text{ joule} = 0.24\text{ calories}$.

Standard conditions

The specific environment ($1\text{ M}$ concentration and pH $7.0$) used to determine the standard free-energy change ($\Delta G^{\circ}$).

$\Delta G^{\circ}$ of ATP hydrolysis

The standard free-energy change for $ATP \rightarrow ADP + P_i$ is $-30.5\,kJ/mole$.

$\Delta G^{\circ}$ of glucose combustion

The complete oxidation of glucose ($C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O$) has a $\Delta G^{\circ}$ of $-2867\,kJ/mole$.

ATP yield from mitochondrial NADH

Each NADH produced in the mitochondrial matrix yields approximately $2.5$ ATP per glucose oxidation stage.

ATP yield from cytosolic NADH

NADH produced in the cytosol yields fewer ATP ($1.5$ each) because transport into the mitochondria requires energy.

$F_0F_1$ complex

Another name for ATP synthase, consisting of a transmembrane proton carrier and a catalytic head.

Lactic acid

The product of anaerobic metabolism in muscle cells when pyruvate accepts electrons from NADH to regenerate $NAD^+$.

Ethanol

A product of anaerobic fermentation in yeast where acetaldehyde accepts electrons from NADH.

Fatty acid oxidation

The breakdown of fatty acids in mitochondria to produce acetyl CoA, NADH, and $FADH_2$ for ATP production.

Peroxisomes

Organelles where the oxidation of very long chain fatty acids occurs, producing heat instead of ATP.