BSC 114: Metabolism and Cellular Respiration

Comprehensive vocabulary flashcards covering thermodynamic principles, enzyme kinetics and regulation, and cellular respiration pathways.

Metabolism

The chemical reactions occurring in an organism that involve the building and breakdown of carbon molecules to harness or release energy.

Phototrophs

Organisms that capture energy from sunlight, including plants, cyanobacteria, and heliobacteria.

Chemotrophs

Organisms that derive energy from chemical compounds, including animals, most bacteria, sulfur-oxidizing bacteria, and hydrogen bacteria.

Autotrophs

Organisms capable of synthesizing organic molecules using carbon obtained from inorganic sources such as carbon dioxide ($CO_2$).

Heterotrophs

Organisms that obtain organic carbon molecules by consuming other organisms or organic compounds.

Anabolism

The set of chemical reactions that build complex macromolecules from smaller subunits, requiring an energy input such as $ATP$, resulting in $+\Delta H$, $-\Delta S$, and a positive $\Delta G$.

Catabolism

The set of chemical reactions that break down complex molecules into simpler subunits, releasing energy as $ATP$, resulting in $-\Delta H$, $+\Delta S$, and a negative $\Delta G$.

Adenosine Triphosphate (ATP)

The universal cellular energy currency composed of the nitrogenous base adenine, a ribose sugar, and three phosphate groups linked by high-potential-energy, unstable covalent bonds.

Kinetic Energy

The form of energy associated with an object's motion or movement.

Potential Energy

Energy that is stored rather than associated with movement, which can be released following a change in position, structure, or covalent bonding.

First Law of Thermodynamics

The physical law stating that energy cannot be created or destroyed; it can only be transformed from one form into another, keeping total energy constant.

Second Law of Thermodynamics

The physical law stating that every energy transformation increases the entropy (disorder) of the universe, meaning transformations are not $100\%$ efficient and free energy available to do work decreases.

Entropy ($S$)

A measure of randomness or disorder in a system that increases throughout the universe when energy transformations release energy as heat.

Gibbs Free Energy ($G$)

The amount of energy available to perform work under conditions of uniform temperature and pressure, expressed as $\Delta G = \Delta H - T\Delta S$.

Exergonic Reaction

A spontaneous chemical reaction that releases energy, characterized by a negative change in Gibbs free energy ($\Delta G < 0$).

Endergonic Reaction

A nonspontaneous chemical reaction that requires a net input of free energy, characterized by a positive change in Gibbs free energy ($\Delta G > 0$).

Energetic Coupling

A biological mechanism where an unfavorable endergonic reaction ($\Delta G > 0$) is driven by pairing it with a favorable exergonic reaction ($\Delta G < 0$), yielding an overall negative net $\Delta G$.

Enzyme

A biological catalyst (mostly proteins, though some are RNA) that accelerates metabolic reactions without being consumed in the process.

Activation Energy ($E_A$)

The initial amount of energy required to destabilize chemical bonds and reach the transition state so that a reaction can proceed; lowered by enzymes without altering $\Delta G$.

Active Site

The specific region of a folded enzyme that physically binds substrates and stabilizes the transition state during catalysis.

Competitive Inhibition

A regulatory mechanism in which an inhibitor directly competes with the substrate by binding to the active site of the enzyme, reducing the reaction rate.

Noncompetitive Inhibition

A regulatory mechanism where an inhibitor binds to a site other than the active site, inducing a conformational change in the enzyme that reduces its catalytic rate.

Cofactor

A non-protein chemical compound or metallic ion bound to an enzyme that is necessary for biological activity; includes inorganic ions as well as organic coenzymes and vitamins.

Allosteric Regulation

The modification of an enzyme's activity resulting from the binding of an activator or inhibitor at a regulatory site away from the active site.

Cooperativity

A specific type of allosteric regulation where substrate binding to one catalytic subunit stabilizes the active conformation across all other subunits.

Negative Feedback

A control mechanism where the downstream end product of a biochemical pathway allosterically inhibits an enzyme that catalyzes an earlier reaction in the pathway.

Cellular Respiration

A major catabolic pathway that breaks down carbohydrates and other fuel molecules, transferring released energy to form $ATP$ while producing $CO_2$ and $H_2O$.

Substrate-Level Phosphorylation

The direct transfer of a phosphate group from a phosphorylated organic intermediate molecule to $ADP$ to produce $ATP$, occurring during glycolysis and the citric acid cycle.

Oxidative Phosphorylation

The generation of $ATP$ fueled by the oxidation of electron carriers ($NADH$ and $FADH_2$) in the electron transport chain, which creates a transmembrane proton gradient used by ATP synthase.

Oxidation

The chemical process in which a substance loses electrons or decreases electron density; in cellular respiration, glucose is oxidized into carbon dioxide ($CO_2$).

Reduction

The chemical process in which a substance gains electrons or increases electron density; in cellular respiration, oxygen ($O_2$) is reduced to water ($H_2O$).

Glycolysis

The anaerobic first stage of cellular respiration occurring in the cytoplasm, breaking down one $6$-carbon glucose into two $3$-carbon pyruvate molecules, yielding net $2\,ATP$ and $2\,NADH$.

Preparatory Phase of Glycolysis

Phase $1$ of glycolysis (steps $1$-$3$), during which $2\,ATP$ molecules are consumed to phosphorylate glucose into fructose 1,6-bisphosphate.

Cleavage Phase of Glycolysis

Phase $2$ of glycolysis (steps $4$-$5$), in which the $6$-carbon sugar fructose 1,6-bisphosphate is cleaved into two $3$-carbon phosphorylated molecules: glyceraldehyde 3-phosphate and dihydroxyacetone phosphate.

Payoff Phase of Glycolysis

Phase $3$ of glycolysis (steps $6$-$10$), which produces $4\,ATP$ via substrate-level phosphorylation, $2\,NADH$, and two molecules of pyruvate.

Pyruvate Oxidation

The second stage of cellular respiration occurring in the mitochondrial matrix, converting each pyruvate ($3C$) into acetyl-CoA ($2C$), releasing $CO_2$ and producing $1\,NADH$ per pyruvate.

Citric Acid Cycle

An $8$-step cyclic metabolic pathway in the mitochondrial matrix that fully oxidizes acetyl-CoA, producing $3\,NADH$, $1\,FADH_2$, $1\,ATP$ (or GTP), and $2\,CO_2$ per acetyl unit.

Electron Transport Chain (ETC)

Four protein complexes (Complexes I-IV) located in the inner mitochondrial membrane that shuttle electrons from reduced carriers ($NADH$, $FADH_2$) to oxygen, pumping $H^+$ into the intermembrane space.

Coenzyme Q (CoQ)

A lipid-soluble electron carrier embedded in the inner mitochondrial membrane that accepts electrons from Complexes I and II, reducing to $CoQH_2$, and transfers them to Complex III.

Cytochrome c

A mobile electron carrier protein that shuttles electrons from Complex III to Complex IV, where molecular oxygen ($O_2$) is reduced to water ($H_2O$).

ATP Synthase

A multi-subunit enzyme complex composed of a membrane-spanning channel subunit ($F_o$) and a catalytic subunit ($F_1$) that harnesses the electrochemical proton gradient to phosphorylate $ADP$ into $ATP$.

Lactic Acid Fermentation

An anaerobic pathway occurring in animal muscle cells and bacteria where pyruvate is directly reduced to lactic acid to regenerate $NAD^+$ for glycolysis, yielding $2\,ATP$ per glucose.

Ethanol Fermentation

An anaerobic pathway occurring in plants and fungi where pyruvate releases $CO_2$ to form acetaldehyde, which is reduced by $NADH$ to form ethanol and regenerate $NAD^+$ for glycolysis.

Glycogen

A large, heavily branched storage polysaccharide made of glucose units attached to a central protein, stored in animal liver and muscle tissues.

Starch

A large, branched storage polysaccharide composed of glucose chains found in plants (such as potatoes, wheat, and corn).

$\beta$-Oxidation

The metabolic process that breaks down fatty acids into two-carbon acetyl-CoA units, generating $NADH$ and $FADH_2$ without directly producing $ATP$.

Phosphofructokinase-1 (PFK-1)

The key allosteric enzyme that catalyzes step $3$ of glycolysis; activated by high levels of $ADP$ and $AMP$ (low energy) and allosterically inhibited by high levels of $ATP$ and citrate (high energy).