Functional Biology: Energy, Enzymes, Cellular Respiration & Photosynthesis

Vocabulary practice flashcards covering Unit 3 (Bioenergetics, Free Energy, Reaction Energetics, Enzyme Kinetics, and Regulation) and Unit 4 (Metabolism, Aerobic Cellular Respiration, Fermentation, and Photosynthesis).

Potential Energy

Stored energy associated with position, structure, or arrangement; in cells, it includes chemical potential energy stored in covalent molecular structure.

Gibbs Free Energy ($G$)

The portion of system energy available to do useful work and drive biological processes under cellular conditions.

$$\Delta G$$

The change in free energy in a reaction, defined by $\Delta G = G_{\text{products}} - G_{\text{reactants}}$, which determines whether a process releases energy or requires energy input.

Exergonic Reaction

A thermodynamically favorable reaction characterized by $\Delta G < 0$, in which products have lower free energy than reactants and free energy is released overall.

Endergonic Reaction

A non-spontaneous reaction characterized by $\Delta G > 0$, in which products have higher free energy than reactants, requiring energy input or energetic coupling to proceed.

Anabolic Pathways

Metabolic pathways that synthesize complex products from simpler substrates, generally requiring an input of energy.

Catabolic Pathways

Metabolic pathways that break down complex substrates into simpler products, generally releasing chemical energy.

Condensation / Dehydration

A chemical reaction commonly associated with anabolic, endergonic pathways that joins simpler units to build larger molecules (polymers) with the removal of water.

Hydrolysis

A chemical reaction commonly associated with catabolic, exergonic pathways that breaks covalent bonds in polymers to produce simpler units using water.

Transition State

The highest free-energy peak on a reaction-energy curve, representing the unstable arrangement of atoms through which reactants must pass to become products.

Activation Energy ($E_A$)

The difference in free energy between the reactant level and the peak of the transition state on a reaction progress graph.

Enzyme

A biological catalyst that accelerates reaction rate by lowering activation energy ($E_A$) without altering the free energies of reactants/products or the overall $\Delta G$.

Active Site

The specific physical pocket or catalytic region of an enzyme where substrate molecules bind to facilitate reaching the transition state.

Competitive Inhibitor

A regulatory or inhibitory molecule that directly binds to the active site of an enzyme, physically blocking substrate binding.

Allosteric Inhibitor

An inhibitor that binds to a distinct regulatory site separate from the active site, inducing a conformational change in enzyme shape that alters its catalytic activity.

Negative Feedback Inhibition

A regulatory mechanism in multistep pathways where an accumulated end product binds to and inhibits an enzyme acting earlier in the pathway, preventing excess synthesis.

ATP (Adenosine Triphosphate)

A ribonucleotide composed of adenine, ribose, and three phosphate groups used by cells to drive endergonic processes through exergonic hydrolysis.

Terminal Phosphoanhydride Linkage

The covalent bond between the second and third phosphate groups of ATP that is cleaved during exergonic hydrolysis ($\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i$) to release free energy.

Oxidation

The loss of high-energy electrons (often observed as the loss of hydrogen or gain of oxygen), transferring chemical energy away from the oxidized molecule.

Reduction

The gain of high-energy electrons (often observed as the gain of hydrogen or loss of oxygen), storing chemical energy in the reduced molecule.

Glucose ($C_6H_{12}O_6$)

A six-carbon monosaccharide storing significant chemical potential energy in its covalent bonds, which are progressively oxidized during cellular respiration.

Aerobic Cellular Respiration

An overall exergonic pathway described by $C_6H_{12}O_6 + 6\,\text{O}_2 \rightarrow 6\,\text{CO}_2 + 6\,\text{H}_2\text{O} + \text{released energy captured in ATP}$, where glucose is oxidized and $\text{O}_2$ is reduced.

Mitochondrial Matrix

The innermost compartment bounded by the inner mitochondrial membrane; site of pyruvate oxidation and the citric acid (Krebs) cycle.

Cristae

The extensive folds of the inner mitochondrial membrane that house the components of the electron transport chain and ATP synthase.

Intermembrane Space

The compartment situated between the outer and inner mitochondrial membranes into which protons ($\text{H}^+$) are pumped to generate an electrochemical gradient.

Glycolysis

The initial cytosolic stage of cellular respiration that converts $1\,\text{glucose}$ into $2\,\text{pyruvate}$, yielding a net of $2\,\text{ATP}$ and $2\,\text{NADH}$.

Pyruvate Oxidation

The matrix transition stage that converts $2\,\text{pyruvate}$ into $2\,\text{acetyl-CoA}$, $2\,\text{CO}_2$, and $2\,\text{NADH}$ per glucose molecule.

Citric Acid Cycle (Krebs Cycle)

The matrix stage that oxidizes $2\,\text{acetyl-CoA}$ per glucose to yield $4\,\text{CO}_2$, $6\,\text{NADH}$, $2\,\text{FADH}_2$, and $2\,\text{ATP}$.

Electron Transport Chain (ETC)

A series of membrane-bound complexes in the inner mitochondrial membrane that receive electrons from $\text{NADH}$ and $\text{FADH}_2$ to drive $\text{H}^+$ pumping into the intermembrane space.

ATP Synthase

A membrane protein complex powered by the flow of protons ($\text{H}^+$) down their electrochemical gradient to synthesize ATP during oxidative phosphorylation and photophosphorylation.

Fermentation

An anaerobic metabolic pathway following glycolysis that regenerates $\text{NAD}^+$ from $\text{NADH}$, yielding only $2\,\text{net ATP}$ per glucose through substrate-level phosphorylation.

Lactate Fermentation

A type of fermentation occurring in animal muscle cells during high-demand or oxygen-limited conditions that reduces pyruvate to lactate to regenerate $\text{NAD}^+$.

Alcohol Fermentation

A type of fermentation occurring in yeast cells that converts pyruvate into ethanol and $\text{CO}_2$ to regenerate $\text{NAD}^+$.

Photosynthesis

An overall endergonic anabolic pathway described by $6\,\text{CO}_2 + 6\,\text{H}_2\text{O} + \text{light energy} \rightarrow C_6H_{12}O_6 + 6\,\text{O}_2$, where water is oxidized to $\text{O}_2$ and $\text{CO}_2$ is reduced to carbohydrate.

Stroma

The fluid-filled space within a chloroplast surrounding the thylakoid membranes where the Calvin cycle takes place.

Thylakoid Membrane

The internal membrane system of chloroplasts, organized into stacks called grana, containing light-absorbing chlorophyll pigments and the photosynthetic ETC.

Chlorophyll

The photosynthetic pigment in thylakoid membranes that absorbs strongly in the blue/violet and red regions of the light spectrum while reflecting green light.

$$\text{NADP}^+ / \text{NADPH}$$

The primary electron-carrier pair in photosynthesis; $\text{NADP}^+$ accepts high-energy electrons from light reactions to become $\text{NADPH}$, carrying reducing power to the Calvin cycle.

Photosystems II and I (PSII & PSI)

Multiprotein complexes in thylakoid membranes; electrons originate from water splitting at PSII, pass through an ETC, get re-energized at PSI, and reduce $\text{NADP}^+$ to $\text{NADPH}$.

Rubisco

The primary enzyme of the Calvin cycle that catalyzes carbon fixation by combining inorganic $\text{CO}_2$ with the five-carbon acceptor RuBP.

RuBP (Ribulose 1,5-bisphosphate)

The five-carbon acceptor molecule that binds $\text{CO}_2$ during carbon fixation and must be regenerated using ATP for the Calvin cycle to continue.

Glyceraldehyde 3-phosphate (G3P)

The three-carbon sugar output produced by reduction and energy input ($\text{ATP}$ and $\text{NADPH}$) in the Calvin cycle, used by plant cells to assemble glucose and other carbohydrates.

Starch and Cellulose

Two plant polysaccharides assembled from glucose; starch serves as an energy storage molecule, whereas cellulose functions as a structural building block.

Glycogen

The primary animal glucose-storage polysaccharide, structurally distinguished from plant starch by having a more highly branched arrangement.