Cellular Biology: Membranes, Energy, Photosynthesis, and Respiration

Practice vocabulary flashcards spanning lipid bilayer mechanics, thermodynamics, enzyme kinetics and regulation, light-dependent and light-independent photosynthesis, and cellular respiration and fermentation pathways.

Amphipathic

A property of a molecule describing the presence of both hydrophilic (polar) and hydrophobic (nonpolar) regions, as seen in phospholipids and membrane-spanning proteins.

Phospholipid

An amphipathic lipid consisting of a hydrophilic head and two hydrophobic hydrocarbon tails that spontaneously forms micelles or bilayers in aqueous solutions.

Fluid-Mosaic Model

The model of the cell membrane describing it as a dynamic structure with the consistency of olive oil, where phospholipids move laterally as fast as $2\,\mu\text{m}$ per second and proteins are embedded or associated with the bilayer.

Selective Permeability

The characteristic of a membrane that permits small, nonpolar molecules ($O_2$, $CO_2$, $N_2$) to cross rapidly while exhibiting lower permeability to small uncharged polar molecules ($H_2O$), and very low permeability to large polar molecules (glucose) and small ions ($Cl^-$, $K^+$, $Na^+$).

Diffusion

The spontaneous net movement of solute molecules down a concentration gradient resulting from constant, random thermal motion.

Membrane Fluidity and Permeability Factors

Four factors altering lipid bilayer behavior: tail length (shorter tails increase permeability), saturation (unsaturated tails with kinks increase permeability), temperature (higher temperatures increase permeability), and cholesterol (hydrophobic steroid rings pack tightly and decrease permeability).

Osmosis

The diffusion of water across a semipermeable membrane from an area of lower solute concentration to an area of higher solute concentration to equalize concentrations.

Aquaporin

A specialized channel protein spanning the membrane that facilitates the rapid, efficient diffusion of water molecules across the lipid bilayer.

Tonicity

The relative concentration of solutes in solutions separated by a membrane, categorized into isotonic (equal concentration), hypotonic (lower external solute, causing cell swelling or lysis), and hypertonic (higher external solute, causing cell shrinkage or crenation).

Facilitated Diffusion

A passive transport process that moves solutes down their concentration gradient without energy input, assisted by membrane proteins functioning as channels (e.g., aquaporins, ion channels) or carriers (e.g., GLUT-1).

Active Transport

The process of moving substances across a cell membrane against their concentration or electrochemical gradient, requiring energy input in the form of $\text{ATP}$ (e.g., the sodium-potassium pump).

Gibbs Free Energy Equation

The thermodynamic equation $\Delta G = \Delta H - T\Delta S$, where $\Delta G$ is the change in free energy, $\Delta H$ is enthalpy, $T$ is temperature in Kelvin, and $\Delta S$ is entropy.

Enthalpy ($H$)

The total energy in a molecule, driven primarily by differences in potential energy; reactions with $\Delta H < 0$ are exothermic (release heat), while those with $\Delta H > 0$ are endothermic (absorb heat).

Entropy ($S$)

The amount of disorder present in a system; when products are less ordered than reactants, $\Delta S > 0$, and when products are more ordered, $\Delta S < 0$.

Exergonic Reaction

A spontaneous chemical reaction with $\Delta G < 0$ that releases energy, wherein the products possess less free energy than the reactants.

Endergonic Reaction

A non-spontaneous chemical reaction with $\Delta G > 0$ that absorbs energy, wherein the products possess more free energy than the reactants.

Transition State

A very short-lived molecular configuration at a local energy maximum featuring partial chemical bonds that cannot be isolated as an individual stable molecule.

Activation Energy ($E_a$)

The minimum kinetic energy required to initiate a chemical reaction by straining reactant bonds to achieve the transition state.

Enzyme

A protein catalyst that speeds up chemical reactions without being consumed or permanently altered, acting by stabilizing the transition state and lowering the activation energy ($E_a$).

Active Site

The specific region of an enzyme that binds substrate molecules and facilitates their chemical transformation into products.

Competitive Inhibition

A reversible regulatory mechanism in which an inhibitor molecule directly competes with the substrate for binding to the enzyme's active site (e.g., malonate competing with succinate in the Krebs cycle).

Allosteric Regulation

The modification of an enzyme's activity resulting from a regulatory molecule binding to a site other than the active site, inducing conformational shifts between active (relaxed / R state) and inactive (tense / T state) forms.

Feedback Inhibition

A regulatory mechanism in which an abundance of the end product of a biosynthetic pathway allosterically inhibits the enzyme regulating entry into that pathway to stop further production.

Transposon

A 'jumping gene' capable of moving to new genomic locations, first discovered by Nobel laureate Barbara McClintock in the $1950\text{s}$; heat-adapted fungal strains display a $5\times$ higher rate of transposon transposition.

Barbara McClintock

The geneticist who discovered transposons ('jumping genes') in maize in the $1950\text{s}$ and was awarded the Nobel Prize in $1983$.

Chloroplast

The specialized photosynthetic organelle of plants and algae containing an outer membrane, an inner membrane, an aqueous stroma, and thylakoid sacs stacked into grana; photosynthetic plant cells typically contain $40$–$50$ chloroplasts.

Thylakoid

A flattened, membrane-bound sac inside a chloroplast containing chlorophyll and accessory pigments organized into photosystems that execute the light-dependent reactions.

Stroma

The fluid-filled matrix surrounding thylakoids inside the chloroplast inner membrane, serving as the site of the light-independent Calvin cycle reactions.

Chlorophyll

The major photosynthetic pigment consisting of a light-absorbing porphyrin ring head with a magnesium ($Mg$) ion and a hydrophobic phytol tail anchoring it in the thylakoid membrane, absorbing red and blue light and reflecting green light.

Photosystem II (PSII)

A protein-pigment complex in the thylakoid membrane featuring a $P680$ reaction center that splits water into $O_2$, protons, and electrons ($2\,H_2O \rightarrow 4\,H^+ + O_2 + 4\,e^-$), transferring electrons to pheophytin to establish a proton gradient.

Plastoquinone (PQ)

A lipid-soluble mobile electron carrier that shuttles electrons from Photosystem II to the cytochrome complex while translocating protons from the chloroplast stroma into the thylakoid lumen.

Photosystem I (PSI)

A protein-pigment complex in the thylakoid membrane featuring a $P700$ reaction center that receives electrons from plastocyanin (PC) and uses light energy to pass electrons to ferredoxin and $\text{NADP}^+$ reductase, forming $\text{NADPH}$.

Photophosphorylation

The production of $\text{ATP}$ from $\text{ADP}$ and $\text{P}_i$ catalyzed by ATP synthase, driven by the proton-motive force across the thylakoid membrane established during light-dependent reactions.

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the leaf enzyme consisting of $8$ active sites that fixes carbon dioxide onto RuBP during the Calvin cycle, but also catalyzes photorespiration when oxygen binds.

Calvin Cycle

The light-independent cyclic pathway occurring in the stroma with three phases: fixation ($3\,\text{RuBP} + 3\,CO_2 \rightarrow 6\,3\text{PGA}$), reduction ($6\,3\text{PGA} + 6\,\text{ATP} + 6\,\text{NADPH} \rightarrow 6\,\text{G3P}$, yielding $1\,\text{G3P}$), and regeneration ($5\,\text{G3P} + 3\,\text{ATP} \rightarrow 3\,\text{RuBP}$).

Alpha (\alpha) Glycosidic Linkage

A glycosidic linkage producing a helical, less stable polysaccharide structure without interchain hydrogen bonds, easily broken down for energy storage (e.g., starch and glycogen).

Beta (\beta) Glycosidic Linkage

A glycosidic linkage producing solidly packed, straight-chain polymers stabilized by numerous hydrogen bonds between monomers, conferring mechanical stability for cellular structure (e.g., cellulose, chitin, peptidoglycan).

Glycolysis

The cytosolic ten-step metabolic pathway converting one glucose into two pyruvates, yielding a net of $2\,\text{ATP}$ (substrate-level phosphorylation) and $2\,\text{NADH}$.

Phosphofructokinase (PFK)

The key regulatory enzyme of glycolysis that is allosterically inhibited by high levels of $\text{ATP}$ (shifting it to the low-affinity T state) and activated by $\text{AMP}$ and fructose-2,6-bisphosphate (shifting it to the R state).

Pyruvate Dehydrogenase (PDH)

The multienzyme complex in the mitochondrial matrix that links glycolysis to the citric acid cycle by oxidizing pyruvate into acetyl CoA, $CO_2$, and $\text{NADH}$; inhibited by high concentrations of products via phosphorylation.

Citric Acid Cycle

The eight-reaction cyclic pathway located in the mitochondrial matrix that oxidizes acetyl CoA to $CO_2$, producing $3\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{ATP}$ (or $\text{GTP}$) per acetyl CoA ($2$ turns per glucose molecule).

Electron Transport Chain (ETC)

A sequence of four protein complexes (Complexes I-IV) and electron shuttles (ubiquinone and cytochrome c) located in the inner mitochondrial membrane that sequentially transfer electrons to oxygen ($O_2$), pumping protons into the intermembrane space.

ATP Synthase

A multi-subunit rotary enzyme containing $F_0$ (membrane rotor channel) and $F_1$ (catalytic head) units that utilizes the proton-motive force across a membrane to synthesize $\text{ATP}$ from $\text{ADP}$ and $\text{P}_i$.

Thermogenin

An uncoupling protein found in the inner mitochondrial membrane of brown fat cells that allows protons to flow back into the matrix without synthesizing $\text{ATP}$, releasing energy exclusively as heat.

2,4-Dinitrophenol (DNP)

A chemical uncoupler that carries protons directly across the mitochondrial inner membrane, dissipating the proton gradient so $\text{ATP}$ synthase cannot produce $\text{ATP}$ despite ongoing oxygen consumption and rapid electron transport, causing hyperthermia, fatigue, and sweating.

Fermentation

An anaerobic cytosolic metabolic pathway that sustains glycolysis by transferring electrons from $\text{NADH}$ to pyruvate or its derivatives, regenerating $\text{NAD}^+$ in the absence of an operational electron transport chain.

Lactic Acid Fermentation

An anaerobic metabolic pathway occurring in animal muscle cells and certain bacteria where pyruvate is directly reduced to lactate, regenerating $\text{NAD}^+$; lactate can be converted back to pyruvate when oxygen becomes available.

Alcohol Fermentation

An anaerobic pathway in yeast and certain microorganisms where pyruvate is converted into acetaldehyde and then reduced to ethanol and $CO_2$, regenerating $\text{NAD}^+$; ethanol cannot be reconverted to pyruvate and is excreted.