Module 2 Exam Review: Cell Biology, Bioenergetics, and Metabolism

Comprehensive vocabulary flashcards covering macromolecule structure, membrane transport, cell anatomy, thermodynamics, enzyme kinetics, cellular respiration, fermentation, and photosynthetic pathways from the Module 2 review.

Organic Molecule

A molecule characterized by containing at least one $\text{C–H}$ bond, which may also contain other elements such as $\text{P}$, $\text{N}$, $\text{O}$, and $\text{S}$.

Polysaccharides (Glycans)

Biological polymers composed of monosaccharide monomers connected by glycosidic bonds, which function in cellular energy storage and cell recognition/signaling.

Nucleic Acids

Informational macromolecules ($\text{DNA}$ and $\text{RNA}$) composed of nucleotide monomers (consisting of a 5-carbon sugar, a phosphate group, and a nitrogenous base) linked by phosphodiester bonds, which store and retrieve genetic information.

Polypeptides (Proteins)

Biological polymers made of amino acid monomers joined by peptide bonds, which carry out structural roles, catalytic enzymatic activities, and cell signaling.

Lipids

A class of biological macromolecules that are not true polymers, grouped instead by shared physical properties (hydrophobic hydrocarbon interactions); they function in membrane structure, long-term energy storage, and signaling.

Primary Structure

The specific sequence and order of amino acids in a polypeptide chain, stabilized by covalent peptide bonds.

Secondary Structure

Local conformational folding into $\alpha$-helices and $\beta$-pleated sheets, stabilized by hydrogen bonding between peptide backbone groups without the involvement of amino acid R-groups.

Tertiary Structure

The overall three-dimensional folding of a single polypeptide chain, stabilized by hydrogen bonds, hydrophobic interactions, van der Waals forces, ionic bonds, and covalent interactions between R-groups or between R-groups and the backbone.

Quaternary Structure

The overall macromolecular shape formed by the combination and assembly of multiple individual polypeptide subunits into a single functional complex.

Nonpolar Amino Acid R-Groups

Hydrocarbon-based amino acid side chains that lack electrical charges or highly electronegative atoms, making them hydrophobic and insoluble in water.

Polar Amino Acid R-Groups

Uncharged amino acid side chains containing partial charges or electronegative atoms ($\text{O}$, $\text{N}$, or $\text{S}$) that allow them to form hydrogen bonds and readily dissolve in water.

Electrically Charged Amino Acid R-Groups

Highly hydrophilic amino acid side chains carrying a net negative charge (acidic) or net positive charge (basic) at physiological pH, allowing strong electrostatic interactions and hydrogen bonding.

Fluid Mosaic Model

A membrane model describing the lipid bilayer as a dynamic, flexible structure with lateral movement of lipids and proteins (fluid) embedded with a diverse mixture of proteins, carbohydrates, and other components (mosaic).

Archaea Membrane Lipids

Membrane lipids distinct from Bacteria and Eukarya characterized by monolayer organization, ether linkages, branched isoprene hydrocarbon tails, and L-glycerol stereochemistry.

Cis-Unsaturated Fatty Acids

Fatty acids containing one or more carbon-carbon double bonds with hydrogen atoms on the same side, creating rigid kinks that prevent tight packing and increase membrane fluidity.

Cholesterol (Membrane Buffer)

A sterol lipid that buffers membrane fluidity across changing temperatures by restraining phospholipid movement to prevent excessive permeability at high temperatures and hindering tight packing to prevent freezing/gelling at low temperatures.

Simple Diffusion

The passive transport of small, nonpolar molecules directly across the lipid bilayer down their concentration gradient without transport proteins or energy input, exhibiting non-saturable kinetics.

Facilitated Diffusion

The passive transport of large, polar, or charged molecules down their concentration gradient via membrane channel or carrier proteins, exhibiting saturable kinetics.

Active Transport

The movement of molecules across a cellular membrane against their concentration or electrochemical gradient, requiring transport proteins and cellular energy input ($\text{ATP}$).

Osmotic Tonicity in Animal Cells

The behavior of animal cells in response to surrounding solute concentrations: shriveling in a hypertonic environment (water leaves), remaining normal in an isotonic environment, and swelling or lysing in a hypotonic environment (water enters).

Endosymbiotic Theory

The evolutionary theory stating that mitochondria and chloroplasts originated from free-living prokaryotes that were engulfed by an ancestral eukaryotic host cell, supported by their circular DNA, prokaryote-like ribosomes, and division by binary fission.

Endomembrane System

A coordinated network of eukaryotic organelles (including the nuclear envelope, rough ER, smooth ER, transport vesicles, Golgi apparatus, lysosomes, and secretory vesicles) that work together to synthesize, modify, package, and transport lipids and proteins.

Free (Cytoplasmic) Ribosomes

Ribosomes unattached to membranes that synthesize proteins destined to remain in the cytosol or travel to the interior of the nucleus, mitochondria, or chloroplasts.

Rough Endoplasmic Reticulum (Rough ER)

A ribosome-studded organelle of the endomembrane system where proteins destined for secretion, plasma membrane insertion, or lysosomes are synthesized and folded.

Second Law of Thermodynamics

The physical law stating that the entropy (disorder) of an isolated system always increases; living organisms maintain local internal order by performing thermodynamic work and releasing heat and waste, increasing universal entropy.

Gibbs Free Energy ($\Delta G$)

A thermodynamic property defined by $\Delta G = \Delta H - T\Delta S$; reactions with $\Delta G < 0$ are exergonic and proceed spontaneously, while reactions with $\Delta G > 0$ are endergonic and require an energy input.

Steady-State (Homeostasis)

A dynamic condition of open biological systems that continuously consume energy to maintain stable, non-equilibrium internal concentrations of metabolic intermediates.

Chemical Equilibrium

A state in which forward and reverse reaction rates are exactly equal, resulting in no net change in reactant and product concentrations, characterized by $\Delta G = 0$.

Activation Energy ($E_a$)

The energy barrier required to reach the transition state in a chemical reaction; enzymes lower this barrier to accelerate reaction rates without altering the overall reaction enthalpy change ($\Delta H$).

$V_{\max}$ (Maximum Velocity)

The maximum rate at which an enzyme-catalyzed reaction can proceed, reached when all enzyme active sites are fully saturated with substrate.

$K_m$ (Michaelis Constant)

The substrate concentration at which the reaction velocity reaches exactly half of $V_{\max}$; a low $K_m$ indicates high enzyme-substrate affinity.

Competitive Inhibition

A mode of enzyme regulation where an inhibitor molecule directly competes with the substrate by binding to the active site, physically blocking substrate entry.

Noncompetitive (Allosteric) Inhibition

A regulatory mechanism in which an inhibitor binds to an allosteric site away from the active site, inducing a conformational change in the enzyme that reduces substrate binding or catalysis.

Photoautotroph

An organism (such as a plant or cyanobacterium) that uses sunlight as its energy source and inorganic $\text{CO}_2$ as its carbon source to generate biomass.

Chemoautotroph

An organism (such as deep-sea vent bacteria or archaea) that captures energy from chemical reactions and fixes inorganic $\text{CO}_2$ to build organic molecules.

Photoheterotroph

An organism (such as purple and green non-sulfur bacteria) that utilizes sunlight for metabolic energy but depends on pre-existing organic carbon sources.

Chemoheterotroph

An organism (such as an animal or fungus) that derives both its metabolic energy and carbon supply from pre-formed organic compounds via chemical reactions.

Substrate-Level Phosphorylation

The direct transfer of a phosphate group from a phosphorylated organic intermediate to $\text{ADP}$ to form $\text{ATP}$, occurring in glycolysis and the citric acid cycle.

Oxidative Phosphorylation

The process of generating $\text{ATP}$ from $\text{ADP}$ and $\text{P}_i$ coupled to redox reactions in an electron transport chain and driven by a proton-motive force across a membrane.

$\text{NAD}^+ / \text{NADH}$ Electron Shuttle

A vital coenzyme that acts as an electron carrier: oxidized $\text{NAD}^+$ accepts high-energy electrons from food molecules to form reduced $\text{NADH}$, which delivers them to Complex I of the respiratory electron transport chain.

Chemiosmosis

The biological process in which free energy released during electron transfer is used to pump protons ($\text{H}^+$) across a membrane, generating an electrochemical proton gradient that drives $\text{ATP}$ synthase.

Anaerobic Respiration

A cellular respiration pathway that utilizes an electron transport chain and chemiosmosis but substitutes alternative inorganic terminal electron acceptors (such as $\text{NO}_3^-$, $\text{SO}_4^{2-}$, $\text{Mn}^{4+}$, or $\text{Fe}^{3+}$) in place of $\text{O}_2$.

Fermentation

An anaerobic metabolic pathway that regenerates $\text{NAD}^+$ in the absence of an active electron transport chain by using organic molecules (such as pyruvate or acetaldehyde) as electron acceptors, producing only the net $2\,\text{ATP}$ from glycolysis.

Beta-Oxidation

The catabolic process occurring in the mitochondrial matrix that cleaves fatty acid hydrocarbon chains two carbons at a time into acetyl-$\text{CoA}$, producing $\text{NADH}$ and $\text{FADH}_2$.

Chlorophyll Absorption Spectrum

The wavelength profile demonstrating that photosynthetic chlorophyll pigments strongly absorb high-energy blue (around $400\,\text{nm}$–$450\,\text{nm}$) and red light (around $650\,\text{nm}$–$680\,\text{nm}$) while reflecting green light.

Non-Cyclic Electron Flow (Z-Scheme)

The standard light reaction pathway in oxygenic photosynthesis that couples PSII ($\text{P680}$) and PSI ($\text{P700}$) to extract electrons from water, release $\text{O}_2$, build an electrochemical proton gradient, and produce $\text{ATP}$ and $\text{NADPH}$.

Cyclic Electron Flow

A photosynthetic light reaction pathway utilizing only PSI, where excited electrons loop back from ferredoxin to the thylakoid electron transport chain to generate extra $\text{ATP}$ via a proton gradient without generating $\text{NADPH}$ or $\text{O}_2$.

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the stroma enzyme that fixes inorganic $\text{CO}_2$ to the five-carbon sugar $\text{RuBP}$ in the first step of the Calvin cycle, which can also bind $\text{O}_2$ to initiate photorespiration.