Principles of Biology: Organic Molecules, Cellular Organization, and Membrane Biology

Comprehensive practice flashcards covering organic macromolecules, cellular evolution and structures, and membrane transport dynamics based on Chapters 3, 4, and 5 of Principles of Biology.

Prebiotic Soup

The slow accumulation of spontaneously formed organic molecules (such as amino acids and nucleotides) in early oceans over a long period prior to the existence of living cells.

Dehydration Reaction

When two monomers or molecules are covalently joined together with the concurrent removal of one net molecule of water ($\text{H}_2\text{O}$).

Hydrolysis Reaction

A chemical process that breaks down a polymer into smaller subunits or monomers by adding a molecule of water ($\text{H}_2\text{O}$).

Monosaccharide

The simplest form of carbohydrate, consisting of a single sugar unit that cannot be broken down by hydrolysis into a simpler carbohydrate.

Disaccharide

A carbohydrate composed of two monosaccharide units joined covalently by a glycosidic bond via a dehydration reaction; examples include sucrose (glucose + fructose), lactose (glucose + galactose), and maltose (glucose + glucose).

Polysaccharide

A complex carbohydrate polymer formed by many monosaccharide units linked by glycosidic bonds, functioning in energy storage (starch in plants, glycogen in animals) or structural support (cellulose in plant cell walls, chitin in fungal walls and arthropod exoskeletons).

Triglyceride

A lipid formed by joining one glycerol molecule to three fatty acids via ester bonds through dehydration reactions, serving as an energy-dense storage biomolecule yielding approximately $9\,\text{kcal/g}$.

Saturated Fatty Acid

A fatty acid whose hydrocarbon chain contains no carbon-carbon double bonds, allowing the straight chains to pack tightly together.

Unsaturated Fatty Acid

A fatty acid containing one (monounsaturated) or more (polyunsaturated) carbon-carbon double bonds, which introduce kinks into the hydrocarbon chain and prevent tight packing.

Phospholipid

An amphipathic lipid consisting of a glycerol backbone linked to two hydrophobic fatty acid tails and a hydrophilic head containing a phosphate group and a charged/polar region (such as choline).

Steroid

A class of lipids characterized by a core structure of four fused carbon rings, such as cholesterol, which maintains membrane fluidity and serves as a precursor for steroid hormones.

Amino Acid Structure

A monomer of proteins consisting of a central $\alpha$-carbon bonded to an amino group ($-\text{NH}_2$ or $-\text{NH}_3^+$), a carboxyl group ($-\text{COOH}$ or $-\text{COO}^-$), a hydrogen atom, and a variable side chain ($R$ group).

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid through a dehydration reaction.

Primary Structure

The precise linear sequence of amino acids in a polypeptide chain encoded by genetic information.

Secondary Structure

Repeating spatial patterns in a polypeptide, primarily the $\alpha$ helix and $\beta$ pleated sheet, stabilized by hydrogen bonds along the polypeptide backbone.

Tertiary Structure

The complete three-dimensional conformation assumed by a single polypeptide chain as secondary structural elements and random coiled regions fold together.

Quaternary Structure

The association of two or more individual polypeptide chains (subunits) that bind together to assemble a functional multimeric protein.

Anfinsen Ribonuclease Experiment

A landmark 1961 biochemical study by Haber and Anfinsen demonstrating that ribonuclease denatured by $\beta$-mercaptoethanol and urea can spontaneously refold into its active native structure when denaturants are removed, proving amino acid sequence dictates tertiary folding.

Nucleotide

The monomeric subunit of nucleic acids, consisting of three components: a five-carbon sugar, a phosphate group, and a nitrogenous base.

Complementary Base Pairing

Specific hydrogen bonding between nitrogenous base pairs in nucleic acids, linking adenine with thymine ($\text{A}-\text{T}$) in DNA (or uracil in RNA, $\text{A}-\text{U}$) and guanine with cytosine ($\text{G}-\text{C}$).

Cell Theory

A foundational biological concept established by Matthias Schleiden (1838), Theodor Schwann (1839), and Rudolf Virchow stating that: 1. All organisms consist of one or more cells; 2. Cells are the smallest units of life; 3. New cells originate only from pre-existing cells via cell division.

Miller–Urey Experiment

A 1953 experiment simulating primitive Earth's reducing atmosphere ($\text{H}_2\text{O}$, $\text{H}_2$, $\text{CH}_4$, $\text{NH}_3$) using electrical sparks to demonstrate the abiotic synthesis of organic precursors such as hydrogen cyanide, formaldehyde, and amino acids.

Carbonaceous Chondrite

A class of carbon-rich meteorites that contain organic molecules, amino acids, and nucleic acid bases, supporting the extraterrestrial hypothesis for the origin of organic precursors on Earth.

Protocell

A prebiotically produced boundary-enclosed aggregate of macromolecules that maintains an internal chemical environment distinct from its surroundings and displays primitive life-like properties.

Liposome

A hollow, fluid-filled spherical vesicle enclosed by a lipid bilayer that forms spontaneously when specific lipids are dispersed in water; their formation can be catalyzed by clay.

Chemical Selection

A process occurring when a specific chemical or mutant RNA in a mixture increases in frequency relative to others due to functional advantages (such as enhanced catalytic self-replication), driving prebiotic chemical evolution.

RNA World Hypothesis

The hypothesis proposing a primordial period during the origin of life when RNA carried out both genetic information storage and catalytic enzymatic functions (ribozymes) before DNA and proteins evolved.

Resolution

The ability of a microscope to distinguish two adjacent points as separate and distinct objects, serving as a measure of visual clarity ($0.2\,\text{mm}$ for unaided human eye; $0.2\,\mu\text{m}$ for light microscopy; $0.1\,\text{nm}$ for electron microscopy).

Differential Interference Contrast (DIC) Microscopy

An optical light microscopy method (also known as Nomarski microscopy) that uses optical modifications to improve image contrast in unstained living specimens, especially for viewing whole cells and large internal organelles.

Transmission Electron Microscopy (TEM)

A type of electron microscopy in which a beam of electrons is transmitted through ultrathin slices of heavy-metal-stained samples to reveal detailed internal cellular fine structures.

Scanning Electron Microscopy (SEM)

A type of electron microscopy in which an electron beam scans across the heavy-metal-coated exterior surface of a sample to generate a three-dimensional image.

Proteome

The entire collection of proteins synthesized by a specific cell type at a given time or encoded by an organism's genome, which determines the cell's specialized structures and biochemical capabilities.

Surface Area-to-Volume Ratio

The critical geometric relationship ($\text{SA/V}$) that constrains cell size; as cell volume expands cubically ($V = \frac{4}{3}\pi r^3$), surface area increases only quadratically ($A = 4\pi r^2$), limiting nutrient import and waste export.

Cytosol

The fluid-filled aqueous region of a eukaryotic cell that lies inside the plasma membrane but outside all membrane-bound organelles.

Catabolism

The metabolic breakdown of complex molecules into smaller, simpler components, often yielding energy.

Anabolism

The metabolic synthesis of cellular molecules and macromolecules from simpler chemical building blocks, requiring an input of energy.

Microtubule

A long, hollow cylindrical protein filament composed of tubulin subunits that maintains cell shape, organizes organelles, forms cilia/flagella, and aids intracellular transport.

Intermediate Filament

A tough, twisted ropelike cytoskeletal filament intermediate in diameter between actin filaments and microtubules that provides mechanical rigidity and structural strength to cells.

Actin Filament

A thin, spiral cytoskeletal fiber (also termed microfilament) composed of actin subunits that supports cell shape, provides cytoplasmic strength, and facilitates cell motility.

Motor Protein

An ATP-powered mechanochemical protein structured into head, hinge, and tail domains (e.g., kinesin, dynein, myosin) that exerts mechanical force along cytoskeletal tracks to carry cargo, move filaments, or bend structures.

Droplet Organelle

A non-membrane-bound cellular compartment formed via liquid-liquid phase separation that concentrates RNA and protein molecules in a distinct chemical environment, exemplified by the nucleolus.

Nuclear Envelope

The double-membrane boundary enclosing the nucleus whose outer leaflet is continuous with the endoplasmic reticulum membrane and which is perforated by nuclear pore complexes.

Nuclear Pore Complex (NPC)

An enormous macromolecular gatekeeper spanning the nuclear envelope composed of approximately 500 to 1000 nucleoporin proteins that regulates macromolecular transit between nucleus and cytosol.

Rough Endoplasmic Reticulum (Rough ER)

A membrane network studded with ribosomes on its cytosolic face that synthesizes, sorts, and glycosylates proteins destined for the endomembrane system, lysosomes, membranes, or extracellular secretion.

Smooth Endoplasmic Reticulum (Smooth ER)

A ribosome-free portion of the endoplasmic reticulum that functions in lipid modification and synthesis, detoxification of toxins, carbohydrate metabolism, and calcium ion storage.

Cisterna

A individual flattened, fluid-filled membrane sac or disc that encloses a single internal lumen within the endoplasmic reticulum and the Golgi apparatus.

Golgi Apparatus

A stack of flattened cisternae that receives, sorts, processes (via proteolysis and glycosylation), and packages proteins and lipids into transport vesicles destined for secretory and endomembrane pathways.

Cotranslational Sorting

A protein sorting pathway in which an emerging ER signal peptide halts cytosolic translation and directs the ribosome to the ER membrane, allowing synthesis directly into the ER lumen.

Post-Translational Sorting

A protein targeting pathway where polypeptides complete synthesis entirely on free cytosolic ribosomes before sorting signals direct their uptake into destinations such as the nucleus, mitochondria, chloroplasts, or peroxisomes.

Lysosome

A single-membrane-bound animal organelle rich in acid hydrolases functioning at low pH to degrade endocytosed matter, damaged organelles, and macromolecules.

Peroxisome

A small single-membrane organelle found in all eukaryotic cells that breaks down toxins and uses catalase to convert harmful hydrogen peroxide into water and oxygen gas ($2\text{H}_2\text{O}_2 \rightarrow 2\text{H}_2\text{O} + \text{O}_2$).

Semiautonomous Organelles

Organelles (mitochondria and chloroplasts) that contain their own circular genome, replicate internally by binary fission, but still depend on nuclear genes for many of their internal components.

Endosymbiosis Theory

The evolutionary theory proposing that mitochondria and chloroplasts originated as free-living bacteria (proteobacteria and cyanobacteria, respectively) engulfed by ancestral eukaryotic host cells in an endosymbiotic relationship.

Extracellular Matrix (ECM)

An interconnected extracellular network of structural and adhesive proteins (such as collagen, elastin, fibronectin, and laminin) and polysaccharides secreted by animal cells to provide strength, structural support, tissue organization, and cell signaling.

Fluid-Mosaic Model

The membrane architecture model proposed by S. Jonathan Singer and Garth Nicolson (1972) describing biological membranes as a dynamic, two-dimensional semifluid lipid bilayer embedded with mobile proteins, glycoproteins, and glycolipids.

Leaflet

One of the two distinct, asymmetrical phospholipid single layers that compose a biological membrane bilayer (the cytosolic leaflet and the extracellular leaflet).

Transmembrane Protein

An integral membrane protein having one or more hydrophobic domains (commonly $\alpha$ helices) physically spanning across the interior of the phospholipid bilayer.

Lipid-Anchored Protein

An integral membrane protein anchored in the lipid bilayer via a covalent bond between one of its amino acids and a lipid molecule.

Peripheral Membrane Protein

A protein noncovalently associated with the membrane by electrostatic or hydrogen bonds to phospholipid polar heads or projecting regions of integral membrane proteins, extractable by high salt or pH shifts.

Flippase

An ATP-dependent membrane enzyme that catalyzes the transbilayer movement ("flip-flop") of phospholipids from one membrane leaflet to the opposite leaflet.

Lipid Raft

A distinct microdomain of lipids with high concentrations of cholesterol and specific membrane proteins that floats together as a cohesive unit within the plasma membrane to regulate cell signaling and endocytosis.

Simple Diffusion

Passive transit of a solute across a biological membrane down its concentration gradient directly through the phospholipid bilayer without the assistance of a transport protein.

Facilitated Diffusion

The passive transport of a solute across a membrane down its concentration or electrochemical gradient with the direct assistance of a transmembrane channel or carrier protein.

Active Transport

The energy-requiring transport of solutes across a membrane against a concentration or electrochemical gradient mediated by specific transport proteins.

Electrochemical Gradient

A dual gradient consisting of both a chemical concentration differential and an electrical potential across a membrane that influences charged ion movement.

Osmosis

The net passive movement of water molecules across a selectively permeable membrane from an area of lower solute concentration (higher water concentration) to an area of higher solute concentration (lower water concentration).

Crenation

The cellular shrinkage that occurs when an animal cell without a rigid cell wall is placed into a hypertonic external solution and loses water via osmosis.

Osmotic Lysis

The swelling and bursting of a cell resulting from the excessive influx of water when placed into a hypotonic environment.

Plasmolysis

The shrinking of a plant, bacterial, or fungal cell's protoplast away from its surrounding rigid cell wall when placed into a hypertonic medium due to water loss.

Aquaporin (CHIP28)

A membrane channel protein identified by Peter Agre (1992) as CHIP28 ($28\,\text{kDa}$) in erythrocytes and kidney cells that facilitates rapid, selective water diffusion across biological membranes.

Uniporter

A carrier transport protein that binds and transports a single ion or solute molecule across a membrane in one direction.

Symporter

A secondary active cotransporter protein that transports two or more distinct ions or solutes across the membrane simultaneously in the exact same direction.

Antiporter

A transport protein (exchanger) that translocates two or more distinct solutes across a biological membrane in opposite directions.

$$\text{Na}^+/\text{K}^+\text{-ATPase}$$

An electrogenic primary active antiporter pump that hydrolyzes one ATP molecule to export $3\,\text{Na}^+$ and import $2\,\text{K}^+$ against their respective gradients, alternating between E1 and E2 conformations.

Gap Junction

An animal intercellular junction assembled from hexameric connexin protein complexes (connexons) in neighboring cells that align to form an open channel permitting direct passage of ions and small signaling molecules.

Plasmodesma

A membrane-lined cytoplasmic channel piercing adjacent plant cell walls that contains a central desmotubule linking smooth ER networks to allow intercellular communication and nutrient transit.

Exocytosis

A vesicular transport process in which intracellular cargo packed within Golgi-derived membrane vesicles is secreted outside the cell as the vesicle membrane fuses with the plasma membrane.

Receptor-Mediated Endocytosis

A selective endocytic uptake mechanism in which specific extracellular ligands bind cell-surface receptors, triggering receptor aggregation, coat protein recruitment, and membrane invagination into an internal vesicle.

Cadherins

Calcium-dependent ($\text{Ca}^{2+}$) cell adhesion molecules that form cell-to-cell anchoring junctions, connecting to actin filaments in adherens junctions and intermediate filaments in desmosomes.

Integrins

Calcium-independent cell adhesion molecules that anchor animal cells to the extracellular matrix (ECM), linking to intermediate filaments in hemidesmosomes and actin filaments in focal adhesions.