Cell Biology – Organelles, Proteins & Enzymes (Lecture 1–2)

Vocabulary flashcards covering organelles, protein structure, folding, regulation, degradation, enzymes, and bioenergetics concepts from the lecture notes.

Eukaryotic Cell

Cell type whose interior is subdivided into membrane-bound organelles with discrete functions.

Prokaryotic Cell

Cell type that carries out all cellular functions in a single, non-compartmentalized space lacking membrane-bound organelles.

Organelle

Specialized sub-compartment within a eukaryotic cell that performs a specific biochemical function.

Ribosome

Large rRNA–protein complex in cytosol or ER that translates mRNA into polypeptide chains.

Proteasome

Multi-protein complex that degrades ubiquitin-tagged proteins into short peptides.

Cytosol

Aqueous fluid (pH ≈7) inside the cell in which organelles and macromolecules are suspended.

Cytoplasm

Collective term for the cytosol plus all macromolecules and organelles it contains.

Fluorescent Protein (FP)

Protein from jellyfish/coral that emits visible light when excited and is used as a genetic cell or organelle label.

Protein

Most abundant cellular macromolecule; polymer of amino acids folded into a 3-D structure to perform diverse functions.

Amino Acid

Building block of proteins, linked covalently via peptide bonds to form polypeptides.

Peptide

Short polymer of 2–50 amino acids; longer chains (>≈50 aa) are considered proteins.

Primary Sequence

Linear order of amino acids in a protein read from N-terminus to C-terminus.

Secondary Structure

Local non-linear folding of a peptide chain (e.g., α-helix, β-sheet) stabilized by hydrogen bonds.

Tertiary Structure

Three-dimensional folded shape of a single polypeptide stabilized by multiple bond types.

Quaternary Structure

3-D arrangement of a multi-subunit protein complex (e.g., dimers, trimers, tetramers).

Protein Domain

Distinct region within a protein that folds independently and confers a specific function.

Conformational Change

Alteration of a protein’s 3-D shape that modulates its activity or interactions.

Protein Affinity

Strength with which a protein binds another molecule; high affinity = tight binding.

Chaperone Protein

Helper protein that assists nascent polypeptides in folding into their correct tertiary structure.

Denaturation

Unfolding of a protein from tertiary back to secondary structure, leading to loss of function.

Protein Aggregate

Insoluble cluster of misfolded proteins that can be toxic, especially to neurons.

Ubiquitin

Small protein covalently attached to proteins to mark them for proteasomal degradation.

Central Dogma

Flow of genetic information: DNA → mRNA (transcription) → protein (translation).

Proteome

Complete set of proteins expressed in a specific cell type or condition.

Post-Translational Modification (PTM)

Chemical modification (e.g., phosphorylation, ubiquitination) made to a protein after translation.

Enzyme

Protein catalyst that accelerates a specific chemical reaction without being consumed.

Catalysis

Process by which an enzyme lowers activation energy to speed up a reaction.

Substrate

Reactant molecule that binds an enzyme’s active site and is converted into product.

Active Site

Region of an enzyme where the substrate binds and the catalytic reaction occurs.

Activation Energy

Energy barrier that must be overcome for a chemical reaction to proceed; lowered by enzymes.

Kinase

Enzyme that catalyzes transfer of a phosphate group from ATP to a substrate (phosphorylation).

Phosphorylation

Addition of a phosphate group to a molecule, altering its shape, charge and interactions.

ATP (Adenosine Triphosphate)

Cellular energy currency containing high-energy phosphoanhydride bonds.

ATP Hydrolysis

Exergonic reaction in which ATP + H₂O → ADP + Pi, releasing usable chemical energy.

Coupling

Linking of an exergonic reaction (e.g., ATP hydrolysis) to drive an endergonic reaction.

Exergonic Reaction

Reaction with negative ΔG⁰ that proceeds spontaneously and releases energy.

Endergonic Reaction

Reaction with positive ΔG⁰ that requires input of energy to proceed.

Gibbs Free Energy (ΔG⁰)

Thermodynamic measure of reaction spontaneity; negative values favor spontaneous reactions.

Inorganic Phosphate (Pi)

Free phosphate ion released during ATP hydrolysis and used in phosphorylation reactions.

Motor Protein

Protein (e.g., kinesin, dynein, myosin) that converts chemical energy into mechanical movement along cytoskeletal tracks.

Microtubule

Cytoskeletal filament composed of tubulin; track for motor proteins and organizer of cell shape.

Affinity Change

Alteration in binding strength caused by protein conformational shifts, enabling dynamic interactions.

Proteasomal Degradation

ATP-dependent process in which proteasomes digest ubiquitin-tagged proteins into peptides.

Electron Tomography

Imaging technique that reconstructs 3-D cellular ultrastructure, revealing crowded organelle organization.

Membrane Compartmentalization

Separation of cellular processes into distinct lipid-bilayer–bounded spaces, enabling multifunctional eukaryotic cells.

Fluorescence Labeling

Use of genetically encoded fluorescent proteins to visualize specific cells, organelles or proteins in vivo.

Hydrolysis

Chemical reaction that splits a bond by adding water (e.g., peptide bond cleavage, ATP hydrolysis).

Lock-and-Key Model

Concept that enzyme active sites have shapes complementary to their substrates’ geometry.

Induced Fit

Model in which enzyme changes shape upon substrate binding to facilitate catalysis.