Biomolecules, Enzymes & Cell Biology – Vocabulary

A comprehensive set of vocabulary flashcards covering key biomolecular, enzymatic and cellular terms from the lecture notes.

Phospholipid

A lipid composed of a glycerol backbone, two hydrophobic fatty acids, and one hydrophilic phosphate/ alcohol head group; forms biological membranes.

Hydrophobic core

The interior region of a phospholipid bilayer created by fatty-acid tails that blocks charged or polar molecules.

Unsaturated fatty acid

Fatty acid containing one or more C=C cis bonds; introduces kinks, increases membrane fluidity and lowers melting point.

Hydrophilic head group

The polar phosphate-containing portion of a phospholipid that faces the aqueous environment.

Amphipathic

Describes molecules with both hydrophobic and hydrophilic regions, e.g., phospholipids.

Lipid bilayer

Double-layered sheet of amphipathic lipids that constitutes cell membranes.

Micelle

Spherical aggregate of single-layered lipids used to absorb lipids and fat-soluble vitamins.

Amino acid

Monomer of proteins containing a central (α) carbon, amino group, carboxyl group, hydrogen, and variable R-group.

R-group

Side chain attached to the α-carbon of an amino acid; determines chemical properties.

Zwitterion

Dipolar form of an amino acid that bears both positive (NH3⁺) and negative (COO⁻) charges at physiological pH.

Biological buffer

Substance like an amino acid whose amino and carboxyl groups accept/donate H⁺ to minimize pH changes.

pKa

pH at which half of a functional group is protonated; ~1.8 for –COOH and ~9 for –NH3⁺ in amino acids.

Isoelectric point (pI)

The pH at which an amino acid or protein carries no net charge.

Essential amino acids

Nine amino acids (Phe, Val, Thr, Trp, Ile, Met, His, Leu, Lys) that must be obtained from the diet.

Peptide bond

Amide linkage formed by condensation between the carboxyl of one amino acid and amino of another.

Primary structure

Linear sequence of amino acids in a polypeptide chain.

Secondary structure

Regular local folding (α-helices, β-pleated sheets) stabilized by backbone hydrogen bonds.

Alpha helix (α-helix)

Coiled secondary structure with 3.6 residues per turn and H-bonds between every 4th peptide bond.

Beta pleated sheet (β-sheet)

Secondary structure where two or more polypeptide strands align side by side, forming flat sheets via H-bonds.

Tertiary structure

Overall 3-D folding of a single polypeptide stabilized by H-bonds, ionic bonds, hydrophobic interactions and disulfide bridges.

Quaternary structure

Association of two or more polypeptide chains to form a functional protein complex.

Disulfide bond

Covalent S–S linkage between two cysteine residues; stabilizes tertiary/quaternary structure.

Hydrogen bond

Non-covalent attraction between a hydrogen attached to electronegative atom and another electronegative atom; key in protein structure.

Hydrophobic interaction

Non-polar side chains clustering to avoid water, driving protein folding.

Warfarin

Anticoagulant drug that inhibits vitamin K epoxide reductase, blocking γ-carboxylation of clotting factors.

Vitamin K epoxide reductase

Enzyme that regenerates active vitamin K; target of warfarin.

Post-translational modification

Chemical alteration of proteins after synthesis (e.g., phosphorylation, acetylation, hydroxylation, cross-linking).

Acetylation

Addition of an acetyl group, often to the N-terminus or lysine residues, altering protein function.

Hydroxylation

Insertion of OH group into proline/lysine residues, important in collagen stability.

Phosphorylation

Attachment of phosphate group to serine, threonine, or tyrosine residues; regulates activity.

Cross-linking

Covalent linkage between polypeptide chains (e.g., disulfide bonds) that stabilizes 3-D structure.

Proteome

Entire set of proteins expressed by a genome, cell or organism; ~1 million in humans.

Enzyme

Biological catalyst that accelerates reactions by lowering activation energy without being consumed.

Active site

3-D pocket on an enzyme where substrate binds and reaction occurs.

Specificity

Ability of an enzyme to select a particular substrate or reaction.

Contact residue

Active-site amino acid that binds substrate, positioning it for catalysis.

Catalytic residue

Active-site amino acid whose chemical groups participate directly in bond-breaking/forming.

Lock-and-key model

Concept that enzyme active site is pre-shaped to fit its substrate exactly.

Induced-fit model

Concept that substrate binding induces conformational change in enzyme for optimal catalysis.

Proximity effect

Catalytic enhancement by bringing substrates together in correct orientation within active site.

Strain effect

Catalysis via slight distortion of substrate bonds, making them easier to break.

Orientation effect

Catalysis by aligning reactive groups of substrate toward catalytic residues.

Microenvironment effect

Catalytic influence of active-site environment (e.g., hydrophobic pocket) on reaction rate.

Acid-base catalysis

Enzyme mechanism using proton donors/acceptors in active site to stabilize transition state.

Cofactor

Non-protein helper (metal ion, coenzyme, prosthetic group) required for enzyme activity.

Prosthetic group

Tightly or covalently bound cofactor, e.g., heme in cytochromes.

Coenzyme

Organic, loosely bound cofactor that carries electrons or groups, e.g., NAD⁺.

Apoenzyme

Protein portion of an enzyme lacking its necessary cofactor.

Holoenzyme

Catalytically active enzyme consisting of apoenzyme plus cofactor.

First law of thermodynamics

Energy cannot be created or destroyed, only transformed.

Second law of thermodynamics

Entropy of an isolated system always increases; processes proceed toward disorder.

Enthalpy (H)

Heat content or total energy of a system; negative ΔH is exothermic.

Entropy (S)

Measure of disorder; higher S indicates greater randomness.

Gibbs free energy (G)

Energy available to do work; ΔG = ΔH – TΔS determines spontaneity.

Lysozyme

Antibacterial enzyme that hydrolyzes β(1→4) glycosidic bonds in peptidoglycan; key catalytic residues Glu35 & Asp52.

Michaelis constant (Km)

Substrate concentration that yields half-maximal velocity; indicates enzyme-substrate affinity.

Competitive inhibitor

Molecule that resembles substrate and binds active site, raising Km but not Vmax.

Non-competitive inhibitor

Molecule that binds a site other than active site, lowering Vmax without changing Km.

Allosteric inhibitor

Regulator that binds allosteric site, stabilizing enzyme’s inactive conformation and lowering activity.

Allosteric activator

Regulator that binds allosteric site, stabilizing active conformation and increasing activity.

Cell theory

Principles stating all living organisms are composed of cells, which arise from pre-existing cells.

Light microscopy

Technique using visible light to visualize tissues and cells.

Fluorescent microscopy

Imaging method using fluorescent tags to visualize cellular structures.

Electron microscopy

High-resolution imaging using electron beams to see organelles and macromolecules.

X-ray crystallography

Technique to determine macromolecular structures by diffraction of X-rays through crystals.

Cytoplasm

Cell contents outside nucleus, including cytosol, organelles, cytoskeleton and inclusions.

Nucleus

Membrane-bound organelle housing DNA and controlling gene expression.

Nucleolus

Dense nuclear region where rRNA is transcribed and ribosomal subunits are assembled.

Nuclear envelope

Double membrane surrounding nucleus, containing nuclear pores for traffic control.

Nuclear lamina

Protein meshwork lining inner nuclear membrane, providing structural support and DNA organization.

Euchromatin

Lightly stained, transcriptionally active, loosely packed chromatin (10 nm fiber).

Heterochromatin

Dark-stained, transcriptionally inactive, densely packed chromatin (30 nm fiber).

Golgi apparatus

Stack of flattened cisternae that modifies, sorts and packages proteins and lipids.

Rough endoplasmic reticulum (RER)

Membranous network studded with 80S ribosomes; synthesizes, folds and glycosylates proteins.

Smooth endoplasmic reticulum (SER)

Membrane network lacking ribosomes; lipid synthesis, detoxification, calcium storage.

Mitochondrion

Double-membrane organelle producing ATP via aerobic respiration; contains own DNA and 70S ribosomes.

Ribosome

Non-membranous organelle (70S or 80S) that translates mRNA into polypeptides.

Lysosome

Single-membrane vesicle containing acidic hydrolases for intracellular digestion.

Peroxisome

Single-membrane organelle housing oxidative enzymes (e.g., catalase) for fatty-acid oxidation and detoxification.

Centrosome

Microtubule-organizing center comprising two centrioles; organizes mitotic spindle.

Microtubule

Cytoskeletal filament of tubulin; supports cell shape, transport, and chromosome movement.

Cilium

Short, hair-like projection with 9+2 microtubule axoneme; moves fluid across cell surface.

Flagellum

Long whip-like structure with 9+2 microtubules; propels cells such as sperm.

Endomembrane system

Interconnected membranes (nuclear envelope, ER, Golgi, vesicles, lysosomes, plasma membrane) for protein/lipid trafficking.

Eukaryote

Cell type with nucleus, membrane-bound organelles, 80S ribosomes and cytoskeleton.

Prokaryote

Cell lacking nucleus and membrane-bound organelles; possesses nucleoid and 70S ribosomes.

Fibroblast

Spindle-shaped connective-tissue cell that secretes collagen, elastin and glycosaminoglycans.

Adipocyte

Large spherical cell storing neutral fat; synthesizes hormones and provides insulation.

Macrophage

Phagocytic white blood cell deriving from monocytes; secretes growth factors and cytokines.

Mast cell

Connective-tissue cell containing histamine-rich granules; mediates allergic responses.

Stem cell

Undifferentiated cell capable of self-renewal and producing specialized cell types.

White blood cell (leukocyte)

Immune cell (e.g., neutrophil, lymphocyte, eosinophil, basophil) defending against pathogens.