BY4001: Biomolecules, Membranes, and Enzymes

Comprehensive vocabulary flashcards covering biomolecules (lipids, carbohydrates, nucleic acids, proteins), membrane structure and transport mechanisms, and enzyme kinetics and catalysis.

Glycerol

A three-carbon polyol molecule containing three reactive $\text{--OH}$ groups that serve as the attachment points for fatty acids in triglycerides and phospholipids.

Triglyceride (Triacylglycerol)

A storage lipid composed of a glycerol backbone ester-linked to three fatty acid chains, synthesized via condensation reactions with the loss of water.

Ester Linkage

The covalent bond formed between the hydroxyl group ($\text{--OH}$) of glycerol and the carboxyl group ($\text{--COOH}$) of a fatty acid during a condensation reaction.

Saturated Fatty Acid

A hydrocarbon chain containing no carbon-carbon double bonds ($\text{C=C}$), allowing tight molecular packing and resulting in a solid state at room temperature.

Unsaturated Fatty Acid

A hydrocarbon chain possessing one or more carbon-carbon double bonds ($\text{C=C}$) that introduce kinks, preventing close packing and increasing fluidity (liquid at room temperature).

Phospholipid

An amphipathic lipid consisting of a glycerol backbone attached to two hydrophobic fatty acid tails and one hydrophilic, charged phosphate head group, forming the structural basis of cell membranes.

Pyranose Ring

A six-membered cyclic hemiacetal sugar ring formed by a reversible intramolecular reaction between the hydroxyl group on carbon 5 ($\text{C5}$) and the aldehyde group on carbon 1 ($\text{C1}$) of glucose.

Glycosidic Linkage

A covalent bond formed between two monosaccharides by a condensation reaction, such as the $\alpha 1\text{--}4$ linkage in maltose or the $1\text{--}2$ linkage between glucose and fructose in sucrose.

Starch

A plant storage polysaccharide consisting of $\alpha\text{-glucose}$ monomers joined predominantly by $\alpha 1\text{--}4$ glycosidic linkages in helical forms such as amylose and branched forms like amylopectin.

Glycogen

An extensively branched animal storage polysaccharide composed of $\alpha\text{-glucose}$ units linked by $\alpha\text{-glycosidic}$ bonds, stored as granules within cells.

Cellulose

A structural plant polysaccharide composed of $\beta\text{-glucose}$ monomers joined by $\beta 1\text{--}4$ glycosidic linkages; forms linear, unbranched microfibrils held together by hydrogen bonds that are indigestible by humans.

Nucleotide

The monomer of nucleic acids, consisting of a pentose sugar (ribose or deoxyribose), a nitrogenous base attached to $1'\text{C}$, and one or more phosphate groups attached to $5'\text{C}$.

Phosphodiester Linkage

The covalent bond connecting adjacent nucleotides in a polynucleotide chain, linking the $3'\text{C}$ hydroxyl group of one sugar to the $5'\text{C}$ phosphate group of the next.

Ribose vs. Deoxyribose

Five-carbon pentose sugars found in nucleic acids; ribose contains a hydroxyl group ($\text{--OH}$) at carbon $2'$, whereas deoxyribose possesses a hydrogen atom ($\text{--H}$) at carbon $2'$.

Purines

Nitrogenous bases consisting of a double-ring structure, specifically Adenine (A) and Guanine (G).

Pyrimidines

Nitrogenous bases consisting of a single six-membered ring, specifically Cytosine (C), Thymine (T in DNA), and Uracil (U in RNA).

Chargaff's Rule

The base-pairing principle stating that Adenine always pairs with Thymine (or Uracil) and Cytosine always pairs with Guanine, maintaining a uniform distance across the DNA double helix.

Peptide Bond

The covalent bond joining the carboxyl carbon of one amino acid to the amino nitrogen of another, formed by a condensation reaction with the elimination of water.

L-Amino Acid

The specific stereoisomer of amino acids universally utilized by living systems to synthesize proteins.

Alpha-Helix ($\alpha$-Helix)

A secondary protein structure characterized by a right-handed coil ($3.6_{13}$) stabilized by hydrogen bonds between backbone atoms every $3.6$ residues, possessing a dipole moment with side chains pointing outwards.

Beta-Sheet ($\beta$-Sheet)

A secondary protein structure formed by hydrogen bonds between adjacent extended polypeptide strands, organized in parallel, anti-parallel, or mixed arrangements with side chains alternating above and below the plane.

Tertiary Structure

The overall three-dimensional folding of a single polypeptide chain into a functional conformation, stabilized by hydrophobic interactions, van der Waals forces, hydrogen bonds, ionic bonds (salt bridges), and disulfide bridges.

Quaternary Structure

The structural organization of a protein that consists of two or more interacting polypeptide subunits or monomers (e.g., a tetramer).

Fluid Mosaic Model

The model proposed by J. Singer and G. Nicolson (1972) describing biological membranes as a dynamic fluid lipid bilayer containing a mosaic of laterally moving embedded proteins.

Freeze-Fracture

A specialized preparation technique for scanning electron microscopy that splits frozen biological membranes along the hydrophobic interior of the phospholipid bilayer, revealing embedded membrane proteins.

Lateral Movement vs. Flip-Flop

The two modes of lipid mobility within membranes: rapid lateral drifting within the plane ($\sim 10^7$ times per second) versus extremely rare transverse crossing across the bilayer ($\sim$ once per month).

Cholesterol (Membrane Fluidity Buffer)

A rigid hydrophobic steroid embedded in animal membranes that prevents excessive fluidity at warm temperatures ($37\,^\circ\text{C}$) by restraining phospholipid movement, and prevents solidifying at cool temperatures by hindering close packing.

Membrane Sidedness

The asymmetrical distribution of specific proteins, lipids, and external carbohydrate modifications across the inner and outer faces of the plasma membrane, determined during synthesis in the endoplasmic reticulum and Golgi apparatus.

Selective Permeability

The property of cellular membranes that allows nonpolar, hydrophobic molecules (e.g., hydrocarbons) to dissolve and pass across rapidly, while restricting polar, hydrophilic molecules (sugars, ions).

Passive Diffusion

The spontaneous net movement of solute molecules down their concentration gradient from an area of higher concentration to lower concentration without the expenditure of cellular energy.

Osmosis

The diffusion of water molecules across a selectively permeable membrane from a region of lower solute concentration to a region of higher solute concentration.

Aquaporin

A membrane channel protein with a hydrophilic pore that facilitates the rapid bidirectional transport of water molecules across the biological membrane.

Tonicity

The capacity of a surrounding solution to cause a cell to gain or lose water, classified into isotonic, hypertonic, and hypotonic states.

Plasmolysis

The lethal phenomenon occurring in plant cells in a hypertonic environment, where water exits the cell causing the protoplast to shrink and the plasma membrane to pull away from the cell wall.

Osmoregulation

The cellular control of internal solute concentrations and water balance, exemplified by the contractile vacuole in freshwater Paramecium that pumps out excess water.

Facilitated Diffusion

A form of passive transport where polar or charged substances cross the plasma membrane down their concentration gradient via specific channel proteins or shape-shifting carrier proteins without consuming ATP.

Active Transport

The energy-requiring movement of a substance across a membrane against its concentration gradient, mediated by specific carrier proteins powered by ATP hydrolysis.

Sodium-Potassium ATPase Pump

An electrogenic transport protein in animal cells that hydrolyzes ATP to export three $\text{Na}^+$ ions and import two $\text{K}^+$ ions against their concentration gradients per cycle.

Electrogenic Pump

A primary active transport protein that generates a voltage (membrane potential) across a biological membrane, such as the $\text{Na}^+/\text{K}^+$ pump in animals or the proton pump in plants, fungi, and bacteria.

Cotransport

A mechanism in which the active transport of one solute (such as $\text{H}^+$ by a proton pump) indirectly drives the secondary active transport of another substance (such as sucrose) against its concentration gradient.

Exocytosis

The cellular secretion process where intracellular transport vesicles migrate to, fuse with, and incorporate into the plasma membrane to discharge their contents into the extracellular space.

Phagocytosis

A type of endocytosis ('cellular eating') in which a cell wraps pseudopodia around large particulate matter or microorganisms and packages them within a food vacuole.

Pinocytosis

A non-specific form of endocytosis ('cellular drinking') where droplets of extracellular fluid containing dissolved solutes are engulfed in tiny invaginating vesicles.

Receptor-Mediated Endocytosis

A specialized, highly selective form of endocytosis in which specific extracellular ligands bind to cell-surface receptors concentrated in coated pits, triggering coated vesicle internalization.

Enzyme

A biological macromolecular catalyst (predominantly protein) that increases the rate of chemical reactions (e.g., from $1\,\text{unit/min}$ to $10^6\,\text{unit/min}$) without being consumed and without altering the net free-energy change ($\Delta G$).

Activation Energy ($E_A$)

The initial investment of energy required to contort reactant molecules into an unstable transition state so that chemical bonds can break and reform.

Active Site

The specific localized pocket or groove on an enzyme that binds the substrate and contains the catalytic residues directly involved in lowering the activation energy.

Induced Fit Model

The model of enzyme-substrate binding where the entry of the substrate induces a conformational change in the enzyme, wrapping the active site snugly around the substrate for optimal catalysis.

Maximum Velocity ($V_{\max}$)

The maximum rate achievable in an enzyme-catalyzed reaction when the active sites of all enzyme molecules are saturated with substrate.

Michaelis Constant ($K_M$)

The substrate concentration ($[S]$) at which the reaction velocity reaches exactly half of its maximal velocity ($V_{\max}/2$); reflects enzyme affinity for substrate.