Bio98 Lecture 1: Bonds, Water, and Amino Acids

A set of vocabulary flashcards summarizing the fundamental concepts of bonding, water interactions, and amino-acid chemistry presented in the Bio98 lecture.

Covalent Bond

Strong chemical bond formed by sharing electron pairs between atoms.

Non-polar Covalent Bond

Covalent bond with equal electron sharing, resulting in no charge separation.

Polar Covalent Bond

Covalent bond with unequal electron sharing that creates partial charges (δ+ / δ−).

Peptide Bond

Polar covalent linkage created by dehydration between an amino acid’s carboxyl group and another’s amine.

Ionic Bond

Electrostatic attraction formed after complete electron transfer between oppositely charged ions (metal + non-metal).

Hydrogen Bond

Weak interaction (≈23 kJ mol⁻¹) between a hydrogen attached to an electronegative atom and another electronegative atom with lone pairs.

Van der Waals Interaction

Weak, distance-dependent attraction or repulsion between uncharged atoms due to transient dipoles.

Hydrophobic Interaction

Association of non-polar molecules in water to minimize disruption of hydrogen-bonded water network, increasing system entropy.

Electrostatic Interaction

Attractive or repulsive force between charged groups; includes ionic bonds and charge-charge interactions.

Amphipathic Molecule

Compound containing both hydrophilic (polar) and hydrophobic (non-polar) regions, e.g., phospholipids.

Micelle

Spherical aggregate of amphipathic molecules with hydrophobic cores and hydrophilic surfaces in water.

Phospholipid Bilayer

Double-layered arrangement of amphipathic phospholipids forming cell membranes; hydrophobic tails inside, hydrophilic heads outside.

Colligative Properties

Physical properties of a solvent (freezing point, boiling point, vapor pressure, osmotic pressure) that change with solute particle number, not identity.

Osmosis

Net movement of water across a semipermeable membrane from low to high solute concentration, driven by particle number.

Lock-and-Key Model

Concept that enzyme active sites have shapes complementary to specific substrates, enabling selective binding.

Protein

Large, folded polymer of amino acids that performs structural or catalytic cellular functions.

Proteome

Entire set of proteins expressed by a cell, tissue, or organism at a given time.

Primary Structure

Linear sequence of amino acids in a polypeptide chain.

Secondary Structure

Localized folding patterns (α-helix, β-sheet) stabilized by backbone hydrogen bonds.

Tertiary Structure

Overall three-dimensional shape of a single polypeptide resulting from side-chain interactions.

Quaternary Structure

Arrangement of multiple polypeptide chains (subunits) into a functional protein complex.

Amino Acid

Building block of proteins containing an α-carbon, amino group, carboxyl group, hydrogen, and variable R-group.

Chiral Center

Carbon atom bonded to four different groups; in amino acids (except glycine) gives L or D stereoisomers.

Zwitterion

Dipolar ion form of an amino acid with a deprotonated carboxylate and protonated ammonium at physiological pH.

Hydropathy Index

Numerical scale reflecting an amino acid’s hydrophobicity or hydrophilicity.

Glycine

Smallest amino acid; lacks side chain, achiral, and minimally hydrophobic.

Methionine

Sulfur-containing, non-polar amino acid; often initiates translation and can form thioether bonds.

Cysteine

Polar amino acid with sulfhydryl (–SH) group capable of forming disulfide bonds.

Disulfide Bridge

Covalent –S–S– linkage between two cysteine residues stabilizing protein tertiary/quaternary structure.

Proline

Cyclic imino acid causing kinks in polypeptide chains; acts as a structural ‘hinge.’

Aromatic Amino Acid

Amino acid with aromatic ring (Phe, Tyr, Trp) that absorbs UV light and contributes to hydrophobic core.

Tyrosine

Aromatic amino acid with reactive hydroxyl; frequent phosphorylation site in cell signaling.

Phenylalanine

Hydrophobic aromatic amino acid with benzyl side chain; important for protein core packing.

Tryptophan

Largest aromatic amino acid; indole ring absorbs strongly at 280 nm; contributes to protein fluorescence.

Lysine

Basic amino acid with ε-amino group (pKₐ ≈ 10.5); carries positive charge at physiological pH.

Arginine

Basic amino acid with guanidinium group (pKₐ ≈ 12.5); strongly positively charged, often binds DNA/RNA.

Histidine

Amino acid with imidazole ring (pKₐ ≈ 6); can be protonated or neutral, acting as a natural buffer and metal ligand.

Aspartate

Acidic amino acid with β-carboxylate side chain; negatively charged at physiological pH.

Glutamate

Acidic amino acid with γ-carboxylate side chain; major excitatory neurotransmitter precursor.

Serine

Polar amino acid with hydroxyl side chain; common site for phosphorylation in signaling pathways.

Threonine

Polar, β-branched amino acid with hydroxyl group; also subject to phosphorylation.

Asparagine

Polar, uncharged amino acid with carboxamide side chain; involved in N-linked glycosylation.

Glutamine

Polar amino acid with highest blood concentration; carboxamide side chain transports nitrogen.

Hydrogen Bond Donor

Atom (e.g., N–H, O–H) that supplies hydrogen in a hydrogen bond.

Hydrogen Bond Acceptor

Electronegative atom with lone pair (e.g., O, N) that receives hydrogen in a hydrogen bond.

Van der Waals Radius

Effective size of an atom defining optimal contact distance in space-filling models.

GC Content

Percentage of guanine and cytosine bases in DNA; higher content increases duplex stability via three hydrogen bonds.