Water and Biochemistry Review

A comprehensive set of vocabulary flashcards covering water chemistry, intermolecular forces, organic chemistry basics, biomolecules, scales, and related concepts from the lecture notes.

Dipole

A molecule with a separation of charge resulting in partial positive and partial negative ends; water is a dipole.

Bent geometry

Molecular geometry (as in water) with bond angles less than the ideal tetrahedral angle (~104.5° for H2O).

Partial charges

Partial positive charge on hydrogen and partial negative charge on oxygen in water due to electronegativity differences.

Hydrogen bond

A weak interaction between a hydrogen atom covalently bonded to an electronegative atom and an electronegative atom in another molecule.

O–H covalent bond energy

Energy to break a covalent O–H bond is about 470 kJ/mol.

Hydrogen bond energy

Energy of a hydrogen bond is about 23 kJ/mol, roughly 20 times weaker than a covalent O–H bond.

Hydrogen bond donor

Functional group whose hydrogen atom initiates a hydrogen bond.

Hydrogen bond acceptor

Functional group whose lone pair interacts with the donor in a hydrogen bond.

Hydration layer

Water forms a hydration layer around ions in solution.

Solvation

Process by which solvent molecules surround and stabilize solute particles (e.g., salt dissolution in water).

Solubility in water

Degree to which a substance dissolves in water; polar and charged species are typically more soluble than nonpolar ones.

Solvated ion

An ion surrounded by a shell of solvent (water) molecules.

Hydration energy

Energy released when ions become hydrated by water; part of the overall solvation energy.

Polar molecule

Molecule with an uneven distribution of charge resulting in a dipole moment.

Nonpolar molecule

Molecule with no significant permanent dipole; lacks substantial charge separation.

Hydrophobic effect

Nonpolar groups cluster together in water, excluding ordered water and increasing overall entropy (ΔS).

Entropy

Thermodynamic quantity measuring disorder; often increases (ΔS) during the hydrophobic effect.

Ionic interactions

Electrostatic attractions between charged species; typically ~20–80 kJ/mol.

van der Waals interactions

Weak distance-dependent interactions from temporary and induced dipoles; typically ~1–10 kJ/mol.

Nucleophile

Electron-rich species that donates electrons to an electrophile; often negative or partially negative.

Electrophile

Electron-poor species that accepts electrons from a nucleophile; often positive or partially positive.

Curved arrow notation

Graphical arrows showing movement of electron pairs in reaction mechanisms.

Resonance structure

Alternative Lewis structures for the same molecule with delocalized electrons; shown with a double-headed arrow.

Electron-pushing arrow

A curved arrow used to indicate the movement of electrons during a reaction step.

Equilibrium arrow

Two-headed arrow indicating a reversible chemical reaction.

Formal charge

Formal charge = (valence electrons) – (bonds) – (unshared electrons).

Unshared valence electrons

Lone pairs of electrons not involved in bonding.

Octet rule

Atoms tend to attain eight electrons in their valence shell; carbon commonly forms four bonds.

Valence electrons

Electrons in the outermost shell involved in bonding; e.g., carbon has 4 valence electrons.

Hybridization

Mixing of s and p atomic orbitals to form hybrid orbitals (sp3, sp2, sp) that influence geometry.

sp3

Hybridization with four attached substituents; tetrahedral geometry.

sp2

Hybridization with three attached substituents; trigonal planar geometry and typically a double bond presence.

sp

Hybridization with two attached substituents; linear geometry.

Methyl group

–CH3; a simple alkyl substituent.

Hydroxyl group

–OH functional group (alcohols/phenols).

Amine group

–NH2 (or substituted amines); nitrogen-containing group.

Carbonyl group

C=O functional group found in aldehydes and ketones; highly polar and reactive.

Amide group

–C(=O)–NR2; carbonyl adjacent to nitrogen; common in proteins.

Ether group

R–O–R; oxygen atom linking two carbon fragments.

Phosphoryl group

P=O functional unit present in phosphates/phosphorylated compounds.

Alkene

Hydrocarbon with at least one carbon–carbon double bond (C=C).

Saturated hydrocarbon

Hydrocarbon with only single bonds (alkanes).

Unsaturated hydrocarbon

Hydrocarbon with one or more double bonds (alkenes or alkynes).

Conjugated molecule

Molecule with alternating single and multiple bonds, allowing delocalization of π electrons.

Cis isomer

Geometric isomer where two substituents are on the same side of a double bond.

Protein Data Bank (PDB)

rcsb.org; central repository of biomolecular 3D structures freely available.

Macromolecule

Large biological polymer such as proteins, nucleic acids, carbohydrates, or lipids.

Protein

A polymer of amino acids folded into a functional three-dimensional structure.

Nucleic acid

DNA or RNA; stores and transmits genetic information.

Carbohydrate

Sugars and their polymers; energy source and structural components.

Lipid

Hydrophobic biomolecules forming membranes and energy reserves.