The Chemistry of Life

Vocabulary flashcards covering the fundamentals of the chemistry of life, including atomic structure, electron configurations, bonding types, the properties of water, acid-base chemistry, carbon properties, functional groups, carbohydrates, lipids, nucleic acids, and protein structures.

Atom

The basic unit of matter, composed of three subatomic particles: protons, neutrons, and electrons.

Atomic Nucleus

The central core of an atom formed by protons and neutrons, around which electrons orbit in an electron cloud or shell.

Atomic Mass

The total number of protons and neutrons contained in a specific version of an element.

Isotope

A form of an element that possesses a different number of neutrons than other atoms of the same element while having the same number of protons.

Principal Quantum Number ($n$)

A value characterizing the constant radius and energy level of an electron orbit in the Bohr model, where a larger radius corresponds to higher energy (e.g., $n = 2$ has greater energy than $n = 1$).

Pauli Exclusion Principle

A quantum rule stating that two electrons with the same spin cannot reside in the same electron orbital; electrons must have opposite spins of $+\frac{1}{2}$ (spin-up) or $-\frac{1}{2}$ (spin-down).

Orbital Capacity

The maximum electron holding limit for each sublevel: the $s$ sublevel holds 2 electrons (1 orbital), the $p$ sublevel holds 6 electrons (3 orbitals), the $d$ sublevel holds 10 electrons (5 orbitals), and the $f$ sublevel holds 14 electrons (7 orbitals).

Ionic Bond

A chemical bond formed by the transfer of valence electrons from a metal to a nonmetal, generating a positively charged cation and a negatively charged anion.

Nonpolar Covalent Bond

A covalent bond formed by the equal sharing of electron pairs between two atoms of identical or near-identical electronegativity, resulting in zero difference in electronegativity.

Polar Covalent Bond

A covalent bond in which electrons are drawn closer to the more electronegative atom, creating slight partial positive and negative charges across the bond.

Cohesion

The attractive force between molecules of the same substance, such as water molecules binding to each other via hydrogen bonds to produce surface tension.

Adhesion

The attractive force between different types of molecules, such as water molecules binding to polar glass ($SiO_2$) surfaces.

Capillary Action

The upward movement of liquid against the pull of gravity, occurring when adhesive forces between water and non-water molecules overcome the cohesive forces of water.

Hydrophilic

A property describing polar or charged substances that readily interact with or dissolve in water because their attraction overcomes the cohesive forces of water.

Hydrophobic

A property describing nonpolar substances, such as oils and fats, that do not interact well with water because their lack of polarity cannot overcome water's cohesive forces.

Universal Solvent

A title given to water due to its polar nature, which allows it to surround and dissociate ionic compounds (such as $NaCl$ into $Na^+$ and $Cl^-$) to make solutes available as electrolytes.

High Heat Capacity

The property of water requiring a large amount of energy to raise its temperature, which allows large bodies of water to moderate temperatures and maintain global climate stability.

High Heat of Vaporization

The property requiring substantial heat energy to break hydrogen bonds in liquid water to convert it to gas, enabling evaporative cooling through sweat.

Autoionization of Water

The dynamic equilibrium process wherein water molecules spontaneously transfer a proton among themselves to produce hydronium ($H_3O^+$) and hydroxide ($OH^-$) ions, occurring in approximately 1 in $500{,}000{,}000$ pure water molecules.

Amphoteric

A characteristic of a substance, such as water, that allows it to behave either as an acid by donating a proton or as a base by accepting a proton.

Arrhenius Acid and Base

A classification where an acid is defined as a substance that ionizes in aqueous solution to produce hydrogen ions ($H^+$), and a base is a substance that dissociates in water to release hydroxide ions ($OH^-$).

Brønsted-Lowry Acid and Base

A classification defining an acid as a substance that donates a hydrogen ion ($H^+$) in a solvent and a base as a substance that accepts a hydrogen ion in a solvent.

pH Scale

A measure of acidity defined as the negative decimal logarithm of hydrogen ion concentration ($pH = -\log([H^+])$); each single-unit change represents a tenfold ($10\times$) difference in $H^+$ concentration.

Electrolyte

A solution containing dissolved ions that is capable of conducting electricity.

Tetravalency

The property of carbon having 4 valence electrons in its outer shell, allowing it to form up to 4 covalent bonds to complete its octet.

Catenation

The ability of carbon atoms to form stable covalent bonds with other carbon atoms to generate linear, cyclic, or branched molecular backbones.

Hydrocarbon

An organic molecule composed exclusively of hydrogen and carbon atoms, serving as the core backbone of biochemical compounds.

Functional Group

A specific group of bonded atoms that acts as a unit and confers distinct chemical and physical properties onto organic molecules.

Carbohydrate

A biological macromolecule serving as an energy store and structural material, typically following the general empirical formula $(CH_2O)_n$.

Ketone (in Sugars)

A sugar containing an internal carbonyl group ($C=O$) within its carbon chain, exemplified by fructose.

Aldose

A sugar containing a terminal carbonyl group ($C=O$) located at the end of its carbon chain, exemplified by glucose.

Glycosidic Bond

A covalent $-C-O-C-$ linkage joining two monosaccharides, formed via a dehydration synthesis reaction that releases a water molecule.

Glycogen

A branched polysaccharide of glucose monomers that serves as a storage reserve of chemical energy in animal liver and muscle tissue.

Cellulose

A glucose polymer with distinct glycosidic linkages that forms the structural fibers of plant cell walls, and is the principal component of cotton and linen.

Saturated Fat

A lipid containing no carbon-carbon double bonds, allowing fatty acid chains to pack tightly together and remain solid at room temperature.

Unsaturated Fat

A lipid containing one or more double bonds in its carbon chain that prevent tight packing, causing it to remain liquid at room temperature.

Omega Fatty Acid

An unsaturated fatty acid classified by the carbon position of its first double bond counted from the terminal methyl ($\omega$, omega) end.

Nucleotide

The monomer of nucleic acids, composed of a 5-carbon sugar (ribose or deoxyribose), a nitrogenous base at carbon $1'$ ($1\text{-prime}$), and a phosphate group at carbon $5'$ ($5\text{-prime}$).

Purines

A class of double-ringed nitrogenous bases in nucleic acids consisting of Adenine (A) and Guanine (G).

Pyrimidines

A class of single-ringed nitrogenous bases in nucleic acids consisting of Cytosine (C) and Thymine (T) in DNA.

Phosphodiester Bond

A covalent bond linking the $5'$ phosphate group of one nucleotide to the $3'$ hydroxyl group of another nucleotide to form the nucleic acid backbone.

Nucleosome

A structural packaging unit formed when supercoiled DNA wraps around positively charged histone proteins.

Amino Acid

A building block of proteins composed of a central alpha-carbon bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain (R-group).

Peptide Bond

A covalent bond formed between the carboxyl group of one amino acid and the amino group of another through a dehydration reaction.

Peptidyl Transferase

An enzyme in the ribosomal peptidyl (P) site that catalyzes peptide bond formation between adjacent amino acids during protein synthesis.

Primary Structure

The linear sequence of amino acids joined by peptide bonds synthesized by the ribosome.

Secondary Structure

The local three-dimensional folding of a polypeptide backbone into conformations such as alpha helices or beta-pleated sheets, stabilized by hydrogen bonds.

Tertiary Structure

The complete three-dimensional conformation of a single polypeptide chain formed by non-covalent interactions among amino acid R-groups.

Quaternary Structure

The multimeric structure that results from the assembly of multiple distinct polypeptide subunits into a functional protein complex, such as hemoglobin.