Chapter 2: The Chemistry of Life – Key Terms

Vocabulary-style flashcards covering key terms and concepts from the lecture notes on chemistry of life, atoms, ions, molecules, water, mixtures, energy, organic compounds, and macromolecules.

Atom

The basic unit of an element; composed of a nucleus (protons and neutrons) and surrounding electrons.

Element

A substance with unique chemical properties, identified by its atomic number.

Atomic number

The number of protons in an atom's nucleus; defines the element.

Symbol

One- or two-letter abbreviation for an element based on its name.

Isotope

Atoms of the same element with different numbers of neutrons.

Atomic weight

The weighted average mass of an element’s isotopes as they occur in nature.

Nucleus

The dense center of an atom containing protons and neutrons.

Proton

Positively charged subatomic particle in the nucleus; mass ≈ 1 amu.

Neutron

Electrically neutral subatomic particle in the nucleus; mass ≈ 1 amu.

Electron

Negatively charged subatomic particle surrounding the nucleus; mass negligible.

Amu (atomic mass unit)

Unit of mass used for atoms and subatomic particles; mass of protons/neutrons ≈ 1 amu.

Electron shells (energy levels)

Regions around the nucleus where electrons are located; first shell max 2, second max 8, third max 18.

Valence electrons

Electrons in the outermost shell that determine an atom’s bonding behavior.

Ion

A charged particle formed when an atom gains or loses electrons.

Cation

Positively charged ion

Anion

Negatively charged ion.

Ionic bond

Electrostatic attraction between oppositely charged ions.

Covalent bond

Bond formed by sharing electrons between atoms; can be polar or nonpolar.

Nonpolar covalent bond

Electrons are shared equally, with no charge separation.

Polar covalent bond

Covalent bond with unequal sharing of electrons, creating partial charges.

Hydrogen bond

Weak attraction between a slightly positive H in one molecule and a slightly electronegative atom (O/N) in another.

Van der Waals forces

Weak, brief attractions due to momentary dipoles; important in molecular interactions.

Mixture

Substances physically blended but not chemically combined.

Solvent

Substance in which solutes dissolve; water is the universal solvent.

Solute

Substance dissolved in a solvent.

Hydrophilic

Able to dissolve in water; polar or charged.

Hydrophobic

Not easily dissolved in water; nonpolar.

Solution

Solute particles are <1 nm and do not scatter light; solute stays dissolved.

Colloid

Mixture with 1–100 nm particles that scatter light; particles stay dispersed.

Suspension

Mixture with particles >100 nm that settle out over time.

Emulsion

Suspension of one liquid in another (e.g., oil in water).

Glycogen

Branched energy-storage polysaccharide in liver and muscles.

Starch

Energy-storage polysaccharide in plants.

Cellulose

Structural polysaccharide in plants; not digestible by humans; dietary fiber.

Carbohydrate

Hydrophilic organic molecule with formula (CH2O)n; main energy source.

Monosaccharide

Simple sugar (e.g., glucose, fructose, galactose).

Disaccharide

Two monosaccharides linked together (e.g., sucrose, lactose, maltose).

Polysaccharide

Long chains of monosaccharides; include glycogen, starch, cellulose.

Glycolipid

Lipid with carbohydrate group; component of cell membranes.

Glycoprotein

Protein with carbohydrate moiety; involved in mucus and cell recognition.

Proteoglycan

Conjugated molecule with dominant carbohydrate moiety; gelatinous fillers and cushions.

Moiety

Functional part or component of a conjugated molecule (e.g., protein moiety, carbohydrate moiety).

Lipid

Hydrophobic biomolecule with high H:O ratio; includes fats, oils, and cholesterol.

Fatty acid

Chain with carboxyl group at one end and methyl at the other; can be saturated or unsaturated.

Saturated fatty acid

Fatty acid with maximum hydrogens (no double bonds).

Unsaturated fatty acid

Fatty acid with double bonds between carbons.

Polyunsaturated fatty acid

Fatty acids with many double bonds.

Essential fatty acids

Fatty acids that cannot be synthesized by the body and must be obtained from diet.

Triglyceride

Three fatty acids bonded to glycerol; primary form of stored fat; neutral fats.

Phospholipid

Lipid with two fatty acids and a phosphate-containing head; amphipathic; key membrane component.

Eicosanoid

20-carbon signaling lipids derived from arachidonic acid; include prostaglandins.

Prostaglandin

A prostanoid with a 5-carbon ring involved in inflammation, clotting, labor, etc.

Cholesterol

Sterol lipid; parent steroid; essential for membranes and steroid synthesis; mainly synthesized in body.

Steroid

Lipid with four fused rings; includes hormones and bile acids.

Protein

Polypeptide or complex of polypeptides; diverse functions in structure, enzymes, transport, etc.

Amino acid

Amino group, carboxyl group, central carbon, and an R group; 20 standard amino acids.

Peptide

Molecule composed of two or more amino acids linked by peptide bonds.

Polypeptide

Chain of many amino acids; forms a protein.

Primary structure

A protein’s amino acid sequence.

Secondary structure

Alpha helix or beta-pleated sheet held by hydrogen bonds.

Tertiary structure

3D folding of a protein due to hydrophobic effects and other interactions.

Disulfide bridge

Covalent bond between sulfur-containing amino acids (e.g., cysteine) stabilizing structure.

Quaternary structure

Association of two or more polypeptide chains into a functional protein.

Conjugated protein

Protein bound to a non-amino acid prosthetic group.

Prosthetic group

Non-amino acid group tightly bound to a protein (e.g., heme in hemoglobin).

Enzyme

Biological catalyst that speeds up biochemical reactions without being consumed.

Cofactor

Nonprotein partner required for enzyme activity (often metal ions).

Coenzyme

Organic cofactor, often derived from vitamins (e.g., NAD+ from niacin).

ATP

Adenosine triphosphate; main cellular energy currency with high-energy phosphate bonds.

ADP

Adenosine diphosphate; product of ATP hydrolysis.

Phosphorylation

Addition of a phosphate group to a molecule, often regulating activity; mediated by kinases.

GTP

Guanosine triphosphate; a nucleotide involved in signaling and energy transfer.

cAMP

Cyclic adenosine monophosphate; a second messenger in cellular signaling.

Nucleic acid

Biomolecule polymer of nucleotides (DNA and RNA) essential for genetics and protein synthesis.

DNA

Deoxyribonucleic acid; genetic material; typically double-stranded and very long.

RNA

Ribonucleic acid; usually single-stranded with three forms involved in protein synthesis.

Nucleotide

Nucleoside with one or more phosphate groups; building block of nucleic acids.

Adenosine triphosphate (ATP) hydrolysis

ATP breakdown to ADP and Pi releases about 7.3 kcal per mole of energy.

Glycolysis

First stage of glucose oxidation; splits glucose into pyruvic acid.

Aerobic respiration

Glucose breakdown with oxygen to CO2 and H2O; yields more ATP.

Anaerobic fermentation

Glucose to lactic acid in the absence of oxygen.

Osmosis

Movement of water across a semipermeable membrane toward higher solute concentration.

Buffer

A solution that resists changes in pH.

pH

A scale expressing acidity; negative log of H+ concentration; logarithmic.

Acid

Proton donor; substance that releases H+ in water.

Base

Proton acceptor; substance that accepts H+ in water.

Salt/electrolyte

Ionic compounds that dissociate in water to conduct electricity; essential for function.

Solubility (solubility in water)

Ability of a substance to dissolve in water; polarity and charge matter.

Hydration sphere

Water molecules surround and stabilize dissolved ions.

Equivalents (Eq)

Amount of a substance that can neutralize one mole of H+ or OH−; used to express electrolyte quantities.

Milliequivalent per liter (mEq/L)

Common unit for electrolyte concentrations in body fluids.

Molarity (M)

Moles of solute per liter of solution; a measure of concentration.

Mole

Amount containing Avogadro’s number of particles (6.023 × 10^23).

Avogadro’s number

6.023 × 10^23, the number of units in one mole of any substance.

Hydration sphere (revisited)

Water molecules surrounding ions after dissolution to stabilize them.

Solubility vs colloid vs suspension

Different categories of mixtures based on particle size and light scattering.

Amino acid side chain (R group)

Part of an amino acid that determines its properties and identity.

Proteins as catalysts

Many enzymes function as biological catalysts to accelerate reactions.

Nucleotides (general)

Organic compounds with a nitrogenous base, a sugar, and one or more phosphate groups.

Glycogen vs starch vs cellulose (polysaccharides)

Glycogen: animal energy storage; starch: plant energy storage; cellulose: plant structural polysaccharide.