Unit 1 AP BIO

Matter

anything that has mass and takes up space.

Element

a pure substance made of only one type of atom that cannot be broken down chemically.

Atom

the smallest unit of an element that retains its chemical properties.

Proton (p⁺)

positively charged subatomic particle in the nucleus.

Neutron (n⁰)

neutral subatomic particle in the nucleus.

Electron (e⁻)

negatively charged subatomic particle orbiting the nucleus.

Atomic number

number of protons in an atom.

Mass number

total number of protons and neutrons in the nucleus.

Isotope

atoms of the same element with the same number of protons but a different number of neutrons.

Radioactive isotope

unstable isotope that emits radiation as it decays into a more stable form.

Electron shell / energy level

a fixed region around the nucleus where electrons are most likely found.

Valence electrons

electrons in the outermost shell; determine chemical reactivity.

Octet rule

atoms are most stable when they have eight electrons in their outermost (valence) shell.

Molecule

two or more atoms bonded together.

Compound

molecule made of two or more different elements chemically bonded.

Covalent bond

a chemical bond formed when two atoms share one or more pairs of electrons.

Nonpolar covalent bond

electrons are shared equally between atoms (no charge separation).

Polar covalent bond

electrons are shared unequally, creating partial charges (δ⁺ and δ⁻).

Ionic bond

chemical bond formed by the attraction between oppositely charged ions (cation = positive, anion = negative).

Hydrogen bond

weak bond formed between a slightly positive hydrogen atom and a slightly negative atom (often O or N).

Cohesion

tendency of water molecules to stick to each other via hydrogen bonding.

Adhesion

tendency of water to stick to other polar or charged surfaces.

High specific heat

water resists temperature changes because hydrogen bonds absorb heat.

High heat of vaporization

requires large amounts of heat to convert water from liquid to gas.

Ice density

ice is less dense than liquid water because hydrogen bonds create a lattice structure, allowing aquatic life to survive under frozen surfaces.

Solvent

a substance that dissolves solutes (water dissolves polar and ionic substances).

Hydrophilic

molecules that interact with water (polar molecules).

Hydrophobic

molecules that repel water (nonpolar molecules).

pH

measure of hydrogen ion (H⁺) concentration in a solution; scale ranges 0-14.

Acid

substance that increases H⁺ concentration; pH < 7.

Base (alkali)

substance that reduces H⁺ concentration or increases hydroxide ion (OH⁻) concentration; pH > 7.

Buffer

substance that resists changes in pH by accepting or donating H⁺ ions. Example: bicarbonate buffer in blood.

Organic chemistry

the study of carbon-containing molecules.

Inorganic chemistry

the study of molecules that do not contain carbon-hydrogen (C-H) bonds.

Biomolecule (macromolecule)

large organic molecule essential for life: carbohydrate, lipid, protein, nucleic acid.

Tetravalent

carbon forms 4 covalent bonds.

Single bond

1 pair of shared electrons (C-C).

Double bond

2 pairs of shared electrons (C=C), restricts rotation.

Triple bond

3 pairs of shared electrons (C≡C), strongest & shortest bond.

Carbon skeleton

Chain of carbon atoms forming the backbone of organic molecules.

Functional group

Specific atom group that gives molecules distinctive chemical properties.

Hydroxyl (-OH)

Polar, found in alcohols.

Carbonyl (C=O)

Polar, found in ketones and aldehydes.

Carboxyl (-COOH)

Acidic, found in fatty acids & amino acids.

Amino (-NH₂)

Basic, found in amino acids.

Sulfhydryl (-SH)

Forms disulfide bonds, stabilizes protein structure.

Phosphate (-PO₄)

Acidic, energy transfer (ATP).

Methyl (-CH₃)

Nonpolar, affects gene expression.

R group

Side chain that varies among molecules or amino acids.

Isomer

Molecules with same molecular formula but different structure.

Structural isomer

Different covalent arrangement.

Geometric isomer

Different spatial arrangement around double bonds.

Enantiomer

Mirror-image molecules.

Monomer

Single subunit.

Polymer

Chain of monomers.

Dehydration synthesis (condensation reaction)

Removes water to form a covalent bond.

Hydrolysis reaction

Adds water to break a covalent bond in a polymer.

Carbohydrate

Organic molecule of C, H, O (ratio ~1:2:1); energy storage & structural role.

Monosaccharide

Single sugar molecule; monomer.

Disaccharide

Two monosaccharides joined by glycosidic bond (dehydration). Examples: maltose, sucrose, lactose.

Polysaccharide

Many monosaccharides linked; examples: starch, glycogen, cellulose, chitin, peptidoglycan.

Lipid

Hydrophobic molecule, mostly C & H. Types: fats, oils, phospholipids, steroids, waxes.

Triglyceride

Glycerol + 3 fatty acids.

Saturated fatty acids

No double bonds; solid at room temp.

Unsaturated fatty acids

≥1 double bond; liquid at room temp.

Trans fat

Artificially hydrogenated unsaturated fat.

Phospholipid

Glycerol + 2 fatty acids + phosphate group.

Hydrophilic head

Polar, attracted to water.

Hydrophobic tail

Nonpolar, repelled by water.

Steroid

4 fused carbon rings. Examples: cholesterol, testosterone, estrogen.

Protein

Polymer of amino acids; functions: enzyme, structure, transport, defense, hormones, motion.

Amino acid

Monomer of proteins.

Peptide bond

Covalent bond linking amino acids.

Polypeptide

Chain of amino acids.

Primary structure

Amino acid sequence.

Secondary structure

α-helix & β-pleated sheet (hydrogen bonds).

Tertiary structure

3D folding (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).

Quaternary structure

Multiple polypeptide subunits.

Denaturation

Loss of protein shape & function.

Chaperone proteins

Assist folding.

Prion

Misfolded infectious protein.

Nucleic acid

Polymer of nucleotides; stores & transmits genetic information.

Nucleotide

Monomer: sugar + phosphate + nitrogenous base.

Purines

Adenine (A), guanine (G); double-ring.

Pyrimidines

Cytosine (C), thymine (T, DNA), uracil (U, RNA); single-ring.

DNA

Double-stranded; complementary base pairing (A=T, C≡G).

RNA

Single-stranded; A=U, C≡G.

ATP (adenosine triphosphate)

Adenine + ribose + 3 phosphate groups; energy currency.

Energy released by hydrolysis

→ ADP + Pi.