Biology: Atomic Structure, Chemical Bonds, and Molecules

Proton

Positively charged particle found in the nucleus of an atom.

Neutron

Neutral (no charge) particle found in the nucleus.

Electron

Negatively charged particle found in electron shells orbiting the nucleus.

Ground State

Lowest energy state of an atom; electrons are in the lowest possible energy levels.

Excited State

Higher energy state; electrons absorb energy and jump to higher levels.

Isotopes

Atoms of the same element with different numbers of neutrons.

Half-life

The time required for half the atoms in a radioactive sample to decay.

Radioisotopes

Radioactive isotopes that spontaneously emit radiation.

Tracer

Used to track biological pathways. How used: Radioactive isotopes (like radioactive carbon) are incorporated into molecules and followed using detectors.

Ionic Bond

Transfer of electrons from one atom to another.

Cation

Positive ion (lost electrons).

Anion

Negative ion (gained electrons).

Covalent Bond

Sharing of electrons between atoms.

Molecule

Two or more atoms bonded together.

Nonpolar Bond

Equal sharing of electrons.

Polar Covalent Bond

Unequal sharing of electrons.

Diatomic Molecule

Molecules of two atoms of the same element: H₂, N₂, O₂, F₂, Cl₂, Br₂, I₂.

Non-Polar Molecule

Symmetrical; equal charge distribution. Example: CO₂, CH₄.

Polar Molecule

Asymmetrical; unequal charge distribution. Example: H₂O.

Hydrophilic

Attracted to water; dissolves in water. Examples: salt, sugar, alcohol.

Hydrophobic

Repels water; nonpolar. Examples: oils, fats, wax.

Hydrogen Bonding

Weak attraction between a slightly positive H and slightly negative O or N.

Specific Heat

Water resists temperature change.

Universal Solvent

Water dissolves many substances due to polarity.

Adhesion

Water sticks to other surfaces.

Cohesion

Water molecules stick to each other.

Capillary Action

Cohesion + adhesion allow water to rise in narrow tubes.

Surface Tension

Cohesion at the surface of water forms a 'film.'

Spring Overturn

Seasonal mixing of lake water due to density changes.

Acids

pH < 7; donate hydrogen ions (H⁺).

Bases

pH > 7; accept H⁺ or release OH⁻.

pH Scale

0-14 scale measuring acidity/basicity.

Structural Isomer

Molecules that have the same molecular formula but different arrangements of atoms, resulting in different shapes and properties.

Cis-Trans Isomer

Isomers that differ in the position of atoms around a double bond: cis = groups on the same side, trans = groups on opposite sides.

Enantiomers

Molecules that are mirror images of each other but cannot be superimposed, like left and right hands.

Carbohydrates

Organic molecules made of sugars that provide quick energy and structural support.

Monosaccharides

Single sugar molecules; the basic building blocks of carbohydrates.

Glucose

A simple sugar and the main energy source for cells.

Disaccharides

Two monosaccharides linked together (ex: sucrose, lactose).

Dehydration Synthesis

A reaction that joins two molecules by removing water, forming a larger molecule.

Condensation

Another name for dehydration synthesis—the formation of a bond while releasing water.

Hydrolysis

A reaction that breaks molecules apart by adding water.

Polysaccharides

Large carbohydrate molecules made of many monosaccharides (ex: starch, cellulose, glycogen).

Lipids

Nonpolar molecules such as fats, oils, and steroids used for long-term energy storage, insulation, and cell membranes.

Glycerol

A 3-carbon backbone molecule that joins with fatty acids to form fats.

Fatty Acid

A long hydrocarbon chain that makes up part of a lipid.

Saturated Fat

A fatty acid with no double bonds, straight, and usually solid at room temperature.

Unsaturated Fat

A fatty acid with one or more double bonds, bent, and usually liquid at room temperature.

Steroid

A lipid with four fused carbon rings, including hormones like estrogen and testosterone.

Phospholipid

A lipid that makes up cell membranes; has a hydrophilic (water-loving) phosphate head and hydrophobic (water-fearing) fatty acid tails.

Protein

A large, folded molecule made of amino acids that performs structural, enzymatic, and regulatory functions.

Amino Acid

The building block of proteins; contains an amino group, a carboxyl group, and an R-group.

Polypeptide

A chain of amino acids linked by peptide bonds.

Amine (Amino) Group (-NH₂)

A basic functional group that accepts H⁺.

Conformation

The 3D shape of a protein that determines its function.

Primary Structure

The sequence of amino acids held together by peptide bonds.

Secondary Structure

Local folding into alpha helices or beta sheets stabilized by hydrogen bonds.

Tertiary Structure

The overall 3D shape of one polypeptide, stabilized by hydrogen bonds, ionic bonds, disulfide bridges, and hydrophobic interactions.

Quaternary Structure

The structure formed when multiple polypeptide chains join together.

Keratin

A tough, fibrous protein found in hair, skin, and nails.

Denaturation

The unfolding of a protein due to heat, pH changes, or chemicals, causing loss of function.

X-ray Crystallography

A technique used to determine a molecule's 3D structure.

Bioinformatics

Using computers and software to analyze biological data (DNA, proteins).

Ribonucleic Acid (RNA)

A single-stranded nucleic acid involved in making proteins.

Deoxyribonucleic Acid (DNA)

A double-stranded molecule that stores genetic information.

FG: Amino Group (-NH₂)

Basic; accepts H⁺; found in amino acids.

FG: Hydroxyl Group (-OH)

Polar; makes molecules soluble; found in alcohols.

FG: Phosphate Group (-PO₄³⁻)

Highly charged; involved in energy transfer (ATP).

FG: Methyl Group (-CH₃)

Nonpolar; reduces solubility; used in gene regulation.

FG: Carboxyl Group (-COOH)

Acidic; donates H⁺; found in amino acids and fatty acids.

FG: Carbonyl Group (C=O)

Polar; found in sugars; can be in aldehydes or ketones.