Matter, Atoms, and Biological Macromolecules

This set of vocabulary flashcards covers biological chemistry concepts including atomic structure, chemical bonding, water properties, pH, and the four major classes of biomolecules.

Matter

Anything that has mass and occupies space; it exists in three forms: solid, liquid, and gas.

Atom

The smallest particle exhibiting chemical properties of an element.

Chemical Element

A substance that cannot be broken down to other substances by ordinary chemical means.

Major Elements

The six elements that collectively compose more than $98\%$ of body weight: Oxygen ($65.0\%$), Carbon ($18.0\%$), Hydrogen ($10.0\%$), Nitrogen ($3.0\%$), Calcium ($1.5\%$), and Phosphorus ($1.0\%$).

Neutron

A subatomic particle with a mass of one atomic mass unit ($amu$) and no charge.

Proton

A subatomic particle with a mass of one $amu$ and a positive charge of one ($+1$).

Electron

A subatomic particle with a negative charge of one ($-1$) located in orbitals at varying distances from the nucleus.

Atomic Number

The number of protons in an atom of the element, located above the symbol name on the periodic table.

Average Atomic Mass

The mass of both protons and neutrons, shown below the element's symbol on the periodic table.

Isotopes

Different atoms of the same element that have the same number of protons and electrons but a different number of neutrons.

Radioisotopes

Unstable isotopes that contain excess neutrons.

Octet Rule

The tendency of elements to lose, gain, or share electrons to obtain complete outer shells with eight electrons.

Ion

A charged atom created when atoms gain or lose electrons.

Anion

An ion with a negative charge.

Cation

An ion with a positive charge.

Ionic Bond

An electrical attraction between ions with opposite charges, such as the bond in sodium chloride ($NaCl$).

Molecule

A chemical structure consisting of atoms held together by covalent bonds.

Compound

A chemical substance composed of atoms of two or more different elements.

Molecular Formula

A representation that indicates the number and type of atoms in a molecule, such as $H_2CO_3$ for carbonic acid.

Structural Formula

A representation that indicates the number, type, and arrangement of atoms within a molecule.

Isomers

Molecules with the same number and type of elements but arranged differently in space, potentially resulting in different chemical properties.

Amphipathic Molecules

Large molecules, such as phospholipids, that contain both polar and nonpolar regions.

Hydrogen Bond

A weak attraction between a partially positive hydrogen atom and a partially negative atom in polar molecules.

Cohesion

The attraction between water molecules due to hydrogen bonding.

Surface Tension

The inward pulling of cohesive forces at the surface of water.

Adhesion

The attraction between water molecules and a substance other than water.

Specific Heat

The amount of energy required to increase the temperature of $1\,g$ of a substance by $1^{\circ}C$.

Heat of Vaporization

The heat required for the release of molecules from a liquid phase into a gaseous phase for $1\,g$ of a substance.

Hydrophilic

"Water-loving" substances, such as polar molecules and ions, that dissolve in water.

Hydrophobic

"Water-fearing" nonpolar molecules that do not dissolve in water.

Acid

A proton donor that dissociates in water to produce $H^+$ and an anion, increasing the concentration of free $H^+$.

Base

A proton acceptor that accepts $H^+$ when added to a solution, decreasing the concentration of free $H^+$.

pH

A measure ranging from $0$ to $14$ that represents the relative amount of $H^+$ in a solution; it is the inverse log of the $H^+$ concentration.

Buffer

Substances that help prevent pH changes by accepting $H^+$ from excess acid or donating $H^+$ to neutralize base, such as the carbonic acid and bicarbonate system in blood.

Colloid

A mixture containing protein of size from $1$ to $100\,nm$.

Emulsion

A mixture of water and a nonpolar liquid substance.

Dehydration Synthesis

A reaction during biomolecule synthesis where one subunit loses $-H$ and another loses $-OH$, forming a new covalent bond and producing water.

Hydrolysis

A reaction during biomolecule breakdown where an $-H$ is added to one subunit and an $-OH$ is added to another.

Triglycerides

The most common form of lipid in living things, used for long-term energy storage, structural support, cushioning, and insulation.

Steroids

Lipids composed of four hydrocarbons rings, including cholesterol, steroid hormones, and bile salts.

Eicosanoids

Modified 20-carbon fatty acids synthesized from arachidonic acid that act as local signaling molecules.

Glycogen

The most common polysaccharide in animals, used for storing excess glucose in the liver and skeletal muscle.

Nucleotide

A monomer of nucleic acids composed of a five-carbon pentose sugar, a phosphate group, and a nitrogenous base.

ATP (Adenosine triphosphate)

A central molecule for energy transfer composed of adenine, ribose, and three phosphate groups; energy is released when the covalent bond between the last two phosphate groups is broken.

Peptide Bond

A covalent bond formed between the amine group of one amino acid and the carboxylic group of another.

Primary Structure

The linear sequence of amino acids joined by peptide bonds.

Secondary Structure

Repeating patterns in proteins, such as the alpha helix (spiral coil) or beta sheet (planar pleat).

Tertiary Structure

The final three-dimensional shape of a polypeptide chain, categorized as either globular or fibrous.

Quaternary Structure

The structure present in proteins with two or more polypeptide chains, such as hemoglobin.

Denaturation

A conformational change to a protein that disturbs its activity, often caused by increased temperature or changes in pH.