Biochemistry 101: Atoms, Ions, Bonding, Water, and Basic Biochemical Concepts

Biochemistry

Chemistry as it applies to biology and living systems; connects chemistry to physics and biology.

Chemical Element

The simplest form of matter with unique chemical properties, identified by its atomic number (number of protons).

Atom

The building block that defines elements.

Proton

A subatomic particle with a positive charge ($+1$) located in the nucleus.

Neutron

A subatomic particle with a neutral charge ($0$) located in the nucleus.

Electron

A subatomic particle with a negative charge ($-1$) that orbits around the nucleus and determines chemical reactivity.

Isotopes

Atoms of the same element with varying numbers of neutrons; chemically similar but decay at different rates via ionizing radiation.

Valence Electrons

The outermost electrons that participate in chemical reactions and determine chemical behavior.

Organic Compound

A compound that contains carbon (by course definition).

Inorganic Compound

A compound that generally does not contain carbon (e.g., many minerals and salts).

Ion

A charged particle formed by gaining or losing electrons.

Cation

A positively charged ion (e.g., $\text{Na}^+$).

Anion

A negatively charged ion (e.g., $\text{Cl}^-$).

Ionic Bond

A bond resulting from electron transfer between a cation and an anion; relatively weak in water and dissociates into electrolytes.

Covalent Bond

A bond involving the sharing of electrons between atoms; generally much stronger than ionic bonds.

Polar Covalent Bond

A covalent bond where electrons are shared unequally due to differences in electronegativity, creating partial charges (e.g., in water).

Nonpolar Covalent Bond

A covalent bond where electrons are shared equally between atoms.

Hydrogen Bond

A weaker intermolecular bond formed between an electropositive hydrogen of one molecule and an electronegative atom (like oxygen) of another molecule; crucial for water's properties.

Molecule

Two or more atoms bonded together (e.g., $\text{H}_2\text{O}$).

Compound

A molecule composed of two or more *different* elements (e.g., $\text{H}_2\text{O}$ is a compound; $\text{O}_2$ is not).

Osmosis

The movement of water across a semipermeable membrane driven by solute gradients.

Electrolyte

A substance that produces ions when dissolved in water, allowing the solution to conduct electricity.

Free Radical

An unstable, highly reactive particle with an unusual number of electrons that can damage molecules and cells (e.g., superoxide anion $\text{O}_2^-$).

Antioxidants

Substances that neutralize free radicals (e.g., selenium, vitamins A, C, carotenoids).

Ionizing Radiation

Energy release from changes in the nucleus, including UV, X-rays, alpha, beta, and gamma rays.

Sievert (Sv)

The unit used to measure radiation dose in terms of biological effect ($1 \text{ Sv} = 1000 \text{ mSv}$).

Physical Half-life ($t_{1/2}^{\text{phys}}$)

The time required for 50% of a radioactive isotope to decay to a stable state.

Biological Half-life ($t_{1/2}^{\text{bio}}$)

The time required for the body to metabolize or eliminate half of a substance.