Chapter 2.1: Atoms, Ions & Molecules

Definition of biochemistry

The study of the molecules that compose living organisms.

Four major biological molecules

Carbohydrates, fats, proteins, and nucleic acids.

Importance of biochemistry

Helps us understand cellular structures, physiology, nutrition, and health.

Chemical element

The simplest form of matter that has unique chemical properties.

Property that determines an element's identity

The number of protons in its nucleus.

Atomic number

The number of protons in an atom's nucleus.

Representation of elements on the periodic table

Represented by one- or two-letter chemical symbols alongside their atomic numbers.

Naturally occurring vs. human body elements

91 naturally occurring elements exist; 24 play functional roles in the human body.

Six elements making up about 98.5% of body weight

Oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus.

Trace elements

Elements present in very small amounts that still perform vital biological functions.

Minerals

Inorganic elements obtained from plants and passed through the food chain to humans.

Three major subatomic particles and their charges

Protons: positive ($+$); Neutrons: neutral ($0$); Electrons: negative ($-$).

Subatomic particle locations in an atom

Protons and neutrons are in the nucleus; electrons are in electron clouds or energy levels surrounding the nucleus.

Masses of subatomic particles

Protons and neutrons have a mass of about $1\,\text{amu}$ each; electron mass is negligible.

Condition for an atom to be electrically neutral

It must have equal numbers of protons and electrons.

Atomic mass calculation

Approximately equal to the sum of protons and neutrons in the nucleus.

Valence electrons

Electrons in the outermost energy level that determine an atom's chemical bonding properties.

Bohr model vs. Quantum mechanical model

Bohr model proposes electrons move in fixed circular energy levels; Quantum mechanical model describes electrons in probabilistic orbital clouds.

Isotopes

Forms of the same element that differ in neutron number and atomic mass, but retain identical proton counts and chemical properties.

Radioisotope and radioactivity

A radioisotope is an unstable isotope that decays; radioactivity is the process in which it decays and emits radiation.

Ionizing radiation

High-energy radiation (e.g., X-rays, gamma rays, UV) capable of ejecting electrons from atoms, damaging molecules, and causing mutations.

Physical half-life vs. Biological half-life

Physical half-life is the time needed for 50% of a radioisotope to decay; biological half-life is the time needed for 50% to leave the body.

Radiation dosage measurements and limits

Measured in sieverts (Sv). Average background: $\approx 2.4\,\text{mSv/yr}$; acceptable exposure limit: $50\,\text{mSv/yr}$; fatal dose: $\ge 5\,\text{Sv}$.

Ion, Ionization, Cation, and Anion

An ion is a charged atom/molecule. Ionization is electron transfer. A cation is positively charged (lost electrons); an anion is negatively charged (gained electrons).

Electrolyte

A substance (such as a salt) that ionizes in water to form a solution capable of conducting electricity.

Free radical and Antioxidant

A free radical is an unstable particle with an unpaired electron that damages tissue; an antioxidant neutralizes free radicals.

Molecule vs. Compound

A molecule consists of two or more bonded atoms; a compound must contain two or more different elements.

Molecular formula vs. Structural formula

Molecular formula shows element types and quantities; structural formula displays spatial arrangement and chemical bonds.

Isomers

Molecules that share the same molecular formula but have different structural arrangements.

Glucose formula and molecular weight

Formula: $C_6H_{12}O_6$; Molecular Weight: $180\,\text{amu}$ calculated as $6(12) + 12(1) + 6(16) = 180\,\text{amu}$.

Functions of protons, neutrons, and electrons

Protons determine element identity; neutrons determine isotope mass; electrons determine electrical charge and bonding behavior.