Atoms, Elements, and Chemical Bonds: Foundations of Biological Chemistry

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Atoms and Bonds

Introduction to Atoms and Ions

Atoms are the fundamental units of matter, composed of subatomic particles. When atoms lose or gain electrons, they become ions, which are charged particles essential for many biological processes.

Atom: Smallest unit of matter retaining chemical properties.
Ion: Atom that has lost or gained electrons, resulting in a positive (cation) or negative (anion) charge.
Example: Sodium atom loses an electron to become a positively charged sodium ion (Na+).

Chemical Elements and Compounds

Nature of Matter and Elements

Matter is anything that has mass and occupies space. Elements are pure substances consisting of only one type of atom, each with unique properties. Chemical symbols are often derived from German or Latin origins.

Matter: Anything with mass and volume.
Element: Pure substance with unique atomic structure.
Periodic Table: Organizes elements by atomic number and properties.

Essential and Trace Elements in Biology

Living organisms require certain elements in large amounts (essential elements) and others in minute quantities (trace elements).

Symbol	Element	Atomic Number	Percentage of Human Body Weight
O	Oxygen	8	65.0
C	Carbon	6	18.5
H	Hydrogen	1	9.5
N	Nitrogen	7	3.3
Ca	Calcium	20	1.5
P	Phosphorus	15	1.0
K	Potassium	19	0.4
S	Sulfur	16	0.3
Na	Sodium	11	0.2
Cl	Chlorine	17	0.2
Mg	Magnesium	12	0.1

Additional info: Trace elements such as iron (Fe), zinc (Zn), and iodine (I) are required in very small amounts but are vital for health.

Emergent Properties of Compounds

When elements combine to form compounds, the resulting substance often has properties different from those of the individual elements.

Emergent Property: New characteristics arise when elements combine.
Example: Sodium (a reactive metal) and chlorine (a toxic gas) combine to form sodium chloride (table salt), which is safe to eat.

Atoms and Molecules

Subatomic Particles

Atoms consist of a nucleus containing protons and neutrons, surrounded by electrons in a cloud.

Proton: Positively charged particle in the nucleus.
Neutron: Neutral particle in the nucleus.
Electron: Negatively charged particle orbiting the nucleus.

Units of Measure in Atomic Structure

Atomic Number and Mass Number

The atomic number is the number of protons in an atom, which also equals the number of electrons in a neutral atom. The mass number is the sum of protons and neutrons.

Atomic Number (Z): Number of protons.
Mass Number (A): Number of protons + neutrons.
Notation: AZ (e.g., 12C for carbon with 6 protons and 6 neutrons).

Atomic Mass and the Dalton

Atomic mass is measured in Daltons (Da), where 1 Dalton is approximately grams.

Proton and Neutron: Each weighs about 1 Dalton.
Electron: Negligible mass (about 1/2000 of a Dalton).

Isotopes

Stable and Unstable Isotopes

Isotopes are atoms of the same element with different numbers of neutrons. Stable isotopes do not change over time, while unstable isotopes (radioisotopes) decay, releasing energy.

Stable Isotope Example: 12C and 13C (both carbon, different neutrons).
Unstable Isotope Example: 14C decays to form nitrogen.

Electron Shells and Chemical Nature of Atoms

Electron Shells

Electrons occupy energy levels called shells. The first shell holds 2 electrons, the second holds 8, and the third holds 8.

Valence Electrons: Electrons in the outermost shell, involved in chemical bonding.
Inert Elements: Elements with full valence shells (e.g., noble gases) are chemically unreactive.

Chemical Bonds

Types of Chemical Bonds

Atoms form bonds using their valence electrons. The main types of chemical bonds are:

Polar Covalent Bonds: Electrons are shared unequally due to differences in electronegativity.
Non-Polar Covalent Bonds: Electrons are shared equally.
Ionic Bonds: Electrons are transferred from one atom to another, creating ions.
Hydrogen Bonds: Weak attraction between a hydrogen atom and an electronegative atom.
Van der Waals Forces: Weak, transient attractions due to temporary electron distributions.

Electronegativity

Electronegativity is an atom's tendency to attract electrons. Atoms with high electronegativity (e.g., oxygen) strongly attract electrons, while those with low electronegativity (e.g., sodium) do not.

High Electronegativity: Atom prefers to gain electrons.
Low Electronegativity: Atom prefers to lose electrons.
Neutral Electronegativity: Atom does not strongly prefer gaining or losing electrons.

Electronegativity of Important Elements

Element	Valence Electrons	Electronegativity
Hydrogen	1	Neutral
Carbon	4	Neutral
Nitrogen	5	Slightly electronegative
Oxygen	6	Most electronegative

Non-Polar Covalent Bonds

Atoms with similar electronegativity share electrons equally, forming non-polar covalent bonds.

Example: Methane (CH4), where carbon and hydrogen share electrons equally.

Polar Covalent Bonds

Atoms with different electronegativity share electrons unequally, resulting in partial charges.

Example: Water (H2O), where oxygen attracts electrons more than hydrogen, creating a polar molecule.

Ionic Bonds

One atom donates an electron to another, forming oppositely charged ions that attract each other.

Example: Sodium chloride (NaCl), where sodium loses an electron and chlorine gains it.

Van der Waals Forces

Temporary attractions between atoms due to random electron movement. Individually weak, but collectively significant.

Example: Geckos use van der Waals forces to adhere to surfaces.

Hydrogen Bonds

Weak attraction between a hydrogen atom (partially positive) and an electronegative atom (partially negative) in another molecule.

Example: Hydrogen bonds between water molecules give water its unique properties.

Chemical Reactions and Equilibrium

Balanced Chemical Equations

A balanced equation has the same number and type of atoms on both sides of the reaction.

Example:

Chemical Equilibrium

At equilibrium, the rate of the forward reaction equals the rate of the reverse reaction. The concentrations of reactants and products remain constant.

Example: Water formation and breakdown occur at equal rates in a closed system.

Additional info: Chemical equilibrium is dynamic, not static; reactions continue to occur, but there is no net change in concentrations.