Atoms, Ions, Molecules, and Water: Foundations of Chemical Biology

Atoms, Ions, and Molecules: The Building Blocks of Chemical Evolution

Atoms and Atomic Structure

An atom is the smallest identifiable unit of matter. Four types of atoms—hydrogen (H), carbon (C), nitrogen (N), and oxygen (O)—make up 96 percent of all matter found in organisms today.

• Subatomic particles: Atoms are made of protons (positively charged), neutrons (neutral), and electrons (negatively charged).

• Nucleus: Contains protons and neutrons; electrons orbit the nucleus.

• Atomic number (Z): Number of protons in the nucleus.

• Mass number (A): Sum of protons and neutrons in the nucleus.

• Atomic mass: The actual weight of a specific atom, often close to the mass number.

Isotopes are atoms of the same element with different numbers of neutrons. The atomic weight is the average of all the atomic masses of naturally occurring isotopes.

Particle	Charge	Atomic Mass Unit	Location
Proton	+1	1	Nucleus
Neutron	0	1	Nucleus
Electron	-1	~0	Electron cloud

Formulas:

• $\text{Mass number} = \text{Number of protons} + \text{Number of neutrons}$

• $\text{Atomic number} = \text{Number of protons}$

Atomic Symbols and the Periodic Table

The periodic table organizes elements by atomic number. Each element has a unique symbol and atomic number.

• First shell fits 2 electrons; subsequent shells fit 8 electrons.

• Valence electrons: Electrons in the outermost shell, important for chemical bonding.

• Atoms are stable when their outer shell is full (usually 8 electrons).

• Atoms with incomplete outer shells tend to form chemical bonds.

Example: Chlorine has 7 valence electrons; sodium has 1 valence electron.

Chemical Bonds and Molecules

Ionic Bonds

Ionic bonds form when one atom donates an electron to another, resulting in oppositely charged ions that attract each other.

• Cation: Positively charged ion (loses electron).

• Anion: Negatively charged ion (gains electron).

• Example: Sodium (Na) donates an electron to chlorine (Cl), forming Na+ and Cl-.

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. These bonds are strong and common in biological molecules.

• Nonpolar covalent bond: Electrons are shared equally (e.g., H2 molecule).

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges (e.g., H2O molecule).

Example: In water (H2O), oxygen is more electronegative than hydrogen, so electrons are pulled closer to oxygen, making water a polar molecule.

Properties of Water

Water is Polar

Water molecules have polar covalent bonds, resulting in a partial negative charge near the oxygen atom and partial positive charges near the hydrogen atoms.

• This polarity allows water molecules to form hydrogen bonds with each other.

• Hydrogen bonds are weak individually but strong collectively, giving water unique properties.

Water Stabilizes Temperature

Water absorbs and releases heat more slowly than most other substances, helping to stabilize temperature in organisms and environments.

• Hydrogen bonds require energy to break, so water has a high specific heat.

• Water moderates temperature changes, protecting living organisms from rapid temperature fluctuations.

• When water freezes, hydrogen bonds form a crystalline structure, making ice less dense than liquid water.

Water is an Excellent Solvent

Water's polarity allows it to dissolve many ionic and polar compounds, making it a solvent for biological reactions.

• Hydrophilic substances: Dissolve easily in water (e.g., salts, sugars).

• Hydrophobic substances: Do not dissolve in water (e.g., oils, fats).

• Water forms hydration shells around ions and polar molecules, keeping them dispersed.

Water is Cohesive and Adhesive

Cohesion refers to water molecules being attracted to each other via hydrogen bonding. Adhesion is the attraction of water molecules to other surfaces.

• Cohesion allows for surface tension, enabling water to resist rupture at its surface.

• Adhesion helps water move up plant stems (capillary action).

Example: Water forms droplets and can move up a straw due to cohesive and adhesive forces.

Carbon and Organic Macromolecules

Carbon's Versatility

Carbon atoms have four valence electrons, allowing them to form strong covalent bonds and a variety of complex molecules essential for life.

• Carbon can bond with H, O, N, S, and P atoms, forming diverse organic molecules.

• Carbon skeletons provide structure for macromolecules.

• The chemical behavior of organic molecules is determined by functional groups attached to the carbon skeleton.

Functional Groups in Organic Molecules

Functional groups are specific groups of atoms within molecules that confer particular chemical properties.

Group	Structure	Properties	Example
Amino	-NH2	Acts as a base; can pick up H+	Amino acids
Carboxyl	-COOH	Acts as an acid; can donate H+	Fatty acids
Hydroxyl	-OH	Makes compounds more soluble; forms hydrogen bonds	Alcohols
Phosphate	-PO4	Transfers energy; contributes negative charge	ATP
Sulfhydryl	-SH	Forms disulfide bonds; stabilizes protein structure	Cysteine

Example: The presence of a carboxyl group makes fatty acids acidic, while an amino group makes amino acids basic.

Additional info: These notes expand on the original content by providing definitions, examples, and context for key biological concepts, ensuring a self-contained study guide suitable for exam preparation.