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

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

Atoms and Subatomic Particles

Atoms are the smallest identifiable units of matter and form the basis of all chemical substances. The most common elements in living organisms are hydrogen (H), carbon (C), nitrogen (N), and oxygen (O).

• Atom: Consists of a nucleus (protons and neutrons) surrounded by electrons.

• Proton: Positively charged particle in the nucleus.

• Neutron: Neutral particle in the nucleus.

• Electron: Negatively charged particle orbiting the nucleus.

Key Equations:

• Mass number = Number of protons + Number of neutrons

• Atomic number = Number of protons

• Atomic mass = The actual weight of a specific atom (often close to the mass number)

Isotopes: Atoms of the same element with different numbers of neutrons. The atomic weight is the average of all isotopes' masses, weighted by their natural abundance.

Atomic Symbols and the Periodic Table

The periodic table organizes elements by atomic number and properties. Each element's symbol, atomic number, and mass number are key identifiers.

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

• Octet rule: Atoms are most stable when their outer shell has 8 electrons (except for the first shell, which holds 2).

Chemical Bonds and Molecules

Ionic Bonds

Ionic bonds form when electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Cation: Positively charged ion (loses electrons).

• Anion: Negatively charged ion (gains electrons).

• Example: Sodium (Na) loses an electron to become Na+; chlorine (Cl) gains an electron to become Cl-; they form NaCl (table salt).

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. These bonds are strong and form the backbone of most 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).

Water: Properties and Biological Importance

Polarity of Water

Water molecules are polar due to the unequal sharing of electrons between hydrogen and oxygen atoms. This results in a partial negative charge near the oxygen atom and partial positive charges near the hydrogen atoms.

• Hydrogen bond: Weak attraction between the slightly positive hydrogen atom of one water molecule and the slightly negative oxygen atom of another.

Water as a Solvent

Water's polarity makes it an excellent solvent, especially for ionic and polar substances. It can dissolve many compounds by surrounding them with hydration shells.

• Hydrophilic: Substances that dissolve in water (water-loving).

• Hydrophobic: Substances that do not dissolve in water (water-fearing).

Water Stabilizes Temperature

Water absorbs and releases heat more slowly than many other substances, helping to moderate temperature changes in organisms and environments.

• High specific heat means water can absorb a lot of energy before its temperature rises.

• When water freezes, it becomes less dense, causing ice to float.

Cohesion, Adhesion, and Surface Tension

Water molecules stick to each other (cohesion) and to other surfaces (adhesion) due to hydrogen bonding. These properties contribute to water's high surface tension and its ability to move through plant vessels.

• Cohesion: Attraction between water molecules.

• Adhesion: Attraction between water molecules and other substances.

• Surface tension: The capacity of water to withstand rupture at its surface.

Carbon and Organic Macromolecules

Carbon's Versatility

Carbon atoms can form four covalent bonds, allowing for a diversity of stable, complex molecules. This property is fundamental to the structure of organic molecules in living organisms.

• Carbon forms the backbone of macromolecules such as carbohydrates, proteins, lipids, and nucleic acids.

• 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 have characteristic properties and chemical reactivity.

Group	Structure	Properties	Example
Amino	-NH2	Acts as a base, can pick up H+	Glycine (an amino acid)
Carboxyl	-COOH	Acts as an acid, can donate H+	Acetic acid
Hydroxyl	-OH	Polar, forms hydrogen bonds	Ethanol
Phosphate	-PO4	Contributes negative charge, can release energy	ATP
Sulfhydryl	-SH	Forms disulfide bonds in proteins	Cysteine

Additional info: Functional groups determine the types of chemical reactions organic molecules can participate in, influencing biological activity and molecular interactions.