Atoms, Chemical Bonds, and Biomolecules: Foundations for General Biology

Atoms and Elements in Biology

Major Elements of Biomolecules

Biological molecules are primarily composed of four major elements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). These elements form the backbone of most biomolecules essential for life.

• Isotope: Atoms of the same element with different numbers of neutrons.

• Radioactive Isotope: Unstable isotopes that decay spontaneously, emitting radiation.

• Energy Capacity: Atoms have discrete energy levels (shells) for electrons. Electrons can absorb energy and move to higher shells, or release energy and fall to lower shells.

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

Example: Carbon has 6 electrons: 2 in the first shell, 4 in the second shell. Its chemical properties are determined by these 4 valence electrons.

Chemical Bonds in Biological Molecules

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules. The main types relevant to biology are:

• Covalent Bonds: Atoms share electron pairs to complete their outer shells. These are strong and stable bonds found in most biological molecules.

• Ionic Bonds: Formed when one atom donates an electron to another, resulting in oppositely charged ions that attract each other.

• Hydrogen Bonds: Weak attractions between a hydrogen atom (partially positive) and an electronegative atom (such as oxygen or nitrogen).

Example: Water molecules are held together by hydrogen bonds, which are crucial for many of water's unique properties.

Electronegativity

Electronegativity is the tendency of an atom to attract electrons in a chemical bond. Differences in electronegativity determine bond polarity.

Element	Electronegativity
Oxygen	3.5
Nitrogen	3.0
Hydrogen	2.1
Carbon	2.5

Additional info: The greater the difference in electronegativity between two atoms, the more polar the bond.

Organic Molecules and Functional Groups

Organic Molecules

Organic molecules are the molecules of life, containing carbon and hydrogen. They may also include oxygen, nitrogen, phosphorus, and sulfur.

• Hydrocarbons: Molecules made only of carbon and hydrogen. They are generally hydrophobic.

Monomers and Polymers

Biological macromolecules are often polymers, made by linking monomers together.

• Monomer: A single, basic building block of a larger molecule.

• Polymer: A large molecule made by joining many monomers together.

• Example: Proteins are polymers made of amino acid monomers.

Dehydration and Hydrolysis Reactions

Polymers are formed and broken down by specific chemical reactions:

• Dehydration Reaction: Joins monomers by removing a water molecule.

• Hydrolysis Reaction: Breaks polymers into monomers by adding a water molecule.

Lipids and Phospholipids

Lipids

Lipids are hydrophobic molecules, including fats, oils, and steroids. They are important for energy storage and membrane structure.

• Saturated Fatty Acid: No double bonds between carbon atoms; usually solid at room temperature.

• Unsaturated Fatty Acid: One or more double bonds; usually liquid at room temperature.

Phospholipids

Phospholipids are major components of cell membranes. They have a hydrophilic (water-attracting) head and hydrophobic (water-repelling) tails.

• In water, phospholipids self-assemble into a bilayer, with heads facing outward and tails facing inward.

Functional Groups in Biological Molecules

Common Functional Groups

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

• Hydroxyl (-OH): Polar, hydrophilic

• Carboxyl (-COOH): Acidic, hydrophilic

• Amino (-NH2): Basic, hydrophilic

• Phosphate (-PO4): Acidic, hydrophilic

• Methyl (-CH3): Nonpolar, hydrophobic

Example: Amino acids contain both amino and carboxyl groups.

Summary Table: Types of Chemical Bonds

Bond Type	Strength	Role in Biology
Covalent	Strong	Stable backbone of biomolecules
Ionic	Moderate	Important in salts and some protein interactions
Hydrogen	Weak	Stabilizes DNA, proteins, and water properties

Key Equations

• Electron Shell Capacity: $2n^2$ (where n = shell number)