Chemistry of Life: Atomic Structure, Bonding, and Biological Macromolecules

Chemistry of Life

Major Concepts

• All molecules are made of atoms joined by covalent bonds.

• Types of bonds are determined by electronegativity of atoms involved.

• Water has unique properties due to hydrogen bonds between water molecules.

• The presence of water determines how life functions.

• There are four types of organic molecules essential for life.

Atomic Structure and Elements of Life

Common Elements in Cells

Cells are composed of a limited set of elements, despite the diversity found on Earth. These elements form the basis of biological molecules.

• Most abundant elements: Oxygen (O), Hydrogen (H), Carbon (C), Nitrogen (N)

• Less abundant but important: Sulfur (S), Phosphorous (P)

Structure of Atoms

• Atoms consist of protons (positive charge) and neutrons (neutral) in the nucleus, surrounded by electrons (negative charge) in orbitals.

• Electrons occupy electron shells at varying distances from the nucleus.

• Shell 1 fills with 2 electrons; Shell 2 fills with 8 electrons.

• The valence shell (outermost shell) determines bonding behavior.

Electron Shells of Life Elements

• Atoms are most stable when their outermost shell is filled:

  • Carbon, Oxygen, Nitrogen: stable with 8 electrons in the outer shell.

  • Hydrogen: stable with 2 electrons in its only shell.

Formation and Types of Chemical Bonds

Bond Formation

Atoms interact to achieve stable electron arrangements, forming bonds by either sharing or transferring electrons.

• Covalent bonds: Sharing electrons between atoms.

• Ionic bonds: Transferring electrons, resulting in charged ions.

Electronegativity and Bond Type

Electronegativity is the tendency of an atom to attract electrons. The difference in electronegativity between atoms determines the bond type:

• Order of electronegativity: O > N > C ≈ H

• Large differences lead to ionic bonds.

• Small or no difference leads to nonpolar covalent bonds.

• Intermediate difference leads to polar covalent bonds.

Maximum Number of Bonds

• The number of unpaired electrons in the valence shell determines how many covalent bonds an atom can form.

• Example: Carbon has 4 unpaired electrons and forms 4 covalent bonds.

Nonpolar vs. Polar Covalent Bonds

Nonpolar Covalent	Polar Covalent
Equal (or near equal) sharing of electron pair	Unequal sharing of electron pair
No partial charge on atoms	Partial charges on atoms
Electrons found midway between nuclei	Electrons shift closer to one atom's nucleus

Ionic Bonds

• Ionic bonds are attractions between positively and negatively charged ions (e.g., Na+ and F-).

• Formed when electrons are completely transferred due to large electronegativity differences.

Water: Structure and Properties

Bonding in Water

• Water (H2O) is a small, light molecule that remains liquid at room temperature due to its bonding properties.

• Oxygen is highly electronegative, hydrogen is less so, resulting in polar covalent bonds within the molecule.

• This creates partial positive (δ+) and partial negative (δ-) charges.

Hydrogen Bonding

• Hydrogen bonds form between the partial positive charge of hydrogen in one water molecule and the partial negative charge of oxygen in another.

• Hydrogen bonds are weak but crucial for water's properties and for many biological molecules.

• Conditions for hydrogen bonding:

  • Hydrogen atom in a polar covalent bond (partially positive).

  • Nearby atom with a partial negative charge.

Importance of Hydrogen Bonds

• Hydrogen bonds hold water molecules together, maintaining liquid state and enabling life processes.

• Found in many biological molecules (e.g., between DNA strands, proteins).

Behavior of Molecules in Water

Polar vs. Nonpolar Molecules

• Polar molecules (with polar covalent bonds) are hydrophilic (water-loving), interact with water, and are soluble.

• Nonpolar molecules (with nonpolar covalent bonds) are hydrophobic (water-fearing), do not interact with water, and are insoluble.

Hydrophilic Molecule	Hydrophobic Molecule
Partial charges interact with water	Lacks partial charges, does not interact with water
Soluble in water	Insoluble in water

Exceptions

• Some molecules, like carbon dioxide (CO2), are nonpolar and hydrophobic due to symmetry, even though they contain polar bonds.

Biological Macromolecules

Classes and Monomers

Four major classes of biological macromolecules are essential for life. Their structure and function are influenced by their interactions with water.

Macromolecule Class	Monomer (Building Block)	Polymer Name
Polysaccharides	Monosaccharides	Polysaccharides
Proteins	Amino Acids	Proteins
Nucleic Acids	Nucleotides	Nucleic Acids
Lipids	Fatty acids & other components	Not true polymers

• Polysaccharides, proteins, and nucleic acids are polymers made from their respective monomers.

• Lipids are not true polymers but are essential for cell membranes and energy storage.

Additional info: The interactions of these macromolecules with water are critical for their biological roles, such as enzyme function, genetic information storage, and cellular structure.