The Chemical Foundation of Life

Learning Objectives

• Explain the relationship between atoms and molecules.

• Compare hydrogen bonds and covalent bonds in terms of their mechanisms and strength of attraction between atoms.

• Define electronegativity and describe how it influences electron positions and partial charges in covalent bonds.

• Given a diagram of a simple biomolecule, determine:

  1. Which covalent bonds are polar and which are nonpolar.

  2. Which atoms have partial positive or partial negative charges.

  3. Which parts of the molecule are likely to interact with water via hydrogen bonding.

Life at Small Scales

Introduction to Biological Scales

Biology examines life at a variety of scales, from large organisms to microscopic structures such as atoms and molecules. Understanding the chemical foundation of life requires knowledge of how atoms combine to form molecules, which in turn make up the structures and functions of living organisms.

• Atoms are the fundamental building blocks of matter.

• Molecules are combinations of two or more atoms bonded together.

• Biological processes depend on interactions at the molecular and atomic levels.

• Examples of scales: multicellular organisms (e.g., cats, flowers), fungi, and molecular structures (e.g., DNA).

Basic Atomic Structure

Components of the Atom

Atoms consist of a central nucleus surrounded by electrons. The nucleus contains protons and neutrons, while electrons orbit the nucleus in defined energy levels.

• Protons: Positively charged particles (+1 charge).

• Neutrons: Neutral particles (no charge).

• Electrons: Negatively charged particles (-1 charge) that orbit the nucleus.

• Atomic Number: The number of protons in an atom, which defines the element.

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

• Ions: Atoms that have gained or lost electrons, resulting in a net charge.

Molecules and Chemical Bonds

Formation and Diversity of Molecules

Molecules are formed when atoms bond together through chemical interactions. The arrangement and type of bonds between atoms allow for a vast diversity of molecular structures, which are essential for biological function.

• Molecule: A group of two or more atoms held together by chemical bonds.

• Valence Shell: The outermost electron shell of an atom; electrons here determine chemical reactivity.

• Atoms are most stable when their valence shells are full (usually 2 or 8 electrons).

• Electrons in the valence shell prefer to be paired for stability.

Covalent Bonds

Covalent bonds are formed when atoms share pairs of electrons. These bonds are strong and are fundamental to the structure of biological molecules.

• Covalent Bond: A chemical bond formed by the sharing of electron pairs between atoms.

• Single, double, or triple covalent bonds can form depending on the number of shared electron pairs.

• Example: In a water molecule (H2O), each hydrogen atom shares an electron with oxygen.

Electronegativity and Bond Polarity

Electronegativity is a measure of an atom's ability to attract electrons in a covalent bond. Differences in electronegativity between atoms lead to the formation of polar and nonpolar covalent bonds.

• Electronegativity: The tendency of an atom to attract electrons toward itself in a chemical bond.

• Order of electronegativity (common in biology): O > N > C ≈ H

• Nonpolar Covalent Bond: Electrons are shared equally between atoms of similar electronegativity.

• Polar Covalent Bond: Electrons are shared unequally, resulting in partial charges (δ+ and δ-) on the atoms.

Table: Comparison of Bond Types

Electric Charge Interactions

Intermolecular Forces

Molecules with partial negative and positive charges interact through various types of intermolecular forces. These interactions are crucial for the structure and function of biological molecules.

• Hydrogen Bond: A weak interaction between a hydrogen atom (attached to an electronegative atom like O or N) and another electronegative atom on a different molecule.

• Van der Waals Interactions: Weak attractions between molecules due to temporary changes in electron density.

• Hydrogen bonds are essential for the properties of water and the structure of DNA and proteins.

The Electron-Sharing Continuum

Types of Chemical Bonds

The electron-sharing continuum describes the range of chemical bonds from equal sharing (nonpolar covalent) to complete transfer (ionic bonds).

• Nonpolar Covalent Bonds: Electrons are shared equally.

• Polar Covalent Bonds: Electrons are shared unequally.

• Ionic Bonds: Electrons are transferred from one atom to another, resulting in charged ions.

Chemical Reactions

Overview of Chemical Reactions

Chemical reactions involve the breaking and forming of chemical bonds, resulting in the transformation of substances. Reactions can be reversible or irreversible, and are represented by chemical equations.

• Reactants: Substances that undergo change during a reaction.

• Products: Substances formed as a result of a reaction.

• Reactions are written as equations:

• Example:

• Irreversible Reaction: Proceeds in one direction until reactants are used up. Example:

• Reversible Reaction: Products can revert to reactants. Example:

• Balanced equations have the same number of each type of atom on both sides.

How to Balance Chemical Equations

1. Draw an appropriate arrow to indicate the direction of the reaction.

2. Ensure the number of atoms of each element is equal on both sides of the equation.

• Example (combustion of methane):

Additional info: Images referenced in the notes (e.g., gene library, mushrooms, cats, flowers) illustrate the diversity of life and the importance of molecular interactions at different biological scales.