The Chemistry of Life: Foundations for Biology

The Chemistry of Life

Introduction

The chemistry of life forms the foundation for understanding biological processes. Living organisms are composed of chemical elements, and their structure and function are governed by chemical interactions. This section explores atomic structure, chemical bonds, water's unique properties, functional groups, and the formation of biological macromolecules.

Atoms and Elements

Atomic Structure

• Atom: The smallest unit of matter that retains the properties of an element. Composed of protons, neutrons, and electrons.

• Atomic Number: Number of protons in the nucleus; defines the element.

• Atomic Mass: Sum of protons and neutrons in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus in energy shells; their arrangement determines chemical reactivity.

Example: A neutral atom of oxygen (atomic number 8) has 8 protons, 8 neutrons (most common isotope), and 8 electrons.

Elements in the Human Body

• The Big Four: Hydrogen, carbon, nitrogen, and oxygen make up about 96% of the mass of living organisms.

Element	Symbol	Percentage of Body Mass
Oxygen	O	65%
Carbon	C	18%
Hydrogen	H	10%
Nitrogen	N	3%
Other elements	-	4%

Chemical Bonds

Types of Chemical Bonds

• Covalent Bonds: Atoms share pairs of valence electrons. Can be single, double, or triple bonds.

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

• Hydrogen Bonds: Weak attractions between a hydrogen atom with a partial positive charge and an electronegative atom (often oxygen or nitrogen).

Covalent Bonds and Electronegativity

• Electronegativity: The ability of an atom to attract shared electrons. Oxygen is highly electronegative.

• Nonpolar Covalent Bond: Electrons are shared equally (e.g., H2, CH4).

• Polar Covalent Bond: Electrons are shared unequally, creating partial charges (e.g., H2O).

Ionic Bonds

• Formed when the difference in electronegativity is so great that one atom completely transfers an electron to another (e.g., NaCl).

• Results in the formation of cations (positive ions) and anions (negative ions).

Molecular Shape

• The three-dimensional shape of a molecule is determined by the arrangement of its atoms and electron pairs.

• Molecular shape is crucial for biological function, such as enzyme-substrate recognition or hormone-receptor binding.

• Example: Morphine and endorphins have similar shapes, allowing both to bind to the same brain receptors.

Water: Structure and Properties

Hydrogen Bonds in Water

• Water molecules are polar, with partial positive charges on hydrogen and a partial negative charge on oxygen.

• Hydrogen bonds form between the oxygen of one water molecule and the hydrogen of another, giving water unique properties.

Emergent Properties of Water

1. Cohesion, Adhesion, and Surface Tension

   • Cohesion: Attraction between water molecules.

   • Adhesion: Attraction between water and other polar/charged substances.

   • Surface Tension: Cohesive force at the surface of water, allowing small objects to rest on it.

2. Water as an Efficient Solvent

   • Hydrophilic: Molecules that dissolve in water (ions, polar molecules).

   • Hydrophobic: Molecules that do not dissolve in water (nonpolar compounds).

   • Hydrophobic molecules cluster together via hydrophobic interactions.

3. Expansion Upon Freezing

   • Ice forms a crystal lattice, making it less dense than liquid water; thus, ice floats.

4. Moderation of Temperature

   • Water has a high specific heat, meaning it absorbs or releases a lot of heat with little temperature change.

   • Helps stabilize temperatures in organisms and environments.

   • Formula: $q = m c \Delta T$ (where $q$ is heat, $m$ is mass, $c$ is specific heat, $\Delta T$ is temperature change)

5. Water and Acid-Base Reactions

   • Water can dissociate into hydrogen ions (H+) and hydroxide ions (OH-): $\mathrm{H_2O \rightleftharpoons H^+ + OH^-}$

   • pH is a measure of hydrogen ion concentration: $\mathrm{pH = -\log[H^+]}$

   • Acids increase [H+], bases decrease [H+].

   • Pure water has a pH of 7.

Carbon and Organic Molecules

Carbon Skeletons

• Organic molecules contain carbon atoms bonded to other elements, forming chains or rings.

• Carbon's versatility allows for a variety of molecular structures essential for life.

Functional Groups

• Groups of atoms attached to carbon skeletons that confer specific chemical properties.

Functional Group	Formula	Properties	Example
Amino	-NH2	Acts as a base; attracts protons	Glycine
Carboxyl	-COOH	Acts as an acid; donates protons	Acetic acid
Carbonyl	-CO-	Reactive; forms aldehydes/ketones	Acetone
Hydroxyl	-OH	Polar; forms hydrogen bonds	Ethanol
Phosphate	-PO4	Contributes negative charge; energy transfer	3-Phosphoglyceric acid
Sulfhydryl	-SH	Forms disulfide bonds in proteins	Cysteine

Macromolecules: Polymers and Monomers

Polymer Formation

• Monomer: A single subunit that can join with others to form a polymer.

• Polymer: A large molecule made of repeating monomer units.

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

• Hydrolysis: Breaks polymers into monomers by adding water.

Example: Formation and breakdown of proteins, nucleic acids, and polysaccharides.

The Electron-Sharing Continuum

• Bonds exist on a continuum from equal sharing (nonpolar covalent) to unequal sharing (polar covalent) to complete transfer (ionic).

• Examples:

  • Nonpolar covalent: H2, CH4

  • Polar covalent: NH3, H2O

  • Ionic: NaCl

Summary Table: Properties of Water

Property	Description	Example/Scenario
High Specific Heat	Water resists temperature change	Oceans moderate coastal climates
Solvent of Life	Dissolves polar and ionic substances	Sugar dissolves in tea
Reduced Density as Solid	Ice floats on liquid water	Icebergs float in the ocean

Additional info:

• Understanding the chemistry of life is essential for studying all biological processes, from metabolism to genetics and cell structure.

• Knowledge of chemical bonds and molecular interactions underpins topics such as enzyme function, DNA structure, and membrane dynamics.