Chapter 2: Chemistry – Chemical Bonds, Electronegativity, and Water Properties

Key Concepts in Chemistry for Biology

Overview

Chemistry is fundamental to understanding biological processes. The behavior of atoms and molecules, especially their electrons, determines the types of chemical bonds they form and how they interact in biological systems. This section covers the nature of chemical bonds, electronegativity, molecular polarity, and the unique properties of water.

Chemical Bonds

Covalent Bonds

Covalent bonds are formed when two atoms share pairs of electrons. The number of shared electron pairs determines whether the bond is single or double.

• Single bond: One pair of shared electrons.

• Double bond: Two pairs of shared electrons.

Example: The oxygen molecule (O2) contains a double covalent bond.

Name and Molecular Formula	Electron Distribution Diagram	Structural Formula	Space Filling Model
Oxygen (O2)	Two overlapping electron clouds (each O atom shares two pairs)	O=O	Two red spheres joined together

Electronegativity

Electronegativity is the tendency of an atom to attract shared electrons in a chemical bond. It varies across the periodic table, generally increasing from left to right and from bottom to top.

• Atoms with high electronegativity (e.g., oxygen, fluorine) attract electrons more strongly.

• Electronegativity differences between atoms influence bond type and polarity.

Example: The periodic table shows electronegativity values, with fluorine being the most electronegative element.

Nonpolar Covalent Bonds

Nonpolar covalent bonds occur when the electronegativity difference between atoms is small, resulting in equal sharing of electrons.

• Example: Methane (CH4) has nonpolar covalent bonds between carbon and hydrogen.

• Electronegativity values: C = 2.5, H = 2.1, Difference = 0.4

Name and Molecular Formula	Electron Distribution Diagram	Structural Formula	Space Filling Model
Methane (CH4)	Central C atom with four H atoms, each sharing electrons	H–C–H (tetrahedral arrangement)	Central black sphere (C) surrounded by four white spheres (H)

Polar Covalent Bonds

Polar covalent bonds occur when the electronegativity difference is moderate, causing unequal sharing of electrons and partial charges on atoms.

• Example: Water (H2O) has polar covalent bonds between oxygen and hydrogen.

• Oxygen is more electronegative, resulting in a partial negative charge on O and partial positive charges on H.

Charge distribution in water:

• Oxygen: partial negative (δ−)

• Hydrogen: partial positive (δ+)

Ionic Bonds

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

• Example: Sodium chloride (NaCl) forms when sodium donates an electron to chlorine, creating Na+ (cation) and Cl− (anion).

Atom/Ion	Electron Count	Proton Count	Net Charge
Neutral Sodium	11	11	0
Neutral Chlorine	17	17	0
Sodium Ion (Na+)	10	11	+1
Chloride Ion (Cl−)	18	17	−1

Other Types of Chemical Interactions

Hydrogen Bonds

Hydrogen bonds are weak attractions between the partial positive charge of a hydrogen atom (bonded to an electronegative atom) and the partial negative charge of another electronegative atom (such as oxygen or nitrogen).

• Important in water, DNA, and protein structure.

Van der Waals Interactions

Van der Waals interactions are weak attractions between molecules due to transient regions of positive and negative charge caused by electron movement.

• Significant in nonpolar molecules and biological macromolecules.

Properties of Water

Cohesion, Adhesion, and Surface Tension

Water molecules exhibit strong cohesion (attraction to each other), adhesion (attraction to other substances), and high surface tension due to hydrogen bonding.

• Allows water to form droplets and move through plant vessels.

Temperature Regulation

Water resists changes in temperature because it has a high specific heat and high heat of vaporization.

• It takes significant energy to raise water's temperature or to vaporize it.

Density of Ice

Solid water (ice) is less dense than liquid water due to the arrangement of hydrogen bonds, causing ice to float.

Water as a Solvent

Water dissolves many substances due to its polarity.

• Hydrophilic substances: Compounds with full or partial charges (e.g., salts, sugars) readily dissolve in water.

• Hydrophobic substances: Nonpolar molecules (e.g., oils, waxes) do not dissolve well in water.

Type	Examples	Solubility in Water
Hydrophilic	NaCl, sugar	High
Hydrophobic	Octane, paraffin	Low

Acids, Bases, and pH

Ionization of Water

Water molecules can ionize to form hydronium ions (H3O+) and hydroxide ions (OH−).

• Shorthand: [H+] is used to represent hydronium ion concentration.

Acids and Bases

• Acid: Substance that donates H+ ions (e.g., HCl → H+ + Cl−).

• Base: Substance that accepts or depletes H+ ions (e.g., NH3 + H+ → NH4+).

pH Scale

The pH scale measures the concentration of hydrogen ions in a solution.

• pH is defined as $pH = -\log[H^+]$

• Lower pH = more acidic (higher [H+])

• Higher pH = more basic (lower [H+])

pH Value	Example	Acidity/Basicity
2-3	Vinegar, wine, cola	Acidic
4-6	Tomato juice, rainwater, urine	Acidic
7	Pure water, human blood	Neutral
8-11	Saliva, household ammonia	Basic
12-14	Oven cleaner	Strongly basic

Additional info:

• Hydrogen bonds and van der Waals interactions are crucial for the structure and function of biological macromolecules.

• Water's properties are essential for life, influencing temperature regulation, nutrient transport, and chemical reactions in cells.