Chemical Foundations of Life

Introduction

Understanding life at the molecular level requires knowledge of chemistry and physics. All living organisms are governed by the same fundamental chemical and physical laws.

• Biology is multidisciplinary: It integrates principles from chemistry and physics.

• All living things follow basic laws of chemistry and physics.

Elements of Life

Major Elements in Living Organisms

Life is composed primarily of a few key elements, with the majority of an organism's mass made up of just four elements.

• Matter: Anything that has mass and occupies space.

• Elements: Pure substances that cannot be broken down by chemical means.

• 96% of the human body is composed of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

• The remaining percentage consists of trace elements, which are required in small amounts but are essential for life.

Atoms & Subatomic Particles

Structure of Atoms

Atoms are the smallest units of matter that retain the properties of an element. They are composed of subatomic particles:

• Protons (+): Positively charged, located in the nucleus.

• Neutrons (0): No charge, located in the nucleus.

• Electrons (–): Negatively charged, orbit the nucleus in shells.

• Atomic number: Number of protons in the nucleus.

• Mass number: Sum of protons and neutrons.

Isotopes

Definition and Examples

Isotopes are variants of a particular chemical element that have the same number of protons but different numbers of neutrons.

• Example: Carbon has three naturally occurring isotopes:

  • 12C: 6 protons, 6 neutrons

  • 13C: 6 protons, 7 neutrons

  • 14C: 6 protons, 8 neutrons

• Atomic weight: The average mass of all isotopes of an element, weighted by their natural abundance.

Electron Arrangement

Shells and Valence Electrons

Electrons are arranged in shells around the nucleus. The arrangement of electrons determines the chemical properties and reactivity of an atom.

• Electrons orbit in shells:

  • Shell 1: up to 2 electrons

  • Shell 2: up to 8 electrons

• Valence shell: The outermost electron shell.

• Valence electrons: Electrons in the valence shell; they determine an atom's chemical behavior.

• Atoms with a full valence shell are stable (inert), e.g., noble gases.

• Atoms with incomplete valence shells are reactive (e.g., H, O, C, Na).

Types of Chemical Bonds

1. Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. They are the strongest type of chemical bond in biological molecules.

• Single bond: 2 electrons shared

• Double bond: 4 electrons shared

• Triple bond: 6 electrons shared

• Electronegativity: The ability of an atom to attract shared electrons.

• Nonpolar covalent bond: Equal sharing of electrons (e.g., O2, CH4).

• Polar covalent bond: Unequal sharing of electrons (e.g., H2O), resulting in partial charges (δ–, δ+).

2. Ionic Bonds

Ionic bonds are formed when electrons are transferred from one atom to another, resulting in the formation of ions.

• Cation (+): Atom that loses electrons and becomes positively charged.

• Anion (–): Atom that gains electrons and becomes negatively charged.

• Opposite charges attract, forming ionic compounds (e.g., NaCl).

3. Hydrogen Bonds

Hydrogen bonds are weak attractions between a δ+ hydrogen atom and a δ– atom (such as oxygen or nitrogen) in another molecule.

• Important in water properties (surface tension, cohesion).

• Stabilize the structure of DNA (hold base pairs together).

Redox Reactions

Oxidation and Reduction

Redox (reduction-oxidation) reactions involve the transfer of electrons between molecules.

• Reduction: Gain of electrons (GER: Gain Electrons = Reduction).

• Oxidation: Loss of electrons (LEO: Lose Electrons = Oxidation).

• Mnemonic: OIL RIG (Oxidation Is Losing, Reduction Is Gaining).

• Example: In cellular respiration, glucose is oxidized to CO2, and oxygen is reduced to H2O.

Electron-Sharing Continuum

Types of Electron Sharing

• Nonpolar covalent: Equal sharing of electrons.

• Polar covalent: Unequal sharing of electrons.

• Ionic: Complete transfer of electrons.

Structure & Function

Relationship Between Structure and Function

The properties and functions of molecules depend on their structure, which includes the number and types of atoms and their three-dimensional arrangement.

• Function is always based on structure.

Water: Properties & Importance

Water as a Universal Solvent

Water is essential for life due to its unique chemical and physical properties.

• Polarity: Water molecules have a partial negative charge on oxygen (δ–) and a partial positive charge on hydrogen (δ+).

• Forms hydrogen bonds.

• Interacts with ions and polar molecules.

Hydrophilic vs. Hydrophobic

• Hydrophilic: "Water-loving"; dissolves in water (polar, ionic substances).

• Hydrophobic: "Water-fearing"; does not dissolve in water (nonpolar substances, fats, oils).

Unique Properties of Water

1. Cohesion: Water molecules stick to each other, resulting in high surface tension.

2. Adhesion: Water molecules stick to other substances.

3. Liquid water is denser than ice: Ice floats on water.

4. High specific heat & heat of vaporization: Water absorbs large amounts of heat, moderating climate and body temperature.

Acids, Bases & pH

pH Scale and Definitions

The pH scale measures the concentration of hydrogen ions (H+) in a solution.

• pH is defined as:

• Acid: Releases H+ ions; pH < 7.

• Base: Accepts H+ ions; pH > 7.

• Neutral: [H+] = [OH–]; pH = 7 (pure water).

Quantifying Molecules

Molecular Weight, Moles, and Molarity

• Molecular weight (MW): The sum of atomic masses in a molecule.

  • Example: Sucrose (C12H22O11) = 342 g/mol.

• Mole: 6.022 × 1023 molecules (Avogadro's number).

• Molarity (M): Moles of solute per liter of solution.

Carbon: Backbone of Life

Importance and Properties of Carbon

Carbon is the foundational element in organic molecules due to its versatile bonding properties.

• Cells are approximately 70–95% water; the rest is mostly carbon-based compounds.

• Carbon has 4 valence electrons, allowing it to form four covalent bonds.

• Can form long chains, rings, and complex structures.

• Forms the basis for proteins, DNA, carbohydrates, and lipids.

Functional Groups

Key Functional Groups in Biological Molecules

Functional groups are specific groups of atoms within molecules that determine the chemical behavior of those molecules.

• Hydroxyl (–OH): Polar, forms hydrogen bonds, dissolves sugars.

• Carbonyl (C=O): Found in aldehydes and ketones, present in sugars.

• Carboxyl (–COOH): Acidic, donates H+ (organic acids).

• Amino (–NH2): Basic, accepts H+ (amino acids).

• Sulfhydryl (–SH): Forms cross-links in proteins (stabilizes hair).

• Phosphate (–PO42–): Contributes negative charge, stores energy (ATP).

• Methyl (–CH3): Affects DNA/gene expression and hormones.