Chapter 2: Chemical Basis of Life

Overview

This chapter explores the fundamental chemical principles that underlie biological processes. It emphasizes the connection between chemistry and the evolution of life, focusing on atomic structure, chemical bonding, properties of water, thermodynamics, and the role of carbon in biological molecules.

Key Concepts

• Molecules form when atoms bond to each other. Chemical bonds are based on electron sharing, and the degree of sharing varies depending on the type of bond.

• Of all small molecules, water is the most important for life due to its high polarity and ability to form hydrogen bonds, making it an extremely efficient solvent.

• Energy is the capacity to do work or supply heat, existing as potential or kinetic energy. Chemical energy is a form of potential energy stored in chemical bonds.

• Chemical reactions tend to be spontaneous if they lead to lower potential energy and higher entropy, and nonspontaneous if they require an input of energy.

• Most important compounds in organisms contain carbon.

Basic Atomic Structure

Subatomic Particles

• Protons: Positively charged particles located in the nucleus.

• Neutrons: Neutral particles located in the nucleus.

• Electrons: Negatively charged particles found in orbitals surrounding the nucleus.

Diagram Example: Hydrogen has one proton and one electron; carbon has six protons, six neutrons, and six electrons (with electrons arranged in two shells).

Elements and Isotopes

• Each element is defined by its atomic number (number of protons).

• Isotopes are atoms of the same element with different numbers of neutrons.

• Mass number = number of protons + number of neutrons.

Electron Arrangement and Valence

• Electrons are arranged in shells around the nucleus. Shells closer to the nucleus have lower energy.

• The valence shell is the outermost electron shell; electrons here are called valence electrons.

• Elements commonly found in organisms have at least one unpaired valence electron, which determines their chemical reactivity.

Chemical Bonding

Types of Bonds

• Covalent Bonds: Atoms share pairs of valence electrons. Molecules held together by covalent bonds are called molecules.

• Ionic Bonds: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

Polarity of Covalent Bonds

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

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

Ions and Ionic Compounds

• Cation: Atom that loses an electron and becomes positively charged.

• Anion: Atom that gains an electron and becomes negatively charged.

• Ionic compounds (e.g., NaCl) are formed by the attraction between cations and anions.

Thermodynamics in Biology

Definitions

• System: The part of the universe being studied.

• Surroundings: Everything outside the system.

• Closed System: Cannot exchange matter or energy with surroundings.

• Open System: Can exchange matter or energy with surroundings.

Laws of Thermodynamics

• First Law (Conservation of Energy): The total amount of energy in the universe is constant. Energy cannot be created or destroyed, only changed in form.

• Second Law: Energy conversion is inefficient. The randomness (entropy) of the universe is always increasing, and the organization is always decreasing.

Properties of Water

• Water is a polar molecule due to the difference in electronegativity between oxygen and hydrogen.

• Forms hydrogen bonds with other water molecules, leading to unique properties:

  • Cohesion: Attraction between like molecules (water to water).

  • Adhesion: Attraction between unlike molecules (water to other substances).

  • High specific heat: Absorbs large amounts of energy with little temperature change.

  • High heat of vaporization: Requires significant energy to change from liquid to gas.

  • Density anomaly: Ice is less dense than liquid water, so it floats.

Acids, Bases, and pH

• Water can dissociate:

• pH measures the concentration of hydrogen ions:

• Pure water has a pH of 7.

• Acids: pH < 7; Bases: pH > 7.

• Buffers are compounds that minimize changes in pH.

Energy in Chemical Reactions

• Potential energy is stored in chemical bonds; kinetic energy is energy of motion.

• Spontaneous reactions tend to lower potential energy and increase entropy.

• Gibbs free energy change () determines spontaneity:

  • : Exergonic (spontaneous)

  • : Endergonic (requires energy)

  • : Equilibrium

The Importance of Carbon

• Carbon is highly versatile due to its four valence electrons, allowing it to form single, double, or triple covalent bonds.

• Carbon-containing molecules can have diverse shapes (linear, ring, branched).

• Functional groups (e.g., amino, carboxyl, hydroxyl, phosphate, sulfhydryl) attached to carbon skeletons determine the chemical behavior of organic molecules.

Summary Table: Types of Chemical Bonds

Key Equations

• pH calculation:

• Water dissociation:

• Gibbs free energy: where is enthalpy change, is temperature in Kelvin, and is entropy change.