Chemical Basis of Life

Atoms, Elements, and Isotopes

The study of biology begins with understanding the chemical foundation of life, which is based on atoms and molecules. Atoms are the fundamental units of matter, and their interactions form the basis of all biological processes.

• Atom: The smallest unit of an element that retains the properties of that element. Atoms are composed of subatomic particles.

• Subatomic particles:

  • Proton: Positively charged particle found in the nucleus.

  • Neutron: Electrically neutral particle found in the nucleus.

  • Electron: Negatively charged particle that orbits the nucleus.

• Element: A pure substance consisting of only one kind of atom, defined by its number of protons (atomic number).

Example: A carbon atom has 6 protons, 6 neutrons, and 6 electrons.

Atomic Number and Atomic Mass

Each element is characterized by its atomic number and atomic mass, which determine its identity and properties.

• Atomic number (Z): The number of protons in the nucleus of an atom. This defines the element.

• Atomic mass (A): The sum of protons and neutrons in the nucleus.

• Usually, atoms have equal numbers of protons and electrons, resulting in a net neutral charge.

Formula:

Isotopes

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

• Stable isotopes: Nuclei remain intact (e.g., 12C, 13C).

• Radioactive isotopes: Nuclei decay spontaneously, emitting energy and particles (e.g., 14C).

• Applications: Used in tracing biochemical pathways, medical imaging (PET scans), and dating fossils.

Electron Arrangement and Chemical Bonds

Electron Shells and Valence Electrons

The arrangement of electrons in shells around the nucleus determines how atoms interact and bond with each other.

• Electron shells: Energy levels where electrons are likely to be found.

• First shell: Holds up to 2 electrons.

• Subsequent shells: Hold up to 8 electrons each.

• Valence shell: The outermost occupied shell; atoms are most stable when this shell is full.

• Valence electrons: Electrons in the outermost shell, involved in chemical bonding.

Chemical Bonds

Atoms form chemical bonds to achieve stable electron configurations. The main types of chemical bonds are covalent, ionic, and hydrogen bonds.

• Covalent bonds: Strongest type; two atoms share one or more pairs of electrons.

  • Single bond: One pair of shared electrons.

  • Double bond: Two pairs of shared electrons (stronger than single bonds).

  • Nonpolar covalent bond: Electrons shared equally (e.g., CH4).

  • Polar covalent bond: Electrons shared unequally due to differences in electronegativity (e.g., H2O).

• Ionic bonds: Formed when one atom donates an electron to another, resulting in oppositely charged ions (cation and anion) that attract each other (e.g., NaCl).

• Hydrogen bonds: Weak attractions between the partial positive charge of hydrogen in one polar molecule and the partial negative charge of another atom (often oxygen or nitrogen) in a different molecule. Important in water and biological macromolecules.

Example: Water molecules are held together by hydrogen bonds, which are responsible for many of water's unique properties.

Electronegativity

Electronegativity is a measure of how strongly an atom attracts shared electrons in a bond.

• Atoms with higher electronegativity (e.g., oxygen) pull electrons closer, creating polar bonds.

• Differences in electronegativity determine bond type (nonpolar covalent, polar covalent, or ionic).

Chemistry of Water

Properties of Water

Water is essential for life due to its unique chemical and physical properties, most of which arise from its polarity and ability to form hydrogen bonds.

• Cohesion: Water molecules stick to each other due to hydrogen bonding, resulting in surface tension.

• Adhesion: Water molecules stick to other polar substances, enabling capillary action.

• High specific heat: Water absorbs and retains heat, stabilizing temperatures in organisms and environments.

• High heat of vaporization: Evaporation of water cools surfaces (e.g., sweating).

• Lower density as a solid: Ice is less dense than liquid water, so it floats, insulating aquatic life in winter.

• Excellent solvent: Water dissolves many ionic and polar substances, facilitating chemical reactions in cells.

Water as a Solvent

• Solution: A homogeneous mixture of two or more substances.

• Solvent: The dissolving agent (water in biological systems).

• Solute: The substance dissolved (e.g., salt, sugar).

• Hydrophilic: Substances that dissolve in water (ionic or polar).

• Hydrophobic: Substances that do not dissolve in water (nonpolar, e.g., oils).

Water in Chemical Reactions

• Water participates as a reactant or product in many biological reactions (e.g., hydrolysis, dehydration synthesis).

• Reactants: Starting materials in a chemical reaction.

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

Acids, Bases, and Buffers

Acids and Bases

Acids and bases are substances that affect the concentration of hydrogen ions (H+) in a solution, influencing pH.

• Acid: Increases H+ concentration in solution (e.g., HCl).

• Base: Decreases H+ concentration, either by accepting H+ or releasing OH- (e.g., NaOH).

• Salt: Compound that releases ions other than H+ or OH- when dissolved in water (e.g., NaCl).

Water dissociation:

pH Scale

• Measures the acidity or basicity of a solution.

• Scale ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

• Each unit represents a tenfold change in H+ concentration.

Buffers

Buffers are mixtures of weak acids and bases that resist changes in pH, helping maintain homeostasis in biological systems.

• Example: The bicarbonate buffer system in human blood maintains pH between 7.3 and 7.5.

Buffer system equation:

Introduction to Organic Compounds

Carbon-Based Molecules

Organic compounds are molecules that contain carbon and are fundamental to life. Carbon's ability to form four covalent bonds allows for a diversity of stable structures.

• Organic compounds: Contain carbon atoms bonded to hydrogen, and often to oxygen, nitrogen, phosphorus, or sulfur.

• Carbon can form chains, rings, and complex structures.

• Main classes: Proteins, nucleic acids, carbohydrates, and lipids.

Isomers

Isomers are molecules with the same molecular formula but different structural arrangements, resulting in different properties.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

• Hydroxyl (-OH): Alcohols

• Carbonyl (C=O): Aldehydes and ketones

• Carboxyl (-COOH): Carboxylic acids

• Amino (-NH2): Amines

• Phosphate (-OPO32-): Organic phosphates

Polymers and Monomers

Most large biological molecules are polymers, made by joining smaller units called monomers.

• Polymerization (Dehydration synthesis): Monomers are joined by covalent bonds, releasing water.

• Hydrolysis: Polymers are broken down into monomers by the addition of water.

Example: Proteins are polymers of amino acids; starch is a polymer of glucose.

Summary Table: Types of Chemical Bonds

Review Questions

• What is an atom, element, and isotope?

• What particles make up an atom?

• How are atomic mass and atomic number determined?

• What is a valence shell and how is it related to chemical bonding?

• Compare and contrast the three types of chemical bonds.

• Define and explain the properties of water and their importance for life.

• What are acids, bases, and buffers?

• What are organic compounds, isomers, polymers, and monomers? How are polymers created and broken down?