THE CHEMICAL CONTEXT OF LIFE

Introduction

This chapter introduces the fundamental chemical principles underlying biological processes. Understanding the composition and properties of matter, atomic structure, chemical bonds, and reactions is essential for studying life at the molecular level.

I. Matter Consists of Chemical Elements in Pure Form and Compounds

A. Organisms Are Composed of Matter

• Matter: Anything that has mass and occupies space.

• Element: A substance that cannot be broken down into other substances by chemical means.

• Atom: The smallest unit of an element that retains its chemical properties.

• Compound: A substance consisting of two or more elements combined in a fixed ratio. Example: Water (H2O) is a compound of hydrogen and oxygen.

• About 25 elements are essential for life.

• 96% of living matter is composed of four elements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

• Trace elements: Elements required by an organism in minute quantities (e.g., iron, iodine).

II. Properties of Elements Depend on Atomic Structure

A. Subatomic Particles

• Atoms are composed of three subatomic particles:

  • Protons (positive charge, p+)

  • Neutrons (no charge, n0)

  • Electrons (negative charge, e-)

• Atomic number: Number of protons in the nucleus of an atom.

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

• Atomic mass: The total mass of an atom, approximately equal to the mass number (measured in daltons).

• Isotopes: Atoms of the same element with different numbers of neutrons.

  • Radioactive isotopes: Unstable isotopes that decay spontaneously, emitting radiation. Useful in biological research and medicine (e.g., PET scans).

B. Energy

• Energy: The capacity to do work or cause change.

• Potential energy: Energy that matter possesses because of its location or structure.

• Energy levels (shells): Electrons have different amounts of potential energy depending on their distance from the nucleus. The further from the nucleus, the higher the energy level.

• Valence shell: The outermost electron shell; determines the chemical behavior of an atom.

C. Electron Orbitals

• Electron orbitals: Regions of space around the nucleus where electrons are likely to be found. Each orbital can hold up to two electrons.

• Electron configuration determines how atoms interact and bond with each other.

III. Chemical Bonds and Interactions

A. Chemical Bonds

• Electronegativity (EN): The attraction of an atom for electrons in a covalent bond.

  • Atoms on the left side of the periodic table (e.g., Na, Mg) have low EN.

  • Atoms on the right side (e.g., Cl, F) have high EN.

• Covalent bonds: Bonds formed by sharing electrons between atoms.

  • Single bond: Sharing of one pair of electrons.

  • Double bond: Sharing of two pairs of electrons.

  • Structural formula: Shows the arrangement of atoms (e.g., H—O—H for water).

  • Molecular formula: Indicates the number and type of atoms (e.g., H2O).

  • Valence: The bonding capacity of an atom, usually equal to the number of unpaired electrons in the valence shell.

• Nonpolar covalent bond: Electrons are shared equally between atoms.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges (e.g., in water molecules).

• Ionic bond: Formed when one atom transfers an electron to another, resulting in oppositely charged ions.

  • Cation: Positively charged ion (loses electron).

  • Anion: Negatively charged ion (gains electron).

  • Ionic compounds/salts: Compounds formed by ionic bonds (e.g., NaCl).

B. Hydrogen Bonds and Van der Waals Interactions

• Hydrogen bond: A weak bond between a hydrogen atom (already covalently bonded to an electronegative atom) and another electronegative atom (e.g., O or N).

• Van der Waals interactions: Weak attractions between molecules or parts of molecules that result from transient local partial charges.

C. Bond Strength Comparison

D. Molecules with Biological Functions

• The function of a molecule is related to its shape or structure.

• Molecular shape determines how biological molecules recognize and respond to one another.

IV. Chemical Reactions

A. Chemical Reactions: Making and Breaking Bonds

• Chemical reaction: The process of making and breaking chemical bonds, leading to changes in the composition of matter.

• Reactants: Starting materials in a chemical reaction.

• Products: Ending molecules formed by a chemical reaction.

• Chemical equilibrium: The point at which the forward and reverse reactions occur at the same rate, and the concentrations of reactants and products remain constant.

Additional info:

• Example of a chemical reaction:

• Isotopes are used in radiometric dating and as tracers in metabolic studies.

• Hydrogen bonds are crucial for the properties of water and the structure of DNA and proteins.