Atoms, Molecules, and Water

Introduction

This section introduces the chemical foundations of biology, focusing on the structure of matter, types of chemical bonds, the properties of water, and the importance of acids, bases, and buffers in biological systems.

Levels of Biological Organization and Size Range

Overview of Biological Scale

• Atoms: The smallest units of matter, forming the basis of all substances.

• Molecules: Combinations of atoms held together by chemical bonds.

• Cells: The lowest level of organization capable of performing all activities required for life.

• Organisms: Composed of many cells and higher-order structures.

Biological structures range in size from atoms (about 0.1 nm) to entire organisms (meters in length). Light and electron microscopes are used to visualize structures at different scales.

Composition of Matter

Elements and Atoms

• Matter: Anything that takes up space and has mass.

• Element: A substance that cannot be broken down into other substances by chemical means; composed of only one type of atom.

• There are 92 natural elements; about 25 are essential for life.

• Four elements—carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)—make up about 96% of living matter.

• Trace elements (e.g., Fe, I, Zn, Cu) are required in minute amounts.

Atomic Structure

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

• Composed of subatomic particles:

  • Protons: Positive charge, found in the nucleus.

  • Neutrons: No charge, found in the nucleus.

  • Electrons: Negative charge, orbit the nucleus in electron shells.

• The number of protons defines the element.

Chemical Bonds and Molecules

Types of Chemical Bonds

• Covalent Bonds: Sharing of electron pairs between atoms.

  • Single bond: Sharing of one pair of electrons.

  • Double bond: Sharing of two pairs of electrons.

  • Nonpolar covalent bond: Equal sharing of electrons.

  • Polar covalent bond: Unequal sharing of electrons, leading to partial charges.

• Ionic Bonds: Transfer of electrons from one atom to another, resulting in oppositely charged ions (cations and anions) that attract each other.

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

Importance of Chemical Bonds

• Chemical bonds determine the structure and function of molecules.

• Interactions between molecules (e.g., enzyme-substrate binding) often depend on hydrogen bonds and other weak interactions.

Water: Structure and Properties

Molecular Structure of Water

• Water (H2O) consists of two hydrogen atoms covalently bonded to one oxygen atom.

• The molecule is polar, with a partial negative charge near the oxygen and partial positive charges near the hydrogens.

• Hydrogen bonding between water molecules leads to unique properties.

Emergent Properties of Water

• Cohesion: Water molecules stick together via hydrogen bonds, aiding transport in plants.

• Moderation of Temperature: Water has a high specific heat, buffering temperature changes.

• Expansion Upon Freezing: Ice is less dense than liquid water, allowing it to float.

• Versatile Solvent: Water dissolves many substances due to its polarity.

Water as a Solvent

• Solvent: The dissolving agent (e.g., water).

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

• Solution: A homogeneous mixture of solvent and solute.

• Water forms hydration shells around ions and polar molecules, facilitating dissolution.

• Hydrophilic substances: Attracted to water (ionic or polar compounds).

• Hydrophobic substances: Repel water (nonpolar compounds, e.g., oils).

Acids, Bases, and pH

Dissociation of Water

• Water molecules can dissociate into hydrogen ions (H+) and hydroxide ions (OH-).

• In pure water at 25°C:

• Hydronium ion (H3O+): A water molecule with an extra proton.

Acids and Bases

• Acid: Increases the concentration of H+ in a solution (proton donor).

• Base: Decreases the concentration of H+ (proton acceptor or produces OH-).

• Strong acids and bases dissociate completely in water; weak acids and bases reversibly release and accept protons.

pH Scale

• pH is a measure of hydrogen ion concentration:

• Neutral solution: pH = 7 ( M)

• Acidic solution: pH < 7

• Basic solution: pH > 7

Buffers

• Buffer: A substance that minimizes changes in pH by accepting or donating H+ as needed.

• Example: The carbonic acid/bicarbonate buffer system in blood helps maintain pH between 7.37 and 7.43.

• Buffer equilibrium:

Table: Types of Chemical Bonds

Key Terms and Definitions

• Atom: Smallest unit of an element.

• Molecule: Two or more atoms held together by covalent bonds.

• Compound: Substance consisting of two or more different elements combined in a fixed ratio.

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

• Solvent: The dissolving agent in a solution.

• Solute: The substance dissolved in a solution.

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

• Hydrophilic: Water-attracting.

• Hydrophobic: Water-repelling.

• Buffer: Substance that resists changes in pH.

Summary

• Understanding atoms, molecules, and water is fundamental to biology.

• Chemical bonds determine the structure and function of biological molecules.

• Water's unique properties support life on Earth.

• Acids, bases, and buffers are crucial for maintaining stable conditions in living organisms.

Additional info: Some explanations and definitions were expanded for clarity and completeness based on standard biology textbooks.