Atoms, Molecules, and Life

Introduction

Understanding chemistry is fundamental to biology because the interactions between atoms form the basis of all biological organization. This section covers the structure of atoms, the nature of chemical bonds, and the properties of water that are essential for life.

Atoms and Subatomic Particles

Structure of the Atom

• Atom: The smallest unit of matter that retains the physical and chemical properties of an element.

• Atoms are composed of three main subatomic particles: protons, neutrons, and electrons.

• Protons determine the atomic number and identity of an element.

• Neutrons contribute to the atomic mass and can vary in number, resulting in isotopes.

• Electrons are involved in chemical bonding and determine the atom's reactivity.

Elements and Isotopes

• Element: A substance that cannot be broken down into other substances by chemical reactions. Each element is composed of one type of atom.

• Atomic number: The number of protons in an atom, unique to each element.

• Atomic weight: The sum of protons and neutrons in an atom.

• Isotopes: Atoms of the same element with different numbers of neutrons, resulting in different atomic weights.

Electron Shells

• Electron shells are three-dimensional spaces around the nucleus where electrons are likely to be found.

• Electrons are arranged in shells based on their energy levels; shells farther from the nucleus have higher energy.

• The chemical behavior of an atom is determined by the number of electrons in its outermost shell (valence shell).

• Atoms with incomplete valence shells are reactive; those with full shells are inert.

Chemical Bonds: Joining Atoms to Make Molecules

Types of Chemical Bonds

• Chemical bond: An attraction that holds two atoms together.

• Molecule: Two or more atoms held together by chemical bonds, representing the smallest unit of a compound.

• Compound: A substance composed of two or more elements in a fixed ratio (e.g., NaCl).

• Mixture: Two or more elements and/or compounds in a variable ratio (e.g., air).

Formation of Ions and Ionic Bonds

• Ion: A charged atom or molecule.

• Anion: Negatively charged ion.

• Cation: Positively charged ion.

• Ionic bond: Formed by the attraction between oppositely charged ions after electron transfer. Ionic compounds are often crystalline solids (salts).

Sharing Electrons: Covalent Bonds

• Covalent bond: A bond formed when two atoms share electrons to fill their outer shells.

• Single covalent bond: Shares one pair of electrons.

• Double covalent bond: Shares two pairs of electrons.

Nonpolar vs. Polar Covalent Bonds

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

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges on the molecule.

• Polar molecules have regions of partial positive and negative charge.

Hydrogen Bonds

• Hydrogen bond: A weak attraction between a hydrogen atom covalently bonded to one atom and another electronegative atom (often oxygen or nitrogen).

• Hydrogen bonds are much weaker than covalent bonds but are crucial for the structure and function of biological molecules.

• They help stabilize the three-dimensional shape of large molecules and can form between or within molecules.

Water and Life

Properties of Water

• Cells are 70-95% water; water covers about 70% of Earth's surface.

• Water molecules are polar and can form hydrogen bonds with each other.

Cohesion and Surface Tension

• Cohesion: Attraction between molecules of the same kind (e.g., water molecules sticking together).

• Surface tension: The force that allows the surface of a liquid to resist external force, due to cohesive hydrogen bonding at the surface.

Solvent Properties

• Hydrophilic: Substances with an affinity for water; easily dissolve in water (e.g., salts, sugars).

• Hydrophobic: Substances that do not have an affinity for water; do not dissolve easily (e.g., oils).

• Water is a versatile solvent due to its polarity and ability to form hydrogen bonds.

Thermal Properties

• Water helps moderate temperature changes due to its high specific heat and high heat of vaporization.

• Specific heat: The amount of energy required to raise the temperature of 1 gram of a substance by 1°C.

• Heat of vaporization: The quantity of heat required to convert 1 gram of liquid to gas.

• Water expands upon freezing, causing ice to float and insulate aquatic environments.

Solutions, Acids, and Bases

Solution Concentration

• Solute concentration: The amount of solute in a given volume of solution.

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

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

• Molecular weight: The sum of the atomic masses of all atoms in a molecule.

Acids, Bases, and pH

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

• Acid: Increases the concentration of H+ in solution.

• Base: Reduces the concentration of H+ (often by increasing OH-).

• pH scale: Measures the acidity of a solution, ranging from 0 (most acidic) to 14 (most basic).

• The pH scale is logarithmic: a change of one pH unit represents a tenfold change in H+ concentration.

• Most biological solutions have a pH between 6 and 8.

Buffers

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

• Buffers are combinations of H+ donors and acceptors (e.g., bicarbonate buffer in blood).

• They help maintain a constant pH in biological systems.

Key Equations and Concepts

• Relationship between [H+] and [OH-]:

• Molarity:

• Specific heat:

• Heat of vaporization:

Summary Table: Types of Chemical Bonds

Example: Bicarbonate Buffer System

• Helps maintain blood pH by balancing H+ and HCO3- ions.

Additional info: The notes above have been expanded for clarity and completeness, including definitions, examples, and key equations relevant to introductory college biology.