Atoms, Molecules, and Life

Introduction

Chemistry is fundamental to biology because the interactions between atoms form the basis of all biological organization. Understanding the structure and behavior of atoms, molecules, and their interactions is essential for comprehending life processes.

Atoms: The Basic Unit of Matter

Definition and Structure

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

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

Subatomic Particles

• Protons and neutrons are found in the nucleus.

• Electrons are found in electron shells surrounding the nucleus.

Elements and Isotopes

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

The 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, forming 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, which contains nitrogen, oxygen, carbon dioxide).

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 called salts and usually form crystals.

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, Adhesion, and Surface Tension

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

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

• Water has higher surface tension than most liquids.

Solvent Properties of Water

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

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

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

Thermal Properties of Water

• Water helps moderate temperature changes due to:

  • High specific heat: The amount of energy required to raise the temperature of 1 gram of water by 1°C is high (1 calorie/gram).

  • High heat of vaporization: The amount of energy required to convert 1 gram of water from liquid to gas is high.

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

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: particles (Avogadro's number).

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

Acids, Bases, and pH

Acids and Bases

• Water can dissociate into hydrogen ions () and hydroxide ions ():

• Acid: Increases the concentration of in a solution.

• Base: Reduces the concentration of (often by increasing ).

The pH Scale

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

• pH is defined as:

• Each pH unit represents a tenfold change in concentration.

• Neutral solution: ()

• Acidic solution: ()

• Basic solution: ()

Buffers

• Buffers: Substances that minimize changes in pH by accepting or donating ions as needed.

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

• They help maintain a stable pH in biological systems, which is crucial for proper cellular function.

Summary Table: Key Properties of Water

Example: Bicarbonate Buffer System

• The bicarbonate buffer system helps maintain blood pH by balancing and ions.

Additional info: The notes above provide a foundational understanding of atomic structure, chemical bonding, water chemistry, and acid-base balance, all of which are essential for further study in biology, including cell structure, metabolism, and physiology.