Basic Chemistry for Biology

Atoms and Their Structure

Atoms are the fundamental building blocks of matter and the smallest unit of an element that retains its chemical properties. Understanding atomic structure is essential for studying biological molecules and processes.

• Atom: The smallest particle of an element, consisting of a nucleus and electrons.

• Nucleus: The central part of the atom containing protons and neutrons.

• Proton: Positively charged particle found in the nucleus.

• Neutron: Neutral particle found in the nucleus.

• Electron: Negatively charged particle orbiting the nucleus in energy levels.

Energy Levels and Electron Configuration

Electrons occupy specific energy levels (shells) around the nucleus. The arrangement of electrons determines the chemical properties and reactivity of an atom.

• Each energy level can hold a certain number of electrons:

  • First level: 2 electrons

  • Second level: 8 electrons

  • Third level: 8 electrons (for main group elements)

• All occupied energy levels must be full for an atom to be stable (noble gas configuration).

• Example: An atom with 8 electrons: 2 in the first level, 6 in the second. Not stable, as the second level is not full.

Elements and the Periodic Table

Elements are pure substances that cannot be broken down into simpler substances. The periodic table organizes all known elements by their atomic number and properties.

• There are 90 naturally occurring elements.

• Only 25 elements are essential for living organisms; 96% of human mass is made up of carbon (C), hydrogen (H), nitrogen (N), and oxygen (O).

• Atomic Number: Number of protons in the nucleus; also equals the number of electrons in a neutral atom.

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

Ions and Isotopes

Ions and isotopes are variations of elements that play important roles in biological systems.

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

  • Positive ion (cation): Fewer electrons than protons.

  • Negative ion (anion): More electrons than protons.

• Isotope: Atoms of the same element with different numbers of neutrons (e.g., Carbon-12, Carbon-13, Carbon-14).

Chemical Bonds

Atoms combine to form compounds and molecules through different types of chemical bonds, which are crucial for the structure and function of biological molecules.

• Covalent Bond: Atoms share pairs of electrons. Found in most organic compounds (e.g., H2O, O2).

• Polar Covalent Bond: Electrons are shared unequally, resulting in partial charges (e.g., water).

• Nonpolar Covalent Bond: Electrons are shared equally (e.g., H2 gas).

• Ionic Bond: Electrons are transferred from one atom to another, creating oppositely charged ions that attract (e.g., NaCl).

• Hydrogen Bond: Weak attraction between a hydrogen atom (partially positive) and another electronegative atom (often oxygen or nitrogen). Important in water and biological macromolecules.

Water: Structure, Properties, and Importance

Structure and Polarity of Water

Water (H2O) is a polar molecule due to the unequal sharing of electrons between oxygen and hydrogen atoms. This polarity leads to many of water's unique properties.

• Oxygen has a higher electronegativity, pulling electrons closer and creating a partial negative charge on oxygen and partial positive charges on hydrogens.

• Polarity allows water molecules to form hydrogen bonds with each other.

Properties of Water

Water's properties are essential for life and are largely due to its polarity and ability to form hydrogen bonds.

• Cohesion: Attraction between water molecules, leading to surface tension.

• Adhesion: Attraction between water molecules and other substances, causing phenomena like the meniscus in a graduated cylinder and capillary action.

• High Specific Heat Capacity: Water absorbs large amounts of heat before changing temperature, helping regulate temperature in organisms and environments.

• Evaporative Cooling: As water evaporates, it removes heat, cooling surfaces (e.g., sweating).

• Versatile Solvent: Water dissolves many substances due to its polarity, making it the "universal solvent" in biological systems.

Solutions and pH

Water forms solutions by dissolving solutes. The pH scale measures the concentration of hydrogen ions (H+) in a solution, indicating its acidity or basicity.

• Solution: Homogeneous mixture of solute (substance dissolved) and solvent (substance doing the dissolving; water is the universal solvent).

• pH Scale: Ranges from 0 (most acidic) to 14 (most basic); pH 7 is neutral (pure water).

• Acid: Substance that increases H+ concentration (pH < 7).

• Base: Substance that increases OH- concentration (pH > 7).

Chemical Equations in Biology

Understanding Chemical Equations

Chemical equations represent the reactants and products in a chemical reaction. They are fundamental for describing metabolic processes in biology.

• Reactants: Substances that undergo change during a reaction.

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

• Chemical Equation Example:

• Coefficients: Numbers before compounds/elements indicating the number of molecules or atoms involved (e.g., 6CO2 means 6 molecules of CO2).

• Subscripts: Numbers within chemical formulas indicating the number of atoms in a molecule (e.g., H2O has 2 hydrogen atoms).

Summary Table: Types of Chemical Bonds