Basic Chemistry for Biology

Atoms and Their Structure

Atoms are the fundamental building blocks of matter and the smallest units of elements that retain their chemical properties. Understanding atomic structure is essential for grasping biological processes at the molecular level.

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

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

• Proton: Positively charged particle found in the nucleus.

• Neutron: Neutrally charged 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 energy level: 2 electrons

  • Second energy level: 8 electrons

  • Third energy 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 has 2 in the first level and 6 in the second; it is not stable because 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.

Isotopes and Ions

Atoms of the same element can have different numbers of neutrons (isotopes) or different numbers of electrons (ions).

• Isotopes: Atoms with the same number of protons but different numbers of neutrons (e.g., Carbon-12, Carbon-13, Carbon-14).

• Ions: Charged atoms formed by gaining or losing electrons.

  • Positive ions (cations): Fewer electrons than protons.

  • Negative ions (anions): More electrons than protons.

Chemical Bonds and Molecules

Types of Chemical Bonds

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

• Covalent Bond: Atoms share pairs of electrons. Found in most organic molecules (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, O2).

• 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 (in a polar bond) and another electronegative atom (e.g., between water molecules).

Polarity and Water

Water is a polar molecule, meaning it has regions of partial positive and negative charge due to unequal sharing of electrons between oxygen and hydrogen.

• Oxygen is more electronegative, pulling electrons closer and creating a partial negative charge on the oxygen atom and partial positive charges on the hydrogens.

• This polarity allows water to form hydrogen bonds with other water molecules and with other polar substances.

Properties of Water

Cohesion and Adhesion

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

• Cohesion: Attraction between molecules of the same substance (water to water), leading to surface tension.

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

Thermal Properties and Solvent Abilities

• High Specific Heat Capacity: Water absorbs and retains heat, moderating temperature changes in organisms and environments.

• Evaporative Cooling: As water evaporates (e.g., sweating), it removes heat from surfaces, helping regulate body temperature.

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

Solutions and pH

Solutions are mixtures where one substance (solute) is dissolved in another (solvent). Water is the most common biological solvent.

• Solute: Substance being dissolved (e.g., salt, sugar).

• Solvent: Substance doing the dissolving (e.g., water).

• pH: Measures the concentration of hydrogen ions (H+) in a solution; scale ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

• Acids: Substances that increase H+ concentration (pH < 7).

• Bases: Substances that increase OH- concentration (pH > 7).

Chemical Equations in Biology

Reactants, Products, and Balancing Equations

Chemical equations represent the transformation of reactants into products. Balancing equations ensures the conservation of mass and atoms.

• Reactants: Substances present before the reaction.

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

• Coefficients: Numbers placed before compounds to indicate the number of molecules involved.

• Subscripts: Numbers within chemical formulas indicating the number of atoms of each element in a molecule.

Example Equation:

• Glucose and oxygen react to form carbon dioxide, water, and energy (cellular respiration).

Summary Table: Key Atomic and Chemical Concepts