Study Guide: Basic Chemistry for Biology (Atoms, Bonds, and Molecules)

Basic Chemistry in Biology

Major Elements in Living Things

Living organisms are primarily composed of a few key elements that are essential for life processes.

• Most Common Elements: The four elements most abundant in living things are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N).

• Trace Elements: These are elements required by an organism in only minute quantities, such as iron (Fe), iodine (I), and zinc (Zn).

• Example: Iron is a trace element necessary for oxygen transport in blood.

Structure of the Atom

An atom is the smallest unit of matter that retains the properties of an element.

• Subatomic Particles: Atoms are composed of protons (positively charged), neutrons (neutral), and electrons (negatively charged).

• Atomic Number: The number of protons in an atom, which defines the element.

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

• Electron Distribution: Electrons are arranged in shells or energy levels around the nucleus. The arrangement affects chemical reactivity.

• Valence Shell: The outermost electron shell, which determines bonding behavior.

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Example: Carbon-12 and Carbon-14 are isotopes of carbon.

Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds.

• Covalent Bonds: Atoms share pairs of electrons. Can be single, double, or triple bonds depending on the number of shared electron pairs.

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

• Nonpolar Covalent Bonds: Electrons are shared equally between atoms.

• Ionic Bonds: Electrons are transferred from one atom to another, creating charged ions (cations and anions) that attract each other.

• Hydrogen Bonds: Weak attractions between a hydrogen atom (already covalently bonded to a more electronegative atom) and another electronegative atom.

• Van der Waals Interactions: Weak, temporary attractions between molecules due to transient charge differences.

• Example: Table salt (NaCl) is formed by ionic bonding between sodium and chlorine.

Molecular Shape and Its Importance

The shape of a molecule is determined by the arrangement of its atoms and the bonds between them. This shape is crucial for the molecule's function in biological systems.

• Functionality: The specific shape of a molecule determines how it interacts with other molecules (e.g., enzyme-substrate specificity).

• Example: The double helix structure of DNA is essential for its function in genetic information storage.

Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, leading to changes in the composition of matter.

• Reactants: Substances that start a chemical reaction.

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

• Example: Photosynthesis converts carbon dioxide and water (reactants) into glucose and oxygen (products).

Key Vocabulary

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

• Element: A substance that cannot be broken down into other substances by chemical means.

• Atom: The basic unit of an element.

• Neutron: A subatomic particle with no charge, found in the nucleus.

• Proton: A positively charged subatomic particle in the nucleus.

• Electron: A negatively charged subatomic particle orbiting the nucleus.

• Atomic Number: Number of protons in an atom.

• Atomic Mass: Total number of protons and neutrons.

• Valence Shell: The outermost electron shell.

• Isotope: Atoms of the same element with different numbers of neutrons.

• Compound: A substance formed from two or more elements in fixed proportions.

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

• Molecular Formula: Shows the types and numbers of atoms in a molecule (e.g., H2O).

• Ion: An atom or molecule with a net electric charge.

• Cation: A positively charged ion.

• Anion: A negatively charged ion.

• Electronegativity: The ability of an atom to attract electrons in a bond.

• Reactants: Starting materials in a chemical reaction.

• Products: Substances produced by a chemical reaction.

Summary Table: Types of Chemical Bonds

Bond Type	Description	Strength	Example
Covalent	Atoms share electron pairs	Strong	H2O (water)
Ionic	Transfer of electrons creates ions	Strong (in dry conditions)	NaCl (table salt)
Hydrogen	Attraction between H and electronegative atom	Weak	Between water molecules
Van der Waals	Temporary attractions due to transient charges	Very weak	Gecko feet adhesion

Key Equations

• Atomic Mass Calculation:

$\text{Atomic Mass} = \text{Number of Protons} + \text{Number of Neutrons}$

• General Chemical Reaction:

$\text{Reactants} \rightarrow \text{Products}$