Atoms, Elements, and Chemical Bonds

Introduction

This section introduces the chemical foundations of biology, focusing on the structure of atoms, the nature of elements, and the types of chemical bonds that enable the formation of complex biological molecules. Understanding these concepts is essential for grasping how living systems are built and maintained at the molecular level.

Learning Objectives

• Compare chemical bonds and interactions, including hydrogen bonds, covalent bonds, polar covalent bonds, and ionic bonds.

• Explain the structure of atoms and how atomic structure contributes to chemical behavior and bonding.

• Describe the importance of trace elements in human health.

Elements and Atoms

Definition and Classification

• Element: A substance that cannot be broken down into other substances by chemical means. Each element is defined by its number of protons.

• Atom: The smallest unit of an element that retains the properties of that element.

• There are about 25 essential elements for life, with four (carbon, hydrogen, oxygen, nitrogen) making up about 96% of living matter.

• Trace elements are required in minute amounts but are vital for health (e.g., iodine, iron).

Table: Major and Trace Elements in the Human Body

Importance of Trace Elements

• Trace elements are required in very small amounts but are essential for proper physiological function.

• Iodine deficiency can lead to thyroid gland problems, such as goiter.

Atomic Structure

Subatomic Particles

• Protons: Positively charged particles found in the nucleus; number of protons defines the element (atomic number).

• Neutrons: Neutral particles found in the nucleus; contribute to atomic mass.

• Electrons: Negatively charged particles orbiting the nucleus in specific energy levels (shells).

Atomic Number and Mass Number

• Atomic number (Z): Number of protons in the nucleus of an atom.

• Mass number (A): Sum of protons and neutrons in the nucleus.

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

Electron Arrangement

• Electrons occupy energy levels or "shells" around the nucleus.

• The chemical properties of an atom are largely determined by the number and arrangement of electrons, especially those in the outermost shell (valence electrons).

• First shell holds up to 2 electrons; second shell up to 8 electrons.

Periodic Table and Chemical Properties

Periodic Table Organization

• Elements are arranged by increasing atomic number.

• Rows (periods) correspond to the number of electron shells.

• Columns (groups) correspond to the number of electrons in the outer shell (valence electrons).

Valence Electrons and Reactivity

• Atoms with incomplete valence shells are more chemically reactive.

• Atoms tend to gain, lose, or share electrons to achieve a full valence shell (usually 8 electrons, known as the octet rule).

Chemical Bonds

Types of Chemical Bonds

• Covalent Bonds: Atoms share pairs of electrons to fill their valence shells. Can be single, double, or triple bonds.

• Polar Covalent Bonds: Unequal sharing of electrons due to differences in electronegativity (e.g., in water molecules).

• Nonpolar Covalent Bonds: Equal sharing of electrons (e.g., in O2 or H2 molecules).

• Ionic Bonds: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other (e.g., NaCl).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom (important in water and DNA structure).

Electronegativity

• Electronegativity is an atom's attraction for shared electrons in a covalent bond.

• Differences in electronegativity determine whether a bond is nonpolar covalent, polar covalent, or ionic.

Summary Table: Types of Chemical Bonds

Applications and Examples

• Water: The polar covalent bonds and hydrogen bonding in water give it unique properties essential for life.

• Biological molecules: The structure and function of proteins, nucleic acids, and other biomolecules depend on the types and arrangements of chemical bonds.

• Health: Deficiencies in trace elements (e.g., iodine) can lead to significant health issues.

Additional info:

• Radioactive isotopes can be used as tracers in medical diagnostics.

• Atomic mass is measured in daltons (1 dalton ≈ mass of 1 proton or neutron).