Atomic Structure, Elements, and Chemical Bonds: Foundations of General Biology

Atomic Structure and Matter

Introduction to Matter, Elements, and Atoms

All living and non-living things are composed of matter, which is governed by the laws of physics and chemistry. Understanding the structure of matter is fundamental to biology, as it underpins the composition and behavior of all biological molecules.

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

• Element: A pure substance consisting of only one kind of atom (e.g., Oxygen, Hydrogen).

• Atom: The smallest unit of an element that retains the properties of that element (e.g., O, H, C).

• Molecule: Two or more atoms joined together (e.g., O2, H2, H2O).

• Compound: A molecule that contains more than one element (e.g., H2O, C6H12O6).

Elements Essential for Life

About 25 elements are essential for life, with a few making up the majority of living matter.

• Major elements: Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N) constitute about 96% of the human body mass (excluding water).

• Other essential elements: Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg).

• Trace elements: Required in minute amounts (e.g., Iron (Fe), Iodine (I), Zinc (Zn)).

Atomic Structure

Subatomic Particles

Atoms are composed of three main subatomic particles:

• Protons: Positively charged particles found in the nucleus; determine the atomic number.

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

• Electrons: Negatively charged particles orbiting the nucleus in electron shells; determine chemical behavior.

Atomic Number, Mass, and Isotopes

• Atomic Number (Z): Number of protons in the nucleus; unique to each element.

• Atomic Mass: Total number of protons and neutrons (measured in Daltons).

• Isotopes: Atoms of the same element with different numbers of neutrons. Some isotopes are stable, while others are radioactive and decay over time, emitting particles and energy.

Example: Carbon-12 (12C) and Carbon-14 (14C) are isotopes of carbon.

Electron Shells and Valence

• Electrons are arranged in shells around the nucleus, each with a specific energy level.

• The first shell holds up to 2 electrons; the second and third shells hold up to 8 electrons each.

• Valence electrons: Electrons in the outermost shell; determine the reactivity of the atom.

• Atoms with full valence shells are chemically inert (noble gases), while those with incomplete shells are reactive.

Chemical Bonds and Electronegativity

Types of Chemical Bonds

Atoms with incomplete outer shells can share or transfer electrons to achieve stability, forming chemical bonds.

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

• Ionic Bonds: Atoms transfer electrons, resulting in oppositely charged ions that attract each other (e.g., Na+ and Cl- in NaCl).

• Hydrogen Bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like O or N) and another electronegative atom.

Electronegativity and Bond Polarity

• Electronegativity: A measure of how strongly an atom attracts electrons in a bond. Increases across a period and decreases down a group in the periodic table.

• Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., H2, O2).

• Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

• Ionic Bonds: Large differences in electronegativity lead to electron transfer and formation of ions.

Electronegativity Difference and Bond Type:

• Difference < 0.4: Nonpolar covalent

• Difference 0.4–2.0: Polar covalent

• Difference > 2.0: Ionic

Common Ions in Biology

Ion Name	Symbol	Charge	Electron Change
Sodium ion	Na+	+1	Lost 1 electron
Chloride ion	Cl-	-1	Gained 1 electron
Potassium ion	K+	+1	Lost 1 electron
Calcium ion	Ca2+	+2	Lost 2 electrons
Magnesium ion	Mg2+	+2	Lost 2 electrons
Hydrogen ion	H+	+1	Lost 1 electron

Summary Table: Types of Chemical Bonds

Bond Type	Description	Relative Strength	Example
Covalent	Atoms share electron pairs	Strongest	H2O, O2
Ionic	Transfer of electrons; attraction between ions	Intermediate	NaCl
Hydrogen	Attraction between H and electronegative atom	Weakest	Between water molecules

Key Equations

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

• Electronegativity Difference: $\Delta EN = |EN_1 - EN_2|$

Additional info:

• Some content, such as the periodic table and specific isotope applications, was inferred from standard biology curricula.

• Tables were reconstructed and expanded for clarity and completeness.