Atomic Structure, Electron Configuration, and Chemical Bonds in Biology

Atomic Structure and Electron Shells

Introduction to Atomic Structure

Atoms are the fundamental units of matter, composed of a central nucleus (containing protons and neutrons) surrounded by electrons. The arrangement of electrons in shells around the nucleus determines the chemical properties and reactivity of each element.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles that occupy regions called electron shells around the nucleus.

Example: A helium atom has 2 protons, 2 neutrons, and 2 electrons.

Electron Shells and Energy Levels

Electrons occupy specific energy levels or shells around the nucleus. Each shell can hold a certain maximum number of electrons, and electrons fill the lowest available energy levels first.

• First shell: Holds up to 2 electrons.

• Second shell: Holds up to 8 electrons.

• Third shell: Holds up to 8 electrons (for main group elements).

• Each shell is further divided into orbitals, which are regions of space where electrons are likely to be found.

• Electrons in the same orbital must have opposite spins.

Additional info: The arrangement of electrons in shells and orbitals is described by the Aufbau principle, Pauli exclusion principle, and Hund's rule.

Electron Configuration and the Periodic Table

The periodic table is organized based on atomic number and electron configuration. The distribution of electrons among shells and orbitals determines the chemical behavior of each element.

• Elements in the same group (column) have similar valence electron configurations and similar chemical properties.

• The valence shell is the outermost electron shell, and its electrons are called valence electrons.

Example: Carbon (atomic number 6) has the electron configuration 1s2 2s2 2p2.

Elements Essential to Life

Major Elements in the Human Body

Living organisms are composed primarily of a small number of elements. The most abundant elements in the human body are:

Element	Symbol	Percentage of Body Mass (including water)
Oxygen	O	65.0%
Carbon	C	18.5%
Hydrogen	H	9.5%
Nitrogen	N	3.3%
Calcium	Ca	1.5%
Phosphorus	P	1.0%
Potassium	K	0.4%
Sulfur	S	0.3%
Sodium	Na	0.2%
Chlorine	Cl	0.2%
Magnesium	Mg	0.1%
Trace elements	-	<0.01%

Additional info: Trace elements such as iron (Fe), zinc (Zn), and iodine (I) are essential in very small amounts for biological processes.

Elements, Compounds, and Emergent Properties

Elements and Compounds

An element is a substance that cannot be broken down into simpler substances by chemical means. A compound is a substance consisting of two or more elements in a fixed ratio, with properties different from its constituent elements.

• Emergent properties: New characteristics that arise when elements combine to form compounds, which are not present in the individual elements.

Example: Sodium (Na) is a soft, reactive metal; chlorine (Cl) is a toxic gas. Together, they form sodium chloride (NaCl), common table salt, which is safe to eat.

Valence Electrons and Chemical Reactivity

Valence Electrons

The valence electrons are the electrons in the outermost shell of an atom. These electrons determine how an atom interacts with other atoms and participate in chemical bonding.

• Atoms with a full valence shell are chemically stable (e.g., noble gases).

• Atoms with incomplete valence shells are chemically reactive and tend to form bonds to achieve stability.

Example: Neon (Ne) has a full valence shell and is inert, while sodium (Na) has one valence electron and is highly reactive.

Chemical Bonds

Types of Chemical Bonds

Atoms form chemical bonds to achieve stable electron configurations. The main types of chemical bonds are:

• Ionic bonds: Formed by the transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent bonds: Formed by the sharing of valence electrons between atoms.

• Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom.

Ionic Bonds

Ionic bonds occur when one atom donates an electron to another, creating positively charged (cation) and negatively charged (anion) ions. These ions are held together by electrostatic attraction.

• Example: Sodium (Na) donates an electron to chlorine (Cl), forming Na+ and Cl-, which combine to make NaCl.

Covalent Bonds

Covalent bonds involve the sharing of one or more pairs of electrons between atoms. Each shared pair constitutes a single covalent bond.

• Single bond: One pair of shared electrons (e.g., H—H).

• Double bond: Two pairs of shared electrons (e.g., O=O).

• Structural formula: Shows the arrangement of atoms and bonds (e.g., H—O—H for water).

Example: In water (H2O), each hydrogen shares one electron with oxygen, forming two single covalent bonds.

Electronegativity and Bond Polarity

Electronegativity is an atom's ability to attract shared electrons in a chemical bond. The difference in electronegativity between two atoms determines the type of bond formed:

• If the difference is > 2.0, the bond is ionic.

• If the difference is < 2.0, the bond is covalent.

• If the difference is small (< 0.5), the bond is nonpolar covalent (electrons shared equally).

• If the difference is moderate (0.5–2.0), the bond is polar covalent (electrons shared unequally).

Bond Type	Description	Example
Nonpolar covalent	Electrons shared equally	H2, O2
Polar covalent	Electrons shared unequally, partial charges	H2O
Ionic	Complete transfer of electrons, full charges	NaCl

Additional info: Electronegativity increases across a period and decreases down a group in the periodic table.

Hydrogen Bonds

Hydrogen bonds are weak interactions that occur when a hydrogen atom covalently bonded to a highly electronegative atom (such as oxygen or nitrogen) is attracted to another electronegative atom. These bonds are crucial in stabilizing the structures of biological molecules like DNA and proteins.

• Example: The attraction between water molecules due to hydrogen bonding gives water its unique properties.

Summary Table: Electron Shells and Orbitals

Shell	Maximum Electrons	Orbitals Present
1 (K)	2	1s
2 (L)	8	2s, 2p
3 (M)	8 (main group)	3s, 3p

Additional info: Higher shells can hold more electrons, but for main group elements, the third shell is usually filled with 8 electrons before the fourth shell begins to fill.

Key Equations

• Maximum electrons per shell: $2n^2$ (where n = shell number)

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