Atoms, Elements, and Chemical Bonds: Foundations for General Biology

Atoms and Elements

Introduction to Atoms and Elements

Understanding living organisms begins with knowledge of the chemical building blocks that compose them. Atoms are the fundamental units of matter, and elements are pure substances consisting of only one type of atom. Biological molecules are primarily made from a small subset of elements, including carbon, hydrogen, oxygen, and nitrogen.

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

• Element: A pure substance made of only one kind of atom; 92 naturally occurring elements exist.

• Periodic Table: Organizes elements by increasing atomic number and groups elements with similar properties.

• Common Biological Elements: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Sulfur (S), Phosphorus (P).

Example: Water (H2O) is composed of hydrogen and oxygen atoms.

Atomic Structure

Atoms consist of subatomic particles: protons, neutrons, and electrons. The arrangement and number of these particles determine the atom's identity and properties.

• Proton (p): Positively charged particle found in the nucleus; defines the atomic number.

• Neutron (n): Neutral particle found in the nucleus; contributes to atomic mass.

• Electron (e): Negatively charged particle found in orbitals around the nucleus; involved in chemical bonding.

Subatomic Particle	Charge	Mass	Location
Proton (p)	+1	1 AMU	Atomic nucleus
Neutron (n)	0	1 AMU	Atomic nucleus
Electron (e)	-1	~0 AMU	Orbitals outside nucleus

Atomic Number: Number of protons in the nucleus; determines the element.

Atomic Mass: Sum of protons and neutrons.

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

Example: Carbon-14 (14C) has 6 protons, 8 neutrons, and 6 electrons.

$\text{Atomic number} = \text{number of protons}$ $\text{Atomic mass} = \text{number of protons} + \text{number of neutrons}$ $\text{Number of neutrons} = \text{atomic mass} - \text{atomic number}$

Electron Arrangement and Shells

Electrons occupy energy levels or shells around the nucleus. The arrangement of electrons determines chemical reactivity and bonding.

• First shell holds up to 2 electrons.

• Second shell holds up to 8 electrons.

• Electrons fill lower energy shells first.

• Valence electrons: Electrons in the outermost shell; involved in chemical bonding.

Example: Carbon has 6 electrons: 2 in the first shell, 4 in the second shell.

Molecules and Chemical Bonds

Molecules

Molecules are formed when two or more atoms bond together. The molecular formula indicates the number and type of atoms in a molecule.

• Methane: CH4 (one carbon, four hydrogens)

• Glucose: C6H12O6 (six carbons, twelve hydrogens, six oxygens)

Chemical Bonds

Chemical bonds hold atoms together in molecules. The main types are covalent and ionic bonds.

• Covalent Bond: Atoms share valence electrons. Strongest type of chemical bond.

• Nonpolar Covalent Bond: Electrons are shared equally (e.g., methane CH4).

• Polar Covalent Bond: Electrons are shared unequally, creating partial charges (e.g., water H2O).

• Ionic Bond: Electrons are transferred from one atom to another, creating ions that attract each other (e.g., sodium chloride NaCl).

Bond Type	Electron Sharing	Strength	Example
Covalent (Nonpolar)	Equal	Strong	CH4
Covalent (Polar)	Unequal	Strong	H2O
Ionic	Transferred	Medium	NaCl

Example: In water, oxygen attracts electrons more strongly than hydrogen, resulting in a polar molecule with partial negative and positive charges.

Special Properties of Water

The polar nature of water gives it unique properties essential for life, such as high cohesion, adhesion, and solvent abilities.

• Cohesion: Water molecules stick to each other.

• Adhesion: Water molecules stick to other surfaces.

• Solvent: Water dissolves many substances, facilitating biological reactions.

Example: Water's polarity allows it to dissolve salts and sugars, supporting cellular processes.

Additional Concepts

Ions and Isotopes

Ions are atoms that have gained or lost electrons, resulting in a net charge. Isotopes are atoms of the same element with different numbers of neutrons.

• Cation: Positively charged ion (loss of electron).

• Anion: Negatively charged ion (gain of electron).

• Isotope Example: Carbon-14 is used in radiocarbon dating.

Electron Placement Rules

Electron placement is crucial for understanding chemical bonding and molecular structure.

• First shell: up to 2 electrons

• Second shell: up to 8 electrons

• Electrons fill shells from lowest to highest energy

Summary Table: Subatomic Particles for Carbon

Subatomic Particle	Number
Protons (p)	6
Neutrons (n)	6
Electrons (e)	6

Practice and Application

Assignments and Practice

• Draw shell models for Carbon, Nitrogen, Oxygen, and Hydrogen using the periodic table.

• Determine the number of each atom in glucose (C6H12O6).

Additional info:

• Electron placement diagrams help visualize chemical bonding and molecular structure.

• Understanding atomic structure is foundational for topics such as metabolism, genetics, and cell biology.