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

Chapter 2: The Chemical Context of Life

Introduction

This chapter introduces the fundamental chemical principles underlying biological systems, focusing on the structure of atoms, the periodic table, subatomic particles, and the types of chemical bonds that form the basis of biological molecules.

Atoms, Elements, and Compounds

Definitions and Key Concepts

• Matter: Anything that has mass and occupies space.

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

• Compound: A substance formed when two or more elements are chemically combined in a fixed ratio.

"Big 4" elements of life: Carbon (C), Hydrogen (H), Oxygen (O), and Nitrogen (N) are the most abundant elements in living organisms.

Subatomic Particles

Structure and Properties

• Proton: Positively charged particle located in the nucleus of an atom.

• Neutron: Neutral particle (no charge) also located in the nucleus.

• Electron: Negatively charged particle found in orbitals surrounding the nucleus.

Particle	Location	Mass	Charge
Proton	Nucleus	1 atomic mass unit (amu)	+1
Neutron	Nucleus	1 amu	0
Electron	Electron cloud/orbitals	~0 (1/1836 amu)	-1

Atomic Number and Atomic Mass

• Atomic Number (Z): Number of protons in the nucleus; defines the element.

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

Example: Sodium (Na) has atomic number 11 and atomic mass 22.990. This means it has 11 protons, and (approximately) 12 neutrons.

Isotopes and Ions

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

• Ion: An atom or molecule with a net electric charge due to the loss or gain of electrons.

Changing Subatomic Particles

Effects on Atomic Identity and Properties

The subatomic particle number changed	What happens?	Example
Protons	Changes the element's identity	6 protons = Carbon, 7 protons = Nitrogen
Neutrons	Creates isotopes of the same element	Carbon-12 vs. Carbon-14
Electrons	Forms ions (charged atoms)	Na → Na+ (loss of 1 electron)

Energy Levels and Electron Shells

Key Terms

• Energy: The capacity to do work or cause change.

• Potential Energy: Stored energy due to position or arrangement.

• Electron Shell: The region around the nucleus where electrons are likely to be found; each shell has a characteristic energy level.

Electrons fill shells in order of increasing energy. The outermost shell is called the valence shell, and electrons in this shell are called valence electrons.

Periodic Table Organization

• Row (Period): Indicates the number of electron shells.

• Column (Group): Indicates the number of valence electrons (for main group elements).

Valence shell electrons determine how an atom reacts chemically.

Chemical Bonds

Types of Bonds

Bond	Definition	Example	Draw It!
Covalent	Sharing of electron pairs between atoms	H2O (water)	O–H
Polar Covalent	Unequal sharing of electrons between atoms	H2O	Oδ-–Hδ+
Nonpolar Covalent	Equal sharing of electrons	O2, H2	H–H
Ionic	Transfer of electrons from one atom to another	NaCl (table salt)	Na+ Cl-
Hydrogen Bond	Attraction between a hydrogen atom and an electronegative atom (like O or N)	Between water molecules	H–O···H
Van der Waals	Weak attractions due to transient local partial charges	Gecko feet adhesion	Additional info: Not easily drawn; shown as dotted lines between molecules.

Electronegativity

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

• Differences in electronegativity determine bond polarity.

Valence Electrons and Bonding Capacity

Determining Covalent Bonds

Element	Total # electrons	Total # valence electrons	Total # covalent bonds
Carbon (C)	6	4	4
Hydrogen (H)	1	1	1
Oxygen (O)	8	6	2
Nitrogen (N)	7	5	3

Example: Carbon forms 4 covalent bonds, oxygen forms 2, nitrogen forms 3, and hydrogen forms 1.

Atomic Structure Notation and Ions

Atomic Notation

• Standard atomic notation: AZX, where A = mass number, Z = atomic number, X = element symbol.

• Example: 126C for carbon-12.

Ion Examples

• Hydrogen atom (neutral): 1 proton, 0 neutrons, 1 electron

• Hydrogen ion (H+): 1 proton, 0 neutrons, 0 electrons

• Fluorine atom (neutral): 9 protons, 10 neutrons, 9 electrons

• Fluorine ion (F-): 9 protons, 10 neutrons, 10 electrons

Summary Table: Subatomic Particles and Atomic Identity

Change	Result	Example
Change in protons	New element	Carbon (6p) → Nitrogen (7p)
Change in neutrons	Isotope	Carbon-12 vs. Carbon-14
Change in electrons	Ion	Na → Na+

Key Equations

• Atomic mass number: $A = Z + N$ where $A$ = mass number, $Z$ = number of protons, $N$ = number of neutrons.

• Number of neutrons: $N = A - Z$

Conclusion

Understanding the structure of atoms, the periodic table, and the types of chemical bonds is essential for studying biological molecules and processes. Mastery of these concepts provides the foundation for exploring more complex topics in biology, such as metabolism, genetics, and cellular structure.