Atoms, Elements, and Chemical Bonds: Study Notes for General Biology

Chapter 2: The Chemical Context of Life

Introduction

This chapter introduces the foundational concepts of chemistry as they relate to biology, including the structure of atoms, the nature of elements and compounds, and the types of chemical bonds that form between atoms. Understanding these principles is essential for studying biological molecules and processes.

Atoms, Elements, and Compounds

Definitions and Key Terms

• Matter: Anything that has mass and occupies space.

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

• Compound: A substance formed when two or more elements are chemically bonded together in fixed proportions.

The "Big 4" Elements of Life

• Carbon (C)

• Hydrogen (H)

• Oxygen (O)

• Nitrogen (N)

These four elements make up the majority of living matter and are essential for biological molecules.

Subatomic Particles

Structure and Properties

Atoms are composed of three main subatomic particles:

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

Changing Subatomic Particles

Changing the number of subatomic particles affects the identity and properties of atoms:

Subatomic Particle Number Changed	What Happens?	Example
Protons	Changes the element	Carbon (6 protons) vs. Nitrogen (7 protons)
Neutrons	Creates isotopes	Carbon-12 vs. Carbon-14
Electrons	Forms ions	Na vs. Na+

Periodic Table and Atomic Structure

Reading the Periodic Table

• Atomic Number: Number of protons in the nucleus. Determines the element.

• Atomic Mass: Sum of protons and neutrons.

• Symbol: One or two-letter abbreviation for the element.

Example: Sodium (Na) has atomic number 11 and atomic mass 22.990.

Electron Shells and Energy Levels

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

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

• Electron Shell: A level of electrons at a characteristic average distance from the nucleus.

Electrons fill shells in order of increasing energy. The outermost shell is called the valence shell.

Electron Distribution and Chemical Properties

The arrangement of electrons in shells determines how atoms interact and bond. Atoms with incomplete valence shells tend to react to achieve stability.

Chemical Bonds

Types of Chemical Bonds

Bond	Definition	Example	Draw It!
Covalent	Atoms share electron pairs	H2O (water)	O-H-O
Polar Covalent	Unequal sharing of electrons	H2O	Oδ-—Hδ+
Nonpolar Covalent	Equal sharing of electrons	O2	O=O
Ionic	Transfer of electrons	NaCl	Na+ Cl-
Hydrogen Bond	Attraction between a hydrogen atom and an electronegative atom	Between water molecules	H—O···H
Van der Waals	Weak attractions due to transient charges	Gecko feet adhesion	Temporary dipoles

Electronegativity

• Electronegativity: The tendency of an atom to attract electrons in a chemical bond.

• Higher electronegativity leads to polar covalent bonds.

Ions and Isotopes

Formation of Ions

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

• Example: Sodium loses one electron to become Na+.

Isotopes

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

• Example: Carbon-12 and Carbon-14.

Valence Electrons and Chemical Reactivity

Valence Shell Electrons

• Valence electrons: Electrons in the outermost shell.

• Determine how atoms bond and react chemically.

Number of Covalent Bonds

Atom	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

Application: Periodic Table and Electron Configuration

How to Read the Periodic Table Entry

• Atomic number = number of protons

• Atomic mass = protons + neutrons

• Symbol = element abbreviation

Example: Carbon (C) has atomic number 6 and atomic mass 12.011.

Electron Distribution

• First shell: up to 2 electrons

• Second shell: up to 8 electrons

• Third shell: up to 18 electrons

Atoms are most stable when their valence shell is full.

Key Equations

• Atomic mass calculation: $\text{Atomic mass} = \text{Number of protons} + \text{Number of neutrons}$

• Number of electrons in a neutral atom: $\text{Number of electrons} = \text{Number of protons}$

Summary Table: Subatomic Particles and Their Effects

Particle Changed	Effect	Example
Proton	Changes element identity	H (1 proton) vs. He (2 protons)
Neutron	Creates isotopes	C-12 vs. C-14
Electron	Forms ions	Na vs. Na+

Practice and Application

• Label the atomic number, atomic mass, and symbol for elements using the periodic table.

• Draw and label atoms, indicating nucleus, electron cloud, protons, neutrons, and electrons.

• Determine the number of covalent bonds an atom can form based on its valence electrons.

• Identify atoms that are not at their lowest energy state in a molecule.

Additional info: These notes expand on the provided questions and tables, adding definitions, examples, and academic context for clarity and completeness.