The Chemical Foundations of Life: Atoms, Elements, and Water in Biology

Chapter 2: The Chemical Foundations of Life

Learning Objectives

• Define matter and elements.

• Describe the relationships between protons, neutrons, and electrons.

• Compare the ways in which electrons can be donated or shared between atoms.

• Explain the ways in which naturally occurring elements combine to create molecules, cells, tissues, organ systems, and organisms.

Life is More Than the Sum of Its Parts

Biological Organization

All living things are composed of matter, which is organized into increasingly complex levels. The fundamental unit of matter is the atom, while the fundamental unit of life is the cell.

• Atoms combine to form molecules.

• Molecules make up organelles and cells.

• Cells form tissues, which build organs and organ systems.

• Organ systems function together in an organism.

Matter, Atoms, and Molecules

Definitions and Properties

• Chemistry is the scientific study of matter.

• Matter is anything that occupies space and has mass.

• Matter exists in three physical states: solid, liquid, and gas.

• Examples: Ice (solid), water (liquid), water vapor (gas).

Atoms: The Building Blocks of Matter

• Atoms are the smallest units of matter that retain the properties of an element.

• Each atom consists of a nucleus (containing protons and neutrons) and a cloud of electrons orbiting the nucleus.

• Protons: Positively charged particles.

• Neutrons: Neutral particles (no charge).

• Electrons: Negatively charged particles.

Atomic Number, Elements, and Isotopes

Atomic Number and Protons

• The atomic number is the number of protons in an atom's nucleus and defines the element.

• All atoms of a given element have the same number of protons.

• Example: Carbon has 6 protons, so its atomic number is 6.

Elements

• An element is a substance that cannot be broken down into other substances by chemical means.

• Each element is represented by a unique symbol (e.g., C for carbon, O for oxygen).

• There are 92 naturally occurring elements.

Isotopes

• Isotopes are atoms of the same element that have different numbers of neutrons.

• Some isotopes are radioactive and decay over time, emitting radiation.

• Example: Carbon-12 (6 protons, 6 neutrons), Carbon-14 (6 protons, 8 neutrons).

Biological Tracers

• Radioactive isotopes can be used as biological tracers in medical imaging and research.

• Example: PET scans use radioactive tracers to visualize metabolic processes in the body.

Elements Essential to Life

Major and Trace Elements

• Four elements make up the majority of living matter: Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N).

• Other elements are required in smaller amounts (trace elements), such as iron (Fe), iodine (I), and zinc (Zn).

Table: Major and Trace Elements in Living Organisms

Element	Symbol	Role in Biology
Oxygen	O	Component of water and organic molecules; required for cellular respiration
Carbon	C	Backbone of all organic molecules
Hydrogen	H	Component of water and most organic molecules
Nitrogen	N	Component of proteins and nucleic acids
Calcium	Ca	Required for bone formation, muscle contraction
Iron	Fe	Component of hemoglobin in blood
Iodine	I	Required for thyroid hormone production
Sodium	Na	Important for nerve function
Potassium	K	Important for nerve and muscle function

Electrons and Chemical Bonds

Electron Arrangement and Reactivity

• Electrons are arranged in energy levels (shells) around the nucleus.

• The valence shell is the outermost electron shell and determines an atom's chemical properties.

• Atoms are most stable when their valence shell is full.

Ions and Ionic Bonds

• An ion is an atom that has gained or lost one or more electrons, acquiring a charge.

• Cation: Positively charged ion (lost electrons).

• Anion: Negatively charged ion (gained electrons).

• Ionic bonds form between oppositely charged ions.

• Example: Sodium (Na) donates an electron to chlorine (Cl), forming Na+ and Cl-, which attract each other to form NaCl (table salt).

Covalent Bonds

• Covalent bonds form when two atoms share one or more pairs of electrons.

• These are the strongest type of chemical bond in biological molecules.

• Example: Two hydrogen atoms share electrons with one oxygen atom to form a water molecule (H2O).

Important Ions in Biological Systems

• Ions play critical roles in physiological functions such as nerve signaling, muscle contraction, and maintaining fluid balance.

• Common biological ions include Na+, K+, Ca2+, Mg2+, Cl-, and HCO3-.

The Periodic Table

Organization and Use

• The periodic table arranges elements by increasing atomic number.

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

Water: The Molecule of Life

Properties of Water

• Water is essential for life and is the most prevalent molecule in living things.

• Key properties of water include:

  • Cohesion: Water molecules stick together due to hydrogen bonding.

  • Adhesion: Water molecules stick to other substances.

  • High specific heat: Water resists changes in temperature.

  • Excellent solvent: Water dissolves many substances, facilitating chemical reactions.

Cohesion of Water

• Hydrogen bonds between water molecules result in high surface tension and allow for phenomena such as water transport in plants.

Water and Life

• Life is thought to have originated in water over 3.5 billion years ago.

• Water's unique properties make it indispensable for biological processes, including temperature regulation, nutrient transport, and chemical reactions.

Summary Table: Types of Chemical Bonds

Bond Type	Description	Relative Strength	Example
Ionic	Transfer of electrons from one atom to another	Moderate	NaCl (table salt)
Covalent	Sharing of electron pairs between atoms	Strong	H2O (water)
Hydrogen	Attraction between a hydrogen atom and an electronegative atom (e.g., O or N)	Weak (individually)	Between water molecules

Key Equations and Concepts

• Atomic number: $\text{Atomic number} = \text{Number of protons}$

• Mass number: $\text{Mass number} = \text{Number of protons} + \text{Number of neutrons}$

• Ion formation: $\text{Na} \rightarrow \text{Na}^+ + e^-$

• Covalent bond (water): $2\text{H} + \text{O} \rightarrow \text{H}_2\text{O}$

Additional info: Some context and examples have been expanded for clarity and completeness, including the summary tables and explicit equations.