The Chemical Context of Life: Atoms, Elements, and Chemical Bonds

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Chapter 2: The Chemical Context of Life

Concept 2.1: Matter, Elements, and Compounds

All living organisms are composed of matter, which is anything that takes up space and has mass. Matter is made up of elements, and elements can combine to form compounds with unique properties.

Matter: Anything that occupies space and has mass.
Element: A substance that cannot be broken down into other substances by chemical reactions.
Compound: A substance consisting of two or more elements in a fixed ratio. Compounds have characteristics different from their constituent elements.
Example: Table salt (NaCl) is a compound formed from sodium (a reactive metal) and chlorine (a poisonous gas), but together they form edible salt.

Sodium, chlorine, and sodium chloride

Elements in the Human Body

Only a few elements are essential for life, and these make up the majority of the human body’s mass.

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%

Table of elements in the human body

Concept 2.2: Atomic Structure and Properties of Elements

The properties of elements depend on the structure of their atoms. Atoms are the smallest units of matter that retain the properties of an element.

Atom: The smallest unit of an element that retains its chemical properties.
Subatomic particles: Atoms are composed of protons (positive charge), neutrons (no charge), and electrons (negative charge).
Nucleus: Protons and neutrons are located in the nucleus, while electrons orbit in a cloud around the nucleus.
Dalton: The unit of measurement for atomic mass (1 dalton ≈ mass of one proton or neutron).

Structure of a carbon atom

Atomic Number, Mass Number, and Isotopes

Atomic number: Number of protons in the nucleus; defines the element.
Mass number: Sum of protons and neutrons in the nucleus.
Atomic mass: Approximate total mass of an atom, nearly equal to the mass number.
Isotopes: Atoms of the same element with different numbers of neutrons. Some isotopes are radioactive and decay spontaneously.

Natural isotopes of carbon

Electron Distribution and Chemical Properties

The arrangement of electrons in shells around the nucleus determines an atom’s chemical behavior. The periodic table organizes elements by their electron configurations.

Valence electrons: Electrons in the outermost shell; determine chemical reactivity.
Chemically inert: Elements with full valence shells (e.g., noble gases) are unreactive.

Periodic table with electron distribution diagrams

Concept 2.3: Chemical Bonds and Molecular Formation

Atoms with incomplete valence shells can share or transfer electrons, resulting in chemical bonds that hold atoms together in molecules or compounds.

Covalent Bonds

Covalent bond: Sharing of a pair of valence electrons between two atoms.
Single bond: Sharing of one pair of electrons (e.g., H—H).
Double bond: Sharing of two pairs of electrons (e.g., O=O).
Molecule: Two or more atoms held together by covalent bonds.
Structural formula: Notation showing how atoms are bonded (e.g., H—H).
Molecular formula: Abbreviated notation showing the number of each type of atom (e.g., H2).

Formation of a hydrogen molecule by covalent bonding

Electronegativity and Bond Polarity

Electronegativity: An atom’s attraction for electrons in a covalent bond.
Nonpolar covalent bond: Electrons are shared equally between atoms.
Polar covalent bond: Electrons are shared unequally, resulting in partial charges (δ+ and δ−) on atoms.

Polarity of water molecule

Ionic Bonds

Ionic bond: Attraction between oppositely charged ions formed when one atom transfers electrons to another.
Cation: Positively charged ion (e.g., Na+).
Anion: Negatively charged ion (e.g., Cl−).
Ionic compound (salt): Compound formed by ionic bonds, often found as crystals (e.g., NaCl).

Formation of sodium chloride from sodium and chlorine

Hydrogen Bonds

Hydrogen bond: Weak attraction between a hydrogen atom covalently bonded to one electronegative atom and another electronegative atom (often oxygen or nitrogen).
Hydrogen bonds are important in stabilizing the structures of proteins and DNA, and in the properties of water.

Hydrogen bond between water and ammonia

Additional info: This summary covers the foundational chemical principles necessary for understanding biological molecules and processes, including atomic structure, types of chemical bonds, and the relevance of these concepts to living systems.