Chapter 2: The Chemical Context of Life – Study Notes

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Chapter 2: The Chemical Context of Life

Concept 2.1: Matter Consists of Chemical Elements in Pure Form and in Combinations Called Compounds

This section introduces the foundational chemical principles underlying biological systems, focusing on matter, elements, and compounds.

Matter is anything that takes up space and has mass. All organisms are composed of matter.
Elements are substances that cannot be broken down to other substances by chemical reactions.
Compounds are substances consisting of two or more elements in a fixed ratio. Compounds have characteristics different from those of their constituent elements (emergent properties).

Example: Sodium (Na) and chlorine (Cl) are both dangerous in pure form, but together they form sodium chloride (NaCl), or table salt, which is essential for life.

The Elements of Life

About 20-25% of the 92 natural elements are essential for life.
Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) make up about 96% of living matter.
The remaining 4% is mostly calcium (Ca), phosphorus (P), potassium (K), and sulfur (S).
Trace elements are required in minute quantities (e.g., iron, iodine, zinc).

Table: Elements in the Human Body

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%

Additional info: Trace elements include boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, vanadium, and zinc.

Concept 2.2: An Element's Properties Depend on the Structure of Its Atoms

Atoms are the smallest units of elements that retain their properties. The structure of atoms determines the behavior of elements.

Atoms are composed of subatomic particles: neutrons (no charge), protons (positive charge), and electrons (negative charge).
Neutrons and protons form the atomic nucleus; electrons form a "cloud" around the nucleus.
Proton and neutron mass are nearly identical and measured in daltons.

Atomic Number and Atomic Mass

Atomic number: Number of protons in the nucleus.
Mass number: Sum of protons and neutrons.
Atomic mass: Total mass of the atom, approximately equal to the mass number.

Isotopes

Atoms of the same element with different numbers of neutrons are called isotopes.
Radioactive isotopes decay spontaneously, emitting particles and energy.

Example: Hydrogen has three isotopes: protium (1H), deuterium (2H), and tritium (3H).

The Energy Levels of Electrons

Energy is the capacity to cause change.
Potential energy is energy due to location or structure.
Electrons exist in energy levels called electron shells.
Electrons can move to higher or lower shells by absorbing or releasing energy.

Electron Distribution and Chemical Properties

The chemical behavior of an atom is determined by the distribution of electrons in its shells.
The periodic table arranges elements by electron configuration.
Valence electrons are those in the outermost shell and determine chemical reactivity.
Atoms with full valence shells are chemically inert (e.g., noble gases).

Table: Electron Distribution for the First 18 Elements

Element	Symbol	First Shell	Second Shell	Third Shell
Hydrogen	H	1	-	-
Helium	He	2	-	-
Lithium	Li	2	1	-
Beryllium	Be	2	2	-
Boron	B	2	3	-
Carbon	C	2	4	-
Nitrogen	N	2	5	-
Oxygen	O	2	6	-
Fluorine	F	2	7	-
Neon	Ne	2	8	-
Sodium	Na	2	8	1
Magnesium	Mg	2	8	2
Aluminum	Al	2	8	3
Silicon	Si	2	8	4
Phosphorus	P	2	8	5
Sulfur	S	2	8	6
Chlorine	Cl	2	8	7
Argon	Ar	2	8	8

Electron Orbitals

An orbital is a three-dimensional space where an electron is found 90% of the time.
Each electron shell consists of a specific number of orbitals.

Concept 2.3: The Formation and Function of Molecules Depend on Chemical Bonding Between Atoms

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

Covalent Bonds

A covalent bond is the sharing of a pair of valence electrons by two atoms.
A molecule consists of two or more atoms held together by covalent bonds.
A single bond is the sharing of one pair of electrons; a double bond is the sharing of two pairs.
Structural formulas (e.g., H—H) and molecular formulas (e.g., H2) are used to represent molecules.
Valence is the bonding capacity of an atom.
Electronegativity is an atom's attraction for electrons in a covalent bond.
Nonpolar covalent bonds: electrons are shared equally.
Polar covalent bonds: electrons are shared unequally, resulting in partial charges.

Example: In water (H2O), oxygen is more electronegative than hydrogen, creating a polar molecule.

Ionic Bonds

Atoms sometimes transfer electrons, resulting in charged atoms called ions.
A cation is positively charged; an anion is negatively charged.
An ionic bond is the attraction between a cation and an anion.
Ionic compounds (salts) are often found as crystals (e.g., NaCl).

Weak Chemical Interactions

Most strong bonds in organisms are covalent, but weak bonds (hydrogen bonds, van der Waals interactions) are crucial for the structure and function of large biological molecules.
Weak bonds are reversible, allowing dynamic biological processes.

Hydrogen Bonds

A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (usually O or N in living cells).

Example: Hydrogen bonds hold water molecules together and stabilize the structure of proteins and DNA.

Concept 2.4: Chemical Reactions Make and Break Chemical Bonds

Chemical reactions involve the making and breaking of chemical bonds.
Reactants are the starting molecules; products are the resulting molecules.
All chemical reactions are reversible; the products of the forward reaction can become reactants in the reverse reaction.
Chemical equilibrium is reached when the forward and reverse reactions occur at the same rate, and the concentrations of reactants and products remain constant.

Example: Formation of water:

Photosynthesis:

Additional info: Chemical equilibrium does not mean equal concentrations, but rather a stable ratio of reactants to products.