Chapter 2: The Chemical Context of Life – Study Notes

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Chapter 2: The Chemical Context of Life

Introduction

This chapter explores the fundamental chemical principles that underlie biological processes. Understanding the nature of matter, elements, atoms, and chemical bonds is essential for studying life at the molecular level.

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

Definition of Matter

Matter is anything that takes up space and has mass.
All organisms are composed of matter.

Elements and Compounds

An element is a substance that cannot be broken down to other substances by chemical reactions.
A compound is a substance consisting of two or more elements combined in a fixed ratio.
Compounds have emergent properties that are different from those of their constituent elements.
Example: Sodium (Na, a metal) and chlorine (Cl, a poisonous gas) combine to form sodium chloride (NaCl, table salt), which is edible and safe.

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% consists mainly of calcium (Ca), phosphorus (P), potassium (K), and sulfur (S).
Trace elements are required by organisms in minute quantities (e.g., iron, iodine).

Table: Major Elements in the Human Body

Element	Symbol	Percentage of Body Mass (including water)
Oxygen	O	~65%
Carbon	C	~18%
Hydrogen	H	~10%
Nitrogen	N	~3%
Calcium	Ca	~1.5%
Phosphorus	P	~1%
Potassium	K	~0.4%
Sulfur	S	~0.3%
Sodium	Na	~0.2%
Chlorine	Cl	~0.2%
Magnesium	Mg	~0.1%
Trace elements	-	<1%

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

Atoms and Subatomic Particles

An atom is the smallest unit of matter that retains the properties of an element.
Atoms are composed of subatomic particles:
- Protons: positive charge (+1)
- Neutrons: no charge (0)
- Electrons: negative charge (–1)
Protons and neutrons are located in the atomic nucleus; electrons form a cloud around the nucleus.
Proton and neutron mass ≈ 1 dalton (Da); electron mass is negligible.

Atomic Number and Atomic Mass

Atomic number: number of protons in the nucleus (defines the element).
Mass number: sum of protons and neutrons in the nucleus.
Atomic mass: total mass of the atom, approximately equal to the mass number.

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons.
Radioactive isotopes decay spontaneously, emitting particles and energy.
Radioactive isotopes are used as tracers in medical diagnostics and research (e.g., PET scans).
Radiometric dating uses the decay of radioactive isotopes to date fossils and rocks.
Half-life is the time required for half the atoms of a radioactive isotope to decay.

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

Energy Levels of Electrons

Energy is the capacity to cause change.
Potential energy is energy due to position or structure.
Electrons have potential energy based on their distance from the nucleus; electrons in higher shells have more energy.
Electrons occupy electron shells with characteristic energy levels.

Electron Distribution and Chemical Properties

The chemical behavior of an atom is determined by the distribution of electrons in its electron shells.
Valence electrons are those in the outermost shell (valence shell).
Atoms with a full valence shell are chemically inert (e.g., noble gases).

Electron Orbitals

An orbital is a three-dimensional space where an electron is found 90% of the time.
Each electron shell contains a specific number of orbitals.
No more than two electrons can occupy a single orbital.

Chemical Bonds

Atoms with incomplete valence shells can share or transfer electrons, forming chemical bonds.
Covalent bonds: sharing of a pair of valence electrons between atoms.
Single bond: sharing of one pair of electrons; double bond: sharing of two pairs; triple bond: sharing of three pairs.
Structural formula shows bonding (e.g., H—H); molecular formula shows composition (e.g., H2).
Valence is the bonding capacity of an atom.

Electronegativity and Bond Polarity

Electronegativity is an atom’s attraction for electrons in a covalent bond.
Nonpolar covalent bond: electrons are shared equally.
Polar covalent bond: electrons are shared unequally, leading to partial charges (e.g., in water, H2O).

Ionic Bonds

Occur when one atom strips electrons from another, forming ions.
Cation: positively charged ion; anion: negatively charged ion.
Attraction between cation and anion forms an ionic bond.
Ionic compounds (salts) are often found as crystals (e.g., NaCl).
Most salts are stable when dry but dissociate in water.

Table: Electronegativity Values for Selected Elements

Element	Electronegativity
H	2.20
N	3.04
P	2.19
O	3.44
Cl	3.16
Na	0.93
K	0.82
Ca	1.00
Additional info:	Electronegativity values are based on the Pauling scale.

Weak Chemical Interactions

Hydrogen bonds: form when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom (often O or N).
Van der Waals interactions: weak attractions due to transient local partial charges.
Weak bonds are important for the structure and function of large biological molecules.

Molecular Shape and Function

A molecule’s shape is determined by the positions of its atoms’ valence orbitals.
Molecular shape determines how biological molecules recognize and respond to one another.
Example: Opiate drugs mimic the shape of endorphins and bind to the same brain receptors, producing similar effects.

Concept 2.4: Chemical Reactions Make and Break Chemical Bonds

Chemical Reactions

Chemical reactions are processes that make and break chemical bonds.
Reactants: starting materials; products: resulting materials.
Example: Formation of water:
Photosynthesis:

Reversibility and Equilibrium

All chemical reactions are reversible; products 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.