Chapter 2: The Chemical Context of Life – Study Notes

Chapter 2: The Chemical Context of Life

Overview

This chapter explores the chemical foundations of life, focusing on the elements, atoms, and molecules that compose living organisms. Understanding these concepts is essential for grasping how biological processes occur at the molecular level.

Main Concepts

• What is matter made up of?

• What is biological matter made up of?

• What bonds are seen in biological matter?

• What impact do bonds have in biological matter?

Biology and Chemistry

Interdisciplinary Nature

• Biology is a multidisciplinary science, integrating principles from physics and chemistry.

• Living organisms are subject to the basic laws of physics and chemistry.

• Example: Formica rufa (wood ants) use chemical compounds for defense.

Concept 2.1: Matter, Elements, and Compounds

Definitions

• Matter: Anything that takes up space and has mass.

• Element: A substance that cannot be broken down to other substances by chemical reactions.

• Compound: A substance consisting of two or more elements in a fixed ratio, with properties different from its constituent elements.

Examples

• Sodium (Na) and Chlorine (Cl) are elements; Sodium chloride (NaCl) is a compound with distinct properties.

Concept 2.1B: The Elements of Life

Essential Elements

• About 20–25% of the 92 naturally occurring elements are essential for life.

• CHON: Carbon, Hydrogen, Oxygen, and Nitrogen make up 96% of living matter.

• CaPPSS: Calcium, Phosphorus, Potassium, Sodium, and Sulfur constitute most of the remaining 4%.

• Trace elements are required in minute quantities (e.g., iron, iodine).

Table: Elements in the Human Body

Element	Symbol	Percentage of Body Mass
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%

Trace Elements and Health

• Iodine deficiency can cause goiter, a thyroid gland disorder.

Case Study: Tolerance to Toxic Elements

• Some elements are toxic to organisms.

• Species can adapt to environments with toxic elements (e.g., plants adapted to serpentine soils).

Concept 2.2: Atomic Structure and Properties

Atoms and Subatomic Particles

• Atom: The smallest unit of matter retaining the properties of an element.

• Subatomic particles: Neutrons (no charge), Protons (+1 charge), Electrons (–1 charge).

• Atomic mass = mass of neutrons + mass of protons (measured in daltons).

Structure of the Atom

• Protons and neutrons form the nucleus.

• Electrons form a cloud around the nucleus, determining chemical behavior.

• An orbital is the three-dimensional space where an electron is found 90% of the time.

Electron Orbitals and Shells

• Each electron shell contains a specific number of orbitals.

• No more than 2 electrons can occupy a single orbital.

• Atoms interact to complete their valence shells.

Examples of Orbitals

• First shell: 1s orbital (max 2 electrons).

• Second shell: 2s and three 2p orbitals (max 8 electrons).

Atomic Number and Atomic Mass

• Atomic number: Number of protons in the nucleus.

• Mass number: Sum of protons and neutrons.

• Atomic mass: Total mass, approximately equal to the mass number.

$\text{Atomic Mass} = \text{Number of Protons} + \text{Number of Neutrons}$ $\text{Atomic Number} = \text{Number of Protons}$

Isotopes

• Atoms of the same element with different numbers of neutrons are called isotopes.

• Radioactive isotopes decay spontaneously, emitting particles and energy.

• Applications: Diagnostic imaging (e.g., PET scans), radiometric dating of fossils.

• Half-life: Time required for half the atoms of a radioactive isotope to decay.

Energy Levels of Electrons

• Energy: Capacity to cause change.

• Potential energy: Energy due to position or structure.

• Electrons in atoms have different potential energies depending on their distance from the nucleus.

• Electrons occupy discrete energy levels (shells).

Electron Distribution and Chemical Properties

• The chemical behavior of an atom is determined by the distribution of electrons in its shells.

• The periodic table shows electron distribution for each element.

• Electron distribution diagrams illustrate the arrangement for the first 18 elements.

Valence Shells and Reactivity

• The outermost shell is the valence shell.

• Atoms with incomplete valence shells are reactive and tend to form bonds to achieve stability.

• Maximum stability is achieved when the valence shell is full (usually 8 electrons).

Summary Table: Electron Shell Capacity

Shell	Maximum Electrons
First shell	2
Second shell	8
Third shell	8

Additional info:

• Understanding atomic structure and chemical bonding is foundational for all biological processes, including metabolism, cell structure, and genetic inheritance.