Foundations of Chemistry for Biochemistry Students

Introduction to Chemistry

Overview

Chemistry is the scientific study of matter, its properties, composition, and the changes it undergoes. A foundational understanding of chemistry is essential for biochemistry, as it provides the basis for understanding the molecular processes in living organisms.

Organic vs Inorganic Chemistry

Definitions and Distinctions

• Inorganic Chemistry: The study of compounds derived from non-living sources. Modernly, it includes the synthesis and behavior of inorganic and organometallic compounds.

• Organic Chemistry: Traditionally, the study of compounds from living sources. Modernly, it is defined as the study of carbon compounds.

Application: Biochemistry is primarily concerned with organic chemistry, as it focuses on carbon-based molecules in living systems.

Matter

Definition and Properties

• Matter: Anything that has mass and occupies space.

• Mass: The quantity of matter in a substance.

• Volume: The amount of space matter occupies.

• All substances are comprised of matter, which is made up of particles.

States of Matter

The three classical states of matter are solid, liquid, and gas. The differences in these states are due to the arrangement and movement of their constituent particles.

Solid	Liquid	Gas
Particles arranged in a lattice	Particles arranged in clusters	Particles widely spaced
Strong forces of attraction	Forces of attraction weaker than in a solid, stronger than in a gas	Negligible forces of attraction
Particles only able to vibrate	Particles flow over each other	Particles move in rapid, random motion
Definite shape and volume	Definite volume, no definite shape	No definite shape or volume
Very little compressibility	Very little compressibility	High compressibility

Structure and Function of Atoms

Hierarchy of Matter

• Particles of matter: Atoms

• Atoms: Elements

• Elements: Molecules and Compounds

• Compounds: Mixtures

Element: A substance that cannot be further decomposed by ordinary chemical means. Each element consists of atoms made up of protons, neutrons, and electrons.

Subatomic Particles

Particles	Symbol	Relative mass (atomic mass unit)	Charge
Protons	p	1.007276	+1
Neutrons	n	1.00864	0
Electrons	e-	5.485799 × 10-4	-1

Atomic Structure

• Protons and neutrons are located in the nucleus of the atom.

• Electrons are found in orbitals outside the nucleus.

Atoms are neutral when they contain equal numbers of protons and electrons.

Ions

• Cation: Formed when positive charge (protons) exceeds negative charge (electrons).

• Anion: Formed when negative charge (electrons) exceeds positive charge (protons).

Elements: Atomic Number and Mass

• Atomic number (Z): Number of protons in the nucleus.

• Atomic mass (A) or mass number: Average mass of an atom compared to carbon-12, which is assigned 12 atomic units.

Element notation: $\begin{array}{c} \text{mass number} \\ \text{atomic number}\end{array} \text{Element Symbol}$

Example: Sodium (Na) has atomic number 11 and mass number 23: $\begin{array}{c}23 \\ 11\end{array} \text{Na}$

Magnesium ion (Mg2+) has two more positive charges than negative charges.

Nitrogen is a diatomic molecule: $\mathrm{N}_2$