Unit 1: Chemistry and Organic Molecules

Introduction

Chemistry is fundamental to understanding biological processes. All living things are composed of chemical substances, and the study of chemistry provides the foundation for exploring the structure and function of biological molecules.

Chapter 2: Chemistry

Definition and Scope

• Chemistry is the branch of science that deals with the identification of substances of which matter is composed, their properties, and the ways in which they interact, combine, and change.

• Understanding chemistry is essential for studying the biological nature of life, as all biological structures and functions are based on chemical principles.

In the Hierarchy of Life

Levels of Biological Organization

• Atoms → Molecules → Cells

• Chemistry is considered the central science because it connects physical sciences with life sciences.

• Before studying biology, it is important to understand the chemical basis of life.

Elements and Compounds

• Elements: Pure substances consisting of only one type of atom. There are 92 naturally occurring elements, but only 6 (carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur) make up 99% of the human body.

• Compounds: Substances composed of two or more different elements chemically combined in fixed ratios (e.g., CaCO3).

Modern Atomic Theory

Basic Concepts

• All matter is composed of atoms.

• Matter is anything that has mass and occupies space. It exists in three forms: solids, liquids, and gases.

• Atoms cannot be subdivided, created, or destroyed in ordinary chemical reactions, but these changes can occur in nuclear reactions.

• Atomic structure includes a dense nucleus and a surrounding electron cloud.

• Most of the mass of an atom is concentrated in its nucleus.

• Note: The nucleus of an atom is not the same as the nucleus of a cell.

The Structure of the Atom

Subatomic Particles

• Atoms consist of three subatomic particles:

  • Proton: Positively charged particle found in the nucleus.

  • Neutron: Neutral particle found in the nucleus.

  • Electron: Negatively charged particle found in the electron cloud surrounding the nucleus.

The Periodic Table of Elements

Reading the Periodic Table

• The atomic number indicates the number of protons in an atom.

• The atomic mass (mass number) is the sum of protons and neutrons.

• To determine the number of neutrons:

• In a neutral atom, the number of electrons equals the number of protons.

Building an Atom

Arrangement of Subatomic Particles

• Protons and neutrons are located in the nucleus.

• Electrons occupy orbitals, which are arranged in electron shells around the nucleus.

• The outermost shell is called the valence shell, which determines the atom's bonding capacity (often following the "Rule of 8's" or octet rule).

Ions and Isotopes

• The number of protons determines the element and does not change.

• Atoms can gain or lose electrons to form ions:

  • Cation: Positively charged ion (loss of electrons).

  • Anion: Negatively charged ion (gain of electrons).

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

• Radioactive isotopes spontaneously decay, releasing energy that can damage DNA (e.g., 14C, 65Zn).

Molecular Mass

Definition and Calculation

• Molecular mass is the total mass of all atoms in a molecule.

• Calculation steps:

  1. List the atoms in the molecule.

  2. Find the atomic mass for each atom.

  3. Add the masses together.

• Example: For glucose (C6H12O6): amu

Atomic Bonding

Types of Chemical Bonds

• Bonds form due to attractive forces between atoms, aiming to fill the outer electron shell (valence shell).

• Ionic bonds: Electrons are transferred from one atom to another, resulting in oppositely charged ions that attract each other.

• Covalent bonds: Electrons are shared between atoms.

  • Non-polar covalent bonds: Electrons are shared equally (usually between identical atoms).

  • Polar covalent bonds: Electrons are shared unequally (between different atoms).

• Hydrogen bonds: Weak attractions between the slightly positive hydrogen atom of one molecule and the slightly negative atom (often oxygen or nitrogen) of another molecule.

Examples of Bonding

• Ionic bond example: Sodium (Na) donates one electron to chlorine (Cl), forming Na+ and Cl-, which combine to form NaCl.

• Covalent bond example: Two hydrogen atoms share electrons with one oxygen atom to form water (H2O).

• Hydrogen bond example: Hydrogen bonds between water molecules give water its unique properties.

Properties of Water

Unique Characteristics

• Cohesion: Water molecules stick to each other due to hydrogen bonding.

• Adhesion: Water molecules stick to other substances.

• High surface tension: Water has a strong surface layer due to cohesive forces.

• High heat capacity: Water can absorb or release large amounts of heat with little temperature change.

• Lower density as a solid: Ice is less dense than liquid water, so it floats.

• Excellent solvent: Water dissolves many substances, forming aqueous solutions (solute dissolved in solvent).

Table: Types of Chemical Bonds

Additional info:

• The six elements that make up 99% of the human body are carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur.

• Atomic mass is often measured in atomic mass units (amu).

• Hydrogen bonding is responsible for many of water's life-supporting properties.