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3.1: Atoms to Molecules

Difficulty Level: Basic Created by: CK-12
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Can you see matter?

Matter is all around you. Everything you see is matter. All of this matter is made of small particles. The small particles are made of smaller particles.

What is Matter?

To understand minerals, we must first understand matter. Matter is the substance that physical objects are made of.

Atoms and Elements

The basic unit of matter is an atom ( Figure below ). At the center of an atom is its nucleus . Protons are positively charged particles in the nucleus. Also in the nucleus are neutrons with no electrical charge. Orbiting the nucleus are tiny electrons. Electrons are negatively charged. An atom with the same number of protons and electrons is electrically neutral. If the atom has more or less electrons to protons it is called an ion . An ion will have positive charge if it has more protons than electrons. It will have negative charge if it has more electrons than protons.

Diagram of an atom

The nucleus of an atom is made up of protons (blue) and neutrons (yellow). Electrons (red) orbit around the nucleus.

An atom is the smallest unit of a chemical element . That is, an atom has all the properties of that element. All atoms of the same element have the same number of protons.

Molecules and Compounds

A molecule is the smallest unit of a chemical compound . A compound is a substance made of two or more elements. The elements in a chemical compound are always present in a certain ratio.

Water is probably one of the simplest compounds that you know. A water molecule is made of two hydrogen atoms and one oxygen atom ( Figure below ). All water molecules have the same ratio: two hydrogen ions to one oxygen ion.

Structure of a water molecule

A water molecule has two hydrogen ions (shown in gray) bonded to one oxygen ion (shown in red).


  • An atom has negatively-charged electrons in orbit around its nucleus.
  • The nucleus of an atom is composed of positively-charged protons, and neutrons, which have no charge.
  • An atom that gains or loses electrons is an ion.

Explore More

Use this resource to answer the questions that follow.


  1. What is at the center of an atom? What is at the outside?
  2. How do atoms resemble the blocks in the video?
  3. What is each type of atom called? How are each of these types of atoms different from each other?
  4. How is the structure of the electrons in an atom important? What is this called?
  5. What is it called when two or more atoms bond together?


  1. Describe the parts of an atom. Where are these parts located?
  2. What is an element?
  3. What is a molecule made of?
  4. How is an ion different from an atom?




Smallest unit of a chemical element.
chemical compound

chemical compound

Substance in which the atoms of two or more elements are bound together.


Tiny negatively charged particles that orbit the nucleus.


Pure chemical substance with one type of atom.


Atom with one or more electrons added or subtracted; it has an electrical charge.


Substance that physical objects are made of.


Smallest unit of a compound; it is made of atoms.


Neutral particle in the nucleus of an atom.


Center of an atom, made of protons and neutrons.


Positively charged particle in a nucleus.

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Difficulty Level:



6 , 7

Date Created:

Jan 04, 2013

Last Modified:

Mar 11, 2015
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