Atoms & Molecules

Physical Science

The idea that matter is made up of atoms and molecules provides the basis for understanding the properties of matter.

Benchmark: Elements & Periodic Table

Recognize that all substances are composed of one or more of approximately one hundred elements and that the periodic table organizes the elements into groups with similar properties.

Benchmark: Elements vs. Compounds

Describe the differences between elements and compounds in terms of atoms and molecules.

Benchmark: Chemical Equations

Recognize that a chemical equation describes a reaction where pure substances change to produce one or more pure substances whose properties are different from the original substance(s).


Standard in Lay Terms 

Science states that matter is made up of atoms and molecules, which provide the basis for understanding matter.

Big Ideas and Essential Understandings 

Big Idea

Atoms are far too small to be observed directly with the naked eye, therefore they appear invisible to us. The enormous variety of materials in the world are the result of different combinations of a relatively small number of basic ingredients called elements. The properties of these materials are determined by the atomic and molecular structure.  These atomic properties have lead to the organization of the approximatley 100 elements in the periodic table.  A chemical reaction that produces new substances with different properties can be expressed in a chemical equation.  Atlas for Science Literacy Project 2061

Benchmark Cluster 

MN Standard Benchmarks

Recognize that all substances are composed of one or more of approximately one hundred elements and that the periodic table organizes the elements into groups with similar properties.

Describe the differences between elements and compounds in terms of atoms and molecules.

Recognize that a chemical equation describes a reaction where pure substances change to produce one or more pure substances whose properties are different from the original substance(s).

The Essentials

 See this page.


Physical Science

Content Standard B
As a result of their activities in grades 5-8, all students should develop an understanding of

The structure of matter is difficult for this grade span. Historically, much of the evidence and reasoning used in developing atomic/molecular theory was complicated and abstract. In traditional curricula too, very difficult ideas have been offered to children before most of them had any chance of understanding. The law of definite proportions in chemical combinations, so obvious when atoms (and proportions) are well understood, is not likely to be helpful at this level. The behavior of gases-such as their compressibility and their expansion with temperature-may be investigated for qualitative explanation; but the mathematics of quantitative gas laws is likely to be more confusing than helpful to most students. When students first begin to understand atoms, they cannot confidently make the distinction between atoms and molecules or make distinctions that depend upon it-among elements, mixtures, and compounds, or between "chemical" and "physical" changes. An understanding of how things happen on the atomic level-making and breaking bonds-is more important than memorizing the official definitions (which are not so clear in modern chemistry anyway). Definitions can, of course, be memorized with no understanding at all.

Going into details of the structure of the atom is unnecessary at this level, and holding back makes sense. By the end of the 8th grade, students should have sufficient grasp of the general idea that a wide variety of phenomena can be explained by alternative arrangements of vast numbers of invisibly tiny, moving parts. Possible differences in atoms of the same element should be avoided at this stage. Historically, the identical nature of atoms of the same element was an assumption of atomic theory for a very long time.

When isotopes are introduced later, to explain subsequent observations, they can be a surprise and a lesson in the nature of progress in science. The alternative-teaching atoms' variety at the same time as the notion of their identity-seems likely to be prohibitively confusing to most students.

To that end, students should become familiar with characteristics of different states of matter-now including gases-and transitions between them. Most important, students should see a great many examples of reactions between substances that produce new substances very different from the reactants. Then they can begin to absorb the rudiments of atomic/molecular theory, being helped to see that the value of the notion of atoms lies in the explanations it provides for a wide variety of behavior of matter. Each new aspect of the theory should be developed as an explanation for some observed phenomenon and grasped fairly well before going on to the next.

By the end of the 8th grade, students should know that

  • All matter is made up of atoms, which are far too small to see directly through a microscope. 4D/M1a
  • The atoms of any element are like other atoms of the same element, but are different from the atoms of other elements. 4D/M1b*
  • Atoms may link together in well-defined molecules, or may be packed together in crystal patterns. Different arrangements of atoms into groups compose all substances and determine the characteristic properties of substances. 4D/M1cd*
  • Equal volumes of different materials usually have different masses. 4D/M2*
  • Atoms and molecules are perpetually in motion. Increased temperature means greater average energy of motion, so most substances expand when heated. 4D/M3ab
  • In solids, the atoms or molecules are closely locked in position and can only vibrate. In liquids, they have higher energy, are more loosely connected, and can slide past one another; some molecules may get enough energy to escape into a gas. In gases, the atoms or molecules have still more energy and are free of one another except during occasional collisions. 4D/M3cd
  • The temperature and acidity of a solution influence reaction rates. Many substances dissolve in water, which may greatly facilitate reactions between them. 4D/M4
  • Chemical elements are those substances that do not break down during normal laboratory reactions involving such treatments as heating, exposure to electric current, or reaction with acids. All substances from living and nonliving things can be broken down to a set of about 100 elements, but since most elements tend to combine with others, few elements are found in their pure form. 4D/M5*
  • Carbon and hydrogen are common elements of living matter. 4D/M6c*
  • No matter how substances within a closed system interact with one another, or how they combine or break apart, the total mass of the system remains the same. 4D/M7a*
  • The idea of atoms explains the conservation of matter: If the number of atoms stays the same no matter how the same atoms are rearranged, then their total mass stays the same. 4D/M7b
  • Most substances can exist as a solid, liquid, or gas depending on temperature. 4D/M8** (SFAA)
  • Substances react chemically in characteristic ways with other substances to form new substances with different characteristic properties. 4D/M11** (NSES)
  • If samples of both the original substances and the final substances involved in a chemical reaction are broken down, they are found to be made up of the same set of elements. 4D/M12**
  • The idea of atoms explains chemical reactions: When substances interact to form new substances, the atoms that make up the molecules of the original substances combine in new ways. 4D/M13**


Student Misconceptions 
  • Elementary - and middle - school students may think everything that exists is matter, including heat, light, and electricity. [1]
  • Alternatively, they may believe that matter does not include liquids and gases or that they are weightless materials. [2]
  •, With specially designed instruction, some middle - school students can learn the scientific notion of matter. [3]
  • Middle-school and high-school students are deeply committed to a theory of continuous matter. [4]
  •, Although some students may think that substances can be divided up into small particles, they do not recognize the particles as building blocks, but as formed as basically continuous substances under certain conditions. [5]
  • Students at the end of elementary school and beginning of middle school may be at different points in their conceptualization of a "theory" of matter. [6]
  • Although some 3rd graders may start seeing weight as a fundamental property of all matter, many students in 6th and 7th grade still appear to think of weight simply as "felt weight" -- something whose weight they can't feel is considered to have no weight at all. Accordingly, some students believe that if one keeps dividing a piece of styrofoam, one would soon obtain a piece that weighed nothing. [7]
  • Students of all ages show a wide range of beliefs about the nature and behavior of particles. They lack an appreciation of the very small size of particles; attribute macroscopic properties to particles; believe there must be something in the space between particles; have difficulty in appreciating the intrinsic motion of particles in solids, liquids and gases; and have problems in conceptualizing forces between particles. [8]
  •,, Despite these difficulties, there is some evidence that carefully designed instruction carried out over a long period of time may help middle-school students develop correct ideas about particles. [9]

[1] Stavy, R. (1991). Children's ideas about matter. School Science and Mathematics, 91, 240-244.

Lee, O., Eichinger, D.C., Anderson, C.W., Berkheimer, G.D., Blakeslee, T.S. (1993). Changing middle school students' conceptions of matter and molecules. Journal of Research in Science Teaching, 30, 249-270.

[2] Stavy, R. (1991). Children's ideas about matter. School Science and Mathematics, 91, 240-244.

Mas, C.J., Perez, J.H., Harris, H. (1987). Parallels between adolescents' conceptions of gases and the history of chemistry. Journal of Chemical Education, 64, 616-618.

[3] Lee, O., Eichinger, D.C., Anderson, C.W., Berkheimer, G.D., Blakeslee, T.S. (1993). Changing middle school students' conceptions of matter and molecules. Journal of Research in Science Teaching, 30, 249-270.

[4] Nussbaum, J. (1985). The particulate nature of matter in the gaseous phase. In Driver, R. (Ed.),Children's ideas in science (pp. 124-144).

[5] Pfundt, H. (1981). The atom-he the final link in the division process or the first building block?. Chemica Didactica, 7, 75-94.

[6] Carey, S. (1991). Knowledge acquisition: Enrichment or conceptual change?. In Carey, S. (Ed.), The epigenesis of mind: Essays on biology and cognition (pp. 257-291).

Smith, C., Carey, S., Wiser, M. (1985). On differen-tiation: A case study of development of the concepts of size, weight, and density. Cognition, 21, 257-291.

Smith, C., Snir, J., Grosslight, L. (1987).Teaching for conceptual change using a computer modeling approach: The case of weight/density differentiation.

[7] Carey, S. (1991). Knowledge acquisition: Enrichment or conceptual change?. In Carey, S. (Ed.), The epigenesis of mind: Essays on biology and cognition (pp. 257-291).

[8] Children's Learning in Science (1987). Approaches to teaching the particulate theory of matter.Approaches to teaching the particulate theory of matter..

[9] Lee, O., Eichinger, D.C., Anderson, C.W., Berkheimer, G.D., Blakeslee, T.S. (1993). Changing middle school students' conceptions of matter and molecules. Journal of Research in Science Teaching, 30, 249-270.


"You can't peek!" called out Mr. R.

Tiffany and Jose were just about to lift up the corner of the square that was taped to the paper in front of them. They stopped dead in their tracks and quickly put the corner back down.

"But, Mr. R, we really want to know what type of coin is under the paper!"

"Tiffany, I know you do, but we need to have a bit of discussion about the technology that can be used to do just that." Mr. R replied.

"Let's stop and think for a second. How is the coin under the paper square like an atom."

The students in Mr. R's class had been given a worksheet. Mr. R had placed a piece of paper just larger than a coin. Over the course of his life Mr. R had collected lots of coins from all around the world and now he could put them to good use in his science class room. Every student had a different coin from a different place that was hidden and taped securely to the worksheet. Mr. R was using this activity to demonstrate how science can use indirect observation and inference to create a model. The topic they had just begun to study was matter and more specifically the topic of atoms.

The rules were simple: without puncturing the hiding paper, lifting off the paper and tape, to try and determine what the coin was under the paper.

Kyan raised his hand. "The way I see it, you can't see it so it is like an atom."

"What do you mean, you can't see it?" asked Mr. R.

Sondra raised her hand, "Atoms are too small to see with our naked eyes."

The class giggled when she said 'naked'. Remember they are seventh graders.

Henry spoke up, "Atoms are too small and we can't see individual atoms, so this coin is hidden, kind of like the atoms we can't see."

"If you can't see them, how do you know they are there," asked Mr. R. "How is that like the coin under the paper?"

"You can't see the coin, because it is hidden. Atoms aren't hidden, they are just too small to see," replied Megan.

"We can't see the coin, how can you find out what the coin is?" asked Mr. R.

"Squeeze it and rub it," Jordan answered.

"You could do that and then measure how big it was," Ross replied.

"I think we could squeeze it, rub it to make it show up and then make an impression in clay." Megan replied.

Landry said, "Why don't we do a pencil rubbing like we did for the tree identification lab? That wouldn't break the paper and we could get a picture of the surface of the coin."

Mr. R then pulled the class back together and they went about trying to discover what the coins were about. Student shaded with pencil lead and crayons and colored pencils. They tried different colored pencils and erased portions to try and reveal details.

Mr. R quietly said, "If you can hear my voice, snap your fingers. If you can hear my voice, snap your fingers," and he continued doing this until the class was snapping all together. He had been using this technique since the start of the year and it didn't take long to get the class focused on something he had to say.

"Let's share some things that you are doing that are working well or not so well."

Megan answered, "I found that if I held my pencil on its side, and just lightly shaded, that I could make out letters and the face on the coin".

Other students went around the room and shared what worked and what didn't work in their quest to discover what the coin was under the paper. With that new information and techniques, student went back to work.

A few minutes later Mr. R called them back to the center of the room to debrief about what they had discovered. They shared at their tables where they thought the coins were from based on the image and language/symbols students found on their paper.

"Now can we lift up the paper to see?" asked Landry. He was growing impatient.

"Not just yet. What were some of the difficulties you had with your technique? What were some of the limits?"

A discussion followed about the information gathered.

"Now you can take the paper off and find out how accurate is your information."

The students went to that task quickly and there were lots of comments about being right or wrong as they pealed back the paper and pulled out the coin.

"How is what you did today similar to how scientists have used technology to understand atoms? Write down five things in your notebook to answer that question."


Instructional Notes 

Selected Labs and Activities

  • Introducing Atoms This lesson is the first of a four-part series on static electricity. These lessons are meant to help students understand that static electricity is a phenomenon that involves positive and negative charges. An understanding of static electricity must begin with the concept that all matter is composed of atoms, and all atoms are composed of subatomic particles among which are the charged particles known as electrons and protons.
  • To help show the difference between molecules and atoms students can construct models.
  • Can use marshmallows and toothpicks to construct molecules.
  • Protons, Neutrons, and Electrons Students will put a static charge on a strip of plastic by pulling it between their fingers. They will see that the plastic is attrached to their fingers. Students will be introduced to the idea that rubbing the strip with their fingers caused electrons to move from their skin to the plastic giving the plastic a negative charge and their skin a positive charge. Through these activities, students will be introduced to some of the characteristics of electrons, protons, and neutrons, which make up atoms.
  • The Science of Atoms and Molecules The Science of Atoms and Molecules project offers 24 research-based, field-tested activities for physics, chemistry, and biology. We provide these all freely to teachers and students online. Through the SAM activities' interactive models and simulations, we involve students in active learning. Teachers can register online to receive Teacher Guides for each activity and to gain access reporting functions to track student progress.
  • Build Atoms Yourself One way to find out about the structure of something is to take it apart. Another way is to construct the item from its parts. This interactive model will allow you to build atoms of different elements from a collection of subatomic particles.
  • What is a Chemical Reaction? The teacher will use a small candle flame to demonstrate a chemical reaction between the candle wax and oxygen in the air. Students will see a molecular animation of the combustion of methane and oxygen as a model of a similar reaction. Students will use atom model cut-outs to model the reaction and see that all the atoms.
  • A Catalyst and the Rate of Reaction Students watch a video and do a quick activity to see that a catalyst can increase the rate of the breakdown (decomposition) of hydrogen peroxide. Students will then use salt as a catalyst in a reaction between aluminum foil and a solution of copper II sulfate. Students will be introduced to the concept that a catalyst increases the rate of a chemical reaction but is not incorporated into the products of the reaction.
  • Chemistry in a Bag Students will make observations of  a chemical reaction in studying an indicator acid base reaction.
  • Mystery Powders Use physical and chemical changes to study and make some conclusions about these powders.
  • Yeast Beasts In Action Yeasts are microorganisms. They can break hydrogen peroxide down into water and oxygen gas.In this experiment you will investigate yeast activity in acidic, neutral, and basic mixtures. You will observe yeast activity by measuring pressure caused by the oxygen gas they produce.
  • Respiration in Yeast Here's a simple lab to show how organisms use sugar to make energy.
  • Photosynthesis in Elodea PHOTOSYNTHESIS is the process during which a plant's chlorophyll traps light energy and sugars are produced. In plants, photosynthesis occurs only in cells with chloroplasts.
Instructional Resources 

Instructional Suggestions/Options

  • What is in the box? Without seeing an atom, how can science use behavior and properties to create a model of an atom. Place an object in a paper box, students have to try and figure out what it is based on observation. As explained in the vignette, you can use boxes, or buy Obscaners from Flinn, Scientific or other science suppliers.
  • An interesting trip into history and science is to look at the idea of the atom over its history. You could create a webquest to have students mining the history of this idea as it has changed over time.
  • Get an appreciation of atomic scale with this interactive site from Strange Matter.
New Vocabulary 


  • pure substance   substance made of one kind of material having definite properties
  • element  simplest type of pure substance
  • atom  smallest part of an element that has all the properties of an element
  • chemical symbol  shorthand way of representing an element
  • compound  substance made up of molecules that contain more than one kind of atom; two or more elements chemically combined
  • molecule  combination of atoms formed by a covalent bond
  • chemical formula combination of chemical symbols usually used to represent a compound
  • subscript  number placed to the lower right of a chemical symbol to indicated the number of atoms of the element in the compound
  • chemical equation  expression in which symbols, formulas, and numbers are used to represent a chemical reaction
  • coefficient  number that is placed in front of a symbol or a formula in a chemical equation that indicates how many atoms or molecules of this substance are involved in the reaction.
Technology Connections 
  • Internet connections for students to use interactive sites. Students can find lot of modeling activities online. Whether it is watching molecules move, atoms bond or chemical reactions happen in slow motion.
  • Using probes and probeware you can measure rates of chemical reactions with temperature probes, gas pressure probes, oxygen and carbon dioxide probes and others. See the Yeast Beast activity above for a specific idea.
  • Cameras/flip videos students can take pictures of the atoms they build to study for quizzes. Using clay models, students could create stop action movies of the behavior of atoms and molecules in Brownian motion, diffusion or osmosis.
  • Using the web, discover some trends in the Periodic Table. Students can get a handle on the symbols and letters by finding out what the symbols mean and the origin of elemental names.
Cross Curricular Connections 

Shop classes can be a cross-curricular source for learning about elements.  The shop class could be a source of comparisons for looking at different materials and their properties. Comparing metals, for example, malleability, tensile strength, melting point in looking at atomic structure. As, perhaps a look at polymers of plastics and the relationships in molecules could happen within an industrial tech curriculum tie in.


Additional Resources

  • Interactive periodic tables for students  http://www.ptable.com/
  • Properties of Water Lab This is one of many labs that explore the properties of water and its importance to living things.
  • The Pfizer Foundation Biochemistry Lab The Pfizer Foundation Biochemistry Discovery Lab at the New York Hall of Science encourages visitors to explore such questions as where flower colors come from, how antacids work, how cheese is made and how bees communicate. Built with a $250,000 donation from the Pfizer Foundation, the Biochem Lab is the first hands-on lab in the world that is open to the public and devoted entirely to biochemistry, the chemistry of living things. Visitors discover that molecules - those bits of things too small to see - are the stars of the show.


Assessment of Students

Is air matter? Why or why not?

1.    Yes, because air is not alive.

2.    Yes, because air is made up of atoms.

3.    No, because air cannot be seen.

4.    No, because air does not take up space.

Which of the following is the smallest?

1.    A germ

2.    An atom

3.    The width of a hair

4.    A cell in your body

In the formulas listed below, identify the only pure element.

1.         CO2

2.         C6H12O6

3.         O2

4.         NH3

Assessment of Teachers

  • How do you connect atoms/molecules and chemistry in general to the lives of students? Daily there is content to be referenced: nitrogen in polluted rivers, the dead zone in the Gulf of Mexico, climate change.... How do you bring those into your classroom?
  • Atomic models and how science has created these models based on inference. How do you emphasize the tentative nature of science here?
  • How can you provide your students with hands on/minds on activities that will be developmentally appropriate? How can you change other activities from HS or ES that look appealing to you, but may not be age appropriate?


Struggling Learners 

Struggling and At-Risk

  • Snow, D. (2003). Noteworthy perspectives: Classroom strategies for helping at-risk students (rev. ed.). Aurora, CO: Mid-continent Research for Education and Learning.
  • In 2002, McREL conducted a synthesis of recent research on instructional strategies to assist students who are low achieving or at risk of failure. From this synthesis of research, McREL identified six general classroom  strategies that research indicates are particularly effective in helping struggling students achieve success.
  • Hands on labs like the one in the vignette helps special ed students comprehend concepts better than straight book work.
  • Hands on use like using Obscaners will help at risk students.
  • Instruction in basic skills must be done in concert with the larger task of learning higher-order skills.
English Language Learners 
  • Herr, N. (2007). The sourcebook for teaching science. This page contains strategies to help teachers better attend to the needs of their ELL learners. These strategies are grouped according to the following learning tasks: listening, visualization,       interpersonal communication, laboratory, demonstrations, reading and writing, instruction and vocabulary.
  • Hands-on science learning promotes language connections
Extending the Learning 
  • Teachers First is an educational support website that may help with G/T students
  • Cogito is another website that is available for G/T Students
  • G/T: Students would make 10 to 12 molecules with given material. The material you provide could be anything from beads and dowels to gumdrops and toothpicks. Challenge to students to wire frames or spacefilling models.
  • Or students could make their molecules with materials they brought in. Show the student a 3-D sample of what a model could look, discuss the limitations and challenge them to build a better model, one more accurate and more functional. The could determine size and scale for an atom (ie, a atom can be no smaller than a ping pong ball) and that will determine the materials you choose.(Peterson, M 2011)
  • Multicultural science education.  Official NSTA Position Statement.
  • Freelang.net hosts a English to Ojibwe and Ojibwe to English dictionary that may be used to look up meanings to vocabulary words.
  • Science education should include the use of culturally relevant content (Ferguson, Robert. "If Multicultural Science Education Standards' Existed, What Would They Look Like?." Journal of Science Teacher Education. 19.6 (2008): 547-564. Print.) The value of using such approaches is that they can improve the conversation about beliefs in science and hone beliefs about science for all students.
  • Students should be given opportunities to do science rather than read about it.  Doing science includes reasoning about science.  This kind of science emphasizes the active role of the learner in constructing knowledge. 
Special Education 
  • Technologies for Special Needs Students: In their newsletter, "Tech Trek",  from the National Science Teachers Association, there are suggestions for using technology including voice recognition software
  • Hands on labs like the one in the vignette helps special ed students comprehend concepts better than straight book work.
  • Learning experiences should be as multi-sensory as possible and safe.  Such experiences have an added benefit too.  They are effective with all learners.



Parents can help students study elements, as well as finding help on the internet to help struggling students.