EarthLabs > Climate and the Carbon Cycle: Unit Overview > Lab 1: Living in a Carbon World > 1B: Carbon - It's Elemental

Living in a Carbon World

Part B: Carbon – It's Elemental!

Carbon(C) (from the Latin carbo meaning coal) is one of the most chemically versatile elements in the Periodic Table of Elements. Carbon forms more compounds than any other element in the periodic table and scientists predict that there are more than ten million different carbon compounds in existence today on Earth. Carbon is found in all life forms in addition to sedimentary rocks, diamonds, graphite, coal, gasoline and oil. Carbon is a simple but amazing and versatile element! To find out a little more about carbon watch this short NPR video clip, It's All About Carbon: Episode 2.


Carbon atoms move through the the carbon cycle in many different forms of organic and inorganic carbon-compounds Organic carbon-compounds include most molecules containing both carbon and hydrogen atoms and are made by living things. All living things make and are thus made of organic carbon-compounds. Carbon-compounds such as carbon dioxide (CO2) and calcium carbonate (CaCO3) do not contain both carbon and hydrogen atoms and are called "inorganic carbon-compounds." . These carbon-compounds are chemically transformed in many ways as they move through various components of the carbon cycle. For example, in Lab 1A, you saw that the carbon atoms in carbon dioxide can end up in new carbon compounds such as glucose sugar. Important examples of carbon-compounds you will learn about in this module include:


Activity: Visualizing carbon compounds and their transformations.

In this activity, you will complete a series of tasks that will help you visualize carbon compounds and their transformations. In Tasks 1 and 2, you will use a "ball and stick" molecular model kit that includes carbon, hydrogen and oxygen atoms.

In Tasks 2-5, you will analyze static images of J-mol biomolecules. However, there are two APPS for IPAD/IPhone that allow you to rotate, zoom in and find background information on your J-mol biomolecules. They are Nice Molecules and Molecules.

Materials you will need for your group:

  • 6 ball-and-stick carbon dioxide molecules - (6 carbon atoms, 12 oxygen atoms, 24 electron bond sticks)
  • 6 ball-and-stick water molecules - (6 hydrogen atoms, 12 oxygen atoms, 12 electron bond sticks ) The image on the right illustrates what each molecule looks like.
  • A CHNOPS: Elements in Plant Biomolecules chart. Before you begin, familiarize yourself with the CHNOPS CHART. As you analyze each biomolecule, fill-in the CHNOPS chart and then answer the questions at the end. You may want to have a copy of a periodic table to help you with your chart.
  • Nice Molecules or Molecules IPAD/IPHONE J-mol APP (optional)

Ball and stick molecules:

  • Oxygen atoms are red and have two prongs. Thus, oxygen atoms can make two electron bonds with other atoms, including another oxygen atom.
  • The white or grey sticks represent covalent electron bonds between two atoms. Each stick represents one electron bond. Sometimes carbon and oxygen can form forms double bonds.
Jmol molecules:

Using Jmol software, scientists and non-scientsists can create visualizations of both simple biomolecules and and very large complex biomolecules. The type and number of atoms and how the atoms are connected to each other makes it easy to visualize what a molecule looks like and how one chemical compound differs from other molecules. The best way to interact with JMOL molecules is through APPs for IPAD/IPHONE. You call rotate, zoom in and find background information on all these biomolecules and more.

Nice Molecules for $1.99 This APP is the easiest to use.

Molecules by Sunset Lake Software. This APP is free but is not as easy to use as "Nice Molecules."

Checking In

  1. What elements are carbon dioxide and water made of? Check all that apply. Then click the Check Answers button at the end of the list.
    [CORRECT]
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Task 1. Visualizing Photosynthesis

You learned in Lab 1A that carbon enters the leaves of plants as carbon dioxide - a gas. When carbon dioxide atoms are combined with water molecules transported up from the roots of plants, a new kind of carbon compound is produceda biomolecule called glucose. Glucose is a carbohydrate sugar and provides the basic fuel and building materials for the plant and most other life forms.

Use the six carbon dioxide and six water molecules to model photosynthesis. Here is the net chemical reaction for photosynthesis.

carbon dioxide + water ==>glucose sugar + oxygen

6CO2 + 6H2O ==> C6H12O6 + 6O2


1. Begin by taking the carbon dioxide and water molecules apart.

2. Build your glucose molecule using this J-mol visualization of a glucose molecule above right. If you click to enlarge the J-mol image, you will easily see how the carbon, hydrogen and oxygen atoms are covalently bonded to each other. Use the structure in the J-mol image to guide you in building your glucose molecule. Note: If you have access to the Nice Molecules or Molecules APP, you can can zoom in and rotate the glucose molecule.

3. Next, use the remaining oxygen atoms and bonds to build six O2 molecules (O=O). These oxygen molecules are released to the air and provide some of the oxygen necessary for life on earth.

4. Make sure you fill-in the information for CO2 and glucose in the CHNOPS chart.

Checking In

  1. What elements is a glucose biomolecule made of? Check all that apply and then click the the Check Answers button at the end of the list
    [CORRECT]
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Stop and Think:


1. Explain how is it possible for a plant to make a sugar molecule from carbon dioxide and water?

Task 2: Visualizing Cellular Respiration

Cellular respiration is the process by which all organisms covert the chemical energy in glucose C-C and O=O electron bonds into biochemical energy that cells use to carry out their normal cellular functions. All life depends on this biochemical energy. Although more complicated than other combustion reactions, cellular respiration requires a fuel source such as glucose, and oxygen(O2). Like other combustion reactions, cell respiration produces carbon dioxide (CO2) and water (H2O).



The chemical equation for cellular respiration is:

Glucose + oxygen ==>carbon dioxide and water and energy

C6H12O6 + 6O2==> 6CO2 + 6H2O + energy for cells

1. Model cell respiration by breaking apart the glucose molecules and the oxygen molecules and then recombining the atoms to create CO2 and H2O molecules.



Stop and Think

2. Closely examine the atoms and molecules in both the cell respiration equation and the photosynthesis equation. In what way does photosynthesis and cell respiration form a carbon cycle? Use a drawing to help you illustrate your answer.

Task 3: Visualizing Biosynthesis - Creating new biomolecules.

Biosynthesis is the production of new biomolecules by a living organism. In biosynthesis, simple compounds can be modified, converted into other new carbon-compounds or used to build complex macromolecules. Large, complex molecules made from smaller subunit molecules. Proteins and DNA are examples.

Glucose is an example of a biomolecule biosynthesized from carbon dioxide (CO2) and water (H2O) molecules. Not all glucose sugar is used for cell respiration. Much of the glucose sugar produced via photosynthesis is used to build the biomass of the plant - primarily carbohydrates, fats, proteins, and nucleic acids (DNA and RNA). Like all organisms, a plant can synthesize hundreds of thousands of different types of biomolecules. But how?

To model biosynthesis in plants, you will need:

1. Join with at least one other team.

2. Use your atoms to build the biggest, most complex biomolecule you can. Your biomolecule can take any shape you like. The one rule you must follow is that no "electron prong" is left unconnected to another atom. When you are finished building your new biomolecule, compare them with other biomolecules made by other students.

Can you connect all of the biomolecules in the room? Try it if you have time! Note: To connect your biomolecule with another biomolecule, you may have to remove one hydrogen(H) atom from one biomolecule and one bonded hydrogen and oxygen (O-H) atom from another.

Discussion

Look at the the other biomolecules the class has made from the glucose molecules and nitrogen atoms (optional).
  • How are they similar? How are they different?
  • If you had a thousand glucose molecules, how many different types of biomolecules could you make? Why?
  • Imagine that carbon could only form one electron bond as opposed to four. What effect might this have on the size and diversity of molecules you have been able to build so far?

Task 4: Visualizing important biomolecules made by plants.

The squirrel and the tree on the right both have carbon stored in their cells and tissues. The biosynthesis of complex biomolecules that comprise these cells and tissues is key to understanding how plants, animals and all other living things store carbon.

A typical plant may make hundreds of thousands of different types of biomolecules. For this task, you will look at several examples of plant biomolecules you may have heard of. As you examine the different Jmol images, look carefully for the presence of nitrogen, phosphorus, sulfur and magnesium atoms in addition to carbon, hydrogen and oxygen atoms.

Although the number of nitrogen, phosphorus, sulfur and magnesium atoms in biomolecules are low compared to the number of carbon, oxygen and hydrogen atoms, these atoms are needed to biosynthesize biomolecules that are critical to life. For example, a plant can't make its DNA molecules unless it has a supply of nitrogen, phosphorus and sulfur atoms from the soil in addition to the carbon, hydrogen and oxygen atoms it obtains through photosynthesis. For this reason, plant growth is limited by the availability of nitrogen, phosphorus, magnesium and sulfur atoms in addition to the availability of carbon dioxide, water and light energy.

Note: Your teacher may decide to assign each member of your team a different molecule to examine. If so, you can use a jigsaw activity to teach other members of your team about your biomolecule.

1. Examine the different biomolecules below, use the following color coding scheme below to identify the types of elements in each biomolecule. Don't forget to write the names of the elements found in each biomolecule in your CHNOPS chart.

Fructose Biomolecule. Click to enlarge.

Fructose- a carbohydrate biomolecule: The Fructose biomolecule on the right is one of the many carbohydrate sugars made by plants. When you eat fruit, such as apples and oranges, you are eating some fructose fruit sugar. What elements are needed by plants to biosynthesize fructose biomolecules?


Cellulose Biomolecule Click to enlarge.

Cellulose- a carbohydrate biomolecule: The fibrous and woody parts of plants are all made of cellulose molecules joined together in long chains. The fibrous nature of cellulose provides the structure for plants to stand upright. Trees are approximately 50% to 53% cellulose, depending on the species of the tree. What elements are needed by plants to biosynthesize cellulose biomolecules?


Discussion

When you burn wood in a fireplace and when trees burn in a forest fire, cellulose molecules are broken apart and the atoms are rearranged into many new types of biomolecules. Would it be possible for burning trees to release carbon dioxide and water molecules to the atmosphere when trees burn? Explain why or why not.


Chlorophyll- a photosynthetic pigment biomolecule

Chlorophyll is a green pigment made by both terrestrial and marine plants. Plants use this pigment to absorb energy from the sun for photosynthesis. Chlorophyll reflects green light, so we see plants as green. Notice that each chlorophyll molecule requires one magnesium atom to be complete. Magnesium is an important nutrient found in soil and in fertilizers.

What elements are needed by plants to biosynthesize chlorophyll molecules?



Checking In

    1. If there was not enough magnesium in the soil, you might expect to observe the following in trees: Check all that apply and then click the Check Answers button at the end of the list.
      [INCORRECT]
      [CORRECT]
      [CORRECT]
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Short segment of a DNA molecule. Click to enlarge.
DNA - a nucleic acid macromolecule

DNA is often called the blueprint of life because it contains genetic instructions for all the organisms on Earth. Without DNA, an organism does not get built. This visualization of DNA represents a very small segment of an entire DNA macromolecule. What elements are needed by plants to biosynthesize a DNA molecule?







Cytochrome C . Click to enlarge.
Cytochrome C - a protein macromolecule

Proteins are macromolecules biosynthesized by all living organisms and have diverse functions that are critical to life. For example, Cytochrome c is an a very important protein that is critical for plants and other organisms to carry out cell respiration. Can you find the sulfur atoms and the two iron atoms in this cytochrome protein molecule? What elements are needed by plants to biosynthesize a protein biomolecule?




Checking In

  1. Where do you think a plant gets the nitrogen and phosphorus atoms it needs to biosynthesize DNA molecules? Check all that apply and then click the Check Answers button at the bottom of the list.
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  2. What elements are in ALL of the plant biomolecules you have examined so far? Check all the apply and then click the Check Answers button at the bottom of the list.
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  3. What types of molecules have you visualized that cannot be biosynthesized without nitrogen atoms? Check all that apply and then click the Check Answers button at the bottom of the list.
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  4. If there was not enough nitrogen, phosphorus, sulfur, magnesium or iron in soil, you might expect to observe the following in trees: Check all that apply and then click the Check Answers button at the bottom of the list.
    [INCORRECT]
    [CORRECT]
    [INCORRECT]
    [CORRECT]
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Task 5: Visualizing Combustion and Hydrocarbons




Discussion

Examine the image above of the Deepwater Horizon oil rig burning in the Gulf of Mexico. The rig is bringing up oil from the sediments deep below the water's surface of the Gulf of Mexico. With a partner and/or class, talk about the following:

  • How do you think the carbon cycle is related to this image?
  • How are carbon compounds are being transformed?
  • What role do you think combustion plays in transforming these carbon compounds?


If you drive a car, heat your home, or enjoy a good backyard barbecue, you can't live without combustionThe process of burning something; when a substance such as wood, coal and gas reacts with oxygen to produce carbon dioxide, water vapor, heat and energy and hydrocarbons Hydrocarbons are organic carbon compounds that are made of only carbon and hydrogen atoms . Gasoline, heating oil, and propane for gas barbecues grills are all made of hydrocarbons. To find out some interesting facts about combustion and hydrocarbons, watch this 7 minute video on Combustion and Combustion Equations. Note: Once on the page, click on combustion video on the right to download. Before you watch the video, make note of the following Checking In questions you will need to answer when you are finished with the video.


Checking In

  1. When a fuel such as wood or gasoline are burned, what are the two products that are created? Check all that apply, and then click the Check Answers button at the bottom of the list.
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  2. Fuels, such as gas, oil and coal, are mostly made of...? Check all that apply and then click the Check Answers button at the bottom of the list.
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  3. When a fossil fuel is burned, where does all of the carbon dioxide go? Check all that apply and then click the Check Answers button at the bottom of the list.
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Jmol Methane molecule
Jmol Propane molecule
Fossil fuels are made of hydrocarbons, primarily coal, fuel oil or natural gas, formed from the remains of dead plants and animals that have been stored deep within Earth's rock sediments for millions of years. A common property of all hydrocarbons is that they produce carbon dioxide, steam, and heat energy when burned. This is why hydrocarbons are currently the main sources of electricity and heating for our homes and fuels we use in our cars. Today, the United States gets approximately 87% of its energy from burning these types of fossil fuels. Both methane and propane are two examples of hydrocarbons.

Propane is produced from natural gas and can be found in a liquid state or a gas state. If you have a gas BBQ grill, then the fuel you are using is propane.

The combustion equation for burning propane is:

C3H8(propane) + 5 O2 → 3 CO2 + 4 H2O + heat energy

Methane is a major component of natural gas. Methane is also naturally produced as a by-product when bacteria, cows and termites try to digest plant cellulose. Some research has indicated that cows can burp out more than 130 gallons of methane per day. Unfortunately, methane is a greenhouse gas that contributes to global warming. You will learn a lot more about methane in Labs 3 and 5.

The combustion reaction for methane is:

CH4 (methane) + 2O2 ==> CO2 + 2H2O (steam) + heat energy

Don't forget to fill in the types of elements in your "Elements in Biomolecules " chart.

Where do coal, oil and gas hydrocarbons come from?

Coal formation. Credit: Stephen Greb, Kentucky Geological Survey
We use fossil fuels on a daily basis but where do they come from? And why are they made of carbon and hydrogen atoms? The answer is simplethe carbon and hydrogen atoms in fossil fuels started out in the biomolecules of living things. As you can see by the drawing on the right, coal originally comes from decomposed land plants that have been covered by sedimentary rock and compressed over millions of years.

Next, consider the drawing below to find out where oil and gas comes from. Click to enlarge. Then answer the Checking In question.


Checking In

  1. What carbon cycle process(es) transform some of the carbon compounds from dead sea plants and animals into the carbon dioxide we release when we drive our cars? Check all that apply and then click the Check Answers button at the bottom of the list.
    [INCORRECT]
    [CORRECT]
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Stop and Think

3. In Lab 1B, you have learned about carbon, biomolecules and the key carbon cycle processes that transform one carbon compound into another. Choose two processes and explain how they can change (transform) one carbon-compound into another.

Extensions (Optional)

1. Watch an animation on oil and gas formation in this animation developed by the University of Waikato, New Zealand. Access the animation here: Oil Formation

2. Watch the other videos in the Its All About Carbon series from NPR.


3. Try out a fun biomolecule App for the iPad or iPhone. If necessary, make sure you have your parents' permission to download an App.
  • Nice Molecules for $1.99 This APP is the easiest to use. Gives you Jmols and background information for lots of carbon compounds. If you shake it, it shows a new molecule.
  • Molecules by Sunset Lake Software. This APP is free but is not as easy to use as "Nice Molecules." This is a more sophisticated APP for students who are interested in chemistry and biomolecules. You can download molecules from two comprehensive databases - The Protein Data Bank and NCBI's PubChem.


4. Plants make millions of different kinds of biomolecules many of which are used as food or as medicine. Examples include: caffeine, cocoa(chocolate), aspirin, quinine, rubber and Taxol. Research one plant biomolecule that interests you. Find a J-mol image for the molecule and then give background information about the biomolecule and its use. You can use one of the molecule APPs for I-Pad above to help you find j-mol images. You can take screenshots and then load onto them onto your computer as a picture. You can also use these APPS to find carbon compounds made by animals and other organisms such as bacteria!

5. Watch a video on what the noted Nobel Laureate Richard Feynman says about trees, carbon and air. You will find Feynman's video at the end of the article.


5. Read about nitrogen availability and trees in these these articles:




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