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.
Carbon atoms move through the the carbon cycle in many different forms of carbon-compounds. Important examples of carbon-compounds you will learn about in this module include:
- Carbon dioxide (CO2) - a gas found in the atmosphere, soils and oceans
- Carbohydrate sugar (C6H12O6) - a solid found in plants and other organisms
- Methane (CH4) -a gas found in the atmosphere, soils and oceans
- Calcium carbonate (CaCO3)- a chalky solid found in rocks, oceans and in the skeletons and shells of ocean creatures.
- Hydrocarbons - solids, liquids or gases that when burned, provide us with energy to heat and light our homes and drive our cars.
- Bio-molecules - are complex carbon-compounds produced in living things. Proteins, carbohydrates, fats and oils, and DNA are examples of of bio-molecules.
Essential questions you will explore in Lab 1B are:
- What makes one carbon-compound different from another?
- How can one carbon-compound be transformed into a different carbon- compound? For example, how could carbon dioxide be transformed into a carbohydrate sugar?
- Why are photosynthesis, cell respiration, combustion, biosynthesis and decomposition key transforming processes in the carbon cycle?
- Why are nitrogen, phosphorus, magnesium and sulfur atoms critical to life on Earth and to the carbon cycle?
Use a molecular modeling kit and J-mol molecules to build and visualize carbon-compounds and their transformations
Materials you will need for your group:
6 ball-and-stick carbon dioxide molecules - (6 carbon atoms, 12 oxygen atoms, 24 white bonds) Note: You may need to put these together before you start.
6 ball-and-stick water molecules - (6 hydrogen atoms, 12 oxygen atoms, 12 white bonds) Note: You may need to put these together before you start.
The image on the right illustrates what each looks like.Ball and stick molecules:
- Carbon atoms are black(or gray) and each has four "prongs." Each prong represents an electron bond. Thus, carbon can make four electron bonds with other atoms. Carbon can sometimes form double bonds as in carbon dioxide.
- Hydrogen atoms are white. Hydrogen only has one prong, so it can make only one electron bond with another atom.
- 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 sticks represent electron bonds between two atoms. One white stick represents one electron bond. Sometimes carbon and oxygen can form forms double bonds.
Using Jmol software, scientists and non-scientsists can create visualizations of both simple and very complex molecules. 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. In Jmol interactive sites, you can rotate the molecule and zoom-in to get a closer look at the atoms.
Important: In order to access and see the interactive Jmol molecules, you will need to use a Firefox browser and have Java downloaded. You can download JAVA http://www.java.com/en/download/index.jsp here.
Before you begin the next section, create a two-column "Elements in Plant Biomolecules" chart with the following headings: "Name of Plant Biomolecule" in column 1, and "Types of Elements found in this Biomolecule" in column 2. In the Biomolecules column, write the name of each biomolecule (ex. carbon dioxide) you learn about in this lab. In the Types of Elements column, you will write down the symbols for the elements found in this biomolecule (ex. C for carbon, O for oxygen). You may also download a version of this chart here (Microsoft Word 2007 (.docx) 67kB Apr4 13). You may want to have a copy of a periodic table to help you with your chart.
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. If you click to enlarge the J-mol image on the right , you will easily see how the carbon atoms hydrogen and oxygen atoms are bonded to each other. Use the structure in the image to build your glucose molecule. If you have Java successfully downloaded into your Firefox browser on your computer, you can access the interactive Jmol glucose molecule here. You can use your mouse to rotate the glucose and to zoom in.
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 necessary oxygen for life on earth.
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 cell respirationWhen most people hear the term "respiration," they think about using their lungs to breath in and out. This is not the same process as cell respiration. In order to maintain life, cell respiration is carried out in the cells of every organism. When plants photosynthesize, they convert carbon dioxide and water into energy-rich glucose sugar molecules. Some of the glucose sugar is used to provide energy for the plant's cells. When organisms cell respire, they break apart the energy-rich bonds between the glucose atoms. Energy is released for cells to carry out their normal cellular functions. Breaking down glucose creates carbon dioxide, some of which is released to the atmosphere and some to the soil.
The net chemical equation for cell respiration is:
Glucose + oxygen ==>carbon dioxide and water and energy
C6H12O6 + 6O2==> 6CO2 + 6H2O + energy for cells
Stop and Think2. 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 - Transforming simpler molecules into more complex biomoleculesNot all glucose sugar is used for cell respiration. Much of the sugar made from photosynthesis is used to build the biomass of the plant. The plant's biomass is made primarily of biomolecules such as carbohydrates, fats, proteins, and DNA(nucleic acid).
How can a plant make so many different types of carbon-compounds from just glucose? To begin to answer this question, join with another team. Using the 6 carbon, 12 hydrogen and 6 oxygen atoms from the glucose molecules from both teams, make as many different new carbon-compounds as you can. They can be any size, any shape. The one rule you must follow is that no "electron prong" is left unconnected to another atom. When you are finished building your new carbon compound(s), compare them with carbon-compounds made by other students.
DiscussionLook at the the other carbon compounds the class has made from the glucose molecules.
- How are they similar? How are they different?
- If you had a thousand glucose molecules, how many different types of molecules 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
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, you will see that there are other elements besides carbon, hydrogen and oxygen atoms in some of the biomolecules. Look carefully for the presence of nitrogen, phosphorus, sulfur and magnesium atoms in addition to carbon, hydrogen and oxygen atoms. As you examine each Jmol biomolecule, don't forget to make note of the elements found in each biomolecule in your "Elements in Plant Biomolecules" chart. If you can access the on-line interactive biomolecules, don't forget to rotate and zoom in. You many want to have a Periodic Table of the Elements handy as you do this activity.
Note: Your teacher may decide to assign each member of your team a different molecule to examine. Then, you can then use a jigsaw activity to teach other members of your team about your biomolecule.
As you examine the different biomolecules below, use the following color coding scheme to identify the types of elements in each biomolecule.
- carbon (black or grey)
- oxygen (red)
- hydrogen (white)
- nitrogen (blue)
- phosphorus (orange)
- sulfur (yellow)
- magnesium (green)
Fructose: The Fructose biomolecule on the right is another carbohydrate sugar made by plants. When you eat fruit, such as apples and oranges, you are eating some fructose biomoleculesalso called fruit sugar. You can access the interactive fructose Jmol here. What elements are in fructose? Make sure you write down the types of elements that you observe in fructose in your "Elements" chart.
Cellulose: 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. Access the interactive version of cellulose here. What elements are in cellulose?
DiscussionWhen 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 carbon compounds. 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 green photosynthetic pigment
Access the interactive biomolecule here. What elements are in chlorophyll?
DNA is a science term you have probably heard about on the news, in your science classes, and forensic science shows like CSI. 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 only represents a very small segment of an entire DNA molecule. Access the interactive Jmol DNA molecule at DNA. What elements are in DNA?
Task 5: Visualizing DecompositionConsider the picture on the right. What will happen to the cut trees and the leaf litter over time? Watch this time-lapse visualization of decomposing leaf litter to find out. As you watch the decomposition process, think about what will happen to the biomolecules that the leaves are made of.
Decomposition is an important carbon cycle process that takes place in both soil and in water bodies such as oceans, lakes and ponds. Decomposition is the opposite of the biosynthesis process. Whereas biosynthesis builds larger more complex molecules from smaller molecules, decomposition breaks down larger molecules - such as plant proteins- into smaller molecules and individual atoms.
The decomposition process is carried out by decomposers whose special role is to break down the cells and tissues in dead organisms into large biomolecules and then break those biomolecules down into smaller molecules and individual atoms. Decomposition ensures that the important elements of life - carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, magnesium - can be continually recycled into the soil and made available for life. 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.
Task 6: Visualizing Combustion and 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
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?the 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. Then answer the Checking In question.
Stop and Think3. 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.
Optional Extensions: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. 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, 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 below to help you find j-mol images. You can take screenshots and then load onto them onto your computer as a picture.
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! $1.99 to install. Gives you Jmols and background information for lots of carbon compounds. If you shake it, it shows a new molecule.
- Molecules app from Sunset lake Software. Free! 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.
- NOVA Elements App: Free! Great visuals and background information on elements and the periodic table.
4. Read about nitrogen availability and trees in these these articles:
- Microbe Diet Key to Carbon Dioxide Release
- Global Warming May Increase the Capacity of Trees to Store Carbon
- Nitrogen Study Could "Rock" a Plants World.