Molecular Modeling Tool: E-Chem, Molecular Construction Kit
In living cells a small set of monomers is used to create a large variety of polymers. Each polymer is unique in the number and type of monomers used to build it. Polymer chains can be linear, branching or even circular.
Students use the computer model, the Molecular Construction Kit, to build polymers from monomers. They employ "sticky points", called "functional groups" by scientists, (polarized groups of atoms in molecules capable of linking to each other with covalent bonds) in their explanations of those monomer properties necessary to build linear, branching or circular polymers.
Students will be able to:
Articulate where living beings obtain their monomers, the building blocks of the cell's polymers.
Build a polymer from monomers and employ the concept of "sticky points" (activated atoms on monomers) to explain the formation of linear, branching or circular polymers.
Macro to Micro Connection
Students link physiological functions of cells and organisms with the underlying macromolecules responsible for these functions.
Using available "raw materials", a set of 20 amino acids and a variety of sugars and lipids from the food we eat, our cells must assemble monomers into polymer chains and shape them into parts necessary for the construction of our cells' molecular machines. A monomer is a molecular building block from which polymers are built. A living cell makes its macromolecules by connecting many smaller organic molecules, called monomers. Such chains are called polymers because they are made of many (poly) monomers.
Animals get these monomers from digesting food; plants make them in the process of photosynthesis.
To qualify as a building block for polymers, each monomer must be capable of linking with others. When a monomer's functional group, a specific arrangement of atoms, reacts with a functional group of another monomer, the two molecules link together with a stable covalent bond, one that will not break under normal conditions and will not dissolve in water.The term "sticky point" in this activity refers to the functional group on a molecule capable of forming a covalent bond with a functional group of another molecule.
Students will discover that:
*If there are a bunch of molecules, with just one active functional group (a sticky point) each, only dimers can be made. (Dimers are a set of two molecules joined together.)
*If there is a second sticky point on each monomer, linear polymers such as polysaccharides, proteins or nucleic acids can be made.
*If there are monomers with two sticky points each and monomers with three sticky points, branching polymers such as starch can be made: the third "sticky point" is the site where branching occurs.
Activity Design and Execution: Major Science Concepts Monomer, polymer, macromolecule, functional group Assumed Previous Knowledge: Cell structure, molecule, covalent bonds Time: 1 50-minute classes Modeling Software:
Molecular Construction Kit (CC)
No installation needed if you have internet access. You may need to check that you have version 5 or later for the Flash plugin.
E-Chem (Joe Krajek) http://hice.org/sciencelaboratory/echem/index.html
This is a java application that runs on MAC OS 9 and Windows computers. You will need to install this (and maybe the Java runtime environment). It is easily downloaded from the eChem download site.
Supportive Materials Advanced preparation (if any) *Have software available.
*Review how to use the Molecular Construction Kit in the teacher's worksheet version.
*Print student material
1. Constructing monomers
Our body doesn't assemble monomers atom by atom. That would be like constructing a brick building grain by grain. Yet students should have an idea of how these monomers were joined together.
Have them open E-Chem to build a few monomers. Ask your students to follow the ECHem worksheet: Building an Amino Acid. Ask them to try to build another molecule in their macromolecule set, such as glucose.
2. Breaking down our food into monomers
Ask your students where we get our monomers come from, if we cannot make them. They should be able fairly easily to come up with the idea of the food we take in. Ask: Do we take protein or fats or nucleic acids directly from plants and animals and add it to our own supplies of proteins, fats, sugars and DNA? They might not know, in addition, that we have digestive enzymes specially designed to break down our food into key monomers, rather than breaking everything into constituent atoms.
The digestive system disassembles our food largely into monomers.This simple illustration of digestion may help them conceptualize this aspect of the digestive process. (You might discuss with your students which foods provide which types of building blocks.)
3. How are monomers connected into polymers?
A. Give your students some context: in order to make a polymer such as plastic, polyethylene or a protein, monomers must be brought close to each other and properly aligned in order to make covalent bonds.
You might need to review the concept of covalent bonds that join macromolecules together. You could remind students that substances held together with ionic bonds, in contrast to those held by covalent bonds, can often be dissolved in water, not a practical solution for living beings.
B. Build polymers. Hand Out the Molecular Construction Kit Worksheets.
Molecular Construction Kit worksheet (student) [HTML version] [PDF version]
Molecular Construction Kit Worksheet (teacher) [HTML version] [PDF version]
Ask students to open the Molecular Construction Kit with Internet Explorer, and go to the Construction Kit. The worksheets include both instructions in how to use the model, and the activities themselves. You may choose to let the students explore the model for five minutes before starting the activities, and then have them get into small groups to teach each other what they have found, or review with your class how to use the model. Similarly you may choose to lead them through the first one or two examples on the worksheet. Students should do at least one of each category, and then see how many of the other examples they can explore, either alone or in teams.
IMPT: Remind studentsof the limitations of the model, that in reality the atoms and molecules are always moving, vibrating and bumping into each other.
4. Review the student answers to the Summarizing Question asked at the bottom of their worksheet:
A. The Molecular Construction Kit is a tool for the construction of polymers. How did you get linear or branching polymer chains?
Both the number of sticky points and the shape and orientation of a monomer are important in building linear or branching polymers.
B. Why in the chemical process do engineers increase the production of polymers by raising temperature to several hundreds degrees (or by increasing concentration or atmospheric pressure). How and why will it help?
The faster the molecules move, the more likely they are to collide. The higher the pressure, the closer they are to one another.
5. Looking ahead: What would be an efficient way to build molecules into polymers in a living cell, where the temperature can not be raised above our body's normal temperature, and where high concentration or pressure is not an option either.
Since our body cannot afford very high temperatures or high pressures, we have special molecular machines called enzymes. An enzyme can attract the right monomer to special areas on their surface from many floating around in the cell, then catch another, orienting the sticky points just the way you did it manuallu in the construction kit.
To do so, an enzyme must have a very specific shape resulting from the unique folding process in which a polymer chain becomes a 3D body. They are needed because the probability of the molecules colliding with each other in the way that the "right" sticky points will be aligned in the right way is very low. In real life all molecules are engaged in the random thermal motion. In addition, groups of atoms within molecules vibrate and rotate.
Extensions and Connections
* Investigate the idea of the power of a linear chain made of repetitive building blocks. Why are they useful to a cell? (Long chains are (i) flexible; (ii) easy to control its making through elongation and (iii) easy to code with another linear chain (e.g., RNA). Have students imagine they had a long chain made of paper clips, or a necklace of beads. Ask them to come up with two ways to have the chain form the figure 8 and hold that shape. Tell them they could change the properties of the beads or links, they can add something around it or to it. Have them be creative. (Some students might think to put it in a mold, others might tape the points together, others put magnets etc.)
Monomers to Polymers Index