Activity Overview:
Molecular
Modeling Tool: Charged Strings, Molecular Workbench
Key concept: Every
living cell builds up its complex structures (e.g. membranes,
DNA, molecular machines) by bringing together chains of folded
polymers, using only basic forces such as charge. The attractions
among charged surfaces of complementary shaped polymers helps
to keep them together.
In Charged Strings, students discover the effect of charge on a polymer shapes. Students then go into the Molecular Workbench and see similar polymers, this time in a more realistic modeling environment called "Smart Surfaces", where other forces besides charge are at work. Manipulating charge, they affect the way two molecular units come together, attracted to each other because they have complementary surfaces that carry charged monomers.. Finally, they manipulate a "Splines" model, in which linear molecules line up with each other much the way lipids align in a monolayer.
Learning Objectives:
Students will be able to:
Discuss the role of charged
areas of molecules in folding polymer chains into specific shapes.
Reason about the forces
that bring polymers together into complex cellular structures.
Give several examples of cellular
machinery and compare them to macroscopic tools and machines.
Macro to Micro Connection
Conceptual Prologue
Large polymer chains fold into specific shapes. Chains made from a variety of monomers, such as amino acids, can generate a large variety of shapes useful for cell structures. In the nanoworld of molecules, the shaping occurs as result of forces between interacting molecules and their parts. Basically all those forces behave as electrical charges, weak and strong, where similar charges repel and different charges attract. (In living cells, helper molecules assist the folding.)
In the previous activity students constructed linear or branching polymers using the Molecular Construction Kit. This tool allowed them to build only flat models, Yet molecular polymers have complicated 3D shapes. Models built in Charged Strings, on the other hand, with its 3D view, bring students closer to reality. Using this tool, students explore forces that shape polymers, turning them into the complicated polymer parts that later will be used to build sophisticated machines. Students place charges on different parts of a polymer, predict, observe and render the resulting structure, and even discover that the shape of a polymer may be communicated to another person or another cell in the code of a sequence of charges.
One of the limitations of Charged Strings, nevertheless, is that it doesn't include the effect of temperature, yet in reality each component also vibrates and moves about randomly. The second model, Smart Surfaces, calculates the effect of temperature and displays these movements. It also takes into account so called "weak" electrostatic interactions between neutral monomers that get slightly polarized because of momentary shifts in the electron cloud.
Students use this modeling environment
to observe the way charges can both bring polymers together and
separate them. This model gives students an opportunity
to experiment with molecular self-assembly, a unique property
of living systems that allow larger structures come into being.
In this way, parts can self-assembly into large molecular ensembles
such as membranes, separating cells into compartments, or a flagella
that works as bacteria's driving motor, or ribosome assembling
new proteins. They also get a hint
about how molecular ensembles cannot find each other and thus
be ruined if changes in the monomer sequence affect the
complementarity of the surfaces or the distribution of charges
on the monomers.
| 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: |
Model: Charged Strings NOTE: Computers running Windows Operating
System only. You will need also to install its application, the
3D Cortona Player in order to play it. Download it from: Modeling engine:Molecular
Workbench: |
| Supportive Materials |
*Worksheet: Charged Strings (Student) [HTML] [PDF version] Worksheet: Holding Molecular Structures Together (Student) [HTML] For print or projection: Molecular Counterparts: some molecular tools and machines |
| Advanced preparation (if any) | *Have software available.
*Print student material |
Investigative Question: What forces can bring polymers into larger complexes?
STEPS
You might want to recap: The variety of polymers arises from combinations of monomers. You might quickly review the organic polymers and their monomers with your students:
Proteins made of more than 20 different amino acids
Polysaccharides made of simple sugars
DNA and RNA made of 4 types of nucleic acids
Lipids mostly made of fatty acids connected to glycerol
1. IF you can display these pictures to your students, introduce charged areas on macromolecules.
|
This is a molecule of globin with another molecule, heparin, attached to it. The charge distribution on a protein surface is visible: Red areas (darker areas in center) show an excess of electrons making these area charged negative; areas in blue have a lesser density of electrons and are charged positive. |
The charged areas on molecules help them "stick' to other molecules and perform their function. The blue beads on the lipids in the membrane are charged and therefore bond to water on the outside of the membrane. their double "tails" have no charge and are moved away from water. Charged areas in the brown protein help attract the charged Sodium ions (the orange Na+s) and move them along. |
2.
Explore the connection between charge and shape: Charged Strings
Ask students to open the modeling software Charged Strings. Distribute
the worksheet that supports their exploration of the impact of
differently charged monomers on the shape of a polymer string
(students might think of this as a fragment of hemoglobin). Their
challenge will be to create different shapes from the polymer
fragment by changing the value of charges on the "monomers"
in the polymer fragment.
*Worksheet: Charged Strings (Student) [HTML version] [PDF version]
*Worksheet: Charged Strings (Teacher) [HTML version] [PDF version]
3.
Assembling Shapes Together. Using the Molecular Workbench,
students explore the power of charge and complementarity to pull
molecules into various kinds of alignment.
Worksheet: "Holding Molecular Structures Together": (Student) [HTML]
Discuss: How could linear polymers such as a string of glucose be made stable when heated or otherwise stressed? Students might think of cross-linking (when some monomers have four sticky points, they can cross-link parallel chains into a mesh), twisting (alpha helixes), weaving and cross-hatching (some beta sheet arrangements). If necessary, introduce the terms primary structure and secondary structure.
How can linear chains be assembled into more complex structures? Students might come up with some ideas: make strands stronger by twisting them together into bundles; assembling units together with different orientations, e.g. blocks of a pore, units of hemoglobin; reinforcing (proteins in lipid membrane.) If necessary, introduce the terms tertiary and quatenary structure.
4. Summarize the highlights of the unit with your class. Where are biomolecules found? What are they used for? Diversity arises from varying a small number of monmers. All biological structures are assembled, more or less, using these forces.
(Optional) Consider molecular
machines made of protein
Have students as a class do a quick inventory of simple machines
and what they do (e.g. transporting materials, using energy,
assembling, cutting
, modifying
force and speed 
etc.). Consider
with your students that, much in the way humans build and use
machines for various tasks, cells build and use molecular machines.
Every cell has molecular "levers", "gears,"
"wheels", "pulleys" or "screws"
as well as complex assemblages of these simple machines for various
complex cellular functions, from transport of chemicals through
a membrane to assembling or disassembling polymers. Similar to
our machines that burn gasoline, cellular machines convert the
chemical energy from the food we eat to perform mechanical work,
run chemical reactions or conduct electrical signals.
Give students access to the following pages or display with an
overhead project the web page: Molecular
Counterparts: some molecular tools and machines. [PDF version]
You might want to emphasize a few such molecules, such as the
enzyme lysozyme that catalyzes the breakdown of certain carbohydrates
found in the cell walls of certain bacteria. This enzyme is in
fact a protein - a large polymer made of amino acids - shaped
to hold and cut a molecule. Another good example is melittin
from bee venom, designed to form a hole in a cellular membrane
and let substances in and out.
Hemoglobin is, of course, the preeminent molecular machine, with
its four protein parts (globin strands) shaped to hold the oxygen-carrying
heme gently and flexibly. This structure is effectively ruined
in the case of Sickle cell Anemia, as students can discover in
other activities. Note that most of the cellular machines
are made of proteins, although sometimes they may have other
molecules attached, e.g. sugars or lipids. Discuss with your
students that every machine should have its unique shape and
property. This can be achieved because of unique properties of
monomers that are combined into a polymer. Besides machines,
cells have walls, tunnels, corridors - a whole infrastructure
- made of proteins in combination with polysaccharides and lipids.
To build its architecture, a cell needs a variety of these macromolecules.
A unique set of biopolymers -- RNA and DNA, the carriers of genetic
code -- are made of nucleotide monomers.