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A Message to Teachers
Thank you for using our tools to help your students visualize the molecular world! The
lesson/activity guide that accompanies the Synapse Kit is intended to help you consider different
ways in which you may use these materials. It is not the intent of the Center for BioMolecular
Modeling to require you to work through the entire lesson from start to finish (although you may do
so if you wish). We do encourage (and perhaps insist on) your modification of these lessons and
activities to meet the learning objectives of your specific students or to accommodate the physical
limitations of the environment in which you teach. Enjoy!
Part I: Modeling the Resting Potential
All living cells, including nerve cells, maintain a difference in
the concentration of ions across their membranes. These
ions play an essential role in neuronal signaling. Ions are
unequally distributed between the interior of the cell and the
surrounding fluid. A small excess of negatively charged ions
on the inside of the cell membrane and a small excess of
positively charged ions on the outside of the cell membrane
results in a negatively charged cell interior relative to the
outside environment. This difference in electrical charge
across the membrane can be measured with a voltmeter and
ranges from -60 to -80 mV (millivolts) when the neuron is not
sending a signal. The membrane potential at rest is referred
to as the neuron’s resting potential. For the purpose of this
lab activity, we will consider a neuron with a resting potential
of -70 mV. A membrane that exhibits a membrane potential
is said to be polarized.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 1
Set up the membrane of the axon of a
neuron according to the diagram to the
The permeability characteristics of a
neuron’s plasma membrane are, in part,
determined by specific membrane
transport channels. Channels in the nerve
cell membrane that transport negatively
charged ions are relatively few in number
or are closed and not displayed in the
1a. Label the membrane, the voltagegated sodium channel, the potassium leak
channel, the voltage-gated potassium
channel and the sodium-potassium pump
in the diagram.
Table 1. Average Ion Concentrations Inside and Outside of Mammalian Neurons
Intracellular Concentration
Extracellular Concentration
Potassium (K+)
Sodium (Na+)
Chloride (Cl-)
Large anions (A-), such as
some proteins, inside the cell
Potassium ions (K+) represented by the square purple models and sodium ions (Na+) represented
as round blue models are the key players in establishing the resting potential. According to the
table above, in most neurons, the concentration of Na+ is higher outside the cell while the
concentration of K+ is higher inside the cell. Distribute the sodium and potassium ions to illustrate
this observation in the model you have constructed.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 2
In a resting neuron, what positive ion is most abundant outside of the plasma membrane?
The K+ gradient dictates that potassium ions will flow in what direction?
(K+ flows out of the cell)
What happens to the resting potential of the cell when K+ ions move?
(As K+ ions move out of the cell, the inside of the cell becomes more negative relative to the
outside of the cell.)
What direction does the concentration gradient dictate the Na+ ions flow?
(Na+ ions will flow into the cell)
Carefully examine the sodium-potassium pump. What is the exchange ratio of Na+:K+ ions
of the sodium potassium pump? (HINT: Focus on the shapes in the pump.)
(For every three sodium ions pumped out of the cell two potassium ions are pumped in)
What molecule is necessary for the sodium-potassium pump to work against the chemical
What factors impact establishing the resting membrane potential?
1. The Na+ and K+ gradients are maintained by the sodium-potassium pump. The energy
of ATP hydrolysis is used to actively transport three Na+ out of the cell for every two K+
into the cell.
2. The chemical gradient favors a net flow of the diffusion of K+ through potassium
channels (often called leak channels) out of the cell.
3. Very few Na+ channels are open as compared to K+ channels. Because K+ ions more
readily cross the membrane due to potassium leak channels and Na+ and other ions
can’t readily cross the membrane, K+ outflow leads to a relative negative charge inside
the cell as compared to the outside of the cell.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 3
Optional Activity: Comparing the Voltage-Gated
Sodium Channel to the Voltage-Gated Potassium
How does the voltage-gated potassium channel
distinguish sodium ions from potassium ions?
(Sodium ions travel through their channel in the
hydrated state. The potassium ion channel is
designed so that potassium ions are not
hydrated when they travel through the channel.)
What structural differences can you observe in
the channel pore of these voltage-gated
(The sodium channel is “wider” than the potassium channel to accommodate the hydrated
sodium ion while the potassium channel is narrower to accommodate only the potassium
ion. The voltage-gated potassium channel is “lined” with oxygen atoms that are precisely
spaced to accommodate a potassium ion and not a sodium ion.)
Part II: Modeling the Action Potential
Set up an axonal membrane as shown in the diagram below and to the left. Remember to set up
your model so that there are more extracellular Na+ ions than intracellular Na+ ions and more
intracellular K+ ions than extracellular K+ ions. You will also need to periodically refer to the graph
shown below and to the right as you work your way through the modeling process:
The Action Potential
Changes in membrane potential in a local area of a neuron's
membrane result from changes in membrane permeability.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 4
Next, you will simulate the mechanism that produces an action
potential in the axon of the neuron. Follow the steps below to
model this action potential.
Step 1 - Resting state:
The voltage-gated sodium and potassium channels are closed.
Set your voltmeter at -70 mV.
Step 2 - Depolarization:
A stimulus opens the voltage-gated sodium channels and Na+
follows its concentration gradient into the neuron. The influx of Na+
causes a depolarization across the cell membrane. An action
potential will be triggered if the depolarization reaches threshold
(often between -40 and -55 mV). Set the voltmeter at threshold.
For the purposes of this activity, we will consider the threshold
potential to be -50 mV.
Step 3 - Rising phase of the action potential:
Depolarization opens most of the voltage-gated sodium channels,
while the voltage-gated potassium channels remain closed. Open
the voltage-gated sodium channels and move a few more Na+ into
the neuron. Depolarization continues until the inside of the
membrane is positive with respect to the outside (usually +30 mV).
Set the voltmeter at the peak value of the action potential. When
the patch of neuron membrane is generating an action potential
and its voltage-gated sodium channels are open, the neuron
cannot respond to another stimulus no matter how strong.
Step 4 - Falling phase of the action potential:
Voltage-gated sodium channels become inactivated, blocking Na+
inflow. Voltage-gated potassium channels slowly open permitting
K+ to follow its concentration gradient out of the cell causing the
voltage across the membrane to fall. Position the voltage-gated
sodium channels to their closed and inactive position. Open the
voltage-gated potassium channel and move the K+ ions out of the
neuron. Demonstrate a fall in voltage due to this ion movement on
the voltmeter. Only a stonger than normal stimulus can reopen the
voltage-gated sodium channels at this time.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 5
Step 5 - Hyperpolarization:
The voltage-gated sodium channels begin to reset back to their
original position. Move the voltage-gated sodium channels to
their closed but able to be activated position. The voltage-gated
potassium channels are still open causing the voltage to
undershoot the resting potential. Set the voltmeter to dip below 70 mV.
Step 6 - Repolarization:
Repolarization restores resting electrical conditions but does
NOT restore resting ionic conditions. The ion redistribution is
accomplished by the sodium-potassium pump.
Step 7 - Re-establish the ion distribution:
7.2 & 7.3
7.5 & 7.6
7.1: Bind three three intracellular sodium ions to the appropriate spots in the protein.
7.2: Bring the ATP in close proximity to the pump.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 6
7.3: Sodium ion binding stimulates phosphorylation of the pump protein by ATP. In other words, a
phosphate group is added to the sodium-potassium pump from the ATP molecule. (You
will not be able to demonstrate this step with the model).
7.4: Phosphorylation causes a change in the shape of the protein. You can demonstrate this by
“swinging” the sides of the protein so that it opens to the outside of the cell.
7.5: The shape change reduces the protein’s binding affinity for sodium ions and increases the
binding affinity for potassium ions. Remove the sodium ions from the protein and deposit
them outside the cell and bind two potassium ions to the appropriate spots in the protein.
7.6: Potassium ion binding triggers the release of the phosphate group from the protein. (Again,
you will not be able to demonstrate this step with the model).
7.7: Loss of the phosphate group results in the restoration of the protein’s original shape which
then releases the potassium ions. Swing the sides of the protein back so that they open to
the inside of the cell and deposit the potassium ions.
7.8: Repeat this process one more time.
What value is being used for the resting potential in your model neuron?
What “factors” may cause a change in the voltage established across the membrane this
(A change in voltage may occur as a result of a stimulus such as heat, light, pressure,
chemicals, a change in body position or a change in blood pressure.)
Of what significance is a rise in membrane potential to -55mV to the neuron? Describe what
protein and how it is affected by this change in voltage.
(This particular neuron has reached threshold potential at -55 mV meaning that
depolarization becomes self generating (the all-or-none response). The voltage-gated
sodium channels open allowing sodium ions to follow into the cell.)
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 7
What is meant by depolarization?
(Depolarization is a reduction in membrane
potential – the inside of the membrane becomes
less negative (moves closer to zero) than at
resting potential.)
Color the area on the graph to the right where
depolarization has occurred.
Sketch the axon membrane that has been
depolarized. Be sure to include all channels and
ions in their proper locations and positions.
What events occur at the peak of the action potential?
(The voltage-gated sodium channels are inactivated and the volta ge-gated potassium
channels are opened.)
Why is it important that another action potential cannot be generated during the rising phase
of an action potential?
(Because the voltage-gated sodium channels are open in a particular section of the
membrane, an action potential cannot be generated there. The inward current that
depolarizes the axon ahead of the action potential cannot produce another action potential
behind it ensuring neuron transmission occurs in one direction.)
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 8
Why does the voltage across the neuronal membrane
(When the voltage-gated potassium channels open,
positively charged potassium ions leave the neuron
causing the membrane potential to fall.)
Color the area on the graph to the right where
repolarization has occurred.
Sketch the axon membrane that has been repolarized.
Be sure to include all channels and ions in their proper
locations and positions.
Why does the voltage “undershoot”?
(The voltage-gated potassium channel gates close
more slowly. Excessive K+ efflux results in
Color the area on the graph to the right where
hyperpolarization has occurred.
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 9
Fill in the following to compare voltage fluctuations and ion concentration changes that occur
during an action potential.
Action Potential
Intracellular Na
Extracellular Na
Intracellular K
Extracellular K
Falling to
2p. Why is the sodium-potassium pump necessary after an action potential has been generated?
(While repolarization restores the electrical potential, the resting potential ion distribution has
not been restored. The concentration of sodium and potassium ions is the opposite of what it
should be at resting potential. That is to say that the concentration of potassium ions is greater
outside than inside the cell and the concentration of sodium ions is greater inside than outside
the cell. The sodium-potassium pump is necessary to reset the ion distribution to resting
potential conditions.)
3q. What would happen to a neuron if threshold potential is not reached?
(The neuron would not “fire” an action potential.)
MSOE Center for BioMolecular Modeling
Synapse Kit: Section 1-2 | 10