Faculteit der Natuurwetenschappen, Wiskunde en Informatica

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Ion channel

This short learning module is about ion channels. As an example, the focus of this module will be on the potassium channel. The module closes with the theme of Cell Transport. the module thereby hooks into the theme of evolution Students can work individually on this module by using the student manual. Or the module can be discussed in class.


This learning module is concentric in design. This means that the module can be used in different manners. On the one hand the module can be used in the beginning of the theme cell transport. The gray questions are then skipped and it possible to let the students answer them at the end of the theme. On the other hand the gray questions can be used as kind of bonus. Students that appreciate the subject or understand the theme want some more challenge.


For this module some prior knowledge about ions, the cell membrane, cytoplasm and transport across the cell membrane is needed.


Install Yasara:

1. Go to: www.yasara.org and click on ‘Products’ in the menu.

2. Choose ‘freely download now’ behind Yasara View.

3. Fill out the form. At ‘departement’ you can fill the name of the school. Your email address is only used to send the download-link.

4. In your email you will receive a download-link.

5. Install yasara according the instructions.

6. A short introduction of yasara can be found on this website here or you can send your question to onderwijs@nbic.nl.

Install the files of this module:

1. At the bottom of this page you can find the files needed for this module. Select a file by pressing the right mouse bottom and choose ‘save links as’

2. Choose the map ‘sce’ in Yasara.

3. Save every file as a sce-files.

Configurations in Yasara:

Yasara is a programme to look at protein in 3D.

1. 1. Load a file in yasara: file > load > Yasara scene or PDB-file. In this module only Yasara scene-files will be used. When you want to open the new file, close the protein you are looking: file > newafter that step you can open a new file.

2. To turn the molecule around you can use the mouse.

– Push the left mouse button and move your mouse: turn the molecule

– Push the right mouse button and move the mouse forward and backwards: zoom in and out.

– Grab the protein while pushing the left and right mouse button at the same time, or pushing the mouse-wheel. You can now move the protein to somewhere else.

3. Yasara can show protein structures in many different ways. Use therefore the keys F1 t/m F8.

– Ball-model: F1

– Ball&Stick-model: F2

– Stick-model: F3

– Trace-model: F4

– Tube-model: F5

– Ribbon-model: F6

– Cartoon-model: F7

– In every view you can choose to show the sidechains or not by pressing F8.

Some files are specifically designed to show specific parts of a molecule. By pressing the different conformation options it is possible to lose the specific design. When that happen and you want to see the specific design, just load the file again.

Required material

For the teacher’s guide and the .sce files, email: nijmegen@dnalabs.nl.