Use a Molecule Viewer in High School Biology: STAR Biochem

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Have you ever wanted to show your students what proteins or other molecules actually look like but struggled to use the 3D molecule or protein viewers?  Some of the programs available are really slow to load on not-state-of-the-art computers (who in education has state of the art computers??) and some of them are so difficult to learn how to use for teachers and students who have never used them before.  They often have many features that take a grad school education to even understand what they are!


The Office of Digital Learning at MIT (I am partial to my grad alma mater!) has created a bunch of great resources for high school teachers and students to use and they are all free!  One of these resources is called STAR Biochem.

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STAR Biochem is truly the easiest program to use to to show students an actual protein’s structure and its primary, secondary, tertiary, and quaternary structure.  I have used this in two different ways.


  1.  I have used it on my own computer and projected it on the screen, to show students how to use the program.  I can start up this program each time we mention a protein like hemoglobin, PRP prion, green fluorescent protein, or any other protein of interest.  Students love to see the pretty colors and the nice thing about this program is they can actually understand what each feature is showing!
  2. I have had students play around with the program on school computers.  Using the Java Webstart may work for some classroom computers and STAR Biochem does have several different install options.  Some schools I have worked in I have had great luck with it working on student computers and some schools I have not.


Once you have it installed on your computer or you choose to use the Java Webstart option, here is what you will see.

When you just open it, the screen looks like this:

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STAR Biochem is a viewer.  It’s a program that needs a separate protein or molecular structure info file to actually do anything.  These files are called PDB or JMOL files.  There are two ways to get these files.  You can actually get any PDB file you want from the Protein Data Bank managed by Rutgers (my undergrad alma mater!)  This bank of protein structures contains thousands of published protein structures and after looking up the name of the protein at the protein data bank site, you can Import them into StarBiochem.

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The second way to open a file is to use one of StarBiochem’s samples.  StarBiochem comes with some great sample files that include a lot of proteins or molecules that you would want to view in a high school classroom and you can access them by clicking on the Samples menu.

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In this blog post, I will focus on the samples, because there are a great selection and you might not even need to use the Import function in your classroom.


So click “Select from samples”.  This is the menu you will see.

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And wow.  You can already see that you have easy access to a bunch of proteins that are useful in the high school biology curriculum.


Here are a few ideas of when during the school year you might want to show students these protein structures.


Amyloid beta peptide is the protein implicated in amyloid fiber diseases and you could show several different human variants to show how mutations can change protein structures.


Aquaporin is a membrane channel that carries water across the cell membrane and you could show them this structure during the cell transport chapter.


DNA polymerase, helicase, and the ribosome subunits are really cool to show during your DNA Replication, Transcription, and Translation chapter!


H-ras p21 and Myc are cancer-related proteins.


They even have an influenza protein with an antibody attached for your virus/immunity chapter.


Lysozyme is a lysosome enzyme, great for viewing during your cell and organelle chapter.


Phosophofructokinase is a protein that I love to bring up during the aerobic cellular respiration chapter, because it is a great example of how enzymes are regulated with allosteric and active sites!


Besides proteins, you can also show students individual amino acid structures by clicking the “Amino Acids” tab.


Seriously, go now and load up STAR Biochem and play with it.  It is really intuitive and you can immediately show students the different levels of structure in a beautiful, colorful, 3D way.  The best way to learn about the program is to play with it yourself.


Teaching a biochemistry unit soon, check out my recent blog post about teaching biochemistry.


While you are planning your biochemistry unit, please make sure to stop by my store if you are looking for unique biochemistry resources that can help your students more away from memorizing and into really understanding the beauty of the field where biology and chemistry meet.



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