Background

We are now at the end of the cholesterol biosynthesis pathway, and have seen how cholesterol is synthesized from acetyl-CoA in a series of steps catalyzed by many different enzymes.

Your Mission

Complete the final step of the Cholesterol biosynthesis pathway, the conversion of 7-Dehydrocholesterol to Cholesterol, catalyzed by DHCR7 (corresponding to the highlighted area in this figure below), and give your pathway a name.



  • Download the starter pathway here: met-1-last-start.gpml.
  • Launch PathVisio and open the dowloaded file via File > Open.

    • Add the metabolite node

  • Select Metabolite from the Data Node palette in the Objects tab. Click on the canvas to place the metabolite node.
  • Double-click on node to open its properties.
  • Search for “cholesterol”; Choose any of the entries that just say “cholesterol” (in order of priority ChEBI, LIPIDMAPS, PubChem, CAS); Click OK to select the identifier, and then click OK again to close the node properties window.

    • Draw the conversion between the metabolite nodes

  • Select the Conversion arrow from the MIM interactions palette in the Objects tab. Drag and drop anywhere on the canvas to create the interaction.
  • Drag the plain end (start) of the interaction over a target area on the starting metabolite node (7-Dehydrocholesterol).
  • Drag the arrow end (end) of the interaction over a target area on the ending metabolite node (cholesterol).
  • Right-click on the conversion interaction and select Add anchor, or select the conversion interaction and then use the keyboard shortcut Ctrl+R (Command+R on Mac), to add the anchor.

    • Add the gene product that catalyzes the conversion.

  • Select GeneProduct from the Data Node palette in the Objects tab. Click on canvas to place the gene node.
  • Double-click on node to open its properties.
  • Search for “DHCR7”; Choose any of the entries that just say “DHCR7”; Click OK to select the identifier, and then click OK again to close the node properties window.

    • Draw the catalysis interaction

  • Select the Catalysis arrow from the MIM interactions palette in the Objects tab. Drag and drop anywhere on the canvas to create the interaction.
  • Drag the plain end (start) of the interaction over a target area on the enzyme node.
  • Drag the catalysis end (end) of the interaction over the anchor on the conversion line.
  • (Optional) Align nodes using toolbar actions.

    • Add a pathway name

  • Finally, the pathway needs a title that conforms with our pathway title guidelines.
  • Double-click on the Pathway Information area in the upper-left corner of the pathway to edit the title.
  • Update the pathway title in the Title field. Briefly, the pathway name should be in English, and should be sentence case.

    • Optimize layout

    The overall layout of a pathway in terms of node spacing, placement on the board etc is important to the readability of the pathway at default zoom levels. As a final step in the creation of your pathway model, consider the following aspects of your pathway and adjust the layout accordingly:

    • Minimize white space by using a space efficient and compact layout.
    • Place the pathway diagram in the upper left of the pathway drawing board
    • Use consistent font size (12 or larger)

      • To see a showcase gallery of representative pathway models with efficient and clear layout, visit the WikiPathways Help page.

  • Save your work as a GPML file under File > Save As.
  • Drag-and-drop the GPML file below to check if it is correct.