Lesson 24

A

Locked — confirm your name above to begin.
  • One cell from the tail of a mouse embryo, and one of its genes: Hes7. The cell runs as you watch.
  • Its parts go in one at a time: the gene is transcribed and its mRNA broken down; the mRNA is translated and the protein broken down; the protein binds the gene's own promoter and blocks transcription.
  • Yours to set: the gene's three introns (each is transcribed, then cut out, so each adds minutes before an mRNA is finished), the mRNA's half-life, the protein's half-life.
One cell. The Hes7 gene sits in the nucleus: a promoter, four exons (dark) and three introns (pale). An intron removed is gone from the drawing.Each dot moving along the gene is RNA polymerase transcribing it; the line it trails is the RNA made so far. A finished mRNA is a wavy line outside the nucleus. Each red dot is 10 molecules of Hes7 protein.Red dots on the promoter: Hes7 protein bound there. The bent arrow fades as transcription is blocked.The strip underneath is the last ten hours, darker for more. ▲ marks each peak of the protein.

PartsThe cell starts with its first part alone. Add the next part puts in the next one; a tick box switches a part off and on again.Adding or switching a part starts the cell again, empty.

Hes7

intronsClick an intron to remove it from the gene; click again to put it back.Polymerase has to transcribe an intron before the mRNA can be finished. Introns 1 and 2 are short (2.5 minutes each); intron 3 is long (14 minutes).

To finish

  • Hes7 protein that keeps rising and falling, pulse after pulse
  • Pulses that come closer together than the mouse's
  • Pulses that die away
Stage B is open.
R code 

    

  







  
B

  
Finish Stage A to unlock this section.

  

    
    

      
    
        
  • A row of cells along the back of the embryo, head to the left, tail to the right. Every cell runs stage A's Hes7.
    • 
        
  • The parts go in one at a time: the tail adds cells; Fgf8 is transcribed only in the tail, so its mRNA decays in the cells left behind, and Hes7 stops in a cell once its Fgf8 is low; Fgf8 speeds Hes7.
    • 
        
  • Yours to set: Hes7's introns and its protein's half-life; the half-life of Fgf8 mRNA.
    • 
      

    

  


  

    

      

        A row of cells, head to the left. Each cell is drawn twice: by its Fgf8 mRNA (blue: pale little, dark a lot) and by its Hes7 protein (red: pale little, dark a lot).▼ marks where Hes7 stops. To its left each cell keeps the Hes7 it had when it stopped.Somites: a boundary is drawn where the stopped cells go from low Hes7 to high. A dashed block has no boundary closing it yet.The row grows for 24 hours.
        
        

          
          
          
        

      

      
      

        
PartsAdd the next part puts in the next one; a tick box switches a part off and on again.Adding or switching a part starts the row again.

        

          
          
          
          
        

        

      

    

    

      

        
Hes7

        

          intronsClick an intron to remove it from the gene in every cell; click again to put it back.Introns 1 and 2 are short (2.5 minutes each); intron 3 is long (14 minutes).
          
          
          
        

        

      

      

        
Fgf8

        

      

      

        
To finish

        
    
          
  • Four somites
    • 
          
  • Two stripes of Hes7 in the tail at once
    • 
          
  • Smaller somites 
    • 
          
  • A longer stretch of cells with Hes7 still running 
    • 
          
  • A long stretch with no somite boundary
    • 
        

        
Stage C is open.

      

    

  

  

    

      R code
      


    

  







  
C

  
Finish Stage B to unlock this section.

  

    
    

      
Hox genes sit in clusters on the chromosome, and the order they're arranged matches the order they're expressed along the body axis—anterior genes at one end, posterior at the other. That's co-linearity. It tells you the regulation of these genes is built into how they're packed in DNA.

      
    
        
  • Stage B's row for 64 hours: the whole body. Each somite becomes one vertebra.
    • 
        
  • Hoxc6 and Hoxc10 each switch on in the tail at an hour you set and stay on in every cell made after. A vertebra made with Hoxc6 carries ribs; the ribs end where Hoxc10 begins. The forelimb sits at the first Hoxc6 vertebra, the hindlimb at the first Hoxc10 vertebra.
    • 
        
  • Yours to set: Hes7's introns and its protein's half-life; the hour each Hox gene switches on. The body starts as a mouse.
    • 
      

    

  


  

    

      

        The whole row, head to the left, growing for 64 hours. The top two rows mark the cells with Hoxc6 on (lines) and with Hoxc10 on (crossed lines); under them, stage B's rows.Each somite is drawn by the Hox genes on in its first cell: plain for neither, lines for Hoxc6, crossed lines for Hoxc10.The skeleton underneath: one vertebra for each somite, with its ribs and limbs.
        
        
        

          
          
          
        

      

      
      

        
Hes7

        

          intronsClick an intron to remove it from the gene in every cell; click again to put it back.Introns 1 and 2 are short (2.5 minutes each); intron 3 is long (14 minutes).A change made after the body is finished grows it again.
          
          
          
        

        

      

    

    

      

        
Hoxc6

        

      

      

        
Hoxc10

        

      

      

        
To finish: any twoEach skeleton here was grown by this model at some setting of the three genes.A finished body like it fills its circle: the same stretches long and short, the same limbs.The snake keeps a hindlimb: pythons and boas have a small one.

        
    
          
  • a goose
    • 
          
  • a long-bodied lizard
    • 
          
  • a snake
    • 
        

        
That is the last stage.

      

    

  

  

    

      R code
      


    

  






  
Good job!

  
That is all of Lesson 24. Your completion code is below — copy it and hand it in.