Sickle Cell Anemia Investigation: Day 8/9

This was a day where we did gel electrophoresis. I got my Sickle Cell test kits from Minione. This is the same supplier that we got our gel electrophoresis units from. I ran a kit which wasn’t anything too spectacular or creative here. The gels can be microwaved, loaded, and cool into tiny forms in 15 minutes at the beginning of class. This left students with about 60 minutes to load their DNA in wells and turn on their electrophoresis kits. I had every student group run their DNA all the way through. Running the DNA only took 22 minutes. During the time that it took to run the DNA I had the students complete an assignment made by mini PCR to check their understanding of gel electrophoresis.

I quickly realized that I needed the students to help me aliquot the DNA samples into numbered microcentrifuge vials that corresponded to particular patients. This added several minutes at the beginning of classes but it saved me over a hour of prep time.

My students were pretty focused on this day. I was too so I don’t have many photos. It turns out if you treat students like scientists they act like scientists. One student literally even student “I feel like a real scientist”. AAAAHHH it still gives me all those tingly teacher feelies. 🙂

The next day we talked about the activity one more time. I used a time lapse video that one of the students took.

Many students got really similar results.

After this time I showed HHMI’s video on Sickle Cell Anemia to answer the guiding question, “Why does sickle cell disease only occur in some locations around the globe.”

Educational GOLD!!!
We used this video to discuss how the malaria parasite hijacks blood cells.

Finally, I went through the way that Hb A and Hb S alleles would behave in a zone of low malaria and a zone with high malaria. I made them predict at their table what would happen and explain why. I actually had to be very aggressive to get them to argue. Often we talk about argumentation as an important skill. My students were simply saying things, yet, I knew that they had all the skills necessary to make good predictions based on logic.

Once the students saw what would happen in low malaria zones I made each table develop an argument for what would happen in areas with high malaria. They had to simply support their hypothesis with logic, but they hated this. I’m still mad about their unwillingness to apply what they had learned to a prediction.

In areas with high incidence of malaria the two alleles stabilize producing a high percent of the population that is heterozygote and thus advantaged.

I loved this whole experience, and I thought it was a great story for students to remember how a system can work from a change in DNA all the way to a population being changed. They will remember this information for much longer than a traditional presentation of the material, because it was presented as a story and humans are primed for narrative not a jumble of incoherent facts and events. I can imagine a suite of biological stories that move from DNA science to evolution. This would serve to create a coherent sense of how biology works rather than a patchwork of biological units that the student never ties together.

Narrative gives biology meaning just as it gives our lives meaning. We should use narrative to weave the large concepts of biology together for a view of life with a little more grandeur.

Sickle Cell Anemia Investigation: Day 7

Today we practiced using a micropipet and loading fluid into the wells of gels. I used several resources from miniPCR to do this.

First of all, this is an amazing video resource to help teach your students how to micropipet. I paused it several times and had the students pass around micropipets to practice with.

Next, I had them compete against one another to pipet their solutions as accurate as possible onto micropipetting practice cards.

This activity requires the students to get the correct amount of fluid to fill the tiny circle on the card.
Water and food coloring and glycerin at 10% were used to make a solution that students could work with.
Student groups of two competed with students across the table to have more accurate pipetting skills.
This silicone gel requires no work on my part so I feel I am wasting less time. The students can’t gum it up and jam into it the way they normally do when they are practicing loading gels.
Next, I had students load their gels into the Electrophoresis machines and then submerge them in water. They filled the wells in their silicone practice gel to get the hang of loading a gel.

This was a very successful day and I am glad I spent the time preparing the students on how to do the practice. I also spent much of this day explaining what is actually occurring when a gel is running.

Sickle Cell Investigation: Day 6

Today we had to retreat back to notes just to get clarity on what was going on. I simply had the students answer the first guiding question with notes.

“How does the gene for sickle cell anemia cause such dramatic changes in people’s health?

This brought students through the following:

DNA-> Mutation-> mRNA-> Amino Acid leading to unusual folding of protein -> Clumping of Protein -> Change in cell shape -> Change in cell function -> symptoms of disease


I actually got a new activity that I wanted to try here to teach the students about how the proteins clump. However, I felt that I didn’t have time. I will try new things next year, but sometimes you simply have to pitch the ball right across the plate.

Finally, I went through a powerpoint that was created by miniPCR to explain how gel electrophoresis works.

Sickle Cell Anemia Investigation: Day 5

Today did not go too well. I must remind myself that it is quite a lot for students to jump from DNA to mRNA to Protein Shape & Function to Cell Shape to bodily function. Still, I think today should have worked much better than it did.

We started with a video by BioVisions at Harvard titled Cellular Visions. It shows how many different types of proteins function in a cell.

It also includes a scene of actin polymerizing which I could pause and discuss. Because It would play into our class discussion.

Then we reviewed that cells shape helps them to perform their function and that their shape is determined by a sequence of amino acids. I told several other protein ‘stories’. I then ended with a visual from Utah Genetics that shows cell size and scale so that I could compare a red blood cell and a hemoglobin protein. I still have many students who cannot interpret that cells are much larger than proteins.


Next, I tried to do a hands on activity with the students that I got from HHMI titled How Do Fibers Form. I think the lesson should work but I couldn’t get it to click. I had lots of blinking and phone issues instead of engaged hands and minds.

Essentially, students take cut out paper models of hemoglobin and they try to piece them in a cell to see how the proteins interact and determine the shape of the cell.

Normal Hemoglobin is “closed” when it is carrying an oxygen molecule. That is, it has no open pocket to accept DNA. So the proteins simply bounce off one another .

I pulled up David Goodsell’s Molecule of the month blog to show the students the behavior of this hemoglobin molecule.

I physically move my body to imitate the hemoglobin in a closed configuration. By pretending to catch oxygen.

On the other hand when an oxygen is not bound to the heme group of hemoglobin it enters an “open” configuration.

This molecule is ready to accept an Oxygen. Thus, it is ‘open’ I slink my body around the room like a catcher with his mitt open and ready to receive a ball. *don’t you wish you had a picture of that 🙂

We can model this with a piece of paper that has a hole punch to show that it is open.

I ask the students to show how these proteins might interact if they were bouncing around a cell. None of my students got this at all…There were literally crickets chirping in my Leopard Gecko cage folks… pppsssssssth 🙁

One or two students suggested that they may clump together.

Next, I had them manipulate models of hemoglobin that had been mutated.

Actually, several of the students started stringing them together… but none (literally 0/111) of them put together that this growing chain of proteins could actually push on the cell membrane to change the shape.

some students got this idea that the proteins would clump together
No students had the notion that the proteins would change the shape of the cell.
None of my students got this far.

I actually did a clearer example with better models that I had printed off.

These ‘normal’ hemoglobins wouldn’t clump
This mutated protein has a pocket for binding to occur in.
Here they could really see how the proteins would stack up to form a polymer fiber that pushes out the cell.

By the last hour I simply just showed them how this could work with my overhead projector. Then we went outside with the last 10 minutes of class and played hacky sack.

I am going to try again on Monday.

Sickle Cell Anemia Investigation: Day 4

Today began with a video by John Perry’s series “Stated Clearly” titled “What is a gene?”

Next, students wrote down the learning objective. A protein’s shape determines its function, and the shape occurs due to the sequence of amino acids coded by DNA. I explained that a truck has a specific shape that helps it to do its function of hauling things and a ferrari has a different shape that helps it to do its function of going fast. Proteins too have specific shapes to help them do their own function.

It is a difficult abstraction for students to take to look at a protein model and think that these microscopic things actually have a function.

Though these models of look interesting to a student to assume that one has a function is very difficult. The one on the left BCR-ABL Fusion Protein stimulates cellular division and the right Aquaporin allows water to pass through membranes. This form function can be a stonewall for a 14 year old due to the level of abstraction involved.

In order to help students realize how these proteins function can work I use minitoobers. (*this is not my own original idea.) I tell students that they have to fold their protein using beta pleated sheets a.k.a. zigzags or alpha helicies a.k.a. loops into a shape that can pick up a molecule and transfer it from one partner to the next. I give them 3 minutes to fold their toober into a shape that can make the transfer and then let them show the rest of the class their solution.

Oven mitten design
The trade off!
The Eagle has landed…

Students fold their proteins into many different shapes to perform the function of moving a protein.

A hockey stick solution
GOAL!

I can then show them It turns out these protein things can have many shapes! You can show the kids these proteins too from the Protein Data Bank.

Now we turn our attention to how the sequence of DNA effects the shape of a protein. I am using kits that we purchased from 3dmolecular designs. But, colored push pins will work too. ( I think Drew Ising did a post about this in the past).

I start this by having the students place a positive amino acid (blue) on one end of their mini-toobers and a negative amino acid on the other end.
Next, students evenly space just four hydrophobic amino acids (labeled yellow here) across the mini toober.
Finally, they place four hydrophilic amino acids across the mini toober.

At this point I pause the class and open a concord consortium interactive player on my smartboard.

I ask student to predict how the positive and negative amino acids will behave and how the hydrophobic and hydrophilic amino acids will behave. They can all get it.
Beautiful! Opposites attract! I love this! Thank you to whoever created this.

Now it is the students chance to fold the protein into a shape where the positive and negative amino acids on the ends of their toober attract to one another and the hydrophobic amino acids fold in.

This looks about right?!

At this point I grab one of the students folded protein and I substitute one positive amino acid for a negative amino acid. They can see that it will unravel their protein. Now I try to hit home the reason that a mutation in DNA can cause an impact in an organism.

I had a few Hemoglobin molecules printed off for my classroom. I found the STL files on Thingverse. So, now the kids can see the shape of the protein is different. When only one amino acid is changed.

It turns out that DNA causes a visible change in proteins.