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

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.

Sickle Cell Anemia: Day 3

I did protein synthesis races with students. This is really fun, requires a high level of focus and energy from the teacher. Yet, I have found it to be very simple and effective.

I project a simple sequence of DNA up on the board. One student acts as the RNA Polymerase and transcribes this DNA code into mRNA. As soon as they are done they shove the white board over to their table partner who acts as a ribosome to translate the mRNA into an amino acid with the help of the amino acid codon chart. The team which writes down the correct code first AND has their dry erase marker capped and holds it up wins a Snickers Bar.

I have found that within about 20-30 minutes the majority of my class can turn DNA into mRNA into Amino Acid. It is amazing what the mind can do with social pressure and engagement!

Next, we actually turn these new skills to good use by ‘mapping’ the Beta Globin gene. I open this up by showing the students the NCBI file for the gene . It is still a wonder to me that there is so much DNA that is ‘unused’. This is an activity from 3D Molecular Designs that has the entire 1792 nucleotides of the functional gene printed into one long laminated strip. Students can learn about promoter sequences, reading frames, template strands, introns, exons, and mutations. I currently teach introductory biology classes so I can’t teach about some of the richness there. But, my kids got through the activity and it stretched them. I mainly had students go through and highlight the Amino Acid code of the Beta Globin Gene this helped them realize that there were introns and exons. By having them actually interact with the massiveness of a real gene I think it helps to show how complex genetics really is.

Sickle Cell Anemia Investigation :Day 2

Our goal for this day was to observe how blood typically passes through capillaries.

I went to the store and got 17 feeder goldfish I had them set in a bucket in my garage over-night so the water was nice and cool and their oxygen demands were low.

I mount my iPad so that students can observe the procedure for how to view the capillary bed.

The students have five minutes to view the fish and take a video with their phones. These are mostly uploaded to their social media platforms. I feel that this is actually a compliment. An additional bonus is that my classes later in the day walk in begging to do ‘the fish thing’.

Next, students observe and draw prepared slides of red blood cells and sickle cells.

When I go to close class I explain that one of the complications of sickle cell anemia is that it can cause blood clots. I am careful to draw attention to the fact that the function of blood cells is related to its structure. This is a big theme for us in our discussion of cells. The point of this lesson can’t be missed.

Sickle Cell Anemia Investigation

I want to share how I am leading my students through our unit on molecular biology with a narrative of sickle cell anemia (SCA).

Day 1: Introduce the problem of sickle cell anemia

Living with sickle cell disease Shaniya’s story is a video produced by St. Jude’s Medical Research Hospital. It introduces the real life struggles of a courageous high school student who has Sickle Cell Anemia. Having a narrative that the kids can cling to really helps to engage them in the value of learning about this topic. \

Next, I introduced the driving questions or problem that we will be looking at. 

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

#2 Why has the disease sickle cell anemia become such a widespread problem in certain regions of the world?

I showed the students an image of where the incidence of SCA is in the world.

This is a pause about 20 min. into a 45 minute lesson to get students moving and assess whether they have learned anything and are willing to learn.

I collected these and read them to the class in four minutes. I am careful to praise genuine curiosity and correct early misconceptions about the concept.

Do not apologize for asking for memorization from your students early in a learning cycle. Higher levels of understanding can only come with fundamental vocabulary and clarity. This diagram is simple for my introductory biology course.

At the end of class I made students diagram the process of protein synthesis. They had to copy this diagram three times in their lab notebooks for homework.

Fun Approach to Teaching DNA Structure

Teaching AP Biology students has many challenges, one of them being that by the time my typical student reaches me they are 3 years removed form freshman biology. As much as they may tell you that they already know something, or “We learned this freshman year”, that does not always translate to “we REMEMBER this from freshman year”. Finding new and fun ways to reintroduce concepts to these students is a challenge that I enjoy.

I have the luxury of having a class set of the 3-D Molecular Designs “DNA Discovery Kit” models. This allows me to have each lab group (4-5 students) use their own kit in this activity.

First, I give the groups each a kit and tell them…well, very little.

I say:

Each group gets one “puzzle” and your challenge is to be the first group to successfully put it together. You must use every piece, and it must be free standing on the provided stand.

Then they begin. Now, I don’t even tell them that it is a model of DNA. Most of them figure that out (especially since it says “DNA model” on the box the model comes in) but knowing that it is DNA does not always translate to being able to quickly assemble the model. Students quickly figure out that they do not know the structure of DNA as well as they thought they did since the “already learned this freshman year”.

Many groups start by just fidgeting with pieces to see how they fit, nitrogen bases get paired up pretty quickly and then we hit some snags and the real learning starts to happen as they begin to problem solve. At this point, many groups will attempt various strategies to get the pieces on the stand. this helps them start to figure out how the components of the nucleotides fit together.

The most successful groups will put together full layers first (two full complimentary nucleotides) and then assemble them on the model. At this point they start to make comments about how each side seems to be pointed in a different direction! The groups that figure it out will then start to push through and their models come together quickly.

I will make sure the first group knows that they “won the race” and sometimes have a prize. Then I will begin to give a few suggestions or tips to the struggling groups to get them rolling.

New thing I did this year:

After everyone is done, I had them all look at their model with a piece of paper and pencil and BY THEMSELVES write down 8 characteristics of DNA that their model shows. This gets challenging once they get to 6 or 7. Next, they work in their groups to create a master list of 10 characteristics. Third, I have them infer a purpose for each characteristic. Finally, I will have the group choose what they feel is the most important characteristic and then share that with the class. This is a good opportunity to have a more guided discussion with the class about the characteristics of DNA and the reasons or purposes for these characteristics.

In my experience, this is an activity that the students seem to enjoy AND students do tend to reference the model in subsequent class periods as they work further through our molecular genetics unit and evidence from student assessments supports that this at least has not discouraged student understanding.

This year, after the activity I had a student very excitedly ask if they could put ALL them models together into one BIG strand. YES, of course we can do that! It …sort of worked. (Pictured at the top)