Transcription and Translation Modeling in Biology

4 different already "Unzipped" DNA strands 

When deciding what we'd do in class to help students understand the process of transcription and translation several blog posts gave me inspiration.  I had just done the transcription translation lab from Kim Foglia in AP Bio and I read these posts on making proteins out of beads on the Science Matters blog. Inspiration struck to combine these two labs into one for my class.

RNA nucleotides ready for transcription

I started the process backwards, by deciding which amino acids would be in the finished proteins. Since the pack of beads I already had at home only had 7 different colors, there were only 7 types of amino acids in our proteins. Two of the designed proteins were identical. I wanted students to be able to see that two strands of mRNA with different orders of nucleotides could produce the same protein because there are multiple codons that code for the same amino acid.  The visual also helps during discussions of silent mutations.

Using DNA as the template for transcription

Next, I wrote the mRNA code for each protein, making sure that I used different codons for the amino acids in the matching proteins. Then I wrote the DNA code that would be transcribed into our mRNA strands.  I felt a little like reverse transcriptase as this point! Now that I had all of the codes I wanted, it was time to prepare the model materials,

I made the beaded proteins and labeled them with a number and set them aside as an answer key for students to check when they were finished. I used a sheet of DNA molecules from Biology Corner, and used the RNA nucleotides from Kim Foglia's lab.  I color coded each DNA nucleotide we would use in the lab, laminated them, and lined them up in the correct order for each of the 4 DNA strands that we would start with in the lab. I taped the line of DNA together with two long strips of packing tape-one on the front and one on the back.  I wanted to make sure it was super sturdy since I wanted it to last for several years (OK, true confession, I want them to last forever). This was time consuming, but hopefully won't need to be repeated any time soon (unless someday I have a class with more than 4 lab groups).

Amino acids ready for translation

Kim Foglia's RNA nucleotides fit perfectly with the DNA from Biology Corner, so I printed each type of nucleotide on a different color paper and laminated them before cutting them all out. These I just put in containers for students to take as they are modeling the process of transcription as they build their mRNA molecule.  Since each RNA nucleotide (A, C, G, and U) is a different color, it's easy for us to hold each lab groups' finished mRNA molecules together to compare them.

After they finish transcribing their mRNA molecules, students move onto translating the mRNA code into a protein. Once the proteins are made, we can compare them. We focus on protein 1 and 4, which match. Then we go back to the mRNA molecules and observe that they are not the same.  At this point we can look at the codon chart, talk about multiple codons for the same amino acid, and what it means to have a silent mutation.

Comparing mRNA from strand 1 and 4 since they built identical proteins 

Here's the link to the student lab. And here's the link to the lists of DNA, mRNA, and protein strands.

Visualizing Real DNA and a Model

For my high school level Biology activity dealing with DNA, we complete it in two parts.  First we look at real DNA--a lot of it, so we can actually see it, Then we build a model of it--including the beginning of replicating it.

We begin with extracting DNA from strawberries. Commercially grown strawberries are octoploid (have 8 sets of chromosomes instead of the normal 2).  We talk about what we need to get through to get to the DNA in strawberry cells, and relate it to each part of the procedure.  We mash the strawberries in a bag to break the cell walls, we add some soap to get through the phospholipid membranes of both the cell membrane and nuclear envelope, and salt to help separate some proteins from the DNA and keep them from precipitation out with the DNA.

This year, to separate the juice of the strawberries from the leftover pulp, I cut up flour sack towels. This worked better than the cheesecloth we used last year which let some pulp through. With the flour sack material, students were actually able to squeeze the juice through the towel and into their beaker.

Then students poured the juice into a test tube.  With the test tube held at an angle, they slowly poured ice cold rubbing alcohol into the test tube.  The hope was not to actually mix the two liquids, but form a layer of rubbing alcohol on the top.  The cold alcohol pulls the DNA that is dissolved in the juice out of solution and into the alcohol. Then students see the clear/cloudy with some bubbles come out of the strawberry juice into the rubbing alcohol.

As we're waiting the 15 minutes to allow the maximum amount of DNA to come into the alcohol layer, we begin on creating a model of DNA and then a model of DNA replication.  This is done with licorice, gummy bears, and toothpicks.  One thing I'd like to do differently next time is change to a different color of licorice for the part we are replicating to allow for a discussion of semi-conservative replication.

Here is the student handout for the lab.   The extraction buffer recipe was from this document. I used the 50 mL of dishwasher detergent this year, but last year I used dish washing detergent (way too many bubbles!). I don't have that many lab groups, so 1 liter of extraction buffer was far more than I needed.  Next time I'll use 25 mL of dishwasher detergent, 1 tsp. of salt, brought to 500 mL with water.

Restriction Enzymes and Washi Tape

We're going to do the gel electrophoresis lab in AP Biology this coming week. I love for students to have a visual of what is happening when we get DNA ready for electrophoresis. This visual also helps them as we discuss why some pieces of DNA move faster than others and therefore give us distinct bands.

For our pre-lab conceptual practice we use toilet paper to represent DNA, washi tape to represent the location of specific palindromic restriction sites, and scissors labeled with specific washi tape to represent the restriction enzymes. Students take turns using the restriction enzymes to cut the DNA and then we determine the number and placement of bands on a gel using the number of toilet paper squares that are in each cut piece of DNA. The idea for this came this video on Vimeo.

 

For students to represent their electrophoresis gels, I made a template in Google Slides that I can project onto the whiteboard in the classroom.  Students can mark where they think the toilet paper DNA will migrate to.  Then I switch to the second slide that will reveal the banding pattern of the "criminal".  I like to wait to show that until last, otherwise they figure out who the criminal is before they finish getting all the bands up.  This way, the suspense lasts until all the bands are drawn on the board.

The template in Google Slides also includes the sketch of locations of each of the restriction sites.