A small group of students use the DNA Writer website (on an iPad) to assemble a string of beads to represent a four genes on a piece of DNA.
Meiosis is a little hard to explain and follow, even with the videos to help, so I thought I’d try a more concrete activity — making DNA strands out of beads — to let students use their hands to follow through the process.
I started them off making a simulated human with four genes. They got to choose which genes, and they went with: hair color, number of eyes, height, and eye color. Then each group picked a different version of the gene (a different allele) for their person. Ravenclaw’s, for example, had brunette hair, three eyes, was tall, and had red eyes. Using the DNA Writer translation table , which maps letters and text to codons, they were then able to write out a string of DNA bases with their person’s information. I had them include start and stop codons to demarcate each gene’s location, and put some non-coding DNA in between the genes.
Since DNA is made up entirely of only four bases (A, C, T, and G), students could string together a different colored bead for each base to make a physical representation of the DNA strand. To make this a little easier, I adapted the DNA Writer to print out a color representation of the sequences as well. Most of the students used the color bars, but a few preferred to do their beading based off the original sequence only.
Ravenclaw’s DNA sequence color coded, and translated back to English (note the start and stop codons and the non-coding DNA in between each gene.
Just the beading took about 40 minutes, but the students were remarkable focused on it. Also, based on students’ questions while I was explaining what they had to do, the beading really helped clarify the difference between genes and alleles, and how DNA works.
Ravenclaw’s bead strand.Ravenclaw’s four genes on the DNA string annotated. Note that start and stop codons bracket each gene, and there is non-coding (junk) DNA between each gene.
Each of these DNA strands represents the half-sequence that can be found in a gamete. Next class, we’ll be using our DNA strands to simulate fertilization, mitosis and meiosis. Meiosis, should be most interesting, since it is going to require cutting and splicing the different strands (to simulate changing over), and following the different alleles as four new gametes are produced. This will, in turn, lead into our discussion of heredity.
Figure 1. Students assemble a molecule after translating the instruction from the gene sequence.
Abstract
This simulation was designed to have middle school students practice reading instructions (proteins) from a sequence of genetic bases (DNA) to better understand how gene translation works and learn the types of things that proteins do. The exercise and discussion lasted 55 minutes (with one preparatory homework assignment). Students appeared to have a lot of fun doing the simulation (especially because of the competition between groups) and we had an excellent discussion afterwards.
Introduction
DNA holds the instructions that control what our bodies in the pattern of molecules (nucleobases) that make up our genes. The genes are located in the nucleus of our cells (as well as for all eukaryotes). When genes are expressed, they create proteins that actually get all the work done.
The jobs of proteins can be summed up a three things:
some proteins build structures like muscles,
other proteins are enzymes that catalyze reactions, like the breakdown of food in the digestive system, and
other proteins are used for sending messages.
Using the DNA Writer application for converting text into simulated DNA sequences, I create an exercise for students to practice:
Finding simulated genes in a DNA sequence
translating the genetic code into an instruction (a simulated protein)
performing the different types of jobs that proteins do.
The simulation was modeled as a competitive game, with the class of 7th and 8th graders broken into four groups that competed against one another to see who could complete the instructions the fastest. I cheated, I’m afraid, because what I did not tell them was that, in order to complete the last instruction, the groups would all need to work together, so there would be no single group winner.
This being the first time I’ve tried anything like this, I was not sure how long it would take students to translate the DNA code to english, so a couple days before the simulation I handed out individualized homework assignments so they could practice. I chose science vocabulary words like “protein”, “ribosome”, and “amino acids” for short, simple messages.
Figure 2. This homework assignment consists of a simulated DNA sequence, the translation table, some instructions on how it works that comes from the DNA Writer app (use the printer friendly output option). The assignment can thus be individualized. This message translates as “amino acids”. Students were able to do the translation in less than five minutes. (pdf)
At least I had intended for it to be homework. As soon as they got the handout, and the 2 minute explanation about how it worked, they hashed out the messages in about five minutes.
The trickiest part was that the first few letters they translated did not make any sense, since they’re random sequences meant to represent non-coding DNA. However, once they got to the “start” codon it was pretty easy sailing.
Given how fast they were able to do the translation (and how eager and enthusiastic they were about it), I realized how unfounded were my fears that the translations would take too long for the competitive part of the exercise to work.
The Simulation/Exercise
Materials
There are only a few materials required for this lab:
envelopes – one for each group (size does not matter)
a chain of paperclips (100 seemed to work pretty well) You only need one set of 100 because the groups will be working on this together.
enough parts of a molecule-building kit to make a methane molecule (CH4).
Figure 3. Materials and printouts used in this activity.
Preparation
For each group
Write out the main set of instructions. The instruction I used were:
PULL APART ALL THE PAPERCLIPS
BUILD A METHANE MOLECULE
BUILD A BUTANE MOLECULE
I used the DNA Writer to get the code for each instruction individually then stuck them together in a text editor (like Word) (Note: it might even be better to give them a bead string with the base sequence instructions). These three instructions together looked like this:
Write or print out an address label as a DNA sequence, and stick it on to the envelope.
Since my groups had already named themselves, my addresses were something along the lines of, “Give to Gryffendor”.
Write out a message and stick it into each envelope
My messages were things like: “Do 10 pushups”; or “Dance Gangnam Style”.
Do 10 pushups.
Chain together the paperclips:
The groups will be working together to pull apart the paperclips, so you want enough paperclips so that it takes a few minutes to do. This way the slower groups will have a chance to catch up with the faster groups.
Put the molecule building parts in a jar – one for each group.
Procedure
So I took the class to the gym and stuck each of the four groups on a side of the basket ball court. Each group had a jar of molecule parts (only enough to build a methane molecule), an addressed letter with a message in it, and the long DNA sequence.
The paperclips were in a box in the center circle of the court.
We gathered around the center circle for instructions, which basically consisted of me telling them they had to
deliver their message first,
then do the whatever was in the message delivered to them,
then follow the instructions in the long DNA sequence
They were eager to go.
Results
Methane molecule assembled.
The entire thing went remarkably smoothly, which was somewhat surprising since this is the first time I’ve ever tried anything like this.
It only took 20 minutes from the time they started to when they finally put together the butane molecule.
A few small issues did come up, however.
Since they had only ever decoded a single instruction from a single DNA sequence before, almost all the groups stopped after the first instruction on the long sequence (pull apart the paperclips). I had to point out that a real DNA sequence contains a whole sequence of genes, so they probably ought to continue translating.
Another group tried doing shortcuts, and when they saw that they had parts from the molecule building kit and the instruction was, “BUILD A M”, they assumed that they were just supposed to build any molecule. I had to intervene on that one too.
Figure 4. Each group contributed one person to pulling apart the paperclip chain. Pulling apart the paperclips represents the catalytic breakdown of long polymers in food (starches and proteins for example) by enzymes.
When the person from the third group arrived to help pull apart the paperclips, the two already there complained that more people would just slow them down. I had to point out that they could just break the long chain they were working on into smaller pieces and then everyone could work and the work would go a lot faster. The breaking of the chains is supposed to represent the catalytic effect of enzymes.
One group mistakenly blocked off the first two letters in the DNA sequence instead of the first three (for a codon), and couldn’t figure out why their sequence was not telling them anything. I had to help out with that one, but in our post-simulation discussion it reminded me to talk about transcription errors and how the genetic code can change.
Finally, they were, some more than other, sorely disappointed that there would be no winner. They so wanted to win that they did not want to share their molecule parts to build the butane molecule.
Figure 4. A student holds a butane molecule model.
Discussion
When we were done with the exercise, we gathered around in the center circle to debrief. We reviewed what DNA does and the three things that proteins do:
Assembling the butane molecule from the methane monomers represented the use of proteins to build structures.
Pulling apart the paperclips represented the breakdown of food in the digestive system. Starches, for example, are long chained polymers that are broken down into their constituent sugars by enzymes in saliva and in the stomach.
The envelope with the message was a very literal representation of proteins as message carriers.
I actually forgot to talk about the transcription errors one group was making during our circle discussion, so we ended up talking about it on the following day. One student had remembered the video I showed earlier about gene expression that compared the rate of errors in DNA encoding compared to computer disks. The DNA coding is much more reliable, but when billions upon billions of bases are being coded then errors will still creep in.
This lead to a discussion about mutations, and how some DNA transcription errors could give messages that made no sense and would be ignored, while others could send signals that could affect the body’s functions. The latter types of mutation can be good or bad.
Conclusion
The exercise went remarkably well. Key to it, I think, was the fact that the students were able to so efficiently translate the DNA code to English. Also, the instructions were designed to feed back into things they’d done in the past, like assemble covalent molecules and polymers.
We talked about the Voluntary Human Extinction Project (VHMET) in Environmental Science, when we were covering issues related to overpopulation and the need for genetic diversity. While I’ve never been quite sure just how serious VHMET is, I just came across this 2007 article by Robert Krulwich on NPR about a tribe of pygmies in the mountains bordering China and Burma that chose extinction because of all the genetic problems that were being caused by inbreeding.
Adam Cole has an excellent NPR article on some fascinating researchers who are storing data — text files, web pages, sonnets — on DNA.
This should be a interesting introduction for middle-schoolers to the idea of DNA as a means of storing and transferring information. The question I hope to get is, “How did they do that?”
PBS has a nice list of genetic modifications to four different plants. First on the list is the antifreeze gene from a fish that was inserted into a tomato. The tomato was infected with a bacteria that had the gene in a genetically engineered plasmid. The PBS site also discusses Bt Corn, which produces it’s own pesticide, Golden Rice, which produces it’s own beta-carotene, and the herbicide resistant Roundup Ready Soybeans.
Golden Rice produces beta-carotene, which the body uses to produce Vitamin A. Two genes, one from daffodils and one from a soil bacteria, were inserted into the rice DNA. Image from the International Rice Research Institute (IRRI) via Wikipedia.
George Dvorsky summarizes a new study showing six types of bacteria found in Siberia are able to survive, and even thrive, under Mars-like conditions.
The researchers took these cultures [from Siberian permafrost] and exposed them to similar conditions found on Mars, including a severe lack of oxygen, extreme cold temperatures, and very low pressure (about 150 times lower than the Earth’s, about 7 millibars). The experiment was run over the period of 30 days. Over 10,000 isolates were exposed to these conditions — and they all died.
Except six.
And in fact, these six surviving microbes actually did better under these conditions. Surprised by the result, the researchers took a closer look at the survivors, and following a genetic analysis concluded that they all came from the same genus: an extremely hardy extremophile called Carnobacterium.
