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.
Using English words like “blue eyes” to represent genes in DNA strings with the DNA Writer runs the risk that students start to wonder if actual genes are coded in English.
I’d say it was a small risk, but today I did have that question from a couple of students today.
Fortunately, it was quite easy to disabuse them of the impression: they didn’t actually believe it, but they just had to know for sure.
I did like one of the questions though, “Does that mean that Spanish people have DNA written in Spanish?”
Embedding the Tiles
With that caveat, since I, and a few of my students, like the pretty patterns the DNA Writer produces (see above), I created a way to embed the color sequences into other webpages like this blog.
By default, the embedded image links back to the DNA Writer website, but you can adjust it so that it does not. Instead, the nucleobase tiles will change color when you click on them. The color changing helps keep track of where you are if you’re trying to string the sequence in beads.
For academic purposes, you can also change the message you get when the mouse hovers over the tiles. By default it give the plain English translation, but you can make it say whatever you want, or even have it just show the base sequence.
Hair color tends to come up pretty organically when talking about heredity and genetic traits. Blonde hair in people of European descent is a result of a the interactions of a combination of genes, but the blonde afros of Melanesians appears to be the result of a single mutation of a single gene.
Switching one “letter” of genetic code-replacing a “C” with a “T”-meant the difference between dark hair and blond hair.
One of my students couldn’t get VPython to install and run her computer. She was running Windows 8, and I have not used Windows, much less this version of it to figure out what the problem was. This is one of the challenges with a bring your own device policy. So, instead I gave the lesson on numerical integration using javascript.
If you open the webpage file (index.html) in your browser you should see nothing but the word “Hello”. The template is blank, but it’s ready so students can start with the javascript programming right away, which a few of my programming elective students have done.
For reference, this file (basic-jquery-numeric-int.zip) uses the template to create a program that does numerical integration. Someone using the webpage can enter the limits (a and b) and the number of trapezoids to use (n), and the program calculates calculates the area under the curve f(x) = -x2/4 + x + 4.
It’s a very bare template and doesn’t have any comments, so it’s not useful unless you’re at least a little familiar with html and javascript and just need a clean place to start.
A neat stop-motion movie made by manipulating individual atoms.
This is a great spark-the-imagination video because you can use it to talk about the physics of atoms and molecules, and what is temperature — they had to cool the atoms down to 4 Kelvin to keep them from moving too much.
Now that we have an idea of what a strand of DNA looks like we’re going to start talking about how our genes are passed on to our kids.
During normal time (interphase) our DNA is stored in the nucleus of our cells. Humans have 23 pairs of chromosomes. Of each pair, one comes from your mom and one from your dad.
The 23 pairs of human chromosomes. One chromosome in each pair comes from each parent. Image from the NIH.
When a cell is not reproducing (which is most of the time) the chromosomes are unspooled threads in the cell’s nucleus.
An unspooled strand of DNA in the cell nucleus.
When the cell is preparing to reproduce, each DNA strand duplicates.
Each chromosome duplicates in preparation for cell reproduction.
Then they fold up into the chromosomes and line up in the center of the cell.
DNA folded into chromosomes in the cell nucleus. The centrioles (plastic cups) move to opposite sides of the cell nucleus.
Now this is where interesting things start to happen. In mitosis, each chromosome pairs up with its duplicate, so when these are pulled apart you get two new cells with exactly the same DNA.
Mitosis produces two identical cells. Image from the NIH.
In meiosis however, where the cell breaks apart into reproductive cells called gametes, the two parent chromosomes pair up and exchange some DNA before being pulled apart (the DNA exchange is called crossing over). Since the DNA has duplicated before this happens, when the cell splits, you end up with two new daughters with mixed up DNA. Each daughter nucleus has two chromosomes, like all your other cells, but unlike every other (non-reproductive) cell in your body those chromosomes are different because of the DNA mixing. In addition, in the last step of meiosis (called Meiosis II) each daughter cell splits apart into two more daughter cells (granddaughter cells?) each with only one chromosome.
Meiosis produces four cells (gametes), each of which has only half as many chromosomes as one of your normal cells. Image from the NIH.
Again, it’s important to note that because of the crossing over and the second splitting, when everything is done, you end up with four cells — called gametes –, each of which has its own unique DNA. And unlike the other cells in your body, which have 23 pairs of chromosomes, each gamete only has 23 chromosomes.
Because a normal cell has 23 pairs of chromosomes is called a diploid cell. The gametes with only 23 single chromosomes is called haploid. These haploid gametes are the reproductive cells — eggs and sperm.
Thus, the DNA you contribute to your kids is not the same strands that you have in your cells, but a halved mixture of the two sets of genes you got from your parents.
References
The NIH has an excellent primer called “What is a Cell” on the history of cells, their parts, and how they split.
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.
UCLA professor Peter Nonacs teaches behavioral theory by letting students “cheat” in his “insanely hard” exams by letting them use whatever resources they want, including the web and working together. His objective is to have his students learn game theory by actually practicing it:
Much of evolution and natural selection can be summarized in three short words: “Life is games.” In any game, the object is to win—be that defined as leaving the most genes in the next generation, getting the best grade on a midterm, or successfully inculcating critical thinking into your students. An entire field of study, Game Theory, is devoted to mathematically describing the games that nature plays. Games can determine why ant colonies do what they do, how viruses evolve to exploit hosts, or how human societies organize and function.
My Environmental Science students are facing a similar problem with their final project. It’s a group project — their objective is to revamp the recycling system at school to make it work better — and I’ve been trying to get out of their way as much as possible. Not only do they have to figure out how to solve an environmental problem (they have an outline of how to do so in their text, but they have to figure out how to put it into practice), but they also have to figure out how to work together as a group to get the project done and write up a final report. The latter problem tends to be the harder, but in having to figure out how to lead, follow, and work as a team, it’s probably the more important lesson in the long term.
