iPad apps
sporte | March 8, 2016It's well understood in science education that students are more engaged when they work on problems that matter. Right now, Zika virus matters. Zika is a very scary problem that matters a great deal to anyone who might want to start a family and greatly concerns my students.
I teach a bioinformatics course where students use computational tools to research biology. Since my students are learning how to use tools that can be applied to this problem, I decided to have them apply their new bioinformatics skills to identify drugs that work against Zika virus.
We don't have the lab facilities…
sporte | December 1, 2015When finding a female scientists' data turns into an archeological treasure hunt.
A few months ago, I decided it would be interesting to celebrate various scientific contributions by making images of chemical / molecular structures in the Molecule World iPad app and posting them on Twitter (@MoleculeWorld). Whenever I can, I like to highlight scientific contributions from women on their birthdays. Tomorrow's post will feature Dr. Isabella Karle, an x-ray crystallographer who worked on the Manhattan project and solved structures of interesting molecules like valinomycin and a South American…
sporte | April 11, 2015To have an effect, a molecule must bind to a receptor and trigger a signal. Studying a receptor's structure can give us insights about the way this triggering process works.
Capsaicin is a fascinating molecule that puts the "pep" into peppers. Curiously, the amount of capsaicin in a pepper is measured with a test devised in 1912 by Wilbur Scoville. Dried peppers are dissolved in alcohol, this liquid extract is diluted in water, and trained people determine the pepper's Scoville value by "tasting" the heat.
I wonder how these people are recruited. I like hot sauce but I can't imagine…
sporte | January 16, 2015Pull a spaghetti noodle out of a box of pasta and take a look. It's long and stiff. Try to bend it and it breaks. But fresh pasta is pliable. It can fold just like cooked noodles.
When students first look at an amino acid sequence, a long string of confusing letters, they often think those letters are part of a chain like an uncooked spaghetti noodle. Stiff and unbending, with one end far from the other.
Molecular modeling apps let us demonstrate that proteins are a bit more like fresh pasta.
If we apply rainbow colors (Red Orange Yellow Blue Indigo Violet) to a protein chain, we can see…
sporte | December 26, 2014On pinene and inhibiting enzymes.
People of a certain age may remember a series of really funny commercials featuring Euell Gibbons and his famous question about whether you've ever eaten a pine tree. "Some parts are edible" said Euell.
Perhaps some parts are, but other pine tree products aren't so nourishing. Crystallography365, aka @Crystal_in_city had a couple of fun blog posts about pinene, a chemical made by pine trees, that also inhibits cytochrome P450 2B6.
I was inspired by their posts and by my experience with Cytochrome P450 to go a little farther. We like to use cytochrome…
sporte | August 3, 2014In 1925, dogsledders raced through the frozen Alaskan bush to bring antiserum to the isolated village of Nome. The antiserum arrived in time, saved the lives of many villagers from the horrors of diphtheria, and inspired the Iditarod, a famous race in celebration of the dog sledders' heroic feat.
West Africa could use a similar effort today. Richard Harris's blog at NPR has a good story about doctors' efforts to develop and use antiserum to treat Ebola. According to ABC news, Dr. Kent Brantly, who is being seen at Emory University Hospital was treated with antiserum as was the other aid…
sporte | July 31, 2014What’s the first you think about when you see a spider? Running away? Danger? Fairies? Spiderman?Do you wonder if spider silk is really strong enough to stop a train, like they showed in Spiderman 2?
Whatever your thoughts, you’re probably not thinking about 3D printing in space. Yet, the time might be near when astronauts will be using 3D printers filled with spider silk to make replacement parts in space. I learned about this idea in a presentation from Dr. Ron Sims, Utah State University, at the Bioman conference at Salt Lake Community College a couple of weeks ago.
Spider silk, as I…
finchtalk | May 27, 2014A key concept in science is molecular scale. DNA is a fascinating molecule in this regard.
While we cannot "see" DNA molecules without the aid of advanced technology, a full length DNA molecule can be very long. In human cells, other than sperm and eggs, six billion base pairs of DNA are packaged into 22 pairs of chromosomes, plus two sex chromosomes. Each base pair is 34 angstroms in length (.34 nanometers, or ~0.3 billionths of a meter), so six billion base pairs (all chromosomes laid out head to toe) form a chain that's two-meters long. If we could hang this DNA chain from a hook, it would…
finchtalk | May 5, 2014
Replication fork - http://en.wikipedia.org/wiki/Telomere.
Organisms with linear chromosomes have to solve the problem that DNA replication makes them shorter. This is due to the fact that DNA polymerase can only add bases to the terminal 3'-OH of a DNA chain. The DNA replication initiation complex uses RNA primers to provide the initial 3'-OH and to initiate "lagging" strand synthesis. While one strand can be copied all the way to the end of a chromosome, the other, lagging strand, must be primed at short intervals in order to provide a 3' OH group for DNA polymerase as the replication…
finchtalk | April 24, 2014Today (4/25) is national DNA day. Digital World Biology™ is celebrating by sharing some of our favorite structures of DNA. We created these photos with Molecule World™ a new iPad app for viewing molecular structures.
As we are taught in school, the double stranded DNA molecule is a right-handed helix as determined by Watson and Crick using Franklin's x-ray diffraction images [1]. This B-form of DNA has approximately 10 nucleotides per turn of the helix and is the most common form of DNA found in nature.
Classic structure with the elements colored.
Classic structure with the bases…