Chemistry & Biochemistry
sporte | September 11, 2007Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
technorati tags: molecular models, protein structures, influenza, bioinformatics, Cn3D
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that…
sporte | August 5, 2007
It could be geosmin.
We encountered geosmin once before in our butter but most people notice it, about this time of year, in their tap water.
Geosmin is a volatile compound that's made by soil bacteria like Streptomyces, as well as some plants like sugar beets, and cyanobacteria. It gets blamed quite often for making water taste like dirt. Only a small amount is required (10 nanograms per liter) for detection by the human palate (1) and it's been blamed for adding a "dirt-like" taste to many things like water, wine, apple-juice, and catfish.
So, late in the summer when everyone is…
sporte | August 3, 2007Last Friday, we had another in the series of weird DNA structures. (You can see the first here).
I asked the audience to identify the unusual feature in this molecule. Here's the first picture:
tags: DNA structure, DNA , molecular structure, biochemistry
Here's the answer:
Steve L. guessed it correctly. This is not just DNA, it's a DNA:RNA hybrid. I circled a 2' hydroxyl group here to make it easier to see the difference. (Remember - the "D" in DNA stands for "deoxy.") The oxygens are red and it's easiest to tell the difference between the strands if you count them.
For extra credit -…
sporte | July 27, 2007I've had some requests for some more molecular puzzles since the last one that I posted (see A DNA puzzle ). One person liked it so much he even blogged about it.
So, here's one for you to chew on over the weekend.
This puzzle is a variation of an activity in Exploring DNA Structure, a CD/lab book that I made (with funding from the NSF) and used for some educational research.
tags: DNA structure, DNA , molecular structure, biochemistry
Any ideas?
sporte | January 4, 2007The wind storms and heavy rains that hit Seattle recently, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists.
Under the bridge on Mercer, from the Seattle Times
When the weather is nice, I bike to work. But when the weather gets bad, (I consider rain and 69 mph winds to be BAD), I take the easy way out. On the day of the big windstorm though, driving home was not so easy. A mudslide covered one of my usual paths, blocked two lanes on a very busy street, and stopped traffic well into the depths of the city.
Since we had to get to a soccer…
sporte | November 29, 2006What's the difference between a synthetic drug and an antibiotic?
Sometimes there's no difference at all.
Let's take a look at chloramphenicol and couple of pencillins.
Chloramphenicol kills many different kinds of bacteria by interfering with their ability to make new proteins. Here's a point where language gets tricky. Originally, chloramphenicol was isolated and purified from Streptomyces (a kind of bacteria). But, chloramphenicol is small and chemists are able to synthesize it. So even though we consider antibiotics to be natural products, they don't have to be made in a "natural…
sporte | November 22, 2006If you're still awake tomorrow after the feast and managing to withstand the sopoforic effects of the tryptophan from the turkey and the carbohydrates from the potatoes and pie, you might want to consider doing a little science at home. Fellow SciBlings Tara Smith (here & here), Mike Dunford (here & here), GrrlScientist, and I (here) have all experimented with the wonders of Mentos and carbonated soft drinks.
Orac even found a Mentos and Diet Coke plug for organ donation. I wouldn't have believed it if I hadn't seen it for myself.
Now, it's your turn. According to the WSTA…
sporte | October 4, 2006Awhile back Chemical & Engineering News published a fascinating article called "The Secret Life of Plant Crystals" with some wonderful photos of calcium oxalate crystals. Special cells (called "idioblasts") produce these crystals, with shapes that are unique to each type of plant.
Even though 75% of flowering plants make these crystals, no one knows why they make them and in fact, their functions may be as diverse as their shapes. Some crystals look sharp and dangerous, like thistles or thorns, suggesting that they function to defend a plant from hungry herbivores. Other crystals are…
sporte | September 19, 2006Modified from the original post.
Playing around with molecular structures is one of the more entertaining activities that you can do with digital biology. I've become totally entranced with molecular structures, both because they're a fascinating art form and because every structure has its own story.
I learned this because I ended up writing 69 different structure stories for the "Exploring DNA Structure" instructor guide. This was never in my original plan but my friend Charlotte Mulvihill wrote to ask me about the functions of different structures. I blithely replied that sometimes the…
sporte | September 13, 2006Reposted and slightly modified from Classic DigitalBio.
Some people say that science takes the magic out of everyday life.
Not me!
I've learned some things by reading Science (1) that might give some people nightmares, especially young children. Remember that scene in "The Wizard of Oz" when the trees get ticked off and start hurling apples at poor Dorothy?
Real plants do defend themselves.
Those "Wizard of Oz" trees would really defend themselves by giving poor Dorothy a tummy ache
Pardon me a moment while I apologize to enforcers of precise scientific language.
Okay, okay, real apple trees…
sporte | September 8, 2006Why do I love Cn3D? Let me count the ways.
What does Cn3D do? (Hint: say "Cn3D" out loud).
Seriously, Cn3D is a program that draws lovely pictures of molecular structures by using experimental data from techniques like X-ray crystallography and nuclear magnetic resonance spectroscopy. Surprisingly (to some), and in contrast to many bioinformatics programs, Cn3D is really easy and fun to use.
Have you ever used programs like MS Office? Using Cn3D is at least 10 times easier.
An added benefit is that you don't have to try and find old copies of Netscape or other bits of obsolete software…
sporte | September 5, 2006Ole and Lena's hot dish on a stick probably is explosive if you like to ride on a tilt-a-whirl afterwards. But what do you do if you're far from St. Paul?
Never fear.
There is more to life than hot dish.
I've always known that there were fun chemistry experiments that could be done with peeps, especially in the spring, but I never realized that so much fun could had with candy and soda pop.
In this article, the Disgruntled Chemist tested the explosive properties of different kinds of soda products when combined with minty items like Mentos or peppermint gum. These results are way more…
sporte | August 31, 2006Have you ever wondered about Cheeze Whiz? why new cars have a distinctive smell? or what makes golf balls so springy?
Chemical and Engineering News, published by the American Chemical Society, has a wonderful section that you will certainly appreciate.
"What's that stuff?" is a collection of entertaining stories about the stuff we encounter in everyday life. Each article combines chemistry with history and fun facts in a way that entices the reader to stay awhile and read every one.
Since the stories are written for non-chemists, they make a perfect companion to chemistry courses ranging from…