molecular structures
sporte | August 10, 2007Here's a lovely DNA structure from our friend, human immunodeficiency virus I. I especially like the way that two heart-like shapes appear in the structure.
tags: DNA structure, DNA , molecular structure, biochemistry
Is nature ironic or what?
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 | July 13, 2007Although, I didn't believe it when I first saw it. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my eyes.
Yet here is parallel DNA, with both strands oriented in the same direction, right here on your monitor. And the commenters were correct.
tags: DNA structure, DNA , molecular structure, biochemistry
The image that I posted a couple of days ago was made from part of this same structure. In that image, I hid the rest of the bases to make it easier to see why this structure is so strange.
Here are two images that show the landmarks a…
sporte | July 10, 2007Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon.
In the meantime, here's your puzzle: What's unusual about this pair of bases?
tags: DNA structure, DNA , molecular structure, biochemistry
(Those of you who attended our Chautauqua course - I know you probably know the answer - but don't answer, okay?)
sporte | June 1, 2007How does grass grow in the extremely hot soils of Yellowstone National Park? Could a protein from a virus help plants handle global warming? Okay, that second sentence is wild speculation, but we will try to find the answer to our mystery by aligning our protein sequence to a sequence from a related structure.
tags: plants, bioinformatics, sequence analysis, viruses, fungi, global warming,
Read part I, part II, part III, part IV, and part V, to see how we got here.
This week, in our last installment, we will seek the answers in a related structure.
Last week, I found that my…
sporte | May 25, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues.
Read part I, part II, part III, and part IV to see how we got here.
And read onward to see where will we go.
In our last episode, I discovered a new tab in the protein database (well, new to me anyway).
Related structures
If you select this tab, you get a list of protein sequences that are similar, by blastp, to the amino sequences in protein structures.
Naturally, I clicked the tab, and then the Links link, to see…
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 | January 1, 2007When computers first entered the mainstream, it was common to hear them getting blamed for everything. Did you miss a bank statement? that darned computer! Miss a phone call? - again the computer!
The latest issue of Science had a new twist on this old story. Now, instead of a researcher failing to take responsibility for doing sloppy science, we're back to blaming the computer. Never mind that the lab was using home made software that they "inherited from someone" (and apparently didn't test it) the five retracted papers were the fault of the software! Not the scientists who forgot to…
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 | September 22, 2006and what is the volume of the sea?
This sounds a bit like the beginning of a poem but it's really the answer to the question we posed last week on a Digital Biology Friday.
We can see, in the sequence window, that two strands are both labeled 5' on the left side and 3' on the right. We call this direction "five prime to three prime."
But, when we look in the structure window, we see that the two strands are oriented in the opposite direction relative to each other. The 5' end of one strand is located across from the 3' end of the other strand.
(Note: I added the arrow and labels, this…
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 15, 2006Today, we're going to look for rainbows in double-stranded DNA and see what they can tell us about DNA structure.
First, we're going to get a structure for a double-stranded molecule of DNA and open it in Cn3D.
1K9L
If you want to do this at home and you haven't already downloaded a copy of Cn3D, you may want to read these instructions and get a copy. These directions also show how to download and open the structure. It's pretty simple once you've given it a try.
Hide a strand
Next, we're going to hide one of the strands. To do this, look in the menu bar for the Show/Hide menu and open…
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 6, 2006How can you win a nerd contest if you don't dress the part?
Last year, I started a shop at CafePress to help distribute lab materials and fund my adventures in science education. Part of the fun has been making molecular merchandise to help show everyone that molecular models are beautiful, in their own special way, and help people engage in random acts of science education.
Here are some of my suggestions for molecular wearables that can help you explain why science is fascinating to people that you meet in the grocery store or the coffee shop.
Kissing DNA. Unfortunately, the DNA…
sporte | August 23, 2006Did HIV become resistant to Atazanavir because of a genetic change?
Was that genetic change inherited?
Did HIV evolve?
Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug?
Let's find out.
All of the sequences in the image below (except for the first) come from HIV strains that were isolated from patients who took Atazanavir and no other protease inhibitors. All of the strains of HIV from patients were resistant to the drug.
If an amino acid is different from other strains, the color at that position is changed. Since we see different…
sporte | August 17, 2006When can a really bad virus be used to do something good?
When we can use it to learn.
The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as clearly as HIV. In this series, I'm going to guide you through some experiments on HIV evolution that you can do yourself. You won't even have to put on any special clothing (unless you want to), wash glassware or find an autoclave. And, you don't need to any UNIX commands or borrow a…
sporte | August 9, 2006One of the commenters on a previous post, pointed out that proteases have pretty diverse structures, even though they also share a common function.
What else could I do? I had to take a look. I found structures for chymotrypsin (from a cow) and subtilisin (from a soil bacteria, Bacillus lentus) and used Cn3D to see how they compare (below the fold).
Both enzymes are proteases - that is they cut the peptide bonds in proteins that hold amino acids together. Many of you use proteases routinely, without knowing it or probably even thinking about it. Proteases, including subtilisin have…
sporte | August 4, 2006It seems kind of funny to be thinking of anti-freeze at the moment, with heat waves blanketing the U.S., but all this hot weather makes me miss winter. And so I decided it was time to re-post this from the original DigitalBio.
Winter is coming soon, my bike ride to work was pretty chilly, and it seems like a good time to be thinking about antifreeze. Antifreeze proteins, that is. Antifreeze proteins help keep pudgy yellow meal worms from turning into frozen wormsicles and artic flounder from becoming frozen flat fish.
Funny, but I would have thought that one antifreeze protein would…
sporte | July 10, 2006Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil.
With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure.
Yet here is, on the screen, parallel DNA.
The image that I posted a couple of days ago came from this same structure. In that image, I hid the rest of the bases, to make it easier to see why this structure is so strange.
Here are some images that show the landmarks a bit better. I hid the hydrogens and used different rendering styles to portray the backbone and the…