molecular structures

I'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) ... Read more
i-dc4398c754d67d54c86378e8729b36bc-parallel_DNA.gifAlthough, 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.

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The ... Read more
Okay, 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?

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How 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.

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Read part I, part II, ... Read more

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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 ... Read more

The wind storms and heavy rains that hit Seattle a few years ago, and flooded the Battery Street tunnel, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists.

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, 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 ... Read more

When 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 ... Read more


What'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 ... Read more

and 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. i-3faa77de2c8e6cc50b5fa2cbca9c38b0-rainbow_direction.pngWe can see, in the sequence window, that two strands are both labeled 5' on the left ... Read more
Modified from the original post. i-e0bb5e70117b600f9bf2a270d7bc69f1-telomere1.gifPlaying 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 ... Read more

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