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? tags ...
One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that ...
What’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 ...
It 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 ...
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 ...
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 ...
Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened? Did people quit making databases? No. This year, the "dead" databases (links no longer valid) outnumber the new ones. To celebrate Digital World Biology's release of Molecule World ...
Biology as a second-language: the immersion method Language teachers say the best way to learn a language is by total immersion and even better, spending time in the country where it's spoken conversing with native speakers. See it, hear it, speak it, use it! Put yourself in a position where ...
One 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 ...
Over 2600 genetic diseases have been found where a change in a single gene is linked to the disease. One of the questions we might ask is how those mutations change the shape and possibly the function of a protein? If the structures of the mutant and wild type (normal) ...
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 ...
tags: 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 ...
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 ...
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 ...
Today, 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 ...
Here'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: Is nature ironic or what?
Why 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) ...
Last 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: Here's the answer: Steve L. guessed it correctly. This is not just DNA, it's a ...
If you look below the fold, you can see two molecules locked in a tight embrace. These molecules or their closely related cousins can be found in any cell because their ability to evolve is slowed by their need to interact with each other in the right way. In an ...
This is a fun puzzle. The pink molecule is a protein and the other molecule is a nucleic acid. If I gave you the amino acid sequence of this protein, or the nucleotide sequence of this nucleic acid, what is the probability of finding a similar sequence in a different ...
Last week I posted an image with two molecules ( below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers. DAG made me clarify my question by asking what I meant by ...
Did you know small fragments of DNA are circulating in your blood stream? These short pieces of DNA are left behind after cells self-destruct. This self-destruction, or apoptosis, is a normal process. In the case of fetal development, certain cells in our hands die, leaving behind individual fingers. Immune system ...
On 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 ...
Modified 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 ...
Imagine a simple hike in a grassy part of South America. You hear a rattle and feel a quick stab of pain as fangs sink into your leg. Toxins in the snake venom travel through your blood vessels and penetrate your skin. If the snake is a South American rattlesnake ...
A 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 ...
A 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 ...
Two 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. One protein structure is from a strain ...
Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both ...
This morning I had a banana genome, an orange genome, two chicken genomes ( haploid, of course), and some fried pig genome, on the side. Later today, I will consume genomes from different kinds of green plants and perhaps even a cow or fish genome. I probably drank a bit ...
This video shows how we used the Molecule World iPad app to make an image of a folded insulin peptide. Protein folding brings the amino acid at the beginning of the protein chain near the amino acid at the other end.
In my last post, I wrote about insulin and interesting features of the insulin structure. Some of the things I learned were really surprising. For example, I was surprised to learn how similar pig and human insulin are. I hadn't considered this before, but this made me wonder about the ...
This structure is called a "kissing loop" and I find that name just a bit odd, given the source of the structure. Now, here's the puzzle: Why would I say that the name " kissing loop" is ironic?
Although, 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 ...
Although, 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 grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme. I'm here to help to you make a merry mug with one of our ...
The grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme. Reposted in honor of the holiday and the economy. I'm here to help to ...
Some people, like Imelda Marcos and Dr. Isis have a thing for fancy shoes. I go crazy for gadgets. For my birthday this year, my family bought me a new iPhone! Yeah! So, I've been killing several hours today filling it with cute little iPhone apps. Who knew one little ...
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and ...
Ribosomes are molecular machines that build new proteins. This process of synthesizing a protein is also known as translation. Many antibiotics prevent translation by binding to ribosomal RNA. In the class that I'm teaching, we're going to be looking at ribosome structures to see if the polymorphisms that we find ...
In 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 ...
I love using molecular structures as teaching tools. They're beautiful, they're easy to obtain, and working with them is fun. But working with molecular structures as an educators can present some challenges. The biggest problem is that many of the articles describing the structures are not accessible, particularly those published ...
" By night all cats are gray" - Miguel Cervantes in Don Quixote I've always liked Siamese cats. Students do, too. "Why Siamese cats wear masks" is always a favorite story in genetics class. So, when I opened my January copy of The Science Teacher, I was thrilled to see ...
To 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 ...
When my parents were young, summer made cities a scary place for young families. My mother tells me children were often sent away from their homes to relatives in the country, if possible, and swimming pools were definitely off limits. The disease they feared, poliomyelitis, and the havoc it wrecked ...
Nick's post on Amantadine resistance in swine flu was so interesting, I had to look at the protein structures myself. I couldn't find any structures with the S31N mutation that Nick discussed, but I did find some structures with the M2 protein and Amantadine. Not only are these structures beautiful ...
