molecular structures
sporte | February 28, 2016Did 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 cells leave traces of DNA behind after they’ve tackled invading microbes. DNA can also appear in the blood when people have cancer.
I had the good fortune, last Monday, to hear Matthew Snyder describe this cell-free DNA in a fascinating talk and learn why DNA in the blood can be a…
sporte | December 31, 2015"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 an article on Siamese cat colors and proteins AND molecular genetics (1).
In the article, the authors (Todd and Kenyon) provide some background information on the enzymatic activity of tyrosinase and compare it to the catechol oxidase that causes fruit to brown, especially apples. Tyrosinase catalyzes the first step of a…
sporte | December 17, 2015Imagine 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, Crotalus terrific duressis, one of those toxins will be a phospholipase. Phospholipases attack cell and mitochondrial membranes destroying nerve and muscle function. Without quick treatment, a snakebite victim may be die or suffer permanent damage (1, 2).
The phospholipase from the South American rattlesnake is called crotoxin…
sporte | October 28, 2015When 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 were the stuff of nightmares. Children could wake up with a headache and end up a few hours later, in an iron lung, struggling to breathe.
Poliovirus colored by molecule in Molecule World.
Today, on Jonas Salk's birthday, I read in the NPR blog Goats and Soda, that…
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…
finchtalk | January 30, 2015Something 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 I'll discuss some of the new structure databases below. But first, the numbers.
As summarized in the database issue's introduction, Galperin, Rigden, and Fernández-Suárez tell us this year's issue has 172 papers. 56 of those describe new databases, 98 provide…
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 | December 22, 2014In 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 human insulin we used to give to one of our cats. How do cat and human insulin compare?
It turns out, that all vertebrates produce insulin, even frogs and zebra fish. Human preproinsulin is only 110 amino acids long and even human and fish insulin are pretty similar. Of course, this observation only leads…
sporte | December 13, 2014 Sucrose
Molecules of sucrose tore apart in their bellies letting glucose course free in their veins.
Luckily for us, a system evolved long ago to capture that glucose and minimize it's potential for damage. Removing sugar from the blood and sequestering it in liver, fat, and muscle cells, minimizes the harm that might result if sugars were free to bind to proteins and our bodies were stressed by trying to flush excess glucose out of our system.
This holiday season, we give thanks for insulin and the biotech companies like Genentech that cloned the human gene and began to produce this…
finchtalk | October 7, 2014Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that scale and proportion are best understood using the scientific practice of working with models.
When scientists and engineers work with these concepts at a molecular scale, new kinds of technologies can be created to advance our understanding of the natural world. One example is DNA…
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…
sporte | December 14, 2010It's been interesting to watch as microbiology's own cold fusion debate has been raging. It began with an extraordinary claim about bacteria using arsenate as a replacement when phosphate concentrations are low (1).
It progressed when at least two scientist / bloggers ( here, and here) (not bloggers! the horrror! how uncivil!) gave public "journal club" presentations on blogs (envision dripping slime).
It continued with the science journalists lamenting about having swallowed the hype.
And it seemingly ended with another scientist / blogger's post that seemed to equate discussions of …
sporte | May 2, 2009Nick'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, but you can look at them and see how the protein works and how the drug prevents the protein from functioning.
As Nick mentions, the M2 protein from influenza makes a channel for hydrogen ions within the viral membrane. The channel controls the pH inside the virus by opening and closing.…
sporte | November 30, 2008The 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 you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine.
1. First, we'll go to PubChem at the NCBI. It's not an exclusive (or even last) resort but there are lots of fancy molecules hanging around, just waiting to be discovered and put onto drinking containers.
2. Now, we'll look for a molecule. I'm…
sporte | November 23, 2008Some people, like Imelda Marcos and our new Dr. Isis, have a thing for fancy shoes.
I go crazy for gadgets.
technorati tags: iphone, DNA, molecules, molecular structure, molecular modeling, Science education
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 phone could be so much fun?
One app, I enjoy, is called Molecules.
Molecules lets you download structure files from the Protein Data Bank (PDB) and play with the structures on your phone!
Spreading your fingers…