molecular structures

Scale, 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 ... Read more

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 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 ... Read more

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 ... Read more

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 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 ... Read more

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 ... Read more

Today (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- ... Read more

It'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 ... Read more

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, 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 ... Read more

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 you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine. 1. First, we'll go to ... Read more

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 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!