Charged 2026

Tag: biochemistry

  • How Pymol Lets You Visualize DNA in 3D

    Have you ever wondered how scientists look at proteins or DNA? Here’s the secret- they don’t actually look at physical molecules all that often! Frequently, they use softwares like PyMOL. PyMOL is a widely used molecular visualization program that converts structural data into detailed 3D models, allowing scientists to rotate, zoom, and explore molecules interactively. It was originally developed by Warren Lyford DeLano and has become a standard tool in structural biology and chemistry (DeLano, 2002).

    PyMOL works by reading files that contain the exact positions of atoms in three-dimensional space, often obtained from experimental techniques like X-ray crystallography and stored in databases such as the Protein Data Bank. Using this coordinate data, the program reconstructs molecules and displays them in different visual styles, including sticks, spheres, and ribbon diagrams that highlight protein folding patterns. These visualization approaches are essential for understanding how molecular structure relates to function and are widely used in both research and education (Sehnal et al., 2021).

    What makes PyMOL especially powerful is how interactive and customizable it is. Scientists can highlight specific regions of a molecule, measure distances between atoms, and even model how molecules might interact with each other- something that is especially important in drug design and biochemistry. Because it translates complex data into intuitive visuals, PyMOL helps bridge the gap between abstract molecular concepts and real-world understanding, making it a valuable tool not just for scientists, but also for students learning about the molecular world.

    References:

    DeLano, W. L. (2002). PyMOL: An open-source molecular graphics tool. San Carlos, CA: DeLano Scientific. Available at http://www.pymol.org

    Sehnal, D., Bittrich, S., Deshpande, M., Svobodová Vařeková, R., Berka, K., Bazgier, V., Velankar, S., Burley, S. K., Koča, J., & Rose, A. S. (2021). Mol* Viewer: Modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research, 49(W1), W431–W437. https://doi.org/10.1093/nar/gkab314

    Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235

  • How does food become energy?

    metabolism

  • The Paleo Phenomenon

    It seems like every other day, a friend of mine declares a newfound dedication to the Paleo Diet.  Nicknamed the “Caveman Diet,” Paleo is this season’s slimmer, fitter (but just as raw) Atkins diet.  I first learned about the elusive Paleo from my dedicated Cross-Fitter friend after asking her for an afternoon snack.  I fully expected some Goldfish or hummus-like options but my friend looked carefully in her fridge and gave me a choice between freshly-watered lettuce or coconut flakes.  Apparently my disturbed look alluded to what I was thinking (when did you start hating your taste buds?) because she then confessed to me that she started this Paleo Diet.  She explained how she stopped eating bread, to which I replied “Dear God,” and went on to describe her new enlightened Paleo lifestyle.

    The Paleo diet theoretically takes us back to our ‘caveman’ days when we hunted rodents with rocks and scurried for nuts and berries.  Protein heavy; processed foods are out of the question; dairy is for infants; and sugar is the devil.  I’m not sure how the Paleo people know this, but apparently cavemen never ate any grains whatsoever, so neither can my friend now.  She carries wild canned tuna in her purse, munches on dried jerky meat from a bag fit for an astronaut (right picture), and mumbles about bacon all the time.

    Shocked at the idea that someone couldn’t indulge in croissants, muffins, or baguettes with chunks of melted brie, I left my friend’s place horrified.  I thought of the possibility that lobbyists for the meat industry were behind the whole conspiracy and hated wheat with a passion.  I needed to find out for myself.  What’s the health benefit behind this fad? Is there any?  How has this pandemic spread to several of my friends already?  Will my love of carbs be strong enough to fight the Paleo takeover?

    The premise behind the ‘Paleolithic’ eating is that humans should only eat what we’ve been genetically adapted for.  For 2.5 million years, the length of the Paleolithic Era, our human ancestors were just a bunch of fit muscular naked hunters-and-gatherers.  Human diets changed 10,000 years ago when agriculture was developed, but our 2.5-million-year-old genetics did not change the way we digested food.  Proponents of Paleo blame ‘Industrial Era’ food such as beans, dairy, alcohol and salt for obesity, cardiovascular disease, cancer, diabetes and high blood pressure.  However, I could not find any known cardiovascular benefits to becoming caveman again.  There IS an increased risk of higher cholesterol because of the increased meat intake, so Paleo might not be a good idea if you have high cholesterol already.

    Paleo basically hates carbohydrates.  They attribute carbohydrates to high blood sugar, insulin resistance and eventual morbid obesity.  Doug McGuff, MD and proponent of the Paleo diet, broke it down like this (with perhaps a few more sophisticated explanations):

    Paleo says that in this metabolic state, consuming high fructose corn syrup, sugar, or fructose of any kind will amplify these effects.  The only way to reverse this is with high intensity exercise.

    In theory, I’d say this Paleo diet sounds good.  But all diets sound good in theory until you’re hungry.  Examples- a few of my Paleo zombie comrades have cheated on a few occasions which they don’t want to admit.  They’ll crave a banana nut muffin all week and allow a bite on an upcoming weekend.  The pizza or cookie monster inside of them might emerge at 3 AM on a Saturday night.  They’ve also ordered light spring salads at dinner only to reach for my deep-fried chicken finger basket after they’ve digested their lettuce in 4 minutes flat.  This worries me.  I do have to say, my friends look extremely fit and healthy, and probably the best looking I’ve seen them in the last 6 years I’ve known them.  So something is working.  It could be the strenuous Cross-Fit workouts though.

    I’m very cautious about new hip diets so even after my research I was still not convinced I could get on board with the I-HATE CARBS Movement Paleo diet.  I needed to do some field research.  Meandering through the bookstore, I came across a Paleo Recipe Book and immediately started perusing through the pages.  The recipes looked pretty delicious so I snapped 18 pictures from my iPhone when no one was looking (don’t judge, I’m on school loans) and dashed from the aisle like a bandit.  I thought cooking one of the recipes would really make up my mind.

    I decided to conjure up some balsamic braised short ribs with a carrot puree and frisee parsley salad.  I wasn’t sure what to expect but, I have to say, it was damn good (pictured right).  I started to think maybe I could ‘have Paleo and eat it too’….but only on Sundays, and with friends who could split the grocery cost with me.

    All in all, I might consider going temporarily Paleo if I want to shed a few pounds but I’m gonna stick to my own health theory which is ‘everything in moderation.’  I don’t know about you, but I can’t get used to having my milk and cookies without either milk or cookies.  Plus diets that completely eliminate certain food groups are difficult to follow and can get very pricey.  If anything, I believe cutting red meats or the Weight Watchers diet are the best ways to go.  What diet could you get on board with?

  • Celebrate DNA Day with a Chocolate Smoothie!

    Celebrate DNA Day with a Chocolate Smoothie!

    Happy DNA Day!!!!

    So, it’s April 20th and you want to celebrate DNA day, but aren’t sure how?  What about making chocolate smoothies in honor of Alfred Hershey and Barbara Chase, the rockin’ scientists whose experiment finally convinced everybody that the information for your traits (i.e. genes) was contained in DNA rather than in protein, which was the other contender .  They made their discovery 60 years ago so now’s a good time to call them out.

    Now, 1952 was a prosperous time in America and while folks were makin’ babies, watching TV and buying $0.20/gallon gasoline to fuel their big, beautiful cars, Hershey and Chase were hanging out on Long Island at the Cold Spring Harbor Laboratory, mixin’ up phage (bacteriophage) and E. coli.  Phage are viruses that infect bacteria and when they do that they bring genetic information along with them.  Hershey and Chase had the genius idea that if they labeled the different parts of the phage with radioactivity and then tracked which parts went INTO the bacteria, they could figure out what genes were made of.  So, they labeled the phage protein with radioactive sulfur or the phage DNA with radioactive phosphorous and added it to the bacteria for a little while.  Then they used a blender (like the vintage Waring blender pictured here) to knock off any parts of the phage stuck to the outside of the bacteria and, lo and behold, the radioactive DNA was inside the cells carrying the genes and the radioactive protein got knocked off of the cells and floated away.

    The results of the Hershey Chase experiment paved the way for the golden era of molecular biology and actually made people care about the big paper Watson and Crick put out the next year that proposed the structure of DNA.

    So, HAPPY DNA DAY! Here’s how you can use YOUR blender to pay delicious tribute to these important scientists.