The Humble Phosphate Ion: Making Life “Go”

Author: John Charpentier

Editors; Noah Steinfeld, Tricia Garay, and Scott Barolo

A glance into any organic chemistry or biochemistry textbook reveals a dizzying variety of chemical compounds, reactions and mechanisms. It is not at all obvious why one particular class of reaction, the attachment and detachment of a phosphate group (PO43-) to molecules like nucleotides and proteins, is central to making the chemistry of life “go.”

Proteins: Not Just for Getting Swole, Brah

Fig1
Figure 1. A phosphate ion. Note the negative charges.

Proteins are the working-class heroes of the cell: they get things done. A protein’s function is largely determined by its shape, which in turn is dictated by the linear sequence of chemically distinct amino acid subunits it is composed of. The rules of protein folding are astonishingly complex. Generally speaking, the reluctance of hydrophobic (“water-fearing”) amino acids to project outward into the watery cytoplasm is the primary determinant of protein shape, but electrostatic interactions between amino acid residues are also important. Phosphate groups have three negative charges, which means that when they are linked to or removed from a protein by specialized enzymes, they can dramatically modify its shape and stability, and therefore its function. The phosphorylation/dephosphorylation cycle operates like a switch to regulate protein behavior: add a phosphate and you get a violent Mr. Hyde protein; take it off and you get the amiable Dr. Jekyll.

 

Fig2
Figure 2. Cellular homunculi don’t exist – decisions are made by integrating signaling inputs from the environment to effect changes in gene expression.

So where do we find phosphorylation in biochemistry? The answer is: pretty much everywhere! I will discuss two key examples. Firstly, phosphorylation is important in “cell signaling,” the sensing of messages from outside a cell and their incorporation into cellular decision-making. It’s worth observing that there isn’t anything we’d recognize as a brain in cells – decision-making is an emergent property of the integration of these signals, not the doing of a microscopic cellular homunculus pulling levers or “thinking.”

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Placebos: Tricking the Brain, Targeting the Body

Author: Shweta Ramdas
Editors: Charles Lu, Whit Froehlich, and Scott Barolo

Screen Shot 2017-07-13 at 2.16.39 PM
Placebo or Nocebo?

Last year, when I pooh-poohed my mother’s alternative medicine regimen, she said, “But these actually work well for me, because I believe in them!” My mother had just outsmarted me with science.

The placebo effect is one of the most remarkable yet least understood phenomena in science. It is a favorable response of our body to a medically neutral treatment (sugar pills, anybody?): in other words, a placebo is a fake treatment that produces a very real response. This is attributed to a physical reaction stemming from a psychological response to the administration of therapy. You could say that a patient sometimes gets better anyway—how many times have we waited out the common cold—and you would be right. This natural return to the baseline which can happen is not considered the placebo effect, which is an improvement in response to a treatment.

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Conversations about Science Writing: Nick Wigginton

MiSciWriters member Kristina Lenn chatted with Nick Wigginton, the assistant vice president of research at the University of Michigan, about the importance of communication among researchers and the big responsibility science writers carry in the current political climate.

 

 Anyone who has ever done collaborative research can list the benefits of being able to work with another group and learn about the cultural differences between researchers. Dr. Nick Wigginton knows better than anyone else how important communication is to successful collaborations.

Prior to his tenure at Michigan, Dr. Wigginton received his doctorate in Earth Science, and his dissertation was a collaborative effort by his department, physics, chemistry, and biology. This interdisciplinary gauntlet gave him the tools he needed to succeed as an editor for Science magazine where he needed to address the research and cultures of multiple departments.

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Setting the Tone: How Physics Can Help Us Understand Musical Harmony (Part 2)

Author: Joseph Iafrate

Editors: Christina Vallianatos, Scott Barolo, and Bryan Moyers

*Editor’s Note: This post has several sound files to help readers understand the author’s message better. These sound files can be accessed via bolded links.

Part one of this post explained how physics gave us a new language for talking about musical notes. In part two, we look at combinations of notes. Will two notes sound pleasant together, or will they clash? We can apply what we’ve learned about frequencies to get an answer.

The Harmony of Ratios

If you’ve ever used the Pythagorean theorem, you are well-acquainted with one of Pythagoras’ contributions to society. Pythagoras was an ancient Greek philosopher and mathematician dedicated to discovering mathematical principles in the world around him. During his time, the Greeks already had an idea of which notes sounded good together, a pleasant combination of two or more notes that we call a harmony. Pythagoras and his followers could identify harmony by ear, but they wanted to see if the math that permeated the rest of their worldview had anything to say about this phenomenon.

According to legend, they took two taut strings of different lengths and plucked them at the same time. The sounds seemed to clash with one another. So the Pythagoreans increased the length of one of the strings and tried again. It was a bit better, but the notes still seemed to clash in their ears. So they increased the length again. This kept going until the sounds complemented one another. Eventually they got it just right, and the two notes were in harmony.

Continue reading “Setting the Tone: How Physics Can Help Us Understand Musical Harmony (Part 2)”

Setting the Tone: How Physics Can Help Us Understand Musical Harmony (Part 1)

Author: Joseph Iafrate

Editors: Christina Vallianatos, Scott Barolo, and Bryan Moyers

*Editor’s Note: This post has several sound files to help readers understand the author’s message better. These sound files can be accessed via bolded links. 

At my elementary school, entering the fifth grade meant we could finally join the school band, and for most of us, that was a big deal. I had been set on playing the clarinet for ages, so I was ready and raring to immediately dive into “Hot Cross Buns” and “Mary had a Little Lamb.”

But before we could do that, we had to learn how to name the building blocks of those songs and the sounds we were making: the musical notes. Our learner books instructed us to orient our fingers in a certain way and call the sound that came out a “G.” Western music labels its tones with the letters A through G. There are also modified notes (sharp and flat) such that we reach twelve total note names.

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How Gecko Feet Will Make Your Next Move Easier

Author: Andrew McAllister

Editors: Ana Vasquez, Molly Kozminsky, and Kevin Boehnke

One of the most frustrating parts of moving is dealing with furniture. Most pieces need to be taken apart to fit through doors or into your moving van. Even if you’re lucky enough to have buff friends to help, one lost or stripped screw is enough to make you question your choice to cart everything miles away.

If only things could be simpler. Instead of screws, why not a super strong, reusable, and easy-to-detach piece of tape to hold your furniture together? Sounds like a tall order, but scientists inspired by a gravity-defying lizard, the gecko, are trying to make it a reality.

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#Scijack: Co-opting Twitter for Science Communication

Author: Ada Hagan

Editors: Whit Froehlich, Scott Barolo, and Irene Park

I doubt Dr. Shaena Montanari ever thought that a single Twitter conversation would earn her 3,000 new followers (1,000 within two hours) and help launch a new hashtag. But that’s what happened when she replied to a political tweet that mentioned velociraptors.

fig1 - scijackSource

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