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.”

Continue reading “The Humble Phosphate Ion: Making Life “Go””

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.

Continue reading “Placebos: Tricking the Brain, Targeting the Body”

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.

Continue reading “How Gecko Feet Will Make Your Next Move Easier”

Analyzing without Lysing: Non-Damaging Techniques for Monitoring Cells

Author: Sarah Kearns

Editors: Whit Froehlich, Ada Hagan, and Irene Park

The interior of a cell is inherently complex with a myriad of processes going on all at once. Despite the clean images that are commonly shown in diagrams and textbooks, the parts inside are more of a whirlwind of structural components, proteins, and products (see Figure 1).

23May17-1+2
Figure 1. Left is a cartoon image of a whole cell highlighting the different organelles (cellular compartments). Right is a computer simulation of the cytoplasm, the fluid between organelles. There are thousands of chemical processes going on within it.

Continue reading “Analyzing without Lysing: Non-Damaging Techniques for Monitoring Cells”

Trash Talk

Author: Sara Wong

Editors: Sarah Kearns, Ellyn Schinke, and Shweta Ramdas

Taking out the trash is a despised chore. It’s smelly and heavy, and you have to get off the comfortable couch, put on shoes, and take it all the way to the curb. Yet, we do it because we understand that it is important for the health of our homes and neighborhood, and taking out the trash is better than leaving it in the house.

What you might not realize is that your cells also have to take out the trash. In fact, defects in this process often lead to disease. One example is Niemann-Pick disease, which in severe cases causes death in early childhood. Neimann-Pick disease is caused by defective lysosomes, the trash bins of the cell. In order to understand diseases like Niemann-Pick disease, we must first understand lysosomes.

Continue reading “Trash Talk”

Can Patients with Early-Stage Breast Cancer Skip Chemotherapy?

Author: Lei Wan

Editors: Whit Froehlich and Shweta Ramdas

My mom was diagnosed with cancer two years ago. She had early-stage breast cancer: tumor size of less than five centimeters, fewer than three cancer-positive lymph nodes in the armpit region, and no cancer-positive lymph nodes nearby. But hers was also an aggressive type of cancer. At the time, I was a graduate student in the States and my parents lived in China, so we talked on the phone every two days about the progress of her treatment. She received surgery, radiation, a tailored drug treatment, and chemotherapy. My mom is tough and stubborn. Most of the time she just mentioned the good news that the cancer had been eliminated. Occasionally, she would say that her life was changed by the cancer treatment: for example, she had to quit her job.

I was shocked by my mom’s diagnosis. She is always physically active and mostly eats vegetables. I barely recognized her after the chemotherapy. She had lost 30 pounds and all of her hair, her skin was pale, and her nails were purple. Her face was unrecognizable because of the weight and hair loss, and she looked almost 20 years older.

My mom is cancer-free now, but she is not the same person that she was. Her appetite is half of what it was before, and she cannot lift heavy things. As a graduate student studying cancer biology, I had learned that chemotherapy would cause side effects like the ones I saw in my mom, including hair loss, vomiting, and nail loss. However, until my mom’s physical appearance and life were transformed by chemotherapy, I didn’t realize the magnitude of its impact on patients. Looking at my mom, I wish that we had better options for patients with early-stage breast cancer so they don’t have to suffer these devastating side effects.

Continue reading “Can Patients with Early-Stage Breast Cancer Skip Chemotherapy?”

Of Sporks and Scorpions: Where Do Genes Come From? (Part 1)

Author: Bryan Moyers

Editors: Theresa Mau, Alex Taylor, and Kevin Boehnke

What exactly separates us from other animals?  For that matter, what makes any species or group of species special?  How is life so diverse?  How can cephalopods camouflage themselves so well, and how did platypuses become so bizarre?

Part of the answer is in genes.  Genes are sections of DNA that perform a specific function, usually after being translated into proteins by special cellular machinery.  Every species has genes that code for proteins, but different species have different numbers of genes. Humans have around 20,000, fruit flies have around 18,000, and the tiny water-flea has around 31,000 genes. Different sets of genes produce animals with different structures and functions.

Continue reading “Of Sporks and Scorpions: Where Do Genes Come From? (Part 1)”