BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Nobel Prize

“DNA and miRNAs: The Universal Blueprint of Life – Uniting Unity, Diversity, and Genetic Regulation”

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On November 6, 2024

In Student Post

MicroRNAs (miRNAs) are a recent discovery that has revolutionized how we understand gene control. Imagine these tiny molecules, just 22 nucleotides long, as editors of our genetic script, deciding which genes get to speak and which stay silent. They do this by latching onto messenger RNA (mRNA)—the molecule that carries DNA’s instructions to make proteins—and either block its message or mark it for destruction. This process acts as a fine-tuned control system in our bodies, regulating essential functions and even playing a role in diseases like cancer.

The discovery of miRNAs came almost by accident in the early 1990s, thanks to two scientists, Victor Ambros and Gary Ruvkun. They were studying the roundworm Caenorhabditis elegans, focusing on a gene called lin-4 that, puzzlingly, didn’t seem to produce any protein. Instead, Ambros’s team found it produced a tiny RNA that bound to the mRNA of another gene, lin-14, blocking it from making protein. Around the same time, Ruvkun’s lab confirmed this connection, showing how lin-4 regulated lin-14 through this surprising, previously unknown mechanism. Initially, scientists thought miRNAs might be unique to worms, but as research progressed, they found these tiny regulators in many species, including humans. This was a huge revelation, showing that miRNAs are an ancient and crucial part of life’s genetic toolkit, silently shaping biology across countless forms of life.

Genetics laureatesThis discovery has led Victor Ambros and Gary Ruvkun to receiving the Nobel Prize in Medicine THIS MONTH (October 2024).  It has profound implications, as miRNAs are now known to be involved in various physiological processes and diseases, including cancer, offering potential new avenues for therapeutic intervention and advancing our grasp of genetic regulation mechanisms. miRNAs groundbreaking discovery in humans gives us limitless possibilities in what people could actually do. For instance, an ethical way to use miRNAs is to get rid of the part of the DNA that has the cancer in it to deactivate the cancer and turn it off. 

File:Conceptual overview of multiomics - digital skewed.png
By KajsaMollersen – Own work, CC BY-SA 4.0, Link

Learning about nucleic acids and gene expression is connecting everything we’re studying in AP Biology. DNA unites all living things with a shared genetic code, yet tiny changes in its sequences create the incredible diversity we see. As we dig into how genes work—turning DNA into RNA and then into proteins—it’s MIND BLOWING to see how DNA’s stability lets life continue, while its flexibility fuels evolution and diversity. Discovering microRNAs takes this even further, showing how even the smallest molecules can have huge effects on gene expression and open up possibilities for new treatments. This knowledge doesn’t just help us understand the unity and diversity of life; it gives us powerful tools to tackle big biological and medical challenges ahead.

I’m drawn to the study of biology, especially genetics, because it feels like the key to understanding life at the most fundamental level. The idea that tiny molecules like miRNAs can control complex processes and even influence diseases is fascinating to me. It’s incredible to think that such small miRNA can make such a significant impact on our health and development. The more I learn, the more I’m inspired by how understanding genes and molecular biology can unlock answers to pressing medical challenges and pave the way for new breakthroughs in medicine. This subject enhances my curiosity and makes me eager to contribute to a field with so much potential to change lives. How do you think that miRNA could change enhances in medicine, and what cures could we find with this breakthrough of miRNA?

Predicting Proteins Using AI!

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On October 24, 2024

In Student Post

Proteins are one of the most crucial yet most unpredictable building blocks of life–until recently, that is, when three scientists were awarded the Nobel Prize in Chemistry for their monumental advancements in creating and predicting 3D structures of proteins. 

Proteins are responsible for various functions in living systems that are crucial for survival. They protect us from diseases in the form of antibodies, transport molecules and cellular information within cells, provide structure to our cells, facilitate and speed up vital chemical reactions in the form of enzymes, and carry out countless other functions. Proteins are made up of chains of amino acids, and all amino acids contain a carboxyl group, an amino group, and a side chain. Each side chain has different defining characteristics, and when numerous amino acids are linked together the side chains determine how the protein will fold to form a 3D structure. The unique 3D structure of a protein is the defining factor for that protein’s function, so we must understand the shape of a protein in order to understand its role in the body. 

The 3D structure of the protein AP5M1.

The first recipient of this Nobel Prize, David Baker and his team, created Rosetta, a system which can generate the 3D shape for a protein given its amino acid chain. However, Baker’s most groundbreaking discovery with his software came from reversing this process. He found that when he and his team gave Rosetta a made-up protein structure, it created an amino acid chain that would fold into that 3D shape. To confirm Rosetta’s prediction, they synthesized the suggested amino acid chain in their lab, and a structure exactly like Rosetta’s was produced! This system has since been used to speed up the process of understanding protein functions when a new protein is discovered and to create various proteins that had never existed in nature before, including one that can detect fentanyl and another that can block COVID-19.  

The second recipients, Demis Hassabis and John Jumper, were recognized for their software called AlphaFold (as well as its successor, AlphaFold2), which can predict protein structures given amino acid chains with unparalleled accuracy. AlphaFold could predict protein structure with up to 60% accuracy, and AlphaFold2 can predict protein shapes almost as well as X-ray crystallography, the standard laboratory technique for discovering protein structure and function. The AI model even color codes areas of the predicted protein shape based on its confidence in its accuracy. AlphaFold’s system has correctly predicted the structure of almost every single protein known to scientists at this point!

These protein prediction softwares and their recognition through the honor of the Nobel Prize directly connects to what we have learned about proteins thus far in AP Biology. Proteins are made up of different combinations of the 20 amino acids known to scientists, and their individual shapes are determined by the interactions between the side chains contained within each different amino acid. Due to the varying characteristics of the side chains, we understand that they will each react differently with their surrounding amino acids as well as with the water that surrounds the protein as a whole. These differing interactions cause the amino acids to connect to and react with each other in different ways, thus causing the protein to fold, bend, twist, and invert itself in unique ways which cause the function-determining shape of the protein. The softwares developed by these award-winning scientists help us to predict the shape (and therefore the function) of any given protein by analyzing the side chains’ characteristics and interactions with one another. Their discoveries represent not only a groundbreaking advancement in protein research, but also a monumentally productive use of AI as a resource to scientists attempting to gain a better understanding of the things that make life possible. Do you think that their discoveries will contribute to the revolution of AI in a positive and helpful light, or do you think that the use of AI at a highly developed level will add to the fear associated with technological advancements? 

And The Nobel Prize in Medicine Goes To…

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On October 29, 2019

In Student Post

On October 7th, it was announced that the Nobel Prize in Medicine would be awarded jointly to scientists William G. Kaelin Jr., Sir Peter J. Ratcliffe and Gregg L. Semenza for their contributions in the discovery of how cells detect and react to the levels of oxygen in their environments. Each contributor will be receiving 1/3 of the prize share for their work in this topic.

The “Textbook Discovery”

Before we are able to understand the gravity of the discovery being awarded one of the world’s most prestigious scientific prizes, let’s set up some essential vocabulary we will need to break this concept down. Firstly, HIF-1α is the main protein that has been found to be essential to the identification of Oxygen. We have known that there exists an EPO gene which encodes for a steroid known to increase levels of Oxygen but the discovery of the HIF-1α protein is what is so astounding. What this protein does is regulate the activity of the EPO gene. Another factor which plays a large role in this discovery is the VHL gene, a gene known to be responsible for preventing occurrences of cancer. It was discovered that VHL had a link to the regulation of oxygen when low levels of the gene were linked to low level of oxygen (hypoxia). However, as more VHL was reintroduced, oxygen

levels were restored to normal.

How do HIF-1α proteins, VHL genes and EPO genes come together to create an understanding for how cells react to oxygen variation? Well, for HIF-1α to degrade, a peptide known as ubiquitin must link onto the HIF-1α and begin proteasomal degradation. It just so happens to be that VHL codes for a complex which tags proteins with ubiquitin allowing them to degrade. Finally, it was discovered that Oxygen was what binded theses two together, moving ubiquitin from the VHL over to the HIF-1α protein, thus degrading it. In other words, the more oxygen there is present, the more HIF-1α which gets degraded. Finally, the mechanism by which oxygen levels are controlled has been uncovered.

The Men Behind The Discovery

Over the span of 2 decades of research, three scientists were able to form an understanding on how our bodies respond to one of the most essential molecules in biology.

William G. Kaelin Jr. is a professor of medicine at at Dana-Farber Cancer Institute and Brigham & Women’s Hospital Harvard Medical School. As a cancer researcher, Kaelin’s main contribution was in the creation of a full understanding of the VHL disease which allowed for the link between VHL and HIF-1α to be formed.

Sir Peter J. Ratcliffe is the director of clinical research at the Francis Crick Institute in London. Ratcliffe and his team’s main contribution was establishing the connection between VHL and HIF-1α.

Gregg L. Semenza is a professor in genetic medicine at John Hopkins. His work focused on the EPO gene and how it controlled oxygen levels. He found out how oxygen is regulated, leaving only the cause a mystery.

For even more information on the scientists responsible, look into this New York Times article about them.

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