Category: Biochemistry

Are Omega-3 fatty acids healthy?

Author: Attabey Rodríguez-Benítez

Editors: Jimmy Brancho, Andrew McAllister, and Noah Steinfeld

When I got sick as a child, my great-grandmother used to treat me with unpleasant fish oil. She would say, “bébete esto para que te pongas mejor y tengas un corazón fuerte” (“drink this so you can get better and have a strong heart”). Both of my parents also swore by fish oil, taking these enormous yellow pills, which I did not take myself because I was afraid to choke on them. These large fish oil pills were full of omega-3 fatty acids. My family explained that the supplements helped with high blood pressure, but never explained why they worked. As it turns out, there is still quite a lot of debate in the scientific community as to how omega-3s impact human health.

Microscopic Diversity: How and Why One Gene Creates Many Unique Proteins

Author: Jessica Cote

Editors: Zena Lapp, Christina Vallianatos, and Whit Froehlich

The Human Genome Project is one of the greatest scientific accomplishments in recent history— this international collaboration identified almost all of the ~20,500 genes in the human body, known collectively as the genome. Now that scientists know the details of these genes, they are better able to understand and treat human diseases associated with genetic factors. However, despite the immense effort put forth by over 30 research labs for 13 years (1990-2003), the information we gained from this project is limited. Genes serve as guidebooks for cells in the body to build proteins; genes themselves don’t perform the necessary cellular functions—proteins do. So, while scientists have now known the nitty-gritty of thousands of human genes for a while, the details of their protein products, known collectively as the proteome, are still quite puzzling.

Methylated Memory

Author: Sarah Kearns

Editors: Naiyiri Kaissarian, Patricia Garay, and Shweta Ramdas

If you saw a hippo on campus, you would remember it. But, would you expect that seeing such a pachyderm roaming on a university would alter the expression of your DNA? A recent study found that rats placed in an environment that tested their memory had alterations to their DNA, or epigenetic changes.

For a long while, we have generally known that neurons within the hippocampus of our brains are responsible for memory. The current model for memory storage is due to the plasticity of neuronal connections, but researchers have recently found that it also involves active changes at the genetic level. These changes come from external factors and are linked to retaining long-term memories, which has implications in stress-related learning and memory disorders.

The After-Hours Life of a Protein

Author: Sarah Kearns

Editors: Zena Lapp, Jimmy Brancho, Noah Steinfeld

After you get home from work, perhaps after eating dinner, you may start working on other projects or hobbies. Humans aren’t the only ones that have a life after hours. Recently it’s been discovered that many proteins have roles in the cell outside of their main functions. This peculiar behavior led to the name ‘moonlighting,’ referencing individuals who have multiple jobs. A useful analogy might be a werewolf’s behavior under a full moon: being a person during the day, but a wolf at night.

Trasplante de Órganos de Cerdos a Humanos Podría Ser Posible en el Futuro Gracias a la Ingeniera Genética

Escrita por Attabey Rodríguez Benitez y editado por Cristina Maria Rios.

¿Te imaginas un futuro en el que los humanos podamos recibir órganos de animales en lugar de esperar por un donante? Esto podría ser posible gracias a una investigación llevada a cabo por una colaboración internacional entre laboratorios de Harvard y China que resultó en una publicación en la revista científica Science.

Organ Transplantation from Pigs to Humans Could Be Possible, Thanks to Gene Editing

Author: Attabey Rodríguez Benítez

Editors: Sarah Kearns, Jimmy Brancho, and Whit Froehlich

Can you imagine a future where humans could receive organs from animals instead of having to wait for a donor? Well, this could be possible thanks to evidence from an international collaboration between labs in Harvard and China which resulted in a publication in the prestigious journal Science.

Semen’s Lesser-known Roles in Reproduction

Author: Brooke Wolford

Editors: Andrew McAllister, Molly Kozminsky, and Whit Froehlich

If you’re a millennial who thinks dating in the age of Tinder is difficult, you may find parallels between your dating life and the complexities of reproduction. The process of a sperm meeting an egg to create a cell that successfully implants in the uterine wall and subsequently creates a human is incredibly intricate. Similar to the world of dating, two have to meet, decide they like each other, and then invest time and energy to grow together as a couple. From finding a mate to the biological processes behind pregnancy, reproduction may seem downright impossible. Luckily mother nature has devised sneaky and fascinating ways to improve the chances of a successful pregnancy. Evolution favors those who pass their DNA on to as many offspring as possible, and natural selection has worked for years to optimize reproduction. If only Tinder were that good at getting you a date!

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.”

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).

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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.

Computing Levinthal’s Paradox: Protein Folding, Part 2

Author: Sarah Kearns

Editors: David Mertz, Zuleirys Santana Rodriguez, and Scott Barolo

In a previous post, we discussed how proteins fold into unique shapes that allow them to perform their biological functions. Through many physical and chemical properties, like hydrogen bonding and hydrophobicity, proteins are able to fold correctly. However, proteins can fold improperly, and sometimes these malformed peptides aggregate, leading to diseases like Alzheimer’s.

How can we figure out when the folding process goes wrong? Can we use computers to figure out the folding/misfolding process and develop methods to prevent or undo the damage done by protein aggregates?