bthoole's blog

Part of the reason that wildtype Abl and the Bcr-Abl fusion act so differently is the change in form that occurs. The structure of a protein relates to the function of the protein, so any minor changes could end up changing the function completely. The change expressed in the fusion is what disrupts the regulation that wildtype Abl usually provides and increases the level of signaling beyond wildtype Abl. Wildtype interacts with multiple signal adaptors, phosphatases, transcription factors and cell cycle regulators.  It is tightly regulated and has nuclear import and export signals so it is capable of interacting in the nucleus and cytoplasm. It is regulated by intramolecular interactions and phosphorylation. When Abl kinase becomes Bcr-Abl, the new N-terminus creates a binding site for other proteins, causes the loss of the CAP domain (which is important for cell regulation) and causes the localization to be purely cytoplasmic. Overall, Bcr-Abl has binding sites for cell proliferation signaling pathways that Abl doesn’t have and has a greater kinase activity.

Chronic myelogenous leukemia is a type of cancer that affects the white blood cells, most often in older adults than children. The cancer is caused by a translocation event between chromosome 9 and chromosome 22. The break and results in a changed chromosome 9 and changed chromosome 22 that has the bcr-abl gene. Abl is a non-receptor tyrosine kinase protein, but the fusion with bcr disrupts regulation and increases signaling. Typically, multiple mutations occur that cause disruption and therefore cause cancer, but CML is particular in that it only requires the one mutation due to Abl having many functions and a role in important pathways like DNA damage repair. After the mutation though, it no longer does the repair and instead functions in cytoplasmic pathways like motility, survival, growth and proliferation.  

Cell signaling is how our cells communicate. Our cells must constantly be receiving cells signals to survive, otherwise they will die. Other than signals to survive or die, our cells also receive signals to do things like differentiate, grow and to divide. Cells are not limited to receiving one signal at a time and in fact don’t, receiving multiple signal at the same time. It is possible for the same signal to be received by the same receptor on cells but depending on what the cell type is will affect the outcome in the cell. This allows for one stimulus to apply a signal that many different cells can receive and can cause different actions. Longer pathways allow for more outcomes from a signal. Signal amplification can be applied to signals that travel along multiple steps in a transduction cascade and with more components in the pathway there can be more crosstalk. However, shorter step pathways are still helpful when a signal needs to be transduced fast.

A protein can continually react in the cell unless the cell receives a signal to stop. Then the cell is able to hinder the performance of the protein until it is needed again, thus avoiding having to waste the energy in destroying the protein when not in use and then transcribing and translating a new protein. Post-translational modifications affect an already made protein and are able to regulate that proteins function. Types of post-translational modifications include ubiquitination, phosphorylation and acetylation. Different modifications cause different results in different proteins, but the end result is a modification of the proteins original function. Post-translational modifications are not only for stopping a proteins actions, but also can also cause conformational changes and lead to active states. Nucleotide bonding and hydrolysis can work together in proteins to counterbalance each other. For instance, in the Ras protein, hydrolysis causes the bound GTP to lose a phosphate group and causes Ras to enter an inactive state. Nucleotide bonding acts to replace the now GDP with GTP when the protein needs to be active again. Regulating proteins is essential to making sure the cell runs properly and efficiently. Post-translational modifications are one of the ways this is accomplished.

A methods section of a scientific paper has the potential to have the greatest impact on the lasting legacy of a scientific paper. The methods section is what is used to replicate a paper’s experiment and serves to try and replicate the results. In the fall 2018 Writing in Biology class offered at the University of Massachusetts, Amherst, a project was assigned to demonstrate this point.  I conducted this project by first writing a methods section that included how to find a previously discovered spiderweb, photograph it and then turn the images into a multi-paneled figure.This was followed by another student in the class being given the methods section with the task of following as best as possible so as to try and produce an identical replicate of the final multipanel figure. Once a duplicate figure was made, I set out to identify observable differences between the two figures and from that, infer what could have caused the differences. I noticed that the figures had differences in the layout and size, the panels had differences in the location of the labels as well as the label’s color, capitalization and border, and there was a difference in the map type that was used. There were differences in the objects in the photos, such as a leg in the replicate, the pen that was used for scale, the amount of visible floor and wall tile, a wooden door in the corner of the photo and how much of the heating duct could be seen. From the observable differences, factors could be identified that may have led to the differences seen. The factors identified were the familiarity with the Inkscape program for composing the figures, the angle of the camera, the distance of the photo taken from the object, and the availability and access to resources. Being able to identify differences in an end product and what may have caused them will be an important part in understanding not only the data that this experiment generated, but data that any experiment may produce. Even if the methods section is written as precisely as possible, small variables may still cause an end product to be different and the ability to recognize what is different and why is how best to understand what the experiment’s results mean.

 

    A methods section of a scientific paper has the potential to have the greatest impact on the lasting legacy of a scientific paper. The methods section is what is used to replicate a paper’s experiment and serves to try and replicate the results. In the fall 2018 Writing in Biology class offered at the University of Massachusetts, Amherst, a project was assigned to demonstrate this point.  I conducted this project by first writing a methods section that included how to find a previously discovered spiderweb, photograph it and then turn the images into a multi-paneled figure.This was followed by another student in the class being given the methods section with the task of following as best as possible so as to try and produce an identical replicate of the final multipanel figure. Once a duplicate figure was made, I set out to identify observable differences between the two figures and from that, infer what could have caused the differences. Being able to identify differences in an end product and what may have caused them will be an important part in understanding not only the data that this experiment generated, but data that any experiment may produce. Even if the methods section is written as precisely as possible, small variables may still cause an end product to be different and the ability to recognize what is different and why is how best to understand what the experiment’s results mean.

 

Enzymes are an important class of proteins that help in cellular processes. Enzymes are particular in their binding and can be allosterically regulated. In enzyme-catalyzed reactions, the enzymes lower the activation energy needed for a certain chemical reaction. The free energy of the reactants and products do not change, just the threshold energy level needed for the reaction to commence. Enzymes can lower the activation energy of a chemical reaction in three ways. One of the ways the activation energy is lowered is having the enzyme bind two of the substrate molecules and orient them in a precise manner to encourage a reaction. This can be thought of as lining the binding pockets up for the substrates so that it is not left to random chance that they will collide and be oriented in this way. Another way enzymes can lower the activation energy by rearranging the electrons in the substrate so that there are areas that carry partial positive and partial negative charges which favor a reaction to occur. Lastly, the enzyme can strain the bound substrate which forces it to a transition state that favors a reaction. By manipulating the substrates of the reaction, the enzyme can lower the necessary energy needed to make the reaction occur. The enzyme itself is not a component of the chemical reaction and is the same molecule at the beginning of the reaction as it is at the end.

It is important for cells to be able to react with their surroundings and to do this, cellular molecules need to be able to interact with one another. Most often, cells use proteins to interact and carry out cellular functions. Proteins are able to interact with one another, but it is important that they can interact with non-protein ligands as well. This is achieved through the use of a binding pocket. The binding pocket is a site on the protein that allows the ligand to fit in and non-covalently bond. Non-covalent bonds include ionic and hydrogen bonds as well as van der Waals and hydrophobic interactions. This is not to say that proteins cannot bind to other proteins using a binding pocket, it is just not always used as sometimes the flat surfaces can simply bind two proteins.

               One of the ways that the interactions between proteins and ligands is measured is by their binding affinity. Also known as the dissociation constant, binding affinity is characterized as the concentration of ligand for when half the binding sites in the protein are filled. The smaller the dissociation constant, the tighter the binding interaction will be, meaning there is a strong binding affinity. Conversely, a low dissociation constant means there is a lower affinity for binding.

The causative agent in prion disease is a misfolded protein that causes normally folded protein to misfold and aggregate. This aggregate of proteins leads to brain cell damage and death, although the exact mechanism is not known. This makes prion disease the only known type of infectious agent in which the causative agent is not based in genetic information in either the form of DNA or RNA. One of the commonly known examples of prion disease is Mad-Cow disease, and though there are different types for different species, in humans it is known as CJD. Prions cause whole areas of brain cells to die, which gives the brain the appearance of a sponge and therefore a “spongiform” phenotype.

The term prion, also known as PrP, comes from the combination of the term “proteinaceous infectious only”. It is especially hard to prevent prion disease by any sterilization means because most sterilization techniques are targeted towards DNA and RNA, such as chemical reagents or by heating. This leads to the most common way of contracting the misfolded protein. Although it can spontaneously misfold on its own, the prion is often inducted into a system and then causes other proteins to transform and collect together.

Proteins are built from the monomer Amino Acids and have primary, secondary, tertiary and quaternary levels of structure. A base overview shows that primary structure includes the chemical structure of the protein, secondary involves beta sheets and alpha helices and tertiary combines secondary structure with other folds. Quaternary structure is where the polypeptide is built as it combines different proteins of tertiary structure. A further way to separate protein structure once there are many polymers is to look at functional domains. A domain is a discrete function and/or structural section of a polypeptide. This differs from a subunit, which is a single polypeptide in a protein which is in turn composed of multiple polypeptides. It is important to note that subunits can have domains.