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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.

The interesting thing about ligand-receptor interactions is the sheer number of different ligands and corresponding receptors. Each cell type has different receptors attached to its membrane and thus, many different ligands that can bind it. Each ligand-receptor complex sets in motion a series of chemical reactions in order to fulfill its specific role in the cell. A good example of this epinephrine (adrenaline) because it can interact with many different cell types and correspondingly receptors, but have much different effects from cell to cell.  

This is really cool, but I'm not sure I totally understand the concept. Does the biofilm encompass multiple bacterial cells? Perhaps if each bacterial cell is producing the material necessary for the biofilm, this acts as a form of quorum sensing and results in the local bacteria to begin production.

So when this specific type kinase receives the phosphate group addition, it becomes capable of catalyzing reactions. So as I understand, they are like enzymes that need an external energy source in the form of a phosphate group.

This fact highlights the importance of G-protein coupled receptors in the cell. Because G-protein coupled receptors are so critical in cell signaling, this makes sense. In addition, cellular signaling is a crucial and fundamental component of cellular function, furthering the importance of G-protein coupled receptors.

Are there situations in which the phosphate is removed from kinase A so that the active site is blocked? If the kinase A receives this phosphate group when it is synthesized, then does it have it all of the time? This section states that the subsequent activation by the secondary messenger is key to making the kinase really function, but it seems weird that it kinase A would always be in the primed state.

This reminds me of the way the neurotransmitters are released into the synaptic cleft. When calcium ions interact with specific channels on the terminal end of a neuron, a series of events occurs in which results in the membrane surrounding a given neurotransmitter and releasing into to the extracellular environment. In this case calcium elicits a change membrane rather than the calmodulin.

In tumorous cells, processes completed by RAS and other oncogenes are disrupted in a way that favors the tumors growth. Specific pathways in the cell are victims of this process and they become fundamentally altered as a result. Many drugs have been designed to target specific pathways and specific oncogene. Some of these drugs include bevacizumab and metformin. Although these drugs may have a beneficial effect at first, the cancerous cell soon finds a way to utilize another pathway for the same purpose. This is known as oncogene addiction. The mechanism of this phenomenon is rooted in the rapid evolution and resultant mutation that occurs in cancer cells. Therefore, targeting specific pathways or oncogenes has proven to be ineffective in that long-run. That's why current cancer treatment is focusing on the immune system instead.  

Figure 1 is the original figure panel that I created. The creation of this figure panel was described in the methods in order for someone to recreate. Figure 2 was the replicated figure panel that another student created using the methods. Looking at the format of the two figures, the letters labeling each image are different. In figure 1 they are much larger and easier to see than they are in figure 2. The location of the letters also seems to be higher in the original figure panel than they are in figure 2. Starting with image A in both images, the major difference is the map used. Although both are maps of the campus, figure 2 used an older map than figure 1. In figure 2, the design building is not included because the map is outdated. The map in figure 2 also has a black outline around the campus pond where figure 1 does not have this outline. Figure 2 also lacks the red circle and dot that show the location of where the images were taken that is seen in figure 1. Figure 2 also shows a less zoomed in version of the map. There is space shown above the ILC and below the FAC but these buildings are both slightly cut off in figure 1.  

As a student in the Writing in Biology class at University of Massachusetts Amherst in Fall 2018, I conducted a project to practice scientific writing and replication. In this project, students find a spider web on campus and create a multi-panel figure illustrating the location of the spider web on campus. Students then create methods explaining how the student found the spider web. These methods also describe the steps taken to format the photographs into a multi-panel figure. Upon completing the original methods, a different classmate follows another student’s methods and replicates the multi-panel figure based on those instructions. The students then observe the differences between the original and replicated multi-panel figure, and use factors to infer why the differences are present. This possible differences between the two figures include differences in the size of the objects in the photo, lighting, or cropping of the image. The factors that could have affected the creation of the multi-panel figure included the time of day, sunlight, weather, or discrepancies in the methods. Overall, the purpose of this project is to practice writing concise and descriptive methods for an experiment, as well as provide practice for portraying differences between the two multi-panel figure.

Enzymes are proteins which work as catalysts to speed up the many chemical processes that occurs in an indaviduals body. Enzymes are never used up or changed during the chemical reaction process. At the most, an enzyme may require a cofactor to bind to it, in order to enter its proper conformation. This allows for a certain level of regulation over the enzyme.

Enzymes speed up chemical reactions by decreasing the activation energy of said reaction. However these never thermodynamically effect the chemical reaction. They do this by orientating molecules in an ideal way, pushing molecules closer together and by stabilizing the transition states of the reaction. Through these methods, enzymes allow our body to perform complex chemical reactions rapidly. For instance, the glycolosis of sugar on its own will take years. However, since we need energy all the time, an enzyme is needed to speed up the process.

In the Results section, it is mentioned that in the repica figure, there is no figure of the actual building. This error of not including a significant element of the replication figure was a direct result of the methods section not being clear and elaborative enough. The original methods section was mainly an “overview” of the process of obtaining the elements for the figure, and putting them together. This formatting allowed for mistakes in putting together the figure to happen. Similarly, there is a difference in the actual web between the two figures, since they are not the same web. The web in the original figure is much smaller in size, judging from the objects surrounding it, such as the sidewalk in the original figure, and the window in the second figure. Of course, since there is no scale to measure the two objects you can never be sure. Another significant difference is the map. For the original figure, opensource.eu was used to find a map for the Lederle Graduate Building. The second figure seems to be from a different website, judging by the look of it. The map also has different scales and markers. Another difference between the maps was that the original map was much more zoomed in, and did not have as many buildings around it compared to the second map, which had a few more buildings. The marker of where the spider web was on the map was a significant difference. In the original figure, a simple red dot was used to mark the location, but in the replica, a star was used to mark the location (also a major difference). This again, was most likely due to the lack of detail in the methods section. The labeling of the figure was quite different, as in the original figure, there were only upper-case red font letters. In the replica figure, the label was spelled out “Location” and “Web” describing the different elements. The words were also inside gray boxes. The specific font size/type was not specified in the methods, leaving it to the person trying to recreate this image to pick a font. Overall, I think much more specificity could definitely have been helpful in this project. It would have prevented a lot of the mistakes in replication if the instructions were much more clear and less concise.

The purpose of this activity was to generate a figure panel that displayed a spider web located somewhere on the UMass campus. The process used to create this figure panel will be written into a methods section that will be used by another student in the class to try and recreate the same figure panel. The goal was to have a clear and descriptive methods section that allowed the other student recreate the same figure panel. I decided to look for a spider web around Morrill because it is a pretty central building on campus and all students know this building since this is where class takes place. The images in the figure panel include a close up of the spider web, an image that shows the location of the web from a farther distance and a screenshot of the campus map. The screenshot of the campus is used because it shows where the pictures were taken so that it can easily be located.

I included all the dimensions, including the X and Y locations, as well as the width of each figure so I am unsure how the formatting differs this much. I did fail to include the height for Figures A and B, which may have influenced the final result. Additionally, I did not mention the units of any of the dimensions. Because of these errors in the dimensions, the location of the three boxes were also off. In my methods, I clearly stated to make the font bold, size 36 Times New Roman and fit the letters into the white boxes. The differences in the text may be from my partner misreading my instructions. For the black star, it was difficult to describe the exact size of the star. Since the replicated figure’s dimensions were not the same as the original’s, it caused the star it be in a different location.

Acknowledgements

I would like to acknowledge Katheryn Ruzzoli for taking the time to follow my methods and replicate my multi-panel figure. I would also like to thank Liron Burstein for keeping his eyes out for a spider web on campus for me.

http://www.saferbrand.com/advice/insect-library/insect-education/ogre-fa...

https://australianmuseum.net.au/how-spiders-see-the-world

https://ednieuw.home.xs4all.nl/australian/Deinopidae/Deinopidae.html

    The significant difference between Figure 1 and Figure 1 is that the images contain a different amount of elements. Specifically, from Figure 2, a photo of the Lederle Graduate Research building is missing. This element was added specifically to highlight the location of the web in relation to how large the UMass campus is. Another noticeable difference is that the location of the spider-web is different. In the original figure, the spider web is very close to the ground, as can be seen by the sidewalk being a few inches below the spiderweb. The replica figure seems to have been found on a window. The spider web in the replica figure is also much bigger in size compared to its surroundings, while in the original figure, it can be assumed the spider web is much smaller due to how big its surroundings look compared to the web. The map in the original figure is noticeably much more zoomed in on the graduate building, as it contains much less of the buildings next to it. This is not true for the replica image, where multiple buildings can be seen, in addition to the Graduate building itself. The labeling is also different, wherein the original image, it is uppercase, standalone letters in a red font. In the replica image, the labels are inside gray boxes and use a different font/sizing.