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Draft 2/22

Submitted by lpotter on Fri, 02/22/2019 - 09:47

Introduction

 

For the course writing in biology students were instructed to create a figure representing an interspecific interaction. The goal of the assignment was for each student to write a methods section that could be followed by a peer in the class. The peer was ultimately attempting to replicate the original figure based solely off of the methods section. The replicate figure was compared to the original and analyzed for the purposes of writing a scientific paper.

 

For selecting an interspecific interaction subjects were observed around the campus of the University of Massachusetts Amherst. In the North East area of campus an interspecific relationship was observed between a dog and the dogs owner. This was a clear example of an interspecific relation, this relation would be the one documented. The observation of the relationship was controlled by designating an area of observation. Another control was time of day, the relationship was observed in daylight, a necessity to capture photos of the subject.

 

Draft 2/21

Submitted by lpotter on Thu, 02/21/2019 - 11:41

Lassa virus is a very severe virus that kills nearly 20% of those infected with it. The most interesting thing about this virus is that it is rarely spread from human to human. It is mostly spread through a vector, which in the case of Lassa virus are rodents. This virus is also primarily spread in places where people are in close contact with rodents. In a area in which rats or mice travel from home to home. The virus doesn’t affect the rodents it just lives in them, so they are essentially a reservoir of the virus, they just keep giving and giving. This is very scary in countries where sanitation is poor and rodent control is minimal. Another problem is the virus can live in the rodents experiments and saliva. So when a rodent sneaks into a house and maybe takes a bite out a loaf of bread and people don’t notice or choose to eat it anyways because that is their only food source they can become infected with the Lassa virus. The problem why Lassa is so bad is because it just seems like a common cold or flu for a while so it goes undiagnosed relatively often. But after a certain period of time those infect start to develop a hemorrhagic fever. This means that blood vessels begin to break and host starts internally bleeding. This can cause a lot of internal problems and also causes the body to become rapidly dehydrated. Blood also comes out of the body's orifices. Something that can further transmit the disease.  

Draft 2/20

Submitted by lpotter on Wed, 02/20/2019 - 16:03

I know this isn’t exactly science related but it is related to physics and it was a test that I did. It was on calculating fall damage in fortnite. In fortnite you can building stairs, walls, floors, and pyramids. For my test I used walls to calculate fall damage. The first test I did was three walls up, I walked straight off the side, no fall damage. The first time I experience fall damage was from 3 and ⅔ wall height. The way I got ⅔ of a wall was by using my ability to edit the wall, you can break it into thirds. This first damaging fall dealt 11 damage, which isn’t too significant considering you get 100 health. When you jump from 5 walls high you start to experience significant fall damage, at this height I was dealt 49 fall damage. Jumping from 6 walls high deals 99 fall damage. A death fall would be from 6 and ⅓ walls high. I had a lot of fun figuring this out. I went into playground mode and got a lot of items that I could use to heal before I did the experiment. If anyone does this again and gets different numbers I would be curious to find out what they are.

Perfect paragraph 5

Submitted by lpotter on Tue, 02/19/2019 - 18:31

The ebola virus is very complex. It has many different ways that it can evade the host’s immune system. For example, one way that the virus can “hide” is by using lipids from the host’s cells to make an outer membrane for itself. This lipid membrane tells the host’s immune system that the virus is self and to not attack it. If the virus can evade the immune system it can successfully replicate in the cells of the host. Ebola has been a documented virus for quite some time with the earliest observations dating back to the 1970s. It has only recently made headlines. This is because the virus kills the host so fast that anyone who comes in contact with it dies before the virus can find a new host. So the majority of ebola cases were very limited because infected people couldn't travel to spread it. In 2014 there was an outbreak which ended up killing more than 10,000 people. This was a new strain of ebola, the Zaire strain. This strain is just as deadly as previous ebola strains however it is unique in the fact that it has an extended incubation period, meaning that it kills the host at a slightly reduced rate. This now means that sick people are able to come in contact with more people than with previous cases. This strain is the cause of the current outbreak in which almost 1000 cases have been confirmed.

Draft 2/19

Submitted by lpotter on Tue, 02/19/2019 - 18:27

Today I learned a lot about the ebola virus. The virus has many different ways that it can evade the host’s immune system. For example, one way that the virus can “hide” is by taking lipids from the host’s cells and making a membrane out of those lipids. This lipid membrane tells the host’s immune system that the virus is self and to not attack it. If the virus can evade the immune system it can successfully replicate in the cells of the host. Ebola has been a documented virus for quite some time with the earliest observations dating back to the 1970s. It has only recently made headlines. This is because the virus kills the host so fast that anyone who comes in contact with it dies before the virus can find a new host. So the majority of ebola cases were very limited because infected people couldn't travel to spread it. In 2014 there was an outbreak which ended up killing more than 10,000 people. This was a new strain of ebola, the Zaire strain. This strain is just as deadly as previous ebola strains however it is unique in the fact that it has an extended incubation period, meaning that it kills the host at a slightly reduced rate. This now means that sick people are able to come in contact with more people than with previous cases. This strain is the cause of the current outbreak in which almost 1000 cases have been confirmed.

Draft 2/18

Submitted by lpotter on Tue, 02/19/2019 - 18:15

I was asked to do an extra credit survey for my recent biochem exam. One of the questions asked was what we would do differently studying. I said that I would watch a lot more of the lecture videos before the  exam to clear up any confusion that I couldn’t on my own or from just looking at the slides. I think that re-watching something that you don’t understand is very helpful in figuring out what it really means. It also helps to just confirm what you already know. For example if you don’t understand protein folding you should google it and find some resources that might help explain it a little bit better, but after reading those and learning what it means re-watching the lecture so that you can understand it in the words of the instructor. Because after all they are going to be the ones writing the exam, so it is imperative that you understand what they are trying to say. One other thing that I will try and do for preparation for my next exam is write everything out. Write everything in words as well as in drawings. This will help me personally connect more abstract topics to something that is more tangible.

Draft 2/17

Submitted by lpotter on Sun, 02/17/2019 - 18:08

I have a biochem exam this week so I have been using my thirty minutes of writing each day to go further in depth with topics that I don’t fully understand and want to get a better grasp on. I went to a review session for it to try and help me with some of the topics and one of the questions that the SI asked us really confused me. She asked if the pKa of an amino acid could change and then said the answer to the question was no. She started to explain why it was no then said the question didn’t make sense and scrapped it all together. I made a note of it and tried to figure it out when I got back home. It turns out that in fact the pKa of amino acids can be altered. That is the pKa of the R-group. The pKa’s get altered when a neighboring R-group, which is ionizable, has a similar pKa. This means that the R-groups will be similarly protonated at similar pH levels which means that they will have similar charges. This will cause the R-groups to repel each other and can alter the folding of a protein which will alter the structure. So if an amino acid like glutamic acid (pKa of 4.25) is located close to aspartic acid (pKa of 3.86) they will have the same negative charge at around the same pH. If they are in a cell at physiological pH of 7 they will both be fully deprotonated and have negative charges, this will cause the two groups to repel. Since aspartic acid has a lower pKa it will become deprotonated first and in an effort to prevent repulsion the pKa of glutamic acid will be raised so it doesn’t acquire a negative charge from deprotonation. This helps maintain protein structure.

In class page 23

Submitted by lpotter on Fri, 02/15/2019 - 14:46

Observations

1. The figure on the left has uniform sized images but the figure on the right has one different sized image.

2. The angles at which the photos were taken are different in both figures.

3. The figure on the left had bold text labeling, the figure on the right did not.

4. The figure on the left placed letters slightly away from the edge of the photo, the figure on the right had had the letters lined with the side of the image.

5. The images on the right were brought to the outer edge of the black background whereas on the left they were not.

6. The backgrounds of the images aren’t corresponding.

 

There are multiple differences between both the left and right figures. However, the most apparent difference is the size of images within the figure. For example, the photos on the left figure are all uniform in size, all photos on the right figure are uniform in size except for the photo labeled D. The angle at which every photo was taken is different in both figures, none of which correspond. Additionally the background of the image was different in every instance and again did not correspond with the other figure. The figures are lettered in the same order, A, B, C, D. The font size and placement of the lettering is different between the two separate figures, but remains consistent within the figure itself. Another difference in the lettering is the alignment with the side of the image, on the left figure the letters are left a small distance away from the edge of the photos while in the right figure the letters are lined up with the side of the images. Another difference is that the spacing between the photos and between the edges of the figure on different.

 

Inferences

1. The last image (D) may have been cropped different on the right figure, or the camera was held at a different orientation.

2. The camera was most likely held at different heights, possibly because the person taking the pictures were different heights or maybe one used a tripod and the other did not.

3. The font choice was slightly different between authors, also resulting in a different bolding of the images.

4. The function to align the letters used by both authors may have been in a different software of different function within the same software.

5. The separate authors may have set margins to different widths causing the images to be differently set.

6. It might be a picture of a similar but tree, the angle at which they were photographed may also be different.

 

The difference in size of images between figures may be due to the orientation at which the photographer held the camera for that image, the image may have also been cropped differently. The angle of the photos may be be different because the the height of the photographer may be different, additionally they could have been standing in different places, at or on different things, or using different equipment. These same factors could also contribute to why the background would be different. The font size and placement of letters on the figure could have been caused by a different software used by both authors, or different setting applied to different figures. Similarly the alignment of images to the background within the separate figures may have been due to different software used or different setting applied by the author.

 

Draft 2/14

Submitted by lpotter on Thu, 02/14/2019 - 11:27

Titration curves have always confused me. I was introduced to them as a freshman in college. I didn’t really understand the whole concept of conjugate base and an acid and how they related. I didn’t understand what pKa or Ka meant but now I think after taking upper level courses the relationship between pKa, pH, acids, and conjugate bases all finally makes sense. On a titration curve there are inflection points, this point represents the amount of base required to react one half of the desired acid. At this point the acid becomes half deprotonated and half protonated. Next is the equivalence point, the point that represents the amount of base to react with all of the desired acid. This now makes sense to me why the acid is noted as HA and the conjugate base is noted as A-. The acid (HA) is neutral and when it becomes deprotonated taking on its conjugate base form (A-) it loses a proton and now has a net negative charge. This is how I started to understand the relationship between pKa and pH. Again, at the inflection point the amount of conjugate base is equal to the amount of acid. When you plug this ratio into the Henderson-Hasselbalch equation you get pH=pKa+log(1), log(1)=0. So that means that pH=pKa. Which now makes sense why stronger acids have a lower pKa. It essentially means that they are more will to give up a proton at a lower pH.

 

Draft 2/13

Submitted by lpotter on Wed, 02/13/2019 - 17:51

Change in pH can have serious effects on the structure of a protein which ultimately changes the function of the protein. Changing pH can affect the charge of ionizable groups of amino acids. Amino acids make up polypeptide chains via peptide bonds. These peptide bonds are not affect by a change in pH, however the alpha amino group at the N-terminus of a polypeptide chain (the subunits of proteins), the alpha carboxyl group at the C-terminus of a polypeptide chain, and the ionizable R groups of acidic and basic amino acids, as well as the ionizable R groups of tyrosine and cysteine. pH is directly related to pKa, this is the amount of base require to react with half of the acid present. Which in this case means at which point the ionizable group will start to become primarily deprotonated. The alpha carboxyl group at the C-terminus has a pKa of 2.2, so whenever the pH is above around 3 every alpha carboxyl group will be deprotonated. The pH of a cell is 7 so most of the times the group has a negative charge. The alpha amino group at the N-terminus has a pKa of 9.5, so unless the pH goes above 9.5 this group will remain protonated with a positive charge which it almost always is in the cell. A lot of ionizable R groups have a pKa of around 6-10 so if the pH of a cell is significantly raised or lowered the R groups will become deprotonated or protonated. This will in turn affect the charges of these groups and disrupt the electrostatic interactions they are taking part in causing the protein to fold differently which alters the function of the protein.

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