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Michael Penny

Mrs. Rausch

Biotechnology, Period 6

May 18, 2017

2PZI Protein (Tuberculosis)

The disease Tuberculosis has killed many million people since it has been around, such

as Edgar Allen Poe, Eleanor Roosevelt, and even King Tutankhamen. Even more people have

been infected by it, such as Adolf Hitler, Nelson Mandela, and even Voltaire, the enlightenment

thinker. These people were all diagnosed with tuberculosis, a terrible, and very infectious disease

that can lead to death if left untreated. Common symptoms include weight loss, fever, and

general sickness. Other symptoms include coughing, chest pain, and coughing up of blood.

The ways that this can be spread to someone is through the air - when people with the

disease that are exhibiting symptoms speak, laugh, cough, etc. the Mycobacterium Tuberculosis

is spread through inhalation. This makes it very contagious, but still pretty difficult to contract.

However, when contracted, the Mycobacterium Tuberculosis keeps itself from being killed and

digested in the lungs. However, when in the lungs, it is phagocytized, but it is unable to be killed

because of its cell wall preventing the fusion of the phagosome with the lysosome. This is how

the bacteria infects and what happens when it does infect someone.

However, the specific protein I’ve built encodes the production of a functional kinase.

Basically, what this means, is that the protein that I’ve built, when put into E. Coli, produces an

enzyme that transfers phosphates from ATP to a certain molecule it wants. Essentially, when the

bacteria steals the ATP, it can use it for whatever it needs, like growing or simply surviving. This

is what the protein I’ve built is specifically for, and without it, the TB bacterium would produce
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ATP much more slowly, if at all. With it, it is able to “autophosphorylate” (add a phosphate to a

protein kinase automatically), and produce ATP easier.

I started building the protein on Sunday, the 14th. I thought that it would take longer than

it did, so I went and bought some pipe cleaners from the dollar store on Sunday and twisted the

pipe cleaners together to make a longer string for the backbone on Monday. However, my dogs

got into my room while I was at school on the 15th, and they chewed it up while it was sitting on

my chair. I started the project again with different pipe cleaners on Tuesday, and on the same day

I decided what side chain Amino Acids I would do. I attempted to download Jsmol on Tuesday

also, but when I went to download it, it told me that the Jsmol project was managed by the same

people that made Jmol, and they wouldn’t let people just download Jsmol anymore. I decided to

start again on Wednesday, and I put the finishing touches on my paper on the 17th. I decided to

just use the Jmol in browser, even though it doesn’t let me restrict the view to only a few certain

Amino Acid side chains. I started my modeling (bending and forming) of the backbone, and

when I was finished modeling the backbone, I realized that I was looking at the wrong part of the

protein. I was looking at and modeling [Serine] (115) - [Glycine] (69). After that, I decided to

take a break and form a new backbone. I made one out of purple pipe cleaners, this time, and

modeled [Glycine] (122) - [Arginine (222)]. I modeled these because these were some of the

amino acids that formed the pocket around the ligase, and they even had an alpha helix in it. This

didn’t take me too long, and then I began labeling. This took me a long time, though. I taped the

labels to the corresponding colored pipe cleaner, with white meaning hydrophilic, yellow

meaning hydrophobic, red meaning a negative charge, blue meaning positive charge, and green

meaning a cysteine amino acid. I did all this so that it would be consistent with what the

website/PDF had already written down. I also made the Hydrogen Bonds, but i made those out of
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black pipe cleaner, because that was the only color I had that wasn’t already used. It took me less

time to stick the labels onto the backbone, but I saw that it would take too much space if I kept

the drawings of the structure on each of the labels, so I cut them off of the little papers. Either

way, the model came out great. It looked a little crowded after I put all the labels on it, though. I

learned that I should close my door more carefully when I have a time-consuming project (or

anything important) in my room, so my dogs don’t get to it next time. I also learned that I should

manage my time a little better on a project like this next time, since the labeling took far longer

than I thought it would - if I had started that in class, then it would have been much easier to

finish the project early.