Professional Documents
Culture Documents
Michael Penny
Mrs. Rausch
Biotechnology, Period 6
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
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