BIOL368/F14:Class Journal Week 6

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Isabel Gonzaga

  1. This assignment deepened my understanding by allowing me to visualize the 3D interactions between the amino acid residues. I was also able to see how phenylalanine inserts itself between the base pairs to stabilize the protein structure, a concept which was previously unclear to me due to it's large bulkiness.
  2. I don't entirely understand how to determine protein functioning based off structure. I also get a little confused on how to determine protein domains from looking at tertiary or quaternary structures
    • I think this game would be fun to play. I really like biology and puzzles, and I think that presenting this topic through a gaming format makes it more appealing to work on these sorts of problems.
    • I think this game would help in learning about protein structure. It allows you to stop looking at the problem of HIV functioning through the lens of a biologist, and allows you to break it down into it's most simple and basic parts. It removes the complicated science aspect from the equation and turns protein folding into a fun, interactive game. By being able to play around with the different parts and see the immediate effects of using different amino acid residues, one better understands the different factors that contribute to protein folding.

Isabel Gonzaga 16:07, 6 October 2014 (EDT)

Weekly Assignments

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Electronic Lab Notebook

Chloe Jones

  1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
    • Yes, being able to see the protein structure in a 3-dimensional format definitely helped my understanding of how proteins are composed, and it also helped me visualize amino acids in regards to hydrophilic vs. hydrophobic.
  2. What is not (yet) clear?
    • What still isn’t clear to me is how as protein certain amino acids become oxidized. I’m confused as to how that occurs, and if it only occurs with certain amino acids are or is it possible to happen at any amino acid. Also, I could use a better understanding of the role that certain atoms play in a protein.
  3. Explain whether you would be interested in playing this game and why or why not? Do you think that games like this could assist you in learning about protein structure?
    • I would be interested in playing the game because having a science background I would be curious to see if that would be advantageous. The article says that players come from all walks of life, so I feel as though the game has to have an intriguing and fun aspect because the audience it is capturing isn’t just completely science people.
    • Yes, I do think games like this could assist in learning about protein structure. The assignment for Week 6 through a program where I was given instructions taught me about protein structure, so I think a game where I essentially have to think for myself in a fun manner would definitely aid my ability in understanding protein structure. I think it would increase my knowledge of protein structure to a greater extent because it is in fact a game, so unknowingly I would want to do well in the game, thus allowing me to achieve an understanding of an protein in an exciting way.

Electronic Lab Notebook

Weekly Assignments

Class Journals


Chloe Jones 03:46, 15 October 2014 (EDT)Chloe Jones

Nicole Anguiano

  1. Did you learn anything that deepened your understanding of protein structure from this assignment? If so, what?
    • I learned how the elements of protein structure work together to create the protein's function. While I had always known the hydrophobic molecules stayed towards the inside and hydrophilic molecules appeared on the outside, it was interesting to actually see it in action using Star Biochem. It was also interesting to see how the protein interacted with the 8-oxoguanine molecule and how it's structure enabled it to recognize and repair the molecule.
  2. What is not (yet) clear?
    • I am still not clear on how viewing structure without any sort of direction on where to look could be helpful in making scientific discoveries. I know it likely took much study to determine how DNA glycosylase works, and I want to learn how to be able to begin to reach conclusions from observing protein structures. I know I have a lot to learn in order for the proteins to look like more than just abstract forms and to be able to determine their function and how it is related to their structure. I also unclear how to tell the presence of domains without needing to use a special coloring scheme.
  3. Read the following article from Science Daily News about a relatively recent advance in solving a protein structure from a virus related to HIV.
    • Explain whether you would be interested in playing this game and why or why not?
      • I have played FoldIt before. I played for a while shortly after the paper came out about them finding the structure of the protein using it. I still have an interest in playing it, as I find it to be extremely interesting to play and try to figure out proper protein structure (though from playing the game I know that I had difficulty figuring it out at first). I find this way of attempting to make scientific discoveries very interesting, especially since it can involve members outside the researching scientific community.
    • Do you think that games like this could assist you in learning about protein structure? (I'm not asking you to play it, per se, although you can if you want; I just want you to comment based on reading the article.)
      • I believe that games like this can assist us in learning about protein structure. I am an avid gamer, and I know that gaming helps me to think outside the box and in ways that I wouldn't have normally thought in. Attaching something scientific to a game is a great way to help me to learn. I always have learned best in alternative ways, such as through songs and games such as this. Therefore, I know that a game like this would help me to more deeply learn about protein structure.

Nicole Anguiano
BIOL 368, Fall 2014

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