Zrusso Biol 368 week 6

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DNA Glycosylase Exercise

BIOL368/F11:Week 6

  1. I can identify the DNA molecule and the glycosylate. The DNA is located in a groove right next to a sulfur atom.
  2. Cysteine at position 241 and the sulfur is on the side-chain.
  3. 105:Threonine, 106:Leucine, 107:Alanine, 108:Glutamine, 109:Leucine, 110:Tyrosine, 111:Histidine, 112:Histidine. 113:Tryptophan, 114: Glycine, 115:Serine, 116:Valine, 117:Apartic Acid
  4. Helices, sheets and coils are all present in glycosylate with helices being purple/pink, sheets being yellow, and coils being blue.
    1. amino acids 105-117 make an alpha helix! A picture of this can be found here Media:Picture_for_question_4b_Russo.png
  5. The negatively charged amino acids that are hydrophillic are located on the outside of the protein, this suggests that it works in a polar environment that is mostly positively charged. You can see this in the picture here, Media:Picture_for_question_5a_Russo.png
  6. Question 6 can't be answered because Star Biochem freezes! See it here! Media:Picture_for_question_6_Russo.png
  7. Most likely helix 16 would be responsible for recognizing the damaged guanine in the DNA since it is directly next to the DNA while helix 1 is on the opposite side. See here Media:Picture_for_question_7_Russo.png
    1. It looks like Phenylalanine at position 319 and Glutamine at position 315 get extremely close to the oxidized guanine, as you can see in this picture with the ring of the PHE and the oxygen (red) and nitrogen (blue) close to the oxidized guanine. Media:Picture_for_optional_question_7_Russo.png

Cn3D Exercise

  • It is a quaternary structure because I can see at least four termini of proteins, meaning there are at least two polypeptides in this structure.
  • It has three domains, since I went under 'show' in the menu and selected 'show structures...' and it listed three domains.
  • I can view the amino acid sequence as well as the helices, coils, and sheets. It does allow me to view domains and shows the Ca atom involved which Star did not do. I can also tell from this that there are two polypeptides instead of just one, however I cannot view the side chains or backbone interactions so it is difficult to view how it interacts on the small scale.
  • This picture is similar to my picture for 5a, Media:Picture_for_Cn3D_Russo.png
  • I prefer to use the Star Biochem. While it did crash when trying to view the DNA sequence, that isn't such a big deal since we are dealing with HIV and not DNA. Also while I didn't realize domains or that there were two polypeptides, I'm sure that there is some way for me to see them in Star. If not, I can just switch over to Cn3D to check it, but I would rather use Star as my primary way to view protein structure
    • Also probably has to do with the fact that I got a tutorial with Star and I was just thrown at Cn3d without any guidance.

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Assignment Pages

BIOL368/F11:Week 7

BIOL368/F11:Week 8

BIOL368/F11:Week 9

BIOL368/F11:Week 10

BIOL368/F11:Week 11

BIOL368/F11:Week 12

BIOL368/F11:Week 14