Robert W Arnold Week 6

Electronic Lab Notebook

DNA Glycosylase Exercise

• Downloaded StarBioChem from MIT website.
• Played around with structure by switching angles and views.
• Made atoms 100% to show accurate space-filled model.
• Began to answer exercise questions.

Questions

1. Yes, I can identify the DNA and the hOGG1 protein. The DNA is the smaller, double helical structure attached to the space-filled hOGG1 protein.
2. One of the amino acid sequences containing a sulfur atom is [CYS]241:A SG #2406. This means it is amino acid: cysteine; position; 241.
3. The sulfur is on the side chain because it remained when backbone was unchecked, but disappeared when side chain was unchecked.
4. The 13 amino acids from 105 to 117 are as follows:
   • 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 - Aspartic Acid
5. Yes, helices are found in hOGG1, they are represented by a purplish pink color. Sheets are also found in hOGG1 and are represented by yellow. Coils are also found in a blueish color in the structure.
6. Amino acids 105-117 all form into a helix structure. Here is the helix they form.
7. The negatively charged amino acids are on the outsides of the protein, exposed. This protein is hydrophilic....The helix can be seen here.
8. Program continued to freeze when trying to enlarge DNA for this question. Here is the frozen image.
9. Helix 16 would be more likely to recognize damaged guanine bases because at position 315 it is extremely close to the oxidized gaunine. The two helices can be seen here. Helix 1 and it's side chains can be seen here. and Helix 16 along with it's side chains can be seen