Chris Rhodes Week 6: Difference between revisions

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# Are there helices, sheets, or coils present in hOGG1? What secondary structure do amino acids 105-117 fold into?-> Yes shown below, pink represents helices, yellow represents sheets, and blue represents coils. [[Image:CHR_Image_20111005.png]] [[Image:CHR_Image3_20111005.png]] 105-117 Fold in a helix
# Are there helices, sheets, or coils present in hOGG1? What secondary structure do amino acids 105-117 fold into?-> Yes shown below, pink represents helices, yellow represents sheets, and blue represents coils. [[Image:CHR_Image_20111005.png]] [[Image:CHR_Image3_20111005.png]] 105-117 Fold in a helix
#Are the negatively charged amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is in? [[Image:CHR_Image4_20111005.png]] The negatively charged amino acids are the on the outside of the protein structure indicating that the protein will most likely make hydrogen bonds meaning its environment is hydrophilic.
#Are the negatively charged amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is in? [[Image:CHR_Image4_20111005.png]] The negatively charged amino acids are the on the outside of the protein structure indicating that the protein will most likely make hydrogen bonds meaning its environment is hydrophilic.
# How many base pairs can you count within the double helix? How many base pairs are unpaired? Is the oxidized guanine paired or unpaired? -> 14 base pairs, only 1 is unpaired, the oxidized guanine is the unpaired base, its position is shown below [[Image:CHR_Image5_20111005.png]]
# How many base pairs can you count within the double helix? How many base pairs are unpaired? Is the oxidized guanine paired or unpaired? -> 14 base pairs, only 1 is unpaired, the oxidized guanine is the unpaired base, its position is shown here -> [[Image:CHR_Image5_20111005.png]]
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#*Note: adjusting the size sliders in the nucleic acid tab caused the program to freeze. The values and screenshots taken for the above question were created through the use of size and transparency sliders of the Proteins->Primary tab instead.
    
    


==Links==
==Links==
{{Chris H. Rhodes}}
{{Chris H. Rhodes}}

Revision as of 15:45, 5 October 2011

Questions and Answers

Star Biochem Exercise Star Biochem Site -> Start: Star Biochem will download and open on the computer -> Samples -> DNA glycolase hOGG1 w/DNA

  1. Can you identify the DNA and the HOGG! protein in the structure? Where is the DNA segment? -> The DNA is circled in black and the Protein structure is circled in Red
  2. Identify the name and sequence number of one the amino acids that contains a sulfur atom. Is the sulfur atom in the backbone or sidechain? :[CYS] 241:A SG #2406, Sidechain
  3. List the 13 amino acids numbered 105-117: Threonine, Leucine, Alanine, Glutamine, Leucine, Tyrosine, Histidine, Histidine, Tryptophan, Glycine, Serine, Valine, Aspartic Acid
  4. Are there helices, sheets, or coils present in hOGG1? What secondary structure do amino acids 105-117 fold into?-> Yes shown below, pink represents helices, yellow represents sheets, and blue represents coils. 105-117 Fold in a helix
  5. Are the negatively charged amino acids located on the inside or outside of the protein? What does this suggest about the environment the protein is in? The negatively charged amino acids are the on the outside of the protein structure indicating that the protein will most likely make hydrogen bonds meaning its environment is hydrophilic.
  6. How many base pairs can you count within the double helix? How many base pairs are unpaired? Is the oxidized guanine paired or unpaired? -> 14 base pairs, only 1 is unpaired, the oxidized guanine is the unpaired base, its position is shown here ->
    • Note: adjusting the size sliders in the nucleic acid tab caused the program to freeze. The values and screenshots taken for the above question were created through the use of size and transparency sliders of the Proteins->Primary tab instead.


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