BIOL368/F14:Nicole Anguiano Week 6: Difference between revisions
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(→Star Biochem DNA Glycosylase Exercise: Answered question 6) |
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[[Image:AA105-117Helix.png|thumb|none|upright=2|alt=An alpha helix created by amino acids 105-117.|<b>Figure 4</b>: The alpha helix formed by amino acids 105 to 117.]] | [[Image:AA105-117Helix.png|thumb|none|upright=2|alt=An alpha helix created by amino acids 105-117.|<b>Figure 4</b>: The alpha helix formed by amino acids 105 to 117.]] | ||
*I reset the structure by selecting Reset > Reset structure in the top menu. I selected the Tertiary tab and moved the atom slider to the left to make all the atoms as small as possible. I then selected the negatively charged/acidic radio button. I moved the Atoms Size slider to the right to make the acidic amino acids as large as possible. | *I reset the structure by selecting Reset > Reset structure in the top menu. I selected the Tertiary tab and moved the atom slider to the left to make all the atoms as small as possible. I then selected the negatively charged/acidic radio button. I moved the Atoms Size slider to the right to make the acidic amino acids as large as possible. | ||
[[Image:Acidic_AminoAcids_hOGG1.png|thumb|none|upright=2|alt=The acidic amino acids in hOGG1.|<b>Figure 5</b>: An image displaying the locations of the negatively charged/acidic amino acids in the hOGG1 structure | [[Image:Acidic_AminoAcids_hOGG1.png|thumb|none|upright=2|alt=The acidic amino acids in hOGG1.|<b>Figure 5</b>: An image displaying the locations of the negatively charged/acidic amino acids in the hOGG1 structure.]] | ||
*I reset the structure by selecting Reset > Reset structure in the top menu. I selected the Nucleic Acids tab and moved the Atoms Size slider to 35. I then selected the Protein > Primary tab and moved the Atoms Size slider to 1 and the Bonds Translucency slider to 95. I selected the Nucleic Acids tab again and unchecked the phosophates checkbox and the sugar atoms checkbox. I moved the Atoms Size slider to 70. I clicked on the Non-Peptide tab and moved the Atoms Size slider to 100 so that I could fully observe the oxidized guanine. | |||
===Questions=== | ===Questions=== | ||
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#Are the negatively charged amino acids located on the inside (buried) or outside (exposed) of this protein? What does that suggest about the cellular environment surrounding this protein, is it hydrophobic or hydrophilic? Explain your answer. | #Are the negatively charged amino acids located on the inside (buried) or outside (exposed) of this protein? What does that suggest about the cellular environment surrounding this protein, is it hydrophobic or hydrophilic? Explain your answer. | ||
#*The negatively charged amino acids are located on the outside (exposed) side of the protein (Fig. 5). This suggests that the cellular environment surrounding this protein is hydrophilic and made of a large amount of water. The amino acids on the outside will likely be exposed to the environment that is suitable to them. Negatively charged amino acids are hydrophilic, so the environment must be hydrophilic as well. If the environment was hydrophobic, the hydrophilic amino acids would repel the environment, and likely curve inwards so that they were not facing the outside. | #*The negatively charged amino acids are located on the outside (exposed) side of the protein (Fig. 5). This suggests that the cellular environment surrounding this protein is hydrophilic and made of a large amount of water. The amino acids on the outside will likely be exposed to the environment that is suitable to them. Negatively charged amino acids are hydrophilic, so the environment must be hydrophilic as well. If the environment was hydrophobic, the hydrophilic amino acids would repel the environment, and likely curve inwards so that they were not facing the outside. | ||
#Now let’s explore how DNA glycosylase interacts with DNA to recognize the damaged DNA base within its sequence. DNA is composed of four bases: Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). In this particular structure, the hOGG1 protein is bound to a segment of DNA that contains an oxidized guanine. | |||
##How many DNA base pairs can you count within this double helix? | |||
##*I can count 13 DNA base pairs within the double helix. | |||
##How many DNA bases are unpaired (not paired to its partner on the other strand)? | |||
##*There is one DNA base that is unpaired. | |||
##Is the oxidized guanine base paired or unpaired? Describe the position of the oxidized guanine with respect to the hOGG1 protein and the double helix. What does this suggest about the mechanism that hOGG1 uses to identify damaged DNA bases? | |||
##*The oxidized guanine base is unpaired. The oxidized guanine is towards the center of the hOGG1 protein with the protein wrapping almost fully around it. It is also in the middle of the double helix. This suggest that hOGG1 uses the presence of oxidized guanine to determine whether or not a DNA base is damaged or not. The presence of it indicates the that base is damaged, and the absence of it indicates that the base is undamaged. | |||
==Cn3D Exercise== | ==Cn3D Exercise== |
Revision as of 15:57, 1 October 2014
Star Biochem DNA Glycosylase Exercise
Methods and Results
- First, I downloaded Star BioChem, and began following the instructions from the DNA Glycosylase Exercise worksheet.
- I selected the “DNA glycosylase hOGG1 w/ DNA – H. sapiens (1EBM)” protein from the Samples > Select from Samples menu. I changed the size of the atoms from 20 to 100 to view the protein as a space-filling model.
- Next, I pointed to a sulfur atom in the hOGG1 structure to obtain information about it.
- I selected View > View Specific Regions / Set Center of Rotation, then selected the amino acid in Figure 2. I moved the VDW Radius slider to 1 and unchecked the side-chain box. I observed that the sulfur atom disappeared. I checked the side-chain box and unchecked the backbone box. The sulfur atom remained. From there, I deduced that the Sulfur atom is a part of the side-chain.
- I reset the structure by selecting Reset > Reset structure in the top menu, then scrolled down and found amino acids 105-117.
Number | Amino Acid |
---|---|
105 | Threonine (Thr) |
106 | Leucine (Leu) |
107 | Alanine (Ala) |
108 | Glutamine (Gln) |
109 | Leucine (Leu) |
110 | Tyrosine (Tyr) |
111 | Histidine (His) |
112 | Histidine (His) |
113 | Tryptophan (Trp) |
114 | Glycine (Gly) |
115 | Serine (Ser) |
116 | Valine (Val) |
117 | Aspartic Acid (Asp) |
- Table 1: The identity of amino acids number 105 to 117.
- I clicked on the secondary tab and selected "all" to view all of the different structures (helices, coils, and sheets). I moved the Structures Size slider to the right to make them larger. I selected View > View Specific Regions / Set Center of Rotation, and selected amino acids 105 to 117 by clicking on amino acid 105, holding Shift, then clicking on amino acid 117. I moved the VDM Radius slider to 1 so that I could just see the selected amino acids.
- I reset the structure by selecting Reset > Reset structure in the top menu. I selected the Tertiary tab and moved the atom slider to the left to make all the atoms as small as possible. I then selected the negatively charged/acidic radio button. I moved the Atoms Size slider to the right to make the acidic amino acids as large as possible.
- I reset the structure by selecting Reset > Reset structure in the top menu. I selected the Nucleic Acids tab and moved the Atoms Size slider to 35. I then selected the Protein > Primary tab and moved the Atoms Size slider to 1 and the Bonds Translucency slider to 95. I selected the Nucleic Acids tab again and unchecked the phosophates checkbox and the sugar atoms checkbox. I moved the Atoms Size slider to 70. I clicked on the Non-Peptide tab and moved the Atoms Size slider to 100 so that I could fully observe the oxidized guanine.
Questions
- The hOGG1 structure contains both DNA and protein. Can you differentiate between the DNA and protein components? How did you distinguish the DNA from the protein?
- It is possible to differentiate between the DNA and protein components. The hOGG1 structure's proteins are displayed in the space-filling form, but the DNA is still visible in the ball and stick model (Fig. 1). Therefore, the DNA appears much smaller and thinner than the protein, making it easily distinguishable from the protein.
- hOGG1 contains multiple sulfur atoms.
- Identify the name and sequence number of one of the amino acids in the structure that contains a sulfur atom.
- The sulfur atom in figure 2 is part of cysteine at position 241.
- Is the sulfur atom located in the backbone or in the side chain of the amino acid?
- The sulfur atom is located in the side chain of the amino acid (Fig. 3).
- Identify the name and sequence number of one of the amino acids in the structure that contains a sulfur atom.
- List the 13 amino acids numbered 105 through 117 in order.
- See table 1.
- Within a protein chain, amino acids form local structures called secondary structures.
- Are helices, sheets or coils present in hOGG1? Describe the color that represents the secondary structures you observe.
- Helices, sheets, and coils are all present in hOGG1. Helices are colored pink, sheets are colored yellow-orange, and coils are colored a darker blue-purple color.
- Amino acids 105 through 117 fold into one of the secondary structures. Which secondary structure do they fold into?
- Amino acids 105-107 fold into an alpha helix (Fig. 4).
- Are helices, sheets or coils present in hOGG1? Describe the color that represents the secondary structures you observe.
- Are the negatively charged amino acids located on the inside (buried) or outside (exposed) of this protein? What does that suggest about the cellular environment surrounding this protein, is it hydrophobic or hydrophilic? Explain your answer.
- The negatively charged amino acids are located on the outside (exposed) side of the protein (Fig. 5). This suggests that the cellular environment surrounding this protein is hydrophilic and made of a large amount of water. The amino acids on the outside will likely be exposed to the environment that is suitable to them. Negatively charged amino acids are hydrophilic, so the environment must be hydrophilic as well. If the environment was hydrophobic, the hydrophilic amino acids would repel the environment, and likely curve inwards so that they were not facing the outside.
- Now let’s explore how DNA glycosylase interacts with DNA to recognize the damaged DNA base within its sequence. DNA is composed of four bases: Adenine (A), Thymine (T), Cytosine (C) and Guanine (G). In this particular structure, the hOGG1 protein is bound to a segment of DNA that contains an oxidized guanine.
- How many DNA base pairs can you count within this double helix?
- I can count 13 DNA base pairs within the double helix.
- How many DNA bases are unpaired (not paired to its partner on the other strand)?
- There is one DNA base that is unpaired.
- Is the oxidized guanine base paired or unpaired? Describe the position of the oxidized guanine with respect to the hOGG1 protein and the double helix. What does this suggest about the mechanism that hOGG1 uses to identify damaged DNA bases?
- The oxidized guanine base is unpaired. The oxidized guanine is towards the center of the hOGG1 protein with the protein wrapping almost fully around it. It is also in the middle of the double helix. This suggest that hOGG1 uses the presence of oxidized guanine to determine whether or not a DNA base is damaged or not. The presence of it indicates the that base is damaged, and the absence of it indicates that the base is undamaged.
- How many DNA base pairs can you count within this double helix?
Cn3D Exercise
Methods and Results
Questions
Links
Nicole Anguiano
BIOL 368, Fall 2014
Assignment Links
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