BIOINFORMATICS ASSIGNMENT
BIOINFORMATICS ASSIGNMENT
- Complete Table 1 after using the PEPSTATS tool:
| Total | Number of | % of polar | Number of | % of | ||
| Alpha amylase | Number of | polar amino | amino acids | non-polar | non-polar | |
| amino acids | acids | amino acids | amino acids | |||
| Homo sapiens | ||||||
| (salivary) | 496 | 225 | 45.36 | 271 | 54.63 | |
| Aspergillus | ||||||
| oryzae | 433 | 198 | 45.72 | 235 | 54.27 | |
| Geobacillus | ||||||
| stearothermophilus | 515 | 246 | 47.76 | 269 | 52.24 | |
- Complete Table 2 after obtaining the Percent Identity Matrix with CLUSTAL OMEGA:
| Source of | Homo sapiens | Aspergillus | Geobacillus | |||
| alpha amylase | (salivary) | oryzae | stearothermophilus | |||
| Homo sapiens | ||||||
| (salivary) | 19.44 | 23.90 | ||||
| Aspergillus | ||||||
| oryzae | 19.44 | 100.00 | ||||
| Geobacillus | ||||||
| stearothermophilus | 23.90 | 100.00 |
- In human salivary amylase, the amino acids that make up the active site are aspartate197 (D197), glutamate233 (E233) and aspartate300 (D300) (the numbers indicate the order of these amino acids in the human sequence). Using the BOXSHADE alignment, determine if these amino acids are conserved in the fungal and bacterial amylases.
There are no amino acids conserved in the fungal and bacterial amylases.
- What secondary structures do you recognize? What is the importance of secondary structures?
The alpha helix and the beta sheet. Secondary structures preserve the bond angles and planar configuration of the peptide bond, as well as keep atoms from coming together so closely that they repelled each other through their interactions.
- The percent alpha helix and beta sheet content for all three amylase enzymes is shown in Table 3 below.
| Human | Fungal | Bacterial | |
| % Alpha helices | 27 | 34 | 23 |
| % Beta sheets | 23 | 21 | 30 |
Discuss the differences in alpha helix and beta sheet content between the three amylases. What do these differences signify?
The α amylase contains (β/α) 8-barrel The β amylase contains (α/β)8 TIM barrels γ amylase or glucoamylase contains intermolecular β sheets and majority of α helices. It signifies that the three enzymes are evolutionary related.
- Obtain the 3D structures of all three amylases, and attach them to your assignment. Draw arrows and label an alpha helix and a beta sheet on each structure.
BIOINFORMATICS ASSIGNMENT
- Complete Table 1 after using the PEPSTATS tool:
| Total | Number of | % of polar | Number of | % of | ||
| Alpha amylase | Number of | polar amino | amino acids | non-polar | non-polar | |
| amino acids | acids | amino acids | amino acids | |||
| Homo sapiens | ||||||
| (salivary) | 496 | 225 | 45.36 | 271 | 54.63 | |
| Aspergillus | ||||||
| oryzae | 433 | 198 | 45.72 | 235 | 54.27 | |
| Geobacillus | ||||||
| stearothermophilus | 515 | 246 | 47.76 | 269 | 52.24 | |
- Complete Table 2 after obtaining the Percent Identity Matrix with CLUSTAL OMEGA:
| Source of | Homo sapiens | Aspergillus | Geobacillus | |||
| alpha amylase | (salivary) | oryzae | stearothermophilus | |||
| Homo sapiens | ||||||
| (salivary) | 19.44 | 23.90 | ||||
| Aspergillus | ||||||
| oryzae | 19.44 | 100.00 | ||||
| Geobacillus | ||||||
| stearothermophilus | 23.90 | 100.00 |
- In human salivary amylase, the amino acids that make up the active site are aspartate197 (D197), glutamate233 (E233) and aspartate300 (D300) (the numbers indicate the order of these amino acids in the human sequence). Using the BOXSHADE alignment, determine if these amino acids are conserved in the fungal and bacterial amylases.
There are no amino acids conserved in the fungal and bacterial amylases.
- What secondary structures do you recognize? What is the importance of secondary structures?
The alpha helix and the beta sheet. Secondary structures preserve the bond angles and planar configuration of the peptide bond, as well as keep atoms from coming together so closely that they repelled each other through their interactions.
- The percent alpha helix and beta sheet content for all three amylase enzymes is shown in Table 3 below.
| Human | Fungal | Bacterial | |
| % Alpha helices | 27 | 34 | 23 |
| % Beta sheets | 23 | 21 | 30 |
Discuss the differences in alpha helix and beta sheet content between the three amylases. What do these differences signify?
The α amylase contains (β/α) 8-barrel The β amylase contains (α/β)8 TIM barrels γ amylase or glucoamylase contains intermolecular β sheets and majority of α helices. It signifies that the three enzymes are evolutionary related.
- Obtain the 3D structures of all three amylases, and attach them to your assignment. Draw arrows and label an alpha helix and a beta sheet on each structure.
