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BIOC0008

Quiz

Congratulations! You have now completed the practical

This practical should have reinforced your understanding of torsion angles and their relationship to secondary structure. Secondly you should now understand the power of using structure to analyze how mutations can affect protein function.

Of course there are many other factors that mean a mutation can affect function as well as it being close to (or within) the active/binding site. For example, a mutation distant from the active site may destabilize the protein fold.

Using the answers that you recorded during the tutorial, now answer the following questions. This is only for your own benefit to ensure you have done all the stages correctly and understand what you are doing. These answers are not recorded.

1. What was the residue number of the first residue in the second helix of crambin (1crn)? (a number between 1 and 46)
7
19
22
23
30

2. What was the residue number of the last residue in the second helix of crambin (1crn)? (a number between 1 and 46)
7
19
22
23
30

3. What was the omega angle (peptide bond torsion) between Thr30 and Gly31 (Note that the angles may differ in the second decimal place owing to rounding errors in different versions of PyMol.)
171.5
-171.6
174.6
-178.2

4. What was the omega angle (peptide bond torsion) between Gly31 and Cys32 (Note that the angles may differ in the second decimal place owing to rounding errors in different versions of PyMol.)
171.5
-171.6
174.6
-178.2

5. Which did you conclude was more stable: the pi-helix or the alpha-helix?
pi-helix
alpha-helix

6. In the all-alpha and all-beta proteins, the distribution of spots on the Ramachandran plots was surprisingly similar. Why do you think this is?
Because the alpha and beta regions are simply energetically favoured regions
Because all proteins contain a mixture of secondary structure even if called 'all-alpha' or 'all-beta'

7. Why do you think the Ramachandran plot it useful?
It allows you to distinguish all-alpha and all-beta protein classes
It allows you to assess the quality of a protein structure - low resolution structures have more amino acids in disallowed conformations

8. Which of these residues was NOT listed as being in the active site or binding sites?
38
171
366
503

9. When using OMIM, which mutation corresponded to the .0030 variant?
His32Arg
Ala44Gly
Asn363Lys

10. When using OMIM, which mutation corresponded to the .0044 variant?
His32Arg
Ala44Gly
Asn363Lys

11. When using OMIM, which mutation corresponded to the .0047 variant?
His32Arg
Ala44Gly
Asn363Lys

12. Which of the variants (mutations), is within the main part of the active/binding site?
.0030
.0044
.0047

13. Which of the variants (mutations), is not withing 15A of the active/binding site?
.0030
.0044
.0047

I have completed this work to the best of my ability.

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