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Macromolecules Structure and Dynamic Discussion

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Macromolecules Structure and Dynamic Discussion

General instructions to students:

  1. Word count
    • The word count is a maximum (not plus/minus 10%). There is no minimum word count.
    • Please refer to the specific instructions below regarding what is and what isn’t included in the maximum word count for this assignment.
    • Penalties will be applied for exceeding the word count as follows:
      • Up to 1% (e.g. up to 2020 for a 2000 word maximum) no penalty
      • Up to 10% (e.g. between 2021 and 2200 words) 5 % penalty
      • Up to 20% (e.g. between 2201 and 2400 words) 10 % penalty
      • (i.e. 5% penalty for every 10% above word count)
    • Enter your word count at the bottom of your submission
  2. Submission
    • Your work should be submitted via Turnitin, following the submission link in your module area in Canvas or VITAL (as appropriate).
    • Please make sure that you follow the guidance on ‘Submission procedures for assessed coursework’ which is published in the School Handbook on Canvas.
    • Also refer to the School Handbook in relation to the penalties for Late Submission and possible exemptions.
    • If you have any technical problems submitting to Turnitin by the deadline, you should email your work to the module organiser (copying in, as evidence that you have submitted in time. You should then continue to attempt submitting via Turnitin.
  3. Academic Integrity

The University’s Academic Integrity policy and your annual Academic Integrity declaration

apply to this assessment. If necessary, the full range of penalties (Category A, B, C, D, and E)

will be available to examiners if they discover contraventions of the Academic Integrity

policy. You can consult the University’s Academic Integrity guide for students here:


Please note: Your answer should be written in your own words. Do not use any verbatim (word for word) quotes.



In this assessment, we expect students to write concise and sufficiently detailed answers which correctly use the appropriate terminology. Some questions require you to give background information based on the relevant module content. When you address the question, you should use your knowledge and understanding of the module content. At the higher end of the marking scheme, markers will also be looking for clear and well-founded explanation in your answers. Macromolecules Structure and Dynamic Discussion

Specific instructions:

Answer all questions. If you choose to include diagrams in your answer these should be original (drawn by hand or in PowerPoint or similar) and pasted into the Word document. Please include a figure legend (this will not be included in your word count) and ensure they are labelled. A good figure with just the information you need to explain your answer will help your answer but a bad figure with too much irrelevant information may detract from the quality of your answer.

Type your answers in the word document. Include questions numbers and letters, but do not copy the question text.

Coursework Question(s):

Q1 (20 marks)

3 drugs (A, B and C) bind to a target protein.

  1. a) Using the data in the table plot semi-log binding curves and determine which of the drugs binds most tightly to the target protein? Explain how you reached this conclusion. (4 marks)
  2. b) Using the graph show and explain how you would determine Kd, and calculate approximate Kd and Ka values for hormone binding of each protein, showing how you perform the calculations. (6 marks)
  3. c) Explain how you can determine whether the binding is dominated by a local conformational change (6 marks)
  4. d) Describe 2 types of interaction that could be involved in drug-protein binding. (4 marks)
[Drug] nM q
Drug A Drug B Drug C
1 0.028 0.009 0.017
5 0.11 0.15 0.183
10 0.2 0.27 0.45
20 0.43 0.59 0.8
50 0.71 0.75 0.91
250 0.83 0.97 0.95
1000 1 0.99 0.98



Q2 (20 marks)


  1. a) In the DNA double helix structure, outline the contribution of hydrogen bonds and other forces to the stability of the helix. (3 marks)
  2. b) Explain this effect in terms of the thermodynamics of the individual strands and the solvent in the system. (7 marks)
  3. c) Explain how propellor twisting further contributes to the stability of the helix. (6 marks)
  4. d) What other kind of evidence can be used to address the importance of hydrogen bonds to the specificity of base pairing? (4 marks)


Q3 (20 marks)


  1. a) Explain in ~100 words the structural basis of GPCR receptor activation of heterotrimeric G-protein (10 marks).


  1. b) Illustrate your answer with the Pymol figure that shows the differences between the active and inactive forms of beta2 adrenoceptor GPCR receptor (use PDB entries 4qkx and 5jqh, corresponding to the different activation states). The figure should contain 3 side by side panels with single molecule of the receptor for each the active and inactive conformation displayed side-by-side and aligned in a similar orientation; chose the optimal molecule orientation to demonstrate the main structural changes. Label the conformations as “active” and “inactive”, label transmembrane helix (TM6) with the biggest movement (10 marks).



Q4 (30 marks)

This question relates to proteases and their inhibitors, and to these two PDB structures

PDB code Protease (chain labels) Protease inhibitor (chain label)
1eja Porcine trypsin (A) Bdellastasin (B)
1eia Porcine elastase (A or B) Ascaris inhibitor (C or D)*

* There are two enzyme-inhibitor complexes A:C and B:D in the crystal structure


  1. a) Using the vocabulary you learned in the lecture, describe the evolutionary relationship between porcine trypsin and porcine chymotrypsin and the likely series of events that led to this relationship. (5 marks)
  2. b) The key inhibitory residue of Bdellastasin is Lys34. Produce a PyMOL figure that illustrates the trypsin-inhibitor complex, including the specific interaction of inhibitor Lys34 with the enzyme. Use colour and different representations to improve the legibility of the figure. (7 marks)
  3. c) Produce a similar figure, in the same orientation, to illustrate the interaction of elastase with Ascaris inhibitor, highlighting the Ascaris inhibitor residue that occupies the same position as Lys34. (5 marks)
  4. d) Comment on the comparison between Lys34 and the Ascaris inhibitor residue mentioned above in relation to the enzymes the inhibitors are bound to. (3 marks)
  5. e) Which amino-acid do you think could functionally replace Lys34 of Bdellastasin? Explain your answer (2 marks)
  6. f) Using the vocabulary you learned in the lecture, compare the structures of the two inhibitors and describe the evolutionary relationship, if any, between them. (3 marks)
  7. g) Using the UniProt database discover the name of the Pfam domain contained in the Ascaris inhibitor. It has the UniProt code P07851. Include a screenshot to illustrate where you obtained the information. (2 marks) Including screenshots of the Pfam database, describe which group of species most commonly contain proteins that include this domain and report on how many human proteins contain the domain (3 marks).

Use APA format, double spaced, new times roman

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