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School of Life Sciences

Coursework assessment for Assessment Cycle 2 Resit

(Semester 2, 2022/23)

LIFE203, Structure and Dynamics of Macromolecules

Module organiser: Igor Barsukov

Submission date: Monday 18 August 2023 at 12 pm

Maximum word count: 1500 words

Please read all instructions (general and specific) carefully! Please also make sure to familiarise yourself with the student guidance for written assessments (Canvas > OX-LIFE-Sciences-202223 > Assessment).

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:

o Up to 1% (e.g. up to 2020 for a 2000 word maximum) no penalty

o Up to 10% (e.g. between 2021 and 2200 words) 5 % penalty

o Up to 20% (e.g. between 2201 and 2400 words) 10 % penalty

o Etc. (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 the submission link in your module area in Canvas

· 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 Canvas by the deadline, you must email your work to the module organiser (copying in [email protected] ) by the deadline, as evidence that you have submitted in time. You should then continue to attempt submitting via Canvas.

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:  

https://www.liverpool.ac.uk/media/livacuk/tqsd/code-of-practice-on-assessment/appendix_L_cop_assess_annex1.pdf  

Please note: Your answer should be written in your own words. Do not use any verbatim (word for word) quotes. Your assignment may not contain verbatim (copy-and-paste) material that you have submitted for another assessment, either on this or a different module.

Expectations:

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 explanations in your answers.  

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%, 20 marks)

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

A. Using the data in the table below, plot semi-log binding curves and determine which of the drugs binds with highest affinity to the target protein. Explain how you reached this conclusion. (4 marks)

B. Using the graph, show how you would determine K_d, and estimate approximate K_d and K_a values for drug binding of each protein, explaining how you perform the calculations. (6 marks)

C. Explain how you can determine whether the binding is dominated by a conformational change (6 marks)

D. Describe 2 types of interaction that could be involved in drug-protein recognition. (4 marks)

Q2 (20%, 20 marks)

A. Explain, using a diagram, the generation of supercoiling by the process of transcription. (3 marks)

B.  The enzymes that manipulate supercoiling in cells are called topoisomerases.  Explain the differences between type I and type II topoisomerases. (5 marks)

C. Removal of supercoiling can be carried out by both type I and type II topoisomerases, but which DNA feature, generated by replication, can only be removed by type II?  Explain why. (2 marks).

Q3 (20%, 20 marks)

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

B. Illustrate your answer to part a) with a 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 displaying single chains for each receptor with the active (panel A) and inactive (panel B) conformations displayed side-by-side and (panel C) two conformations 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%, 30 marks)

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

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

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)

B. The key inhibitory residue of Bdellastasin is Lys34. Produce a PyMOL figure and brief legend 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)

C. Produce a similar figure/legend, 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)

D. Comment on the comparison between Lys34 and the Ascaris inhibitor residue mentioned above in relation to the enzymes to which the inhibitors are bound. (3 marks)

E. Which amino acid do you think could functionally replace Lys34 of Bdellastasin? Explain your answer (2 marks)

F. Using the specific, relevant technical terms you learned in the lecture, compare the structures of the two inhibitors and describe the evolutionary relationship, if any, between them. (3 marks)

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).