University of York. BA, BSc, and MSc Degree Examinations Department : BIOLOGY. Title of Exam: Molecular machines. Time Allowed: 2 hours

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1 Examination Candidate Number: Desk Number: University of York BA, BSc, and MSc Degree Examinations Department : BIOLOGY Title of Exam: Molecular machines Time Allowed: 2 hours Marking Scheme: Total marks available for this paper: 100 Sec on A: Short Answer / Problem / Experimental Design ques ons (50 marks) Sec on B: Essay ques on (marked out of 100, weighted 50 marks) The marks available for each ques on are indicated on the paper Instructions: Sec on A: Answer all ques ons in the spaces provided on the examina on paper Sec on B: Answer either ques on A or ques on B. Write your answer on the separate paper provided and a ach it to the back of the ques on paper using the treasury tag provided Materials supplied: CALCULATOR For marker use only: For office use only: Total as % DO NOT WRITE ON THIS BOOKLET BEFORE THE EXAM BEGINS DO NOT TURN OVER THIS PAGE UNTIL INSTRUCTED TO DO SO BY AN INVIGILATOR page 1 of 8

2 SECTION A: Short Answer / Problem / Experimental Design questions Answer all questions in the spaces provided Mark total for this section: How does the high volume occupancy observed inside cells affect motion on the microscopic and nanoscopic scales? (4 marks) 2. a) What happens to the DNA duplex during the scrunching process? (3 marks) b) Why is DNA scrunching thought to be important in both the abortive initiation and promoter escape stages of transcription? (3 marks) page 2 of 8

3 3. The bacterial replisome has several components that contribute to the very high processivity of this molecular machine. Briefly describe three of these components and explain how each enhances processivity. (6 marks) 4. Describe the biochemical evidence that has revealed an intrinsic helicase activity in the ribosome. (5 marks) 5. a) Describe the rigor state for a conventional molecular motor that moves along F-actin or a microtubule. (2 marks) page 3 of 8

4 b) How do the rigor states differ for a conventional myosin and a conventional kinesin in the cross-bridge cycle? (4 marks) 6. a) What is the duty ratio of a motor protein and how is it calculated? (2 marks) b) Define processivity. (1 mark) c) How is the duty ratio of a motor protein related to its processivity? (1 mark) The space above this line should be sufficient for your answer page 4 of 8

5 7. a) Outline an experimental strategy to investigate the stoichiometry of a multi-protein molecular machine in a bacterium using slimfield fluorescence microscopy. (6 marks) b) Why are both the diffraction limit and the time-resolution of a video fluorescence microscopy approach important when studying dynamics in a cell? (3 marks) 8. Förster resonance energy transfer (FRET) experiments are used to determine the distance between two groups in the F 1 module of ATP synthase. These groups are labelled with Cy3 (donor) and Cy5 (acceptor) fluorophores. a) What is the requirement for the absorption and emission spectra of Cy3 and Cy5 in order for FRET to occur? (1 mark) b) Define what is meant by the Förster radius (R o ). (1 mark) page 5 of 8

6 c) Labelling sites on the δ and b 2 sub-domains are chosen for the donor and acceptor, respectively. When the dyes are separated by a distance of 75Å, the FRET efficiency is What would be the FRET efficiency if the donor-acceptor distance decreased by 30%? (4 marks) d) Briefly describe the Binding Change Hypothesis with respect to the F o F 1 ATP synthase. (2 marks) The space above this line should be sufficient for your answer page 6 of 8

7 e) The labelled F 1 module of ATP synthase is embedded in a lipid bilayer. The change in position of the donor relative to the acceptor upon rotation of the rotor is followed via the efficiency of energy transfer, E, as shown below. Briefly explain why this data supports the Binding Change Hypothesis. (2 marks) The space above this line should be sufficient for your answer page 7 of 8

8 SECTION B: Essay question Answer one question on the separate paper provided Remember to write your candidate number at the top of the page and indicate whether you have answered question A or B Mark total for this section: 50 EITHER A) Discuss the evidence which supports the view that nucleic acid-dependent molecular motors can do work and have force-dependent enzymatic properties. OR B) Compare and contrast the structural and functional characteristics of molecular motors that can be classified as rowers or porters. page 8 of 8