University of York. BA, BSc, and MSc Degree Examinations Department : BIOLOGY. Title of Exam: Biochemical reaction mechanisms

Size: px

Start display at page:

Download "University of York. BA, BSc, and MSc Degree Examinations Department : BIOLOGY. Title of Exam: Biochemical reaction mechanisms"

Georgia Smith
6 years ago
Views:

1 Examination Candidate Number: Desk Number: University of York BA, BSc, and MSc Degree Examinations Department : BIOLOGY Title of Exam: Biochemical reaction mechanisms Time Allowed: 1 hour Marking Scheme: Total marks available for this paper: 50 Sec on A: Short answer ques ons (30 marks) Sec on B: Problem ques ons (20 marks) The marks available for each ques on are indicated on the paper Instructions: Answer all ques ons in the spaces provided on the examina on paper Materials Supplied: CALCULATOR For marker use only: For office use only: Module 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 11

2 SECTION A: Short answer questions Answer all questions in the spaces provided Mark total for this section: Name the E.C. class to which enzymes catalysing each of the following reactions belong. (4 marks) (1 for each) page 2 of 11

3 2. The diagram below shows the range of pka values one would normally expect to find for a series of amino acid residue side chains in solution. a) Complete the diagram by matching the name of the following amino acids to each ionization range, (a) to (d): Histidine, Tyrosine, Aspartic Acid, Cysteine. b) Draw the ionisation reaction for the side chain of a lysine residue, and give an estimate of the pka for this residue in solution. c) Explain, giving an example, how the value you quote in (b) may be substantially modified within the active site of an enzyme. page 3 of 11

4 3. A simplified mechanism for the action of bovine alkaline phosphatase is shown below. a) Complete the mechanism by adding curly arrows to pictures I and III to indicate the movement of electrons that will result in II and IV. page 4 of 11

5 b) What features of the enzyme (not shown) stabilise the negatively charged phosphate oxygens during the catalytic cycle? c) What name is given to the intermediate shown in picture III? (1 mark) d) Comment on changes to the stereochemistry at the phosphorous atom during the catalytic cycle. Describe a molecule that could be employed to monitor these changes experimentally. (3 marks) The space above this line should be sufficient for your answer. page 5 of 11

6 4. The structure of the coenzyme pyridoxal phosphate PLP, as found in the enzyme alanine racemase, is shown below, alongside the structure of the amino acid alanine. a) Describe how the PLP coenzyme is bound within the active site in the resting form of alanine racemase.what name is given to this species? (3 marks) b) Using the structures as guides, draw and name the structure of the complex formed between PLP and alanine within the active site of alanine racemase. (3 marks) page 6 of 11

7 5. The electronic configuration of atomic Cl is 1s 2 2s 2 2p 6 3s 2 3p 5. a) Draw out the molecular orbital diagram for Cl 2 based on the assumptions that the orbital splitting patterns are the same as for O 2, and that the 1s, 2s and 2p orbitals are too spatially contracted to contribute to the bonding. b) Consider a 1-electron oxidation of Cl 2. (i) Quantify how the bond order of Cl 2 such a reaction. would change following (ii) Calculate the spin multiplicity of the resultant molecule and explain, with reasoning, whether EPR could be used to follow the progress of the oxidation reaction. page 7 of 11

8 SECTION B: Problem questions Answer all questions in the spaces provided Mark total for this section: a) Acetogenic microbes grow using dihydrogen as an electron donor and carbon dioxide as an electron acceptor, generating carbon monoxide from this process. (i) Write out a balanced reaction for the reduction of protons to form dihydrogen. (1 mark) (ii) The standard reduction potential for proton reduction, E 0 H + / H2, is 0 V vs. SHE (Standard Hydrogen Electrode). Calculate what the value will be under conditions of ph 7, 37 C, 100% H 2 atmosphere. Use the constants R = J K -1 mol -1 and F = C mol -1. (4 marks) (iii) Assuming that under the same conditions the reduction potential for converting CO 2 into CO is V vs. SHE, calculate the Gibbs free energy for respiration for acetogenic microbes growing under these conditions. page 8 of 11

9 b) The following structure depicts carbon dioxide bound to the active site of the enzyme which converts it into carbon monoxide. (i) State, with reasoning, whether you expect the Ni to access higher or lower oxidation states than Fe during the catalytic reduction of carbon dioxide to carbon monoxide. Atomic number of Fe = , atomic number of Ni = (1 mark) (ii) Briefly state similarities and differences between this active structure and the O 2 reducing centre of cytochrome c oxidase. (2 mark) page 9 of 11

7. An ene-reductase (ERED) can catalyse the transformation of trans -cinnamic acid 1 to metabolite 2, in the process generating the cofactor FAD from X. a) Draw the structure of 2 in the box provided.

10 7. An ene-reductase (ERED) can catalyse the transformation of trans -cinnamic acid 1 to metabolite 2, in the process generating the cofactor FAD from X. a) Draw the structure of 2 in the box provided. (1 mark) b) Using the structure of FAD as a guide, name and draw a structure of X in the box provided, using R for the ADP moiety. (3 marks) c) Suggest a means whereby cofactor X may be recycled in the cell for further turnovers of 1. (1 mark) page 10 of 11

11 d) Describe a strategy for industrial production of 2 from 1, using purified ERED and the cofactors you have described, and paying particular attention to the economic factors surrounding the use of cofactors at scale, and a method for monitoring the reaction. (5 marks) The space above this line should be sufficient for your answer. page 11 of 11

BA, BSc, and MSc Degree Examinations

Examination Candidate Number: Desk Number: BA, BSc, and MSc Degree Examinations 2017-8 Department : BIOLOGY Title of Exam: Molecular Biology and Biochemistry Part I Time Allowed: 1 hour and 30 minutes