CH3F5-15 Bioorganic Chemistry
Introductory description
N/A
Module aims
This module aims to highlight the central importance of enzymes as catalysts in biological systems which are involved in the interconversion of all essential cellular metabolites (primary metabolites) and the production of many natural products of importance in medicine and agriculture. In addition this module aims to define the major classes into which secondary metabolites fall according to their structure and to explain how labelled precursors can be used to determine the primary metabolic building blocks from which secondary metabolites are assembled. The module includes descriptions of the molecular mechanisms of the most important enzyme catalysed reactions in natural product biosynthesis and associated coenzyme mechanisms, and some of the methods used to elucidate these mechanisms. Students will learn how the principles of organic chemistry can be critically used to discriminate between different possible mechanisms for a given enzyme catalysed reaction (12 lectures).
In addition this module aims to enable students to link fundamental components of the major classes of molecular interactions that play key roles in recognition processes. Semi-quantitative methods for estimating strengths of these processes will be introduced and used in the analysis and study of well-described systems from biology (enzymes, drug-receptor interactions, non-covalent assemblies) and synthetic systems (small molecule, host-guest, self-assembled architectures). In studying these systems students will become familiar with underlying chemical principles and use some of the tools for computer-aided molecular visualisation and modelling encountered in years 1 and 2. The module is designed in particular to allow students working at the interface between Chemistry and Biology to begin to use these tools but is accessible to students on other Chemistry degree streams as well (10 lectures).
Outline syllabus
This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.
Introduction to natural products (3 lectures)
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Introduction
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Classical methods in biosynthesis - labelling
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Modern methods in biosynthesis
Polyketide biosynthesis (5 lectures) -
Incorporation of labelled precursors into aromatic and complex polyketides
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Enzymology of iterative polyketide biosynthesis
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Enzymology of modular polyketide synthases
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Non-ribosomal peptide synthesis
Terpenoid biosynthesis (2 lectures) -
The mevalonate and non-mevalonate pathways to isoprenoids
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Enzymology of linear polyprenyl pyrophosphate biosynthesis
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Enzymology of polyprenyl pyrophosphate cyclisation reactions
Alkaloid biosynthesis (2 lectures)
plus 3 workshops -
Introduction to molecular interactions.
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Quantifying molecular interactions
Practice with quantifying molecular interactions - workshop 1 -
Quantifying molecular interactions 2
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Hydrogen bonding including examples
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X-ray macromolecular structure determination; PDB and EDS.
Exploring Interactions - workshop 2 (computer - introduction to PyMol and Jmol) -
Electrostatic interactions ; pi-pi interactions: examples
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Hydrophobic effect and introduction to protein folding
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Self-assembly processes in biology and chemistry
Exploring Interactions - workshop 3 (computer) -
Thermodynamics and Isothermal titration calorimetry including worked examples
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NMR-based and other methods for characterising interactions including biological example
Feedback on assessed work - workshop 4
Exploring interactions 3 - workshop 5
Revision Lecture
Learning outcomes
By the end of the module, students should be able to:
- Subject knowledge to an appropriate level.
- Analysis and contextual understanding of contemporary examples
- Ability to interpret and evaluate examples from the literature
Indicative reading list
P.M. Dewick, Medicinal Natural Products, 2nd edition, Wiley, London, 2002.
T.D.H. Bugg, An Introduction to Enzyme and Coenzyme Chemistry, Blackwells, Oxford, 1998.
Modern Physical Organic Chemistry, E. Anslyn, D. Dougherty, University Science Books, 2005.
Alan Cooper, Biophysical Chemistry ( RSC Tutorial Chemistry Text #16, ISBN 0-85404-480-9, Royal Society of Chemistry, Cambridge, 2004) The Theory of Intermolecular Forces Anthony J. Stone, Clarendon Press, Oxford: 1996. [QD831.S8] – advanced.
Bioorganic Chemistry, H. Dugas, 3rd Edition, Springer. Structure and Mechanism in Protein Science, A. Fersht 3rd Edition, Freeman. Supramolecular Chemistry, P. D. Beer, P. A. Gale and D. K Smith OUP Primer, Oxford: 1999. Principles and Methods in Supramolecular Chemistry, H.-J. Schneider, A. Yatsimirsky, Wiley. Introduction to protein structure, C. Branden, J. Tooze, Garland. Supramolecular Chemistry, J. Steed and J. Atwood, Wiley.
RCSB Protein Databank Tutorials at: http://www.rcsb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/intro.html
Research element
e.g. essay, dissertation, individual or group research, research skills activity, etc.
Subject specific skills
Numeracy
Problem solving
Written communication
Independence and initiative
Information literacy and research skills
Digital skills and literacy
Transferable skills
Numeracy
Problem solving
Written communication
Independence and initiative
Information literacy and research skills
Digital skills and literacy
Study time
| Type | Required |
|---|---|
| Lectures | 22 sessions of 1 hour (15%) |
| Practical classes | 8 sessions of 1 hour (5%) |
| Private study | 120 hours (80%) |
| Total | 150 hours |
Private study description
Self study and direct reading: 120 hours
Costs
No further costs have been identified for this module.
You do not need to pass all assessment components to pass the module.
Students can register for this module without taking any assessment.
Assessment group D3
| Weighting | Study time | Eligible for self-certification | |
|---|---|---|---|
| Assessed coursework | 10% | Yes (extension) | |
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Two sequential assessed workshop reports of 2-3 pages. Feedback of report 1 to be provided before 2nd report is submitted |
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| Assessed Work | 5% | Yes (extension) | |
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Part 1 of 2 pieces of assessed work to be completed in Term 1 |
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| Assessed Work | 5% | Yes (extension) | |
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Part 2 of 2 pieces of assessed work to be completed in Term 1 |
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| In-person Examination | 80% | No | |
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Feedback on assessment
Oral and written feedback on assessed work from module leaders. Cohort level examination
feedback provided via Moodle.
Pre-requisites
To take this module, you must have passed:
Courses
This module is Optional for:
- Year 4 of UCHA-F107 Undergraduate Master of Chemistry (with Intercalated Year)
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UCHA-F109 Undergraduate Master of Chemistry (with International Placement)
- Year 3 of F109 MChem Chemistry (with International Placement)
- Year 3 of F111 MChem Chemistry with Medicinal Chemistry (with International Placement)
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UCHA-4M Undergraduate Master of Chemistry Variants
- Year 3 of F105 Chemistry
- Year 3 of F109 MChem Chemistry (with International Placement)
- Year 3 of F126 MChem Chemistry with Med Chem (with Prof Exp)
- Year 3 of F125 MChem Chemistry with Medicinal Chemistry
- Year 3 of F106 MChem Chemistry with Professional Experience
- Year 4 of UCHA-F127 Undergraduate Master of Chemistry with Medicinal Chemistry(with Intercalated Year)
This module is Option list A for:
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UCHA-4 Undergraduate Chemistry (with Intercalated Year) Variants
- Year 4 of F101 Chemistry (with Intercalated Year)
- Year 4 of F122 Chemistry with Medicinal Chemistry (with Intercalated Year)
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UCHA-3 Undergraduate Chemistry 3 Year Variants
- Year 3 of F100 Chemistry
- Year 3 of F121 Chemistry with Medicinal Chemistry
- Year 3 of UCHA-F110 Undergraduate Master of Chemistry (with Industrial Placement)
- Year 3 of UCHA-4M Undergraduate Master of Chemistry Variants