Module

Biophysical Chemistry

Description - summary of the module content

Module description

Designed to bring you the basic toolkit of any biophysical chemist, this module provides: a concise derivation of the thermodynamic states and the associated laws of matter; a mathematical generation and chemical explanation of observation experimental rate laws; and examination of the main forms of spectroscopy available, including application.

This module is therefore mandatory for all Biological & Medicinal Chemistry students and should provide a foundation for future study/research in the sphere of biophysical chemistry. The module is also optional for students on the Biochemistry programme.

This module will cover three fundamental areas of biophysical chemistry:

• Kinetics: If thermodynamics is 'how far' a reaction goes, then kinetics is not just concerned with 'how fast' it takes to get there but also by 'which method.' Observation of reaction extent as a function of time allows scientists to discern more about the mechanism of a reaction.
• Thermodynamics: The study and rationalisation of energy and all its forms including its flow (heat) and utility (work). Rationalisation of any reaction in terms of its benefits but also its feasibility.
• Spectroscopy: Often it is difficult to distinguish reagents from products or by-products, particularly if all particles are in the same phase or (even more challenging) of the same or similar molecular mass. Spectroscopy helps us reach a solution.

Pre-requisites: An A-level (or equivalent) in Chemistry and GCSE (or equivalent) in Mathematics.

Module aims - intentions of the module

This module aims to introduce you to the quantitative description of rates of change of chemical/biological systems both thermodynamically and kinetically, and to introduce the basics of spectroscopy for molecular analysis.

Graduate attributes. Students are expected to develop the following skills:
• Data handling skills – demonstrated use of appropriate laboratory equipment fundamental for measurements in chemistry, and the ability to interpret and analyse resulting datasets
• Application of knowledge – being able to understand core aspects of inorganic chemistry and related mathematical concepts and apply these to solve problems and explain experimental observations.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

• 1. Describe quantitatively functions, limits and rates of change to calculate reaction enthalpies, internal energy changes, equilibrium constants and related thermodynamic parameters for chemical reactions
• 2. Interpret experimental data for reaction rates, including those catalysed by enzymes
• 3. Explain and apply the basic principles of spectroscopy in molecular and structural analysis
• 4. Understand the quantitative description of physical chemistry processes

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

• 5. Describe the basic foundation of physical chemistry
• 6. Identify and interpret trends in data in a sub-discipline of the biological and chemical sciences
• 7. Solve problems and apply basic concepts in a sub-discipline of the biological and chemical sciences
• 8. Describe and begin to evaluate aspects of the biological and chemical sciences with reference to textbooks and other forms of information retrieval
• 9. With some guidance, deploy established techniques of quantitative data analysis within the biological and chemical sciences

ILO: Personal and key skills

On successfully completing the module you will be able to...

• 10. Demonstrate confidence in using mathematical methods in problem solving
• 11. Demonstrate skills in estimation
• 12. With some guidance, study autonomously
• 13. With some guidance, select and properly manage information drawn from books

Syllabus plan

Syllabus plan

Whilst the module’s precise content may vary from year to year, it is envisaged that the syllabus will cover some or all of the following topics:

Thermodynamics

• The perfect gas law and definitions of temperature from a mechanical and historical perspective.
• Internal energy, enthalpy, constant temperature and pressure system classifications and state functions.
• Heat and work as path functions and their relationship with the first law.
• The use of calorimetry and Hess’s law to calculate the standard states of various state functions.
• Mechanical and statistical definitions of entropy and the second and third law of thermodynamics.
• Helmholtz and Gibbs free energies, equilibrium constants and their relationship.

Kinetics

• Reaction rates and their relationship to the experimentally determined rate law, reaction coordinate and intermediates.
• Methods for determining the experimental rate law including the method of initial rates, half-life, integration and isolation.
• Single-substrate enzyme catalysis and associated Michaelis-Menten model including extreme scenarios of activation vs. diffusion control and how to experimentally determine using the Lineweaver-Burk plot.

Spectroscopy

• The electromagnetic spectrum and its general properties including a quantum consideration.
• Diffraction of X-rays and powder structure analysis.
• Absorption and emission of visible and ultraviolet light and luminescence.
• Vibration of infrared radiation and associated spectroscopies.

Learning and teaching

Learning activities and teaching methods (given in hours of study time)

Details of learning activities and teaching methods

Assessment

Formative assessment

Summative assessment (% of credit)

Details of summative assessment

Re-assessment

Details of re-assessment (where required by referral or deferral)

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons judged acceptable by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. If you are deferred for both practical-based reports, you will be required to submit a single lab report based on videos, notes and model data provided by the module convenor. The mark given for a re-assessment taken as a result of deferral will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral – if you have failed the module overall (i.e. a final overall module mark of less than 40%) you will be required to sit a further examination. The mark given for a re-assessment taken as a result of referral will count for 100% of the final mark and will be capped at 40%.

Resources

Indicative learning resources - Basic reading

• N. C. Price, Principles and problems in physical chemistry for biochemists (2001) Oxford
• G. J. Price, Thermodynamics of chemical processes (1998) Oxford
• E. B. Smith, Basic chemical thermodynamics (1990) Oxford
• M. J. Pilling & P. W. Seakins, Reaction kinetics (1995) Oxford
• J. M. Brown, Molecular spectroscopy (1998) Oxford
• S. Duckett & B. C. Gilbert, Foundations of spectroscopy (2000) Oxford

Indicative learning resources - Web based and electronic resources

• ELE page: http://vle.exeter.ac.uk/course/view.php?id=6583
• A list of books, along with an up-to-date account of those licenced for electronic access, may be found here

Module has an active ELE page

Key words search

Kinetics, thermodynamics, biophysical chemistry, enzyme reactions, infra-red spectroscopy, UV-visible spectroscopy, NMR spectroscopy