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 kinetic, chemical explain of observation experimental rate laws and examination of the main forms of spectroscopy available including application.

This module is therefore mandatory for all biochemistry and biomedicinal chemistry students and should provide a foundation for future study/research in the sphere of biophysical chemistry.

Lectures are in three essential areas of biophysical chemistry:

• 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. 
• 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.
• 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.

Practical sessions provide you with the equipment and methodology to derive various physical properties of matter.

To take this module you will need an A Level (or equivalent) in Chemistry and GCSE Mathematics. Those of you with concerns about mathematics will have the opportunity to develop further in the provided tutorials.

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.

We will consider states of matter and their subsequent transformations from a thermodynamic and kinetic perspective and how to explain/predict such phenomena. You will learn to exploit the electromagnetic spectrum through its various interactions with matter to further identify a range of species.

We will help you develop the necessary mathematical skills for a quantitative description of matter.

Graduate attributes. As part of this module you are expected to develop the following skills:

• Laboratory and data handling skills – use of appropriate laboratory equipment fundamental for measurements in physical chemistry, and the ability to interpret and analyse resulting datasets.
• Application of knowledge – being able to understand core aspects of physical chemistry and the associated mathematical concepts and, being able to solve problems.
• People skills – working with your peers during laboratory sessions.

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 of 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 Michael-Menten model including extremes 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.
• Polarisation of light and circular dichroism.
• Diffraction of X-rays and powder structure analysis.
• Absorption and emission of visible and ultraviolet light and luminescence.
• Vibration and rotation of infrared and microwave 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. The practicals are not deferrable because of their practical nature. 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

• Atkins P.W. and de Paula J. Physical Chemistry for the Life Sciences. OUP, ISBN:0-7167-8628-1 (2006)
• J. Fisher and J. R. P. Arnold, Chemistry for Biologists (Instant Notes), BIOS Scientific
• E. B. Smith, Basic Chemical Thermodynamics, Imperial College Press
• M.J. Pilling, P.W. Seakins, Reaction Kinetics - An Oxford Chemistry Primer, Oxford University Press (1995)
• Eds: J. C. Lindon, G. E. Tranter, D. W. Koppenaal, Encyclopedia of Spectroscopy and Spectrometry, Elsevier (2017)

Indicative learning resources - Web based and electronic resources

• ELE page: http://vle.exeter.ac.uk/course/view.php?id=6583 (contains ILOs and/or self-assessment questions for each lecture topic along with the lecture notes and recordings)

Module has an active ELE page

Key words search

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