Biophysical Chemistry

Module titleBiophysical Chemistry
Module codeBIO1346
Academic year2020/1
Credits15
Module staff

Dr Sam Stevens (Convenor)

Duration: Term123
Duration: Weeks

11

Number students taking module (anticipated)

38

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.

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.

In addition, students will undertake a guided ‘at home’ practical with various common household items and conduct academic interviews relating to physical chemistry.

Pre-requisites: 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 scheduled lectures and interactive learning activities.

Module aims - intentions of the module

Scientists need to know 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.
  • People skills – working with your peers during home-based experimental sessions and learn how to interview academics.

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
  • 10. With some guidance, design a practical to test an hypothesis

ILO: Personal and key skills

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

  • 11. Demonstrate confidence in using mathematical methods in problem solving
  • 12. Demonstrate skills in estimation
  • 13. With some guidance, study autonomously
  • 14. With some guidance, select and properly manage information drawn from books
  • 15. Inquire and learn from professionals through a chaired interview scenario.

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:

Mathematics

  • Series
  • Complex Numbers
  • Population Distributions

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.
  • 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)

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad
401100

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled Learning and Teaching7Thermodynamics lectures (7 x 1 hour)
Scheduled Learning and Teaching7Kinetics lectures (7 x 1 hour)
Scheduled Learning and Teaching7Spectroscopy lectures (7 x 1 hour)
Scheduled Learning and Teaching1Revision lecture
Scheduled Learning and Teaching12Tutorials for reviewing practical work and for mathematics skills (4 x 3 hours)
Scheduled Learning and Teaching6Practical classes (2 x 3 hours)
Guided Independent Study14Reviewing past exam papers
Guided Independent Study47Reading recommended text
Guided Independent Study49Reading background to workshops and laboratory experiments

Assessment

Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Revision class at end of module2 hours1-9Oral

Summative assessment (% of credit)

CourseworkWritten examsPractical exams
40600

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Examination602 hours1-8, 11-12Written
Report on home-based practical202000 words1-13Written and oral
Essay based on academic interviews202000 words1-15Written and oral

Re-assessment

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

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
ExaminationExamination1-8, 11-12August Ref/Def
Report on home-based practicalReport on home-based practical1-13August Ref/Def
Essay based on academic interviewsEssay based on academic interviews1-15August Ref/Def

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 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

  • J. Fisher and J. R. P. Arnold, Chemistry for Biologists (Instant Notes), BIOS Scientific
  • 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

Module has an active ELE page

Key words search

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

Credit value15
Module ECTS

7.5

Module pre-requisites

None

Module co-requisites

None

NQF level (module)

4

Available as distance learning?

No

Origin date

01/12/2015

Last revision date

15/07/2020