Biophysical Chemistry


Unit code: CHEM40262
Credit Rating: 10
Unit level: Level 4
Teaching period(s): Semester 2
Offered by School of Chemistry
Available as a free choice unit?: N

Requisites

None

Aims

The aim of this module is to understand the range of physical methods used to characterize the organization, properties and function of biological molecules. Biological systems are very complex, necessitating sophisticated methods to study them at the molecular level. Nonetheless, many of the concepts and analytical methods have their origins in the physical sciences. In this module you will learn about the structure and function relationships of biological macromolecules, and the range of physical methods used to characterise these. You will learn how multi-technique approaches are the rule rather than the exception in biophysical analysis.

 

Overview

Biological Systems and Fundamentals (Prof. P. Barran 4 lectures)

The main molecules, levels of organisation and processes of living organisms are examined. We will recap on the structure of biological macromolecules and how these assemble to functional entities within organisms. This section will equip you with knowledge of structure function relationships for proteins, Nucleic acids and lipids.

Chromatographic Methods and Capillary Electrophoresis (Dr N Lockyer – 3 lectures)

Separation and purification of biomolecules in the liquid phase by methods including affinity chromatography, electrophoresis and lab-on-a-chip.

Metabolomics (Prof R. Goodacre – 3 lectures)

The analysis of small molecules in biological systems can be very useful for the discovery of potential new biomarkers for disease, as well as for validating potential targets for drug therapy and following therapeutic intervention. Methods are described for their robust discovery.

Structural Proteomics (Prof PE Barran – 3 lectures)

Determining the structures of individual proteins and how they assemble into complexes may be carried out using mass spectometry. Bottom up proteomics will be briefly discussed as a means to contrast the use of mass spectrometry to directly probe intact functional protein assemblies.

X-ray Crystallography (Prof D. Leys – 3 lectures)

Knowing the precise 3D structure of biomolecules is essential for understanding their function. X-ray crystallography is the pre-eminent method for determining the 3D structure of biomolecules. This section covers crystal formation, diffraction theory, the phase problem, fitting, refinement and validation of structure.

Computer Simulation and Bioinformatics (Dr R Henchman, – 3 lectures)

The detailed mechanisms of how biomolecules work at the molecular level are difficult to probe experimentally. Computer simulations model and explain the behaviour of biomolecular systems at the molecular level of detail using the fundamental equations of classical and quantum mechanics. Bioinformatics seeks to achieve this in a data-driven computational approach based on algorithms to analyse databases of sequences, structure, and properties. 

Biophysical Case Studies (Multiple lecturers, 3 workshops 1 hour each)

How all these techniques are applied to research problems will be examined in three case studies using papers taken from the scientific literature. This makes clear the capabilities of each technique and how they be used synergistically to complement each other’s strengths.

This section of the course will be taught using a flipped approach where you will be expected to view content on Blackboard using screencasts and then attend workshops to analyse this content.

Teaching and learning methods

Lectures and screencasts supplemented by workshops. Lecturers are available after classes for meetings or at other times as arranged.

Learning outcomes

  •  Be familiar with the main biological macromolecules and principles of biological processes.
  •  Understand the main methods used to characterise biological systems. These include chromatography,  electrophoresis, metabolomics, mass spectrometry, x-ray crystallography, computer simulation and  bioinformatics.
  •  Examine how multiple methods are synergistically used to analyse complex biological systems. Know the  concepts behind metabolic profiling and metabolomics in general.
  •  See how analytical science plays an important role for generating reproducible metabolomics and  proteomic data.
  •  Be familiar with methods used to separate molecules on the basis of mass, size, shape, charge or  combination of these parameters.

 

Transferable skills and personal qualities

1. Problem solving and Analytical Skills - this course has an emphasis on interdisciplinary and on multi-technique approaches and the students will learn that modern science contains large elements of both.

2. Communication and Interpersonal Skills - the workshops and small lecture sizes will encourage student participation and will teach the students how to critique literature in front of their peers.

3. Numerical Skills - in particular the analysis of large 'omics datasets'

Assessment methods

  • Written exam - 100%

Recommended reading

  • Physical Chemistry for the Life Sciences by PW Atkins and J de Paula, 2011, 2nd Edition, Oxford University Press.
  • Physical Biology of the Cell by R. Phillips, J. Kondev, J. Theriot 2012, 2nd Edition, Taylor and Francis. 
  • http://www.chromacademy.com/
  • Biochemistry by J.M. Berg, J.L. Timozcko, L. Stryer, 2012, W. H. Freeman.
  • Molecular Biology of the Cell by B Alberts, A Johnson, J Lewis, M Raff, K Roberts, P Walter, 2008, 5th  Edition, Taylor and Francis.
  • Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis by G.G. Harrigan and R. Goodacre (Eds), 2003, Kluwer Academic Publishers.
  • Mass Spectrometry in Biophysics I. Kaltashov and S.A Eyles 2005, Wiley
  • Principles of Physical Biochemistry by KE van Holde, W Curtis Johnson and P Shing Ho, 2005, 2nd Edition, Prentice Hall.
  • Molecular Modelling and Simulation: An Interdisciplinary Guide, T Schlick, 2010, 2nd Ed., Springer
    ebook:  http://link.springer.com/book/10.1007/978-1-4419-6351-2/page/1

Feedback methods

Workshops are supported by online Blackboard quizzes worked answers. Revision week at the end of semester to answer questions and go over past exam papers.

Study hours

  • Assessment written exam - 2 hours
  • Lectures - 19 hours
  • Practical classes & workshops - 4.5 hours
  • Independent study hours - 74.5 hours

Teaching staff

Nicholas Lockyer - Unit coordinator

Royston Goodacre - Unit coordinator

Richard Henchman - Unit coordinator

David Leys - Unit coordinator

Perdita Barran - Unit coordinator

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