Biophysical Chemistry

CHEM40262 Biophysical Chemistry 10 Semester 2 Undergraduate Level 4 Perdita Barran Unit coordinator Department of Chemistry 1 FHEQ level (Framework for Higher Education Qualifications) ' Masters/Integrated Masters P4 ' European Credit Transfer & Accumulation System Rating : 5.0 Lectures and screencasts supplemented by workshops. Lecturers are available after classes for meetings or at other times as arranged.Biological Systems and Fundamentals (Prof. P. Barran 4 lectures)The main molecules, levels of organization 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 – 4 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 – 4 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 – 4 lectures)Determining the structures of individual proteins and how they assemble into complexes may be carried out using mass spectrometry. 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 – 4 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.Biophysical Case Studies (Multiple lecturers, 2 workshops 2 hours 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. Lectures and screencasts supplemented by workshops. Lecturers are available after classes for meetings or at other times as arranged.Biological Systems and Fundamentals (Prof. P. Barran 4 lectures)The main molecules, levels of organization 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 – 4 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 – 4 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 – 4 lectures)Determining the structures of individual proteins and how they assemble into complexes may be carried out using mass spectrometry. 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 – 4 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.Biophysical Case Studies (Multiple lecturers, 2 workshops 2 hours 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. 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. <ul> <li> Be familiar with the main biological macromolecules and principles of biological processes.</li> <li> Understand the main methods used to characterise biological systems. These include chromatography, electrophoresis, metabolomics, mass spectrometry, x-ray crystallography, computer simulation and bioinformatics.</li> <li> Examine how multiple methods are synergistically used to analyse complex biological systems. Know the concepts behind metabolic profiling and metabolomics in general.</li> <li> See how analytical science plays an important role for generating reproducible metabolomics and proteomic data.</li> <li> Be familiar with methods used to separate molecules on the basis of mass, size, shape, charge or combination of these parameters.</li></ul> 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' Lectures and screencasts supplemented by workshops. Lecturers are available after classes for meetings or at other times as arranged. 1 Written exam 100% 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.  N ·        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:  <a href="http://link.springer.com/book/10.1007/978-1-4419-6351-2/page/1" target="_blank">http://link.springer.com/book/10.1007/978-1-4419-6351-2/page/1</a> Assessment written exam 2 Lectures 19 Practical classes & workshops 4.5 0 74.5