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Module Code - Title:

PH6051 - ADVANCED BIOPHYSICAL CHARACTERISATION TECHNIQUES

Year Last Offered:

2025/6

Hours Per Week:

Lecture

2

Lab

0

Tutorial

1

Other

1

Private

6

Credits

6

Grading Type:

N

Prerequisite Modules:

Rationale and Purpose of the Module:

To develop a fundamental understanding of how modern biochemical and biophysical characterization techniques work. To understand the relationship between molecular structure and function of biological materials. To illustrate these concepts through discussion of their application to biological complexes.

Syllabus:

X-ray crystallography determinations of protein structure; Determining glycosylated and phosphorylated protein structures; Nuclear Magnetic Resonance methods to resolve protein structures; Small Angle X-ray Scattering methods; Cryo-electron microscopy (cryo-EM); Resolution of large multi-protein assemblies; Discussion of topics such as resolving biomolecular structures in biological fluids, proteolysis, ultrafast laser spectroscopy, and structural genomics; The special case of Intrinsically Disordered Proteins; Mapping assembly from protein monomers to oligomers to protofibrils to plaques; Determining nucleotide structures; Resolving nucleotide:protein and nucleotide:sugar complexes

Learning Outcomes:

Cognitive (Knowledge, Understanding, Application, Analysis, Evaluation, Synthesis)

On successful completion of this module, students will: 1) Be able to describe the structure and function of proteins in their native and modified states 2) Be able to recognise the 3D structures of biological materials from single molecules to tissue 3) Be able to explain how X-ray crystallography can resolve atomic scale structure of biomolecules 4) Understand how techniques such as spectroscopy and microscopy can resolve biomolecule structures in solution and surface-bound states 5) Be able to research and discuss topics in the current literature on biophysical characterization

Affective (Attitudes and Values)

On successful completion of this module, students will: 1) Appreciate the relative merits of the plethora of techniques available to resolve biomolecular structures 2) Justify usage of different techniques to understand biological structure-function relationships at the molecular through to tissue level

Psychomotor (Physical Skills)

On successful completion of this module, students will: Construct and analyse computer models of biological structures based on Xray/microscopy data

How the Module will be Taught and what will be the Learning Experiences of the Students:

How the Module will be Taught and what will be the Learning Experiences of the Students: The module will be taught from a theoretical perspective with online lectures and tutorial sessions. The theoretical content will support contemporaneous modules in biopharmaceuticals, predictive modelling tools and cell biology, and will thus form part of a stream within biology which lays an important foundation in biophysics and molecular biology. The tutorials will develop key skills in visualisation and analysis of biological complexes with extraction of biochemical and biophysical properties, which reinforce the lecture content. Computer-based practicals will be undertaken in building crystal models for examination of 3D structure. Research Findings Incorporated in to the Syllabus (If Relevant): Applications from research findings that are current will be used to re-enforce the importance of particular programmatic aspects. For example identification of particular proteins associated with neurodegeneration may be highlighted, with emphasis on comparing the techniques available for 3D structure analysis form high-resolution XRD of idealised structures coupled with indirect determination from NMR in solution through to cryo-EM which is emerging as a medium to high resolution tool to determine large biomolecule assemblies in their native states

Research Findings Incorporated in to the Syllabus (If Relevant):

Prime Texts:

Rupp, Bernhard (2010) Biomolecular crystallography : principles, practice, and application to structural biology , New York : Garland Science
Branden, Carl.; Tooze, John. (1999) Introduction to protein structure , New York : Garland Science

Other Relevant Texts:

Programme(s) in which this Module is Offered:

Semester(s) Module is Offered:

Autumn

Module Leader:

jennifer.cookman@ul.ie