CH3405: Advanced Techniques in Organic and Biological Chemistry

School Cardiff School of Chemistry
Department Code CHEMY
Module Code CH3405
External Subject Code 100422
Number of Credits 10
Level L7
Language of Delivery English
Module Leader Dr James Redman
Semester Autumn Semester
Academic Year 2015/6

Outline Description of Module

In this module, the application of physical techniques and artificially modified biomolecules to problems in structure and mechanism in organic and biological chemistry research will be discussed. Students will appreciate what information can be gained from each technique and learn how to plan experiments and interpret the resulting data for probing structure, dynamics and reactivity.

On completion of the module a student should be able to

  • decide which experimental techniques are most appropriate for solving problems in organic and biological chemistry;


  • understand how chemical, physical and biological techniques can be combined to address complex problems;
  • identify proteinogenic amino acids and common post-translational modifications;
  • explain the chemistry behind the synthesis of peptides;
  • devise chemical syntheses of peptides including modified residues and cyclisation;
  • propose appropriate methodology for protein engineering challenges;
  • summarise the different computational and experimental approaches to engineering proteins;
  • explain the limitations of protein engineering methodologies;
  • describe the chemistry used for creating libraries of proteins;
  • explain the principles of phage display;
  • discuss previous knowledge of photo-chemistry in a biological context;
  • understand how proteins and peptides can be modified for specific light-activatable applications. understand how biophysical techniques are used to study interactions between biomacromolecules, and between small molecules and biomacromolecules;
  • decide which (bio)physical techniques are appropriate for the study of interactions.

 

How the module will be delivered

This module will be delivered in 10 two-hour lectures, supplemented by 3 1-hour class tutorials, covering different aspects of organic and biological chemistry. A series of lectures will introduce the methods that can be used to tackle problems in this area, analytical techniques involved and the theoretical background as well as any strengths or weaknesses associated with them. This will be further broadened and deepened in the class tutorials.

Skills that will be practised and developed

Solution of problems by application of knowledge from different areas of chemistry, physics and biology.

How the module will be assessed

The module will be assessed by a combination of coursework (20%) and written examination (80%). Coursework will be broken down into 3 problem-based pieces of work (6.67% each).

Assessment Breakdown

Type % Title Duration(hrs)
Exam - Autumn Semester 80 Advanced Techniques In Organic And Biological Chemistry 2
Written Assessment 20 Written Assignments N/A

Syllabus content

Principles of UV/Vis, fluorescence, FRET, and circular dichroism spectroscopies as used in biophysical studies. Solution calorimetric techniques, including DSC and ITC.

Surface plasmon resonance (SPR); SPR instrumentation; SPR methods for determining equilibrium constants and kinetics.

Applications of these techniques to the study of biomolecular structure and interactions, including data analysis and estimation of error margins.

Chemical synthesis of peptides; introduction to the need for, and strategies for production of modified peptides (labels, post-translational modifications); types of peptide modification, PTMs, unnatural amino acids, dyes/fluorophores; solid phase synthesis by the Fmoc method; orthogonal protecting groups (e.g. alloc, Dmab, ivDDE, Mtt) strategies for selective peptide modification; cyclic peptide synthesis, with a case study.

Introduction to protein engineering; rationale for engineering proteins and introduction to protein engineering strategies; de novo design, rational computational design; mutagenesis, protein libraries; screening for function – fluorescence, FACS; selection for function – affinity chromatography, phage display.

Light-responsive molecules; combinations of different synthetic and analytical methods in a biochemical research project; applications of photo-active proteins as nano-switches for biological and medical problems. Modern mass spectrometry instruments and methods for study of biomolecules.

Essential Reading and Resource List

Relevant chapters from textbooks, primary literature and reviews will be indicated in the course, and partially supplied as hand-outs or on Learning Central.

Background Reading and Resource List

Peptide synthesis and applications, John Howl, Humana Press, ISBN 9781588293176.

Relevant chapters from textbooks, primary literature and reviews will be indicated in the course, and partially supplied as hand-outs or on Learning Central.


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