In this module, different advanced aspects of Physical Organic Chemistry (part A), Chemical Biology (part B), and Photo-Biochemistry (part C) will be discussed with an emphasis on underlying mechanisms.

Knowledge

• integrate previous knowledge of organic reactivity with new information, typically from kinetic studies, to solve or elucidate organic reaction mechanisms.

• discuss how organic reactions respond to changes in control parameters such as temperature, pressure and solvent composition.

• identify proteinogenic amino acids and common post-translational modifications.
• explain the chemistry behind the synthesis of peptides using the Fmoc protecting group strategy.
• 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.
• explain the outline of an SPR instrument and the physical principles on which it operates.
• describe the stabilizing effect of photo-switchable ligands on peptides.
• discuss previous knowledge of photo-chemistry in a biological context.
• describe labelling strategies of proteins with stable isotopes to enable analysis by magnetic resonance techniques.

Understanding

• decide which experimental techniques are most appropriate for solving problems in organic reaction mechanisms.

• analyse kinetic data using accepted methods to elucidate reaction mechanisms.

• understand how the techniques of physical organic chemistry can find application in solving problems in neighbouring disciplines, such as chemical biology and catalysis.
• devise chemical syntheses of peptides including modified residues and cyclisation.
• propose appropriate methodology for protein engineering challenges.
• devise experiments for probing biomolecular interactions using SPR.
• interpret sensorgram data to deduce equilibrium constants and make qualitative deductions about kinetics.
• understand how chemical, physical and biological techniques can be combined to address complex problems.
• understand how proteins and peptides can be modified for specific light-activatable applications.

This module will be delivered in 10 two-hour lectures, supplemented by 4 1-hour class tutorials, and consists of four distinct blocks, each covering a different aspect 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.

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

The module will be assessed by a combination of coursework (20%) and written examination (80%). Coursework will be broken down into 4 problem-based pieces of work (5% each).

Part A

Solvent isotope effects; determination and interpretation of activation parameters; activation enthalpy; group additivity and molecular mechanics for estimating heats of formation; activation entropy; dependence of entropy and free energy changes on standard states; activation volume; linear free-energy relationships; Brønsted plots; general and specific acid/base catalysis; substituent effects; solvent effects

Part B

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. Biomolecular Interactions; physical principals of surface plasmon resonance (SPR);SPR instrumentation; SPR methods for determining equilibrium constants and kinetics.

Part C

Natural and artificial light-responsive proteins and peptides; primary and secondary (photo)reactions and their mechanisms; applications and analysis including UV/Vis- and fluorescence spectroscopies; protein labelling and analysis; magnetic resonance (NMR and EPR); 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: optogenetics.

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