Chemistry of Biological Processes (E)

CHEM31812 Chemistry of Biological Processes (E) 10 Semester 2 Undergraduate Level 3 Neil Dixon Unit coordinator Eriko Takano Unit coordinator 1 FHEQ level (Framework for Higher Education Qualifications) ' Last part of a Bachelors ' European Credit Transfer & Accumulation System Rating : 5.0 This course is primarily intended for Biochemistry students. To outline the basic principles of (bio)chemistry that will be relevant to an understanding of key biological structures and processes and to understand how it can be applied. Chemical principles review A brief recap of the key concepts that govern molecular structure (ie atomic bonding) and reactivity (ie nucleophile/electrophile; redox reactions; radical reactions).Chemistry underpinning complex biological processes: signalling An overview of various signalling processes is provided: Phosphorylation: kinases/phosphatases  Methylation: both of DNA and proteins, methylases and demethylases ADP-ribosylation: PARP and PARG enzymesChemistry underpinning complex biological processes: N2/CO2 fixation The challenges associated with activation of relatively stable and inert gases N2/CO2 will be presented, as well as Nature’s solutions.      CO2 fixation by distinct enzymes will be discussed, in the context of distinct CO2 fixation pathways (ie not exclusively photosynthetic)     N2 fixation will predominantly focus on the nitrogenase enzyme, and the use of Glu as a N-carrierEnzyme catalysis and engineering An understanding of the following major theoretical concepts: 1.    Theoretical models of enzyme kinetics, with a focus on the Michaelis-Menten / Briggs-Haldane approach 2.    Transition state theory and why the ‘Lock and Key’ hypothesis is flawed An understanding of the mechanisms used by enzymes to enhance reaction rates:  1.    Binding of substrate and/or transition state. Proximity & orientation; Electrostatic catalysis; Preferential binding of the transition state; Induced fit 2.    General acid/base catalysis  3.    Covalent (nucleophilic) catalysis  4.    Metal ion catalysis An understanding of structure activity relationships (SARs) An understanding of the use of protein engineering to investigate enzyme mechanism and substrate binding with the specific examples:  1.    Historically important studies on aminoacyl tRNA synthetase 2.    Chemical and engineering studies with triose phosphate isomerase An understanding of the general approaches to enzyme design: rational vs. directed/forced evolution An understanding of how transition state complementarity is exploited in the design of: 1.    Drugs/inhibitors 2.    Catalytic antibodies 3.    De novo-designed enzymesBiotechnology: Search for new antibiotics •    Application of biochemistry to biotechnology, examples in antibiotics discovery and development.Biotechnology: biofuel development •    Application of biochemistry to biotechnology, examples in biofuel developmentChemistry inspired by Nature     •    The de novo design of proteins with novel fold/functionalities as an example of the developing field of Nature inspired (bio)chemistry. This course is primarily intended for Biochemistry students. To outline the basic principles of (bio)chemistry that will be relevant to an understanding of key biological structures and processes and to understand how it can be applied. On successful completion of the course students should be able to: Describe:<ul> <li> Complex biochemical processes from a chemistry perspective: what are the challenges, what are the solutions used by Nature?</li></ul>Explain:<ul> <li> The application of biochemistry/biotechnology with respect to antibiotics, biofuels, and biocatalysis applications.</li></ul>Develop:<ul> <li> Communications skills: communicate complex information effectively and concisely using the appropriate chemical and biochemical terminology, and chemical structure drawings</li> <li> Problem-solving skills: apply the knowledge gained to deduce the likely properties of particular enzymes/enzyme active sites.</li></ul> <div><ul> <li>Communications skills: communicate complex information effectively and concisely with the understanding of biochemistry from a biologist’s point of view.</li> <li>Problem-solving skills: apply the knowledge gained from combining chemistry and biology for new (industrial) applications.</li></ul></div> Voet and Voet Biochemistry and selected publication provided during lectures. 1 Written exam 80% 9 Set exercise 20% <div>Feedback during the lectures and also using the online course review self-evaluation form.</div> CHEM21162 Chemistry of Biomolecules Pre-Requisite Compulsory BIOL31812 Pre & Co-requisites are CHEM21162None. It is however recommended that students taking this unit have an A grade in Chemistry at AS level as a minimum, CHEM21162 is also strongly recommended. N <div> <ul> <li> Agapakis, C.M., Designing synthetic biology</li> <li> Baltz 2006 J Ind Microbiol Biotech.</li> <li> Medema et al 2011 NRM.</li> <li> Poust S et al Curr Opin Biotechnol 2014.</li> <li> Voet and Voet Biochemistry Part III, Mechanisms of Enzyme Action (Chapters 13-15 in 4th Ed), Part IV, Metabolism (Chapters 17, 21, 22 in 4th Ed)</li> </ul></div>  Assessment written exam 2 Lectures 21 Tutorials 6 0 71