Introductory description

Living organisms are continually degrading and synthesising organic compounds. To effect the conversion of simple organic substrates into the complex polymers of the cell (and vice versa) requires the concerted use of a wide range of enzymes with many different functions. Students will become familiar with the basic methods of studying enzymes in order to understand the mechanisms whereby enzymes are able to catalyse reactions, and to how individual reactions are controlled and integrated into the metabolic pathways of the cell.

Module aims

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

Introduction to enzyme catalysis and the concept of enzyme active site.
Substrate binding via non-covalent interactions.
Energetics and kinetics of enzyme catalysis.
Michaelis-Menten kinetics for enzyme-catalysed reactions.
Importance of transition state stabilisation.
Proximity effects in intramolecular and enzyme-catalysed reactions.
Types of catalysis observed in enzyme-catalysed reactions.
Acid-base catalysis (triose phosphate isomerase, ketosteroid isomerase).
Covalent catalysis (haloalkane dehalogenase, acetoacetate decarboxylase).
Strain in enzyme catalysis (carboxypeptidase A, lysozyme).
Stereospecificity – prochiral selectivity.
Mechanisms of Serine proteases, Cysteine proteases, Metalloproteases and Aspartyl proteases
Phosphoryl transfer and NAD-dependent dehydrogenases
General principles, examples and design of enzyme assays and methods for purification of enzymes.
Identification of key residues in enzymes
Rapid reaction methods and the determination of enzyme reaction rate parameters.
Regulation of enzyme activity in a wider biological context including discussion of enzymes in membranes

Learning outcomes

By the end of the module, students should be able to:

• understand how conversion of simple organic substrates into the complex polymers of the cell (and vice versa) requires the concerted use of a wide range of enzymes with many different functions
• understand research tools and techniques used to measure enzyme kinetics and investigate enzyme mechanisms
• understand how enzymes catalyse reactions
• understand how individual reactions are controlled and integrated into the metabolic pathways of the cell

Indicative reading list

Berg, J., Tymoczko, J. and Stryer, L. Biochemistry, 7th edn. (W. H. Freeman, 2012).

Fersht, A. Enzyme Structure and Mechanism, 2nd edn. (W. H. Freeman, 1984).

Bugg, T. D. H. Introduction to Enzyme and Coenzyme Chemistry, 2nd edn.
(Wiley-VCH, 2004).

Subject specific skills

Understand how to assay enzymes and the features of enzyme catalysis.
Understand the mechanism of action of proteases and their role in the body.
Understand the mechanism of phosphoryl transfer
Understand the functioning of dehydrogenases
Understand the role of key residues involved in protein function and how this information can inform protein engineering.

Transferable skills

Adult learning, self directed learning, team based learning and quantitative skills.