Enzymes in Organic Chemistry

Course manual 2025/2026

Course content

The course “Enzymes in Organic Chemistry” provides a detailed overview of the enzymatic methods currently applied in organic chemical synthesis, both at laboratory and industrial scales. It also offers fundamental knowledge on how enzymes can be engineered to meet the requirements for their use in chemical synthesis. New concepts related to enabling challenging chemical transformations triggered by light using enzymes are also covered (photobiocatalysis). In detail, the course begins with a review and expansion of the fundamental concepts of enzyme catalysis, including enzyme classification and general enzymatic mechanisms. Next, the main classes of enzymes employed in organic synthesis—such as hydrolases, oxidoreductases, transferases, and enzymes for C–C bond formation—are discussed. The related specific synthetic strategies (e.g., kinetic and dynamic kinetic resolution, deracemization, asymmetric synthesis) are introduced progressively and critically analyzed. Furthermore, another aim of the course is to bridge knowledge and concepts between biocatalysis, organic synthesis, and chemo-catalysis within the broad field of synthetic organic chemistry. These concepts are further developed through the introduction of biocatalytic retrosynthesis, which integrates enzyme-catalyzed reactions into traditional chemical retrosynthetic analysis. This is exemplified in a problem session on biocatalytic retrosynthesis, where these concepts are applied. Ad hoc lectures on artificial enzymes illustrate how biocatalysis can be merged with chemocatalysis, in certain cases, to catalyze reactions not known to occur in nature. Similarly, ad hoc lectures on photobiocatalysis demonstrate how the reactivity of radicals generated either by light irradiation of cofactors or reaction intermediates in the active site of the enzyme (direct photoexcitation) or by an exogenous photocatalyst (synergistic photobiocatalysis) can be controlled by enzyme scaffolds, enabling control over the regio- and stereoselectivity of the transformation. Finally, the course provides fundamental knowledge on strategies for enzyme engineering based on directed evolution and rational design.

Study Goals

One of the main goals of the M.Sc. programme in Molecular Sciences is to develop a solid understanding of the reactions and reactivity of organic compounds. In this context, nature catalyzes a vast array of chemical transformations leading to organic molecules of diverse structural complexity. Broadly, the course 'Enzymes in Organic Chemistry' aims to provide a critical overview of synthetic strategies that employ various classes of biocatalysts, as well as their combination with complementary chemical methodologies.

Study materials

Literature

• “Biotransformations in Organic Chemistry”, 6th edition (2011) or 7th edition (2018, latest), Author: Kurt Faber, Publisher: Springer.

Other

• The content is complemented by additional study material that will be available in Canvas. Please, check and download Canvas material.

Objectives

• To classify enzyme families based on type of reaction, substrate converted, cosubstrate and cofactor involved, eventually formed coproduct.
• To explain and sketch the mechanism of selected enzymatic reactions.
• To describe and apply the fundamental definitions in enzyme catalysis and asymmetric synthesis (e.g. activity units, selectivity, turnover, enzymatic kinetic constants, enantiomeric/diastereomeric excess).
• To distinguish among different biocatalytic strategies in organic synthesis and provide examples on those.
• To memorise, summarize, apply, compare and combine the different classes of enzymes in organic synthesis.
• To sketch biocatalytic reactions and pathways for the synthesis of important family of compounds.
• To conceive a retrosynthetic plan for the synthesis of relatively simple organic molecules in which, at least, an enzymatic step is incorporated (i.e., affording an advantage such as shortening the length of the synthesis and/or increasing selectivity and/or reducing generation of waste).
• To assess pros and cons when comparing a biocatalytic reactions with a chemocatalytic or non-catalyzed reaction for a given chemical transformation.
• To illustrate principles and methods in enzyme engineering and analyse pros and cons for each method.
• To describe the basic principles behind tandem and cascade reactions and relate them to major biosynthesis routes.
• To classify multi-step biocatalytic processes (sequential, concurrent, parallel, orthogonal, etc.) and apply them through examples in organic synthesis.
• To define the fundamental terminology in molecular biology and summarize the steps for the preparation of an enzyme in the lab.
• To illustrate principles and methods for the generation of artificial enzymes and related them with concepts of organometallic- and organo-catalysis.
• To illustrate the principles and methods involved in combining enzymes with light, and to analyze their advantages and limitations compared to non-enzymatic methods
• To distinguish among and sketch the different types of biophotocatalytic processes

Teaching methods

• Lecture
• Self-study
• problem solving sessions

See the objectives above. The ILOs (intended Learning Objectives) will be pursued via the Hoorcollege for what concerns Understanding, Remembering and Analyzing, via Problem solving sessions for what concerns Analyzing, Applying and Evaluating, and via home exercises that will be upload in Canvas for what concerns Analyzing, Applying, Evaluating and Creating.

Learning activities

Attendance

This programme does not have requirements concerning attendance (TER part B).

Assessment

Inspection of assessed work

During the lectures and via communication in Canvas.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• dr. Francesco Mutti

Staff

• I. Drienovska PhD
• dr. V. Tseliou