Bio Organic Chemistry

Course manual 2020/2021

Course content

The course Bio-Organic Chemistry provides a detailed overview on the available enzymatic methods (i.e., biocatalysis) that are currently applied in organic chemical synthesis, both in laboratory as well as industrial scale settings. Fundamental concepts of enzyme catalysis such as enzyme classification and general enzymatic mechanisms are reviewed and expanded at the beginning of the course. Then, 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 also gradually introduced 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 bio-organic chemistry. For instance, that is exemplified in the lectures on cascade and tandem reactions in which biocatalytic reactions are combined in one-pot with other chemical transformations—including multi-component reactions—that are of utmost importance for the synthesis of high value chemicals such as pharmaceuticals, libraries of drug candidates, etc. These concepts are further extended by providing an introduction to biocatalytic retrosynthesis, which aims at the implementation of enzyme-catalyzed reactions into traditional chemical retrosynthetic analysis. An ad-hoc lecture on artificial enzymes exemplifies also how biocatalysis can be merged to chemocatalysis, in certain cases, in order to catalyze reactions which are not known to occur in Nature. Finally, the course also provides fundamental knowledge on strategies for enzyme engineering based on directed evolution and rational design.

Study materials

Literature

• The recommended book that covers most of the topics of the course is:

  “Biotransformations in Organic Chemistry”, 6th edition, Kurt Faber, Springer, 2011.

   

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

   

  For those students interested in extending further their knowledge on biosynthesis of natural products:

  “Medicinal Natural Products: A Biosynthetic Approach”, 3rd Edition, Paul M. Dewick, John Wiley & Sons, Ltd, 2009

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 in enzyme engineering and analyze pros and cons for each method

Teaching methods

• Lecture
• Working independently on e.g. a project or thesis
• Self-study

The lectures will provide a critical overview on synthetic strategies that utilize the available classes of biocatalysts and combinations thereof with complementary methodologies. Through presentation of content, direct interaction with students and active problem session, all of the cognitive levels will be trained. In addition, home assignments will be given to the students and solutions will be discussed during the lectures. The execution of the home assignments will imply active search of the scientific literature, organization and selection of the information, critical thinking and final elaboration of original solutions. Knowledge, Comprehension, Analysis, Synthesis and Evaluation skills will be trained.

Learning activities

Attendance

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

Assessment

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

Timetable

The schedule for this course is published on DataNose.

Contact information

Coordinator

• dr. Francesco Mutti

Staff

Staff