2025 (Current Year) Faculty Courses School of Science Department of Chemistry Graduate major in Chemistry
Advanced Bioorganic Chemistry
- Academic unit or major
- Graduate major in Chemistry
- Instructor(s)
- Atsushi Minami
- Class Format
- Lecture
- Media-enhanced courses
- -
- Day of week/Period
(Classrooms) - Class
- -
- Course Code
- CHM.D431
- Number of credits
- 200
- Course offered
- 2025
- Offered quarter
- 3Q
- Syllabus updated
- Mar 19, 2025
- Language
- English
Syllabus
Course overview and goals
The student will learn how microorganisms synthesize biologically active natural products. Specifically, the student will learn the reaction mechanism catalyzed by enzymes, especially focused on key skeletal construction enzymes and modification enzymes. The student will also learn the advanced technologies, especially AI-based structural prediction of the enzymes involved in the biosynthetic event.
Course description and aims
The aim of the course is that the student will understand and consider the how microorganisms synthesize biologically active natural products.
Keywords
biologically active natural products, enzyme catalysis, biosynthesis, chemical biology
Competencies
- Specialist skills
- Intercultural skills
- Communication skills
- Critical thinking skills
- Practical and/or problem-solving skills
Class flow
Lectures
Course schedule/Objectives
| Course schedule | Objectives | |
|---|---|---|
| Class 1 | Introduction to bioorganic chemistry. | Overview of bioorganic chemistry |
| Class 2 | Peptide and protein structure | Understanding of peptide and protein structure |
| Class 3 | 3D-structure prediction of proteins: A practical approach | Learning how to predict protein structure |
| Class 4 | Functional prediction of proteins: A practical approach | Learning how to predict the function of proteins |
| Class 5 | Skeletal construction enzymes: Overview of polyketide synthase (PKS) | Understanding of reaction mechanism catalyzed by polyketide synthases (PKSs) |
| Class 6 | Multimodular type I polyketide synthases: C-C bond formation | Understanding of mechanism of the C-C bond formation catalyzed by type I multimodular PKSs |
| Class 7 | Multimodular type I polyketide synthases: Modification reactions | Understanding of mechanism of the modification reactions catalyzed by type I multimodular PKSs |
| Class 8 | Type II polyketide synthase | Understanding of reaction mechanism catalyzed by type II PKSs |
| Class 9 | Type III polyketide synthase | Understanding of reaction mechanism catalyzed by type III PKSs |
| Class 10 | Terpene synthase: Cyclization mechanism | Understanding of cyclization mechanism catalyzed by terpene synthases |
| Class 11 | Non-ribosomal peptide synthetase: Peptide bond formation | Understanding of peptide bond formation catalyzed by non-ribosomal peptide synthetases |
| Class 12 | Cytochrome P450s: Oxidative modifications | Understanding of oxidative modifications catalyzed by cytochrome P450s |
| Class 13 | Flavin dependent enzymes: Oxidative modifications | Understanding of oxidative modifications catalyzed by flavin dependent enzymes |
| Class 14 | Glycosyltransferases: Glycosylation | Understanding of glycosylation catalyzed by glycosyltransferases |
Study advice (preparation and review)
To enhance effective learning, students are encouraged to spend approximately 100 minutes preparing for class and another 100 minutes reviewing class content afterwards (including assignments) for each class.
They should do so by referring to textbooks and other course material.
Textbook(s)
None
Reference books, course materials, etc.
”Medicinal Natural Products: A Biosynthteic Approach” (Wiley)
related pdfs would be distributed.
Please bring personal PC in the second, third, and fourth lectures. Also, please be prepared to access the campus LAN.
Evaluation methods and criteria
Exercise problems including homework in each class (40%) and a report (60%)
Related courses
- CHM.D334 ： Natural Product Chemistry
- CHM.D401 ： Basic Concepts of Organic Chemistry
Prerequisites
An understanding of the fundamentals of organic chemistry is required for this course.