2022 Organic and Bioorganic Chemistry

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Academic unit or major
Graduate major in Life Science and Technology
Yuasa Hideya  Mihara Hisakazu  Seio Kohji  Ohkubo Akihiro  Tsutsumi Hiroshi  Okada Satoshi 
Class Format
Lecture    (Livestream)
Media-enhanced courses
Day/Period(Room No.)
Tue3-4()  Fri3-4()  
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Course description and aims

[Intermediate-to-advanced Level] In order to understand life phenomena in atomic and molecular levels, a deep knowledge about organic chemistry is indispensable. On the other hand, some graduate students might not have gotten enough education on organic chemistry and yet may face the necessity for grasping their study subjects in atomic level. This organic chemistry course aims to give the fundamentals for "the ability to see the world in atomic and molecular levels" to all the students from the beginners to intermediate students by covering from a high school chemistry to advanced organic chemistry.

Student learning outcomes

In the first six lectures, students will focus on the selected topics in undergraduate organic chemistry, thereby lay a foundation on organic chemistry. In the middle stage, where the conversions of functional groups are detailed, students will learn the fundamentals required for organic synthesis and ability to consider various reaction mechanisms at molecular and atomic levels. In the end, students will be able to thoroughly understand the synthetic pathways to organic compounds at molecular and atomic levels.


Organic reaction mechanism, Organic electron theory, Molecular orbital theory, Functional group conversion, Retro synthesis, , Synthesis of organic compounds

Competencies that will be developed

Specialist skills Intercultural skills Communication skills Critical thinking skills Practical and/or problem-solving skills

Class flow

Four professors are responsible for this course. The lecture will be held through Zoom. Each lecture will start with about 10 min summary of the previous lecture. At the end of each class, the points will be briefed. All the classes are held in English.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Basic organic chemistry and glossary of chemical terms By going over the introductory organic chemistry taught in high school and university, you will be able to explain the octet rule.
Class 2 Nucleophilic substitution reactions You will be able to explain SN1 and SN2 reactions.
Class 3 Elimination reactions You will be able to explain E1 and E2 reactions.
Class 4 Nucleophilic addition to carbonyl group You will be able to explain the reactivity of carbonyl group.
Class 5 Formation and reactions of enols and enolates You will be able to explain aldol reaction and Claisen reaction.
Class 6 Electrophilic addition to alkenes You will be able to explain epoxidation and hydration.
Class 7 Synthesis of organic compound You will be able to conduct retrosynthetic analysis for simple organic compounds.
Class 8 Chemistry of nucleic acids You will be able to explain structure and reactivity of nucleotides.
Class 9 Chemistry of nucleic acid synthesis You will be able to explain phosphoramidite chemistry.
Class 10 Chemistry of carboxylic acids and related compounds You will be able to explain dehydration condensation.
Class 11 Protecting group: Protection of amines and carboxylic acid in peptide syntheses You will be able to explain orthogonality of protecting groups.
Class 12 Chemistry of peptide synthesis You will be able to explain liquid-phase synthesis, solid-phase synthesis, and bioactive peptides.
Class 13 Chemical labeling of proteins You will be able to explain site-selective chemical modification.
Class 14 Protein labeling in live cells You will be able to explain bioorthogonal chemical reactions.

Out-of-Class Study Time (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.



Reference books, course materials, etc.

“ORGANIC CHEMISTRY AN INTERMEDIATE TEXT” second ed., Robert V. Hoffman, WILEY (2004).
Essential graduate courses for bioscience and bioengineering - organic chemistry, H. Yuasa, ed, TokyoTech Press (2011).
Advanced Organic Chemistry, Fifth Edision, Part B: Reactions and Synthesis, F.A. Carey and R. J. Sundberg, Springer (2007). 

Assessment criteria and methods

The home works assigned by each professor (100%).

Related courses

  • LST.A202 : Organic Chemistry I (alkanes and haloalkanes)
  • LST.A207 : Organic Chemistry II (alcohols and alkenes)
  • LST.A212 : Organic Chemistry III (benzene and ketones)
  • LST.A217 : Organic Chemistry IV (carbonyl compounds and amines)
  • LST.A333 : Bioorganic Chemistry

Prerequisites (i.e., required knowledge, skills, courses, etc.)

Knowledge on undergraduate-level organic chemistry

Contact information (e-mail and phone)    Notice : Please replace from "[at]" to "@"(half-width character).


Office hours

All the questions must be through e-mail.

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