2017 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  Fuse Shinichiro  Tsutsumi Hiroshi 
Course component(s)
Mode of instruction
Day/Period(Room No.)
Tue3-4(J221,S222)  Fri3-4(J221,S222)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
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Course description and aims

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 have not 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 four 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 natural products and pharmaceutical drugs at molecular and atomic levels.


Organic reaction mechanism, Organic electron theory, Molecular orbital theory, Functional group conversion, Retro synthesis, Natural product synthesis, Synthesis of medicinal drugs

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. Each lecture will start with about 10 min summary of the previous lecture. At the end of each class, the points will be briefed. Handouts will be given in each class.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Structure of organic compounds Introductory organic chemistry taught in high school and university, Octet rule
Class 2 Reactivity of organic compounds Acids, bases, polarizability
Class 3 Functional groups and their properties Electron withdrawing, resonance
Class 4 Organic reaction mechanisms Drawing "arrows" to indicate electron shifts
Class 5 Functional group conversion 1: derivatization to leaving groups Nucleophilic addition-elimination reaction
Class 6 Functional group conversion 2: nucleophilic substitution Nucleophilicity, leaving ability, solvent effect
Class 7 Functional group conversion 3: addition reaction, oxidation-reduction Multiple bonds
Class 8 Synthesis of natural products Retrosynthetic analysis, C-C bond formations
Class 9 Synthesis of medical drugs Costs, Toxicity, Bioactivity
Class 10 Chemistry of nucleic acids Phosphoric acids, hetero cyclic compounds
Class 11 Protecting group 1: Protection of alcohols and amines in nucleic acid syntheses Ethers, esters, amides
Class 12 Synthesis of natural and artificial nucleic acids DNA, RNA, Antisense oligonucleotides, aptamers
Class 13 Chemistry of carboxylic acids and related compounds Dehydration condensation
Class 14 Protecting group 2: Protection of amines and carboxylic acid in peptide syntheses Orthogonality
Class 15 Synthesis of bioactive peptides Hormones, medicinal drugs



Reference books, course materials, etc.

Essential graduate courses for bioscience and bioengineering - organic chemistry, H. Yuasa, ed, TokyoTech Press (2011).
Organic Chemistry: Structure, Mechanism, and Synthesis, R.J. Ouellette and J. D. Rawn, Elsevier (2014) 
Advanced Organic Chemistry, Fifth Edision, Part B: Reactions and Synthesis, F.A. Carey and R. J. Sundberg, Springer (2007). 

Assessment criteria and methods

Small tests given in the classes (20%). Achievement is evaluated by a term-end examination (80%).

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.)


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