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2024　Functional Chemistry of Biomolecules

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Academic unit or major
Graduate major in Life Science and Technology
Instructor(s)
Yuasa Hideya  Seio Kohji  Ohkubo Akihiro  Tsutsumi Hiroshi  Okada Satoshi  Masaki Yoshiaki 
Class Format
Lecture    (Livestream)
Media-enhanced courses
Day/Period(Room No.)
Mon3-4()  Thr3-4()  
Group
-
Course number
LST.A423
Credits
2
Academic year
2024
Offered quarter
2Q
Syllabus updated
2024/3/14
Lecture notes updated
-
Language used
English
Access Index

Course description and aims

[Intermediate-to-advanced Level]
Functional biomolecules, in which chemical modifications are introduced into nucleic acids, sugars, peptides and proteins, are extremely useful for understanding and controlling biological phenomena at the molecular and atomic level. This course provides a basis for understanding and controlling biological phenomena at the molecular and atomic level by covering a wide range of topics from basic knowledge of the chemical structure and synthesis of biomolecules to advanced applications of functional biomolecules.

Student learning outcomes

In the first three lectures, students learn and acquire basic knowledge of the organic chemistry required for the chemical synthesis and chemical modification of biomolecules. Subsequently, students learn the basic knowledge of the chemical structures of nucleic acids, sugars, peptides and proteins, and then learn in detail how to introduce chemical modifications to them. Furthermore, students will develop the ability to design molecules applicable in medicine and engineering, and to apply optical control of them, as well as improving their understanding of life phenomena at the molecular and atomic level.

Keywords

Biomolecules, Nucleic acids, Sugars, Peptides, Proteins, Photochemistry, Synthetic organic chemistry.

Competencies that will be developed

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

Class flow

Biomolecules, Nucleic acids, Sugars, Peptides, Proteins, Photochemistry, Synthetic organic chemistry.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Organic chemistry for introduction of functional groups to biomolecules I You will be able to understand and explain the chemical reactions of carbonyl compounds, and nucleophilic addition reactions.
Class 2 Organic chemistry for introduction of functional groups to biomolecules II You will be able to understand and explain electrophilic addition reactions, and aromatic substitution reactions.
Class 3 Organic chemical reactions on functional nucleic acids You will be able to understand and explain DNA template synthesis, and the chemical modification of Aptamer by the SELEX method.
Class 4 Nucleic Acid Structure Understand and be able to explain the conformation of nucleosides and nucleic acids.
Class 5 Properties of modified nucleic acids Understand and be able to explain the properties of chemically modified nucleic acids.
Class 6 Application of modified nucleic acids Understand and be able to explain the application of chemically modified nucleic acids.
Class 7 Under what circumstances can light and matter interact? Students will be able to consider the conditions under which light and matter can resonate (Laporte rule, heavy atom effect, El-Sayed rule, hyperfine coupling, etc.).
Class 8 Ways to obtain chemical energy from light and make it function Students will be able to understand the transient phenomena in the interaction between light and matter, such as triplet-triplet annihilation and the magnetic field effect of radical pairs.
Class 9 Points to note when using light for life By learning about the photosensitization mechanism and the deep tissue penetration of light, students will be able to think deeply about the biological applications of light.
Class 10 Protection of amino acid and chemical synthesis of peptide You will be able to understand and explain the chemistry of protection groups for amino acids and the strategy of chemical synthesis of peptides.
Class 11 Bioactive peptides and peptide medicines You will be able to understand and explain chemical synthesis and structure-activity relationships of peptide hormones, antimicrobial peptides, cyclic peptide natural products and their derivatives.
Class 12 Peptide libraries for discovery of peptide medicines You will be able to understand and explain methods for the construction of peptide libraries and discovery of peptide medicines using peptide libraries.
Class 13 Chemical labeling of proteins You will be able to explain site-selective chemical modification of proteins.
Class 14 Protein labeling in live cells You will be able to explain protein modification in live cells by using 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.

Textbook(s)

N/A

Reference books, course materials, etc.

Distributed by each lecturer using T2SCHOLA

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

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