2022 Biomolecular Analysis

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Academic unit or major
Graduate major in Life Science and Technology
Osada Toshiya  Fujii Masaaki  Ishii Yoshitaka  Okada Satoshi  Nozawa Kayo  Kondo Toru 
Class Format
Lecture    (Livestream)
Media-enhanced courses
Day/Period(Room No.)
Mon3-4()  Thr3-4()  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
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Course description and aims

This course is organized into five parts.
The first part describes the vibrational spectroscopy. It includes quantum chemical description of molecular vibrations, normal modes, principle and setup of infrared spectroscopy and Raman scattering, and their examples of several important molecules such as benzenes. The vibrational relaxation will also be shown with examples.
The second part introduces nuclear magnetic resonance (NMR) spectroscopy.
The third part introduces the single-molecule spectroscopy (SMS), used for the spectroscopic analysis of molecular dynamics in biological systems.
The forth part describes basic principle of magnetic resonance imaging (MRI) and its application to molecular imaging.
The firth part of the course deals with an AFM (atomic force microscopy). The AFM has become a powerful tool to study biological samples not only for imaging at the molecular level but also for measuring their mechanical properties. The course begins with an overview of AFM and then goes to applications of AFM to the study of the biological materials.
The last part describesX-ray crystallography and cryo-electron microscopy has provided important insights into macromolecules such as drug-protein complexes and viruses. This lecture summarizes the outline of the principles and applications of these technologies.

Student learning outcomes

By the end of this course, students will be able to:
1) gain understanding of the basic principles of AFM.
2) learn the broad applications of AFM in biological fields
3) understand molecular vibrations and normal modes
4) understand the experimental techniques to measure the molecular vibrations and its applications
5) learn theory and applications of NMR spectroscopy
6) understand theory and application of MRI
7) understand basics and applications of SMS
8)Understanding the X-ray crystallographic and cryo-electron microscopic methods. Familialize with analyses of the three-dimensional structure and complex formation of biomolecules using the methods.


AFM, normal mode, molecular vibration, infrared and Raman spectroscopy, Laser spectroscopy, mass spectrometry, nuclear magnetic resonance, NMR, MRI, single-molecule spectroscopy, microspectroscopy

Competencies that will be developed

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

Class flow

The class starts with reviews of previous class. Towards the end of class, students are often given exercise problems related to the lecture given that day to solve. To prepare for the class, students should read the course schedule section and check what topics will be covered. Required learning should be completed outside the classroom for preparation and review purposes.
Classes are basically done in English, but if necessary we will provide supplementary explanation in Japanese.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Quantum chemical description of molecular vibrations and normal mode Understanding molecular vibration including normal mode
Class 2 Principle and spectra of infrared and Raman spectroscopy Understanding experimental principle and vibrational spectra
Class 3 NMR spectroscopy: (1) Introduction to NMR spectroscopy Understanding of basic theory and applications of NMR spectroscopy
Class 4 NMR spectroscopy: (2) Classical theory and 1D NMR Understanding of classical theory of NMR spectroscopy and 1D NMR
Class 5 NMR spectroscopy: (3) 2-3D NMR and applications to small molecules, proteins, and imaging Understanding of 2-3D NMR and advanced
Class 6 Single-molecule spectroscopy: (1) Microspectroscopy at the single-molecule level Understanding of microspectroscopy at the single-molecule level
Class 7 Single-molecule spectroscopy: (2) Spectroscopic analysis of fluctuations Understanding of spectroscopic measurement and analysis of fluctuations
Class 8 Single-molecule spectroscopy: (3) Applications to biological systems Understanding of applications of single-molecule spectroscopy
Class 9 Magnetic resonance imaging (MRI): (1) Introduction Understanding basic principle of MRI
Class 10 Magnetic resonance imaging (MRI): (2) Contrast agents and molecular imaging Understanding application of MRI to molecular imaging
Class 11 Introduction to atomic force microscopy(AFM) AFM instrumentation, Surface forces, Contact mechanics
Class 12 AFM based single-molecule force spectroscopy Explain the principle and the application of AFM to single molecule.
Class 13 X-ray crystallography and cryo-electron microscopy: (1) Introduction and basic theory Understanding of the principle of diffraction and imaging
Class 14 X-ray crystallography and cryo-electron microscopy: (2) Application to biomolecules Understanding of applications to macromolecules and their impact

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.


No textbook is set.

Reference books, course materials, etc.

Handouts will be distributed at the beginning of class when necessary and elaborated on using PowerPoint slides.

Assessment criteria and methods

Students' knowledge of basic matters, understanding on essential significance and abilities to apply them to problems will be assessed. No midterm and final exams.

Related courses

  • LST.A409 : Physical Biology of the Cell

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

Students must have successfully completed Physical Chemistry I, II, and III (number) or have equivalent knowledge.

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