2019 Biophysical Chemistry

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Academic unit or major
Undergraduate major in Life Science and Technology
Instructor(s)
Taguchi Hideki  Asakura Noriyuki 
Course component(s)
Lecture
Day/Period(Room No.)
Mon5-6(W331)  Thr5-6(W331)  
Group
-
Course number
LST.A341
Credits
2
Academic year
2019
Offered quarter
2Q
Syllabus updated
2019/4/12
Lecture notes updated
-
Language used
Japanese
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Course description and aims

This course deals with a more advanced treatment of the biochemical mechanisms based on physical chemistry and introduces physical chemistry in a variety of biological processes. Topics include physical chemistry of biomolecules, thermodynamics and quantum chemistry for metabolism and photosynthesis. Physical chemistry approaches to biology will provide us the wide range of backgrounds among biotechnology and the bases on applications of biological systems.

Student learning outcomes

By the end of this course, students will be able to:
1) Understand the role of physical chemistry in biological system.
2) Understand basic statistical thermodynamics in biological system.
3) Understand protein folding, protein stability, protein-protein interaction and motor proteins.
4) Explain energy production through biological processes.
5) Explain an electron transfer reaction in proteins
6) Explain the photochemical processes of photosynthesis.

Keywords

Proteins, protein stability, protein folding, protein-protein interaction, motor proteins, statistical thermodynamics, thermodynamics, photochemistry, metabolism, photosynthesis

Competencies that will be developed

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

Class flow

This course mainly consists of lectures. Required learning should be completed outside of the classroom for preparation and review purposes.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Introduction: Biological science in the context of physical chemistry Explain the significance of physical chemistry in biological science.
Class 2 Basic statistical thermodynamics 1- Boltzmann distribution and partition function Explain Boltzmann distribution and partition function.
Class 3 Basic statistical thermodynamics 2- equilibrium constants using statistical thermodynamics Explain equilibrium constants using statistical thermodynamics.
Class 4 Protein folding Explain protein folding and its correlation to protein function. 
Class 5 Protein stability Explain how the stability of proteins is described by physical chemistry.
Class 6 Protein-protein interaction Explain the mode of protein-protein interaction and its physiological importance.
Class 7 Proteins in motion: Motor proteins Explain the molecular mechanism of motor proteins with the aid of ATP hydrolysis.
Class 8 Review of the first half of the courses (classes 1-7) and midterm exam Review the first half of the classes to prepare midterm exam.
Class 9 Thermodynamics and equilibrium on metabolism Explain metabolism based on thermodynamic equilibrium.
Class 10 Theory of electron transfer reaction Explain Franck-Condon principle and Marcus theory.
Class 11 Kinetics of biological electron transfer reaction Explain an electron transfer rate and reorganization energy.
Class 12 Activation energy of biological electron transfer reaction Explain the activation energy of electron transfer and reorganization energy.
Class 13 Photochemistry of proteins Explain photochemical reaction based on quantum mechanics.
Class 14 Photocehemical reaction in photosynthesis I Understand photosynthesis based on electron transfer throry and quantum mechanics
Class 15 Photocehemical reaction in photosynthesis II Understand photoinduced electron transfer and photoinduced energy transfer in photosynthesis processes

Textbook(s)

Distribute handouts or upload materials via OCW

Reference books, course materials, etc.

Physical Chemistry for the Life Sciences (Atkins and De Paula)

Assessment criteria and methods

Midterm exam and final exam including questions of fundermental knowledge on physical chemistry, discription type questions, and calculation problems.

Related courses

  • LST.A201 : Physical Chemistry I
  • LST.A206 : Physical Chemistry II
  • LST.A211 : Physical Chemistry III
  • LST.A331 : Structural Biology
  • LST.A341 : Biophysical Chemistry
  • LST.A409 : Physical Biology of the Cell

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

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

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

Hideki Taguchi: taguchi[at]bio.titech.ac.jp , Noriyuki Asakura : asakura.n.aa[at]m.titech.ac.jp

Office hours

Contact by e-mail in advance to schedule an appointment is desirable.

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