2024 Faculty Courses School of Science Department of Physics Graduate major in Physics
Biophysics II
- Academic unit or major
- Graduate major in Physics
- Instructor(s)
- Michio Matsushita / Satoru Fujiyoshi
- Class Format
- Lecture (Face-to-face)
- Media-enhanced courses
- -
- Day of week/Period
(Classrooms) - 5-6 Mon
- Class
- -
- Course Code
- PHY.C453
- Number of credits
- 100
- Course offered
- 2024
- Offered quarter
- 3Q
- Syllabus updated
- Mar 14, 2025
- Language
- English
Syllabus
Course overview and goals
In the beginning of the 20th century, fermentation was still discussed whether it is life activity of yeast or not. Owing to development in extraction and purification, an enzyme called urease was for the first time crystallized in 1926. This led to the conclusion that enzymes are protein. This course will present recent progress of research of structure and function of proteins.
Course description and aims
By completing this course, students will be able to understand
1) that enzymes are proteins which catalyze biochemical reactions, and
2) that the tetrameric structure of hemoglobin allows adjusting the oxygen affinity to the environment, and
3) that membrane channel proteins are found in cell membrane, many of them are involved in signal transmission.
Keywords
protein, enzyme, catalyst, chemical kinetics, inhibition, hemoglobin, tetramer, oxygen delivery, cooperativity, quarterly or higher order structure, membrane channel, membrane protein, cell membrane, signal transmission, G-protein-coupled seven-pass transmembrane receptor protein, G-protein
Competencies
- Specialist skills
- Intercultural skills
- Communication skills
- Critical thinking skills
- Practical and/or problem-solving skills
Class flow
Some of the concepts which are accepted and used in biology do not exist in physics, for example, “quarterly structure of protein” and may appear strange to physics students. To avoid misunderstanding due to unfamiliar concepts and different terminology, attention will be paid for unfamiliar words to be explained clearly.
Course schedule/Objectives
| Course schedule | Objectives | |
|---|---|---|
| Class 1 | Enzyme catalyzes biochemical reactions | Explain that enzyme is a protein which catalyzes a biochemical reaction. |
| Class 2 | Three-dimensional structure of protein | Explain that in order to function as a catalyst an enzyme must take its specific 3-D structure. |
| Class 3 | Cooperativity in oxygen-delivery by hemoglobin. | Explain that cooperativity among the subunit of tetramer makes oxygen affinity to be dependent on the local environment. |
| Class 4 | Membrane channels and of active potential of the neural system. | Explain how ion channels work to transmit the active potential through an axon. |
| Class 5 | Inter-cellular signal transmission and G-protein. | Explain the function of the G-protein which is coupled to a receptor protein. |
| Class 6 | Initial process of vision | Explain the initial processes of vision. |
| Class 7 | Observing individual events of a single protein. | Explain observation of on-off behavior of a single ion-channel via pico-ampere measurements. |
Study advice (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)
Lecture notes will be distributed.
Reference books, course materials, etc.
1) J. M. Berg, J. L. Tymoczko, and L. Stryer, “Biochemistry”, 7th ed. (2012) W. H. Freeman Co.
2) A. Berk, C. A. Kaisser, et al., “Molecular Cell Biology”, 8th ed. (2016) W. H. Freeman Co.
Evaluation methods and criteria
Evaluated by a final report.
Related courses
- PHY.C343 ： Chemical Physics
Prerequisites
No prerequisites.