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2020　Physical Biology of the Cell

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Academic unit or major
Graduate major in Life Science and Technology
Instructor(s)
Hayashi Nobuhiro  Murakami Satoshi  Taguchi Hideki  Tokunaga Makio  Ishii Yoshitaka 
Class Format
Lecture    (ZOOM)
Media-enhanced courses
Day/Period(Room No.)
Tue3-4(Zoom)  Fri3-4(Zoom)  
Group
-
Course number
LST.A409
Credits
2
Academic year
2020
Offered quarter
4Q
Syllabus updated
2020/9/18
Lecture notes updated
-
Language used
English
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Course description and aims

What is the life? Why? To answer these questions, the aim of this course is to form a habit of considering using basic principles, essential models, and quantitative measures. Seeing the various workings of life and the cells through this physical way of thinking, not the physics with difficult numerical formula, interests and admirations of the physics can be enjoyed. Connecting physical chemistry learned so far with biochemistry, molecular biology, and biology to consider and discuss the "Why?" of concrete biological phenomena leads understanding of essence of life phenomena, and enhance the ability of scientific considering. Advanced materials on molecular mechanisms in life science will be discussed.

Student learning outcomes

1) Overlooking of biological phenomena using number, space, and time as a quantitative measure.
2) On the basis of concrete examples, explaining that maximum of entropy of whole system and minimum of Gibbs energy of the system are basic principles conducting biological phenomena thermodynamically.
3) Learning theory of random walk, soft chain, and Bernoulli-Euler beam, and discussion about structures of biopolymers and cells.
4) Quantitative understanding of biomembrane and membrane proteins, and bioelectricity and action potential generated by the membrane.
5) On the basis of concrete examples, discussion about dynamics of reactions in the cells and biomolecular motor.

Keywords

biopolymer, cell function, biomembrane, protein, bioelectricity, action potential, biomolecule motor, thermodynamics, transport, reaction dynamics, membrane transport

Competencies that will be developed

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

Class flow

The lecture is to be done in order of the contents of the textbook. (Thus, students are encouraged to familiarize the expected contents of the textbook in advance and to review them after the class.) The lecture will be given in English.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Why: Biology by the Numbers --- Application of physical and quantitative thinking to biological problems. (Yoshitaka Ishii) Understand the importance of fundamental physical models and quantitative estimation of the biologycal system.
Class 2 What and Where: Construction Plans for Cells and Organisms --- Development of an intuitive feeling for size and scale to envision the biological processes. (Yoshitaka Ishii) Understand the various units consisting biological system.
Class 3 When: Stopwatches at Many Scales --- Understanding different views of time in biological systems. (Yoshitaka Ishii) Understand the different time scales in biological systems.
Class 4 Mechanical and chemical equilibrium in the living cell. (Nobuhiro Hayashi) Understanding energy providing directions of the biological reactions.
Class 5 Entropy rules! (Nobuhiro Hayashi) Understanding life phenomena through statistical mechanics.
Class 6 Two-state systems: from ion channels to cooperative binding. (Nobuhiro Hayashi) Applying statistical mechanics to bio macromolecules expressing as two states.
Class 7 Random Walks: A random walk model of polymers viewed as rigid segments connected by hinges, and the basics of structures of macroomolecules such as proteins, DNA/RNA and chromosomes.(Makio Tokunaga) Understand the nature and basics of structures of biologycal macromolecues as random processes.
Class 8 Random Walks and the structures of macromolecules: Force spectroscopy measured by single molecule techniques and explanation by random walks. (Makio Tokunaga) Understand the various structures of biological macromolecues viewed as the random walk model.
Class 9 Beam theory: Architecture for cells and skeletons --- Elasticity, stiffness, persistance length and enrtropy viewed as beam deformations result in stretching, bending.(Makio Tokunaga) Understand the architecture of biological macromolecules and assemblies viewed as elasticity and thermodynamics.
Class 10 Structure and function of cell membrane and membrane proteins.(Satoshi Murakami) Understanding of physicochemical features of cell membranes and membrane proteins.
Class 11 Physioogical aspects on membrane proteins. (Satoshi Murakami) Understanding of physiological aspects on channels, pumps, transporters and receptors.
Class 12 Action potential in neurons and Hodgkin–Huxley model. (Satoshi Murakami) Understanding of basic concept of Hodgikin-Huxley model
Class 13 Rate Equations and Dynamics in the Cell. (Hideki Taguchi) Describe dynamics of proteins in the cell using rate equations.
Class 14 Dynamics of Molecular Motors: Translational motor proteins and Rotary motor proteins. (Hideki Taguchi) Explain the molecular mechanism of translational motor proteins and rotary motor proteins.

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)

“Physical Biology of the Cell, 2nd ed.” Phillips et al, Garland Science, 2012

Reference books, course materials, etc.

P. Atkins and J. D. Paula, Physical Chemistry for the Life Science, second edition、Oxford University Press.: P. Atkins and J. D. Paula, Physical Chemistry, eight edition, Oxford University Press. ; ,Student's Solutions Manual to Accompany Atkins' Physical Chemistry, eight edition, Oxford University Press.

Assessment criteria and methods

Reports and/or presentations on demand to check the essential understanding and quantitative discussion are held for the assessment.

Related courses

  • LST.A201 ： Physical Chemistry I
  • LST.A206 ： Physical Chemistry II
  • LST.A211 ： Physical Chemistry III
  • LST.A341 ： Biophysical Chemistry
  • LST.A403 ： Biophysics

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

No prerequisites are necessary, but it is highly suggested that the courses of physical chemistry I, II and biochemistry (and/or protein science) are completed prior to attempting this course.

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

Nobuhiro Hayashi (nhayashi[at]bio.titech.ac.jp, 03-5734-3863)
Yoshitaka Ishii (ishii[at]bio.titech.ac.jp, 045-924-5817)
Makio Tokunaga (mtoku[at]bio.titech.ac.jp, 045-924-5711)
Satoshi Murakami (murakami[at]bio.titech.ac.jp, 045-924-5748)
Hideki Taguchi (taguchi[at]bio.titeich.ac.jp, 045-924-5785)

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