2021 Physical Chemistry II

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Academic unit or major
Undergraduate major in Life Science and Technology
Tokunaga Makio  Hayashi Nobuhiro  Osada Toshiya 
Class Format
Media-enhanced courses
Day/Period(Room No.)
Tue5-6(S621,S622)  Fri5-6(S621,S011)  
Course number
Academic year
Offered quarter
Syllabus updated
Lecture notes updated
Language used
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Course description and aims

The aim is to understand biological functions through interpretation of elementary process of biological phenomenon as physicochemical reaction by learning of fundamental concepts, principles, and laws of physics. Students learn chemical equilibrium, electrical phenomenon, reaction kinetics, and biological process quantitatively from view points of statistical thermodynamics, and deepen their essential skill of consideration of physical phenomenon and chemical change. Taking concrete biological phenomena as the themes, students deepen their essential understanding. Through fundamental learning, ability of development and utilization of science and technology, that is ability of consideration for the applications in the bio science and engineering or clinical fields, is promoted.

Student learning outcomes

1) Understanding of chemical equilibrium, and explaining thermodynamically and statistical thermodynamically the reason why biological reactions occur.
2) Quantitative understanding of electrical phenomenon relating to transport of ion and electron, and explaining theory of solution and membrane transportation, battery, and biological energy.
3) Understanding of reaction kinetics, and construction of rate equation.
4) Discussion of biological reaction mechanism and reaction dynamics by rate equation.
5) Explaining enzymatic reaction and the inhibition as complex biochemical process by physical chemistry.
6) Explaining diffusion, ion transport, and electron membrane transport as elementary process of biological phenomenon by physical chemistry.


statistical thermodynamics, chemical equilibrium, transport, reaction kinetics, reaction dynamics, enzymatic reaction, inhibition, diffusion phenomenon, membrane transport, electron transfer

Competencies that will be developed

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

Class flow

Over the course, students will be conducted according to the text "Physical Chemistry for the Life Sciences" with introductory and detailed explanations. In each class, students are given exercise problems related to the lecture given that day to solve.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Chemical equilibrium: Reaction Gibbs energy, biological standard state, equilibrium constant (Makio Tokunaga) Compute the standard reaction Gibbs energy. Understand the biological standard state, the composition at equilibrium, endothermic reactions, the molecular origin of chemical equilibrium.
Class 2 Chemical equilibrium: Cooperative binding, standard reaction Gibbs energy, thermodynamical stability and unstability, effect of catalyst and temperature on the response of equilibria, coupled reactions (Makio Tokunaga) Understand the binding of oxygen to myoglobin and hemoglobin, the standard reaction Gibbs energy, Le Chatelier's principle, coupled reactions.
Class 3 Chemical equilibrium: Coupled reactions in bioenergeics, high-energy compound and the role of ATP (Makio Tokunaga) Calculate ΔrG for intracellular ATP. Understand the high-energy compound and transfer potential, the role of ATP in cells, ATP formation coupled to glucose oxidation.
Class 4 Chemical equilibrium: Proton transfer equilibria; acid and base, poyprotic acid and amphiprotic systems, buffer solutions (Makio Tokunaga) Understand acids and bases in terms of proton transfer equilibria, buffer capacities, the relationship between pH and pKa/pKb, the solution equilibrium and pKa/pI of amino acids, the buffer capacity of human blood.
Class 5 Thermodynamics of Ion and Electron Transport: Ion solution, biological membranes, membrane potential (Makio Tokunaga) Explain the Debye-Hückel theory, the activity of ionic solution, ΔG of ion transfer, the Goldman equation. Estimate ionic strengths and membrane potentials.
Class 6 Thermodynamics of Ion and Electron Transport : Redox reactions, electrochemical cell, Nernst equation, standard potential (Makio Tokunaga) Understand electrochemical cells in terms of redox reactions, the Nernst equation, the standard potential. Estimate standard potentials and equilibrium constants of cell reactions.
Class 7 Thermodynamics of Ion and Electron Transport : Electron transport and redox reactions in respiratory chain and photosynthesis (Makio Tokunaga) Understand the electron transport, redox reactions and ATP production in the respiratory chain and photosynthesis.
Class 8 Reaction kinetics: Definition, kinetics and rate constants, and order (Nobuhiro Hayashi) Understand the reaction kinetics theory.
Class 9 Reaction kinetics: Determination of rate constants, temperature dependency (Arrhenius equation) (Nobuhiro Hayashi) Represent biological phenomena in terms of rate equations. Interpret theoretically temperature dependency of kinetics.
Class 10 Interpretation of rate equation: Understanding of reaction mechanism (Nobuhiro Hayashi) Understand the reaction mechanism by rate equations.
Class 11 Interpretation of rate equation: Reaction dynamics (Nobuhiro Hayashi) Understand the factors determining the rate constants.
Class 12 Physical and chemical approach to understand complex biochmical processes. Catalytic efficiency of enzymes (Nobuhiro Hayashi) Compute the Michaelis-Menten mechanism of enzyme catalysis. Understand the reactions with inhibition.
Class 13 Complex Biochemical Processes : Biomembrane transport (Nobuhiro Hayashi) Understand the rules controlling the motion of molecules and ions in solution.
Class 14 Reaction kinetics, Rate equation, Complex biochemical processes : summary (Nobuhiro Hayashi) Explain and estimate the reaction kinetics, rate equations, enzyme kinetics, biomembrane transport processes.

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.


Atkins, Paula. Physical Chemistry for the Life Sciences (2nd ed). Tokyo: Tokyo Kagakudojin, 2014; ISBN-13: 978-4807908387. (Japanese)
Atkins, Paula. Physical Chemistry for the Life Sciences (2nd revised ed). Oxford: Oxford University Press; ISBN-13: 978-0199564286. (English)

Reference books, course materials, etc.

Atkins, Paula. Atkins' Physical Chemistry I, II (8th ed). Tokyo: Tokyo Kagakudoji, 2009; ISBN-13: 978-4807906956, 978-4807906963. (Japanese)
Atkins, et al. Atkins' Physical Chemistry (11th ed). Oxford: Oxford University Press, 2018; ISBN-13: 978-0198769866. (English)
Keeler, et al. Student Solutions Manual to accompany Atkins' Physical Chemistry (11th ed). Oxford: Oxford University Press, 2018; ISBN-13: 978-0198807773. (English)
Tinoco, et al. Physical Chemistry: Principles and Applications in Biological Sciences (5th ed.). Tokyo: Tokyo Kagakudojin, 2015; ISBN-13: 978-4807908806. (Japanese)
Tinoco, et al. Physical Chemistry: Principles and Applications in Biological Sciences (5th ed.). Upper Saddle River: Prentice Hall, 2013; ISBN-13: 978-0136056065. (English)
Phillips, et al. Physical Biology of the Cell (1st ed). Tokyo: Kyoritsu shuppan, 2011; ISBN-13: 978-4320057166. (Japanese)
Phillips, et al. Physical Biology of the Cell (2nd ed). New York: Garland Science, 2012; ISBN-13: 978-0815344506. (English)

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

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

No prerequites are necessary, but enrollment in Physical Chemistry I is desirable.

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