2016 Physical Chemistry II

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Academic unit or major
Undergraduate major in Life Science and Technology
Tokunaga Makio  Osada Toshiya  Sogawa Kumiko  Kamachi Toshiaki  Hayashi Nobuhiro  Asakura Noriyuki 
Class Format
Media-enhanced courses
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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: equilibrium constant, cooperative binding, standard reaction Gibbs energy Understand the composition at equilibrium. Compute the standard reaction Gibbs energy in chemical reaction.
Class 2 Chemical equilibrium: Effect of catalyst and temperature on the response of equilibria, Coupled reactions in bioenergeics Understand the van't Hoff equation. Explain ATP formation coupled with glucose oxidation.
Class 3 Chemical equilibrium: Proton transfer equilibria; Acid and Base Understand proton transfer equilibria. Estimate the pH of a solution of a weak acid or a weak base.
Class 4 Chemical equilibrium: Proton transfer equilibria; Amphiprotic systems, Buffer solutions Calculate the fractional concentration of polyprotic acid. Explain the pH stability in buffer solutions.
Class 5 Thermodynamics of Ion and Electron Transport:Transport of ions across biological membranes Explain Debye-Hückel theory and activity of ionic solution. Understand the contents of pages 184–191 of textbook.
Class 6 Thermodynamics of Ion and Electron Transport : Redox reactions Explain the Nernst equation. Understand the contents of pages 192–204 of textbook.
Class 7 Thermodynamics of Ion and Electron Transport : Applications of standard potentials Understand the redox potential and Gibbs energy. Understand the contents of pages 205–210 of textbook.
Class 8 Thermodynamics of Ion and Electron Transport : Electron transfer in bioeneretics Explain the respiratory chain and photosynthesis based on redox reaction. Understand the contents of pages 210–215 of textbook.
Class 9 Reaction kinetics: Definition, kinetics and rate constants, and order Understanding of reaction kinetics theory.
Class 10 Reaction kinetics: Determination of rate constants, temperature dependency (Arrhenius equation) Representation of biological phenomenon by rate equation, theoretical interpretation of temperature dependency of kinetics.
Class 11 Interpretation of rate equation: Understanding of reaction mechanism Understanding of reaction mechanism by the rate equation.
Class 12 Interpretation of rate equation: Reaction dynamics Understanding of factors determining the rate constants.
Class 13 Physical and chemical approach to understand complex biochmical processes. Catalytic efficiency of enzymes Compute the Michaelis-Menten mechanism of enzyme catalysis. Understand the reaction with inhibition.
Class 14 Complex Biochemical Processes : Biomembrane transport Understanding of rules controlling motion of molecules and ions in solution.
Class 15 Complex Biochemical Processes : Electron transfer in biological systems Explain the Marcus theory and compute diffusion equation. Understand the contents of pages 302–310 of textbook.


P. Atkins and J. D. Paula, Physical Chemistry for the Life Science, second edition、Oxford University Press.

Reference books, course materials, etc.

P. Atkins and J. D. Paula, Physical Chemistry, eight edition, Oxford University Press.; P. Atkins and J. D. Paula, Student's Solutions Manual to Accompany Atkins' Physical Chemistry, eight edition, Oxford University Press.; Phillips et al, Physical Biology of the Cell, 2nd ed., Garland Science, 2011.; Ignacio, et al., Physical Chemistry:Principles and Applications in Biological Sciences, Fifth Edition., Pearson.

Assessment criteria and methods

Students' knowledge of basic matters, understanding on essential significance and abilities to apply them to problems will be assessed.
Midterm and final exams 100%.

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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