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2017　Structural Biology

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Academic unit or major
Undergraduate major in Life Science and Technology
Instructor(s)
Murakami Satoshi  Hayashi Nobuhiro 
Class Format
Lecture     
Media-enhanced courses
Day/Period(Room No.)
Mon1-2(W241)  Thr1-2(W241)  
Group
-
Course number
LST.A331
Credits
2
Academic year
2017
Offered quarter
1Q
Syllabus updated
2017/3/17
Lecture notes updated
-
Language used
Japanese
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Course description and aims

Vital phenomena arise from the sum of interweaving chemical reactions of many biomolecules such as proteins and nucleic acids. This allows for individual phenomena to be explained in the terms of physics and chemistry, and unraveling their systematic integration and regulation leads to the understanding of vital phenomena.
This course provides an overview of fundamental thinking required to understand and use interweaving reactions of these biopolymers, often viewed simply as components, as well as methods for analyzing them and the development of research by their use.

Student learning outcomes

By the end of this course, students will be able to:
1) Understand that analysis of the functional structures of biopolymers is essential to understanding the true nature of life.
2) Explain the structure of biopolymers.
3) Explain the functions of biopolymers based on their structures.
4) Analyze and discuss vital phenomena based on the structure of molecules involved in the reaction.
5) Understand the principles behind various analysis methods and utilize them to unravel the functional structure of biopolymers.
6) Utilize structure information in applied development such as drug development and protein engineering research.

Keywords

Tertiary structure of biopolymer, X-ray crystal structure analysis, Nuclear magnetic resonance, Cryogenic temperature electron microscopy observation, Molecular dynamics.

Competencies that will be developed

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

Class flow

This course consists of lectures according to the course schedule, in the order listed.

Course schedule/Required learning

  Course schedule Required learning
Class 1 Outlook: Nucleic acids, Proteins, Sugar, Lipid and more… Explain the proper use of various biopolymers based on their physical properties.
Class 2 Nucleic acids: Structure of DNA~ Structural basis of DNA replication Understanding of function of DNA based on the molecular structure.
Class 3 Nucleic acids: Structure of RNA~Functional RNA, Ribozyme and m-RNA Understanding of function of ribosome and mRNA based on their molecular structures.
Class 4 Proteins: Amino acids, building blocks of proteins. Primary, secondary, tertiary and quaternary structure Understanding of protein structure and the four level of protein structure.
Class 5 Nucleic acids: Structure of RNA~Functional RNA, t-RNA Understanding of function of tRNA based on the molecular structure.
Class 6 Proteins: Reaction mechanism of enzymes at atomic level Understanding of structure- function relationship in enzymes.
Class 7 Proteins: Mechanism of proteins at atomic level (Non-enzymatic reactions, such as DNA binding, ion transfer, etc.) Understanding of structure- function relationship in non-enzyme proteins.
Class 8 Proteins: Functional structure of a protein (Structural change and target recognition: A case study (calmodulin)) A case study: Understanding of a protein based on the molecular structure.
Class 9 Proteins: Post-translational modifications Understanding of regulation of proteins by their post translational modifications based on their molecular structures and physical properties.
Class 10 Review (case studies): Elucidation of molecular mechanism of life phenomena through solution of functional structure using various analytical methods (mass spectrometric analysis, analyses of molecular interactions (SPR, QCM, fluorescent spectrum, etc.), CD, SAXS/SANS, NMR, etc.). Understanding of principles and operations of various analytical methods of biopolymers.
Class 11 Methods in structural biology: NMR and distance geometry Understanding of principles and applications of NMR.
Class 12 Methods in structural biology: cryo-electron microscopy Understanding of principles and applications of cryo-electron microscopy
Class 13 Methods in structural biology: X-ray crystallography Understanding of principles and applications of x-ray crystallography
Class 14 Structure and function: Functional analysis based on structure data Understanding of functional assay based on structure.
Class 15 Structure and function: Utility of the structure data (Structure based drug design) Introduction and discussion on utility of the structural information of proteins for designing inhibitors etc.

Textbook(s)

The textbook is not appointed. Prints related to the class will be handed out on demand.

Reference books, course materials, etc.

“Genes （8th ed.）” BENJAMIN LEWIN, "Introduction to protein structure (2nd. ed.) ” Carl Branden, “Molecular biology of the gene（6th ed）” James D. Watson， “Molecular biology of thecell （5th. ed.）” Bruce Alberts

Assessment criteria and methods

To be evaluated based on the final exam, which contains questions to check students' basic understanding and writing tasks to assess their deeper understanding.

Related courses

  • LST.A201 ： Physical Chemistry I
  • LST.A206 ： Physical Chemistry II
  • LST.A211 ： Physical Chemistry III

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

No prerequites are necessary.

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

S. Murakami:By appointment (murakami[at]bio.titech.ac.jp, ext:5748)
N.Hayashi: By appointment (nhayashi[at]bio.titech.ac.jp, ext3863)

Office hours

Students may approach the instructors at the end of class or visit their offices upon securing an appointment through e-mail.

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