Course syllabus for Structure and dynamics of biomolecules

The course syllabus contains changes
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Course syllabus adopted 2019-02-12 by Head of Programme (or corresponding).

Overview

  • Swedish nameBiomolekylär struktur och dynamik
  • CodeKBB058
  • Credits7.5 Credits
  • OwnerMPBIO
  • Education cycleSecond-cycle
  • Main field of studyBioengineering, Chemical Engineering
  • DepartmentKEMI OCH MOLEKYLÄRBIOLOGI (GU)
  • GradingTH - Pass with distinction (5), Pass with credit (4), Pass (3), Fail

Course round 1

  • Teaching language English
  • Application code 08138
  • Maximum participants20
  • Open for exchange studentsNo

Credit distribution

0118 Laboratory 1.5 c
Grading: UG		 1.5 c
0218 Examination 6 c
Grading: TH		 6 c
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In programmes

Examiner

  • Richard Neutze
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Eligibility

General entry requirements for Master's level (second cycle)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Specific entry requirements

English 6 (or by other approved means with the equivalent proficiency level)
Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling the requirements above.

Course specific prerequisites

Anyone at fourth year within the Bt or K programmes at Chalmers will automatically be accepted. The course will have a significant mathematical component.

Aim

This course aims to provide an understanding of the methods that can be used the determination of protein structure and dynamics. The course will cover how X-ray crystallography and Nuclear Magnetic Resonance Spectroscopy, Electron Paramagnetic Resonance and Electron Microscopy can be used for structure determination. Students will be expected to understand the steps required to solve a protein structure, and the physical concepts which underpin these methods. They will get introduced to spectroscopic methods (based on NMR and vibrational spectroscopy) that can be used for studying protein dynamics at different timescales.

Learning outcomes (after completion of the course the student should be able to)

The course provides advanced knowledge of the methods for studying biomolecular structure and dynamical properties (X-ray diffraction of protein crystals, spin resonance and vibrational spectroscopy, and electron microscopy) and the molecular interplay between biomolecules (DNA - protein-ligand interactions).

It also deals with the theory and basic mathematical concepts (Fourier transform) for spectroscopic and X-ray scattering methods in biology and biochemistry. The course also provides an in-depth knowledge of the biochemical methodology and an understanding how structure, function and dynamics is linked in biological molecules. In relevant context protein structure-based drug design is discussed.

The theoretical and practical parts lie close to the current research and are designed to prepare graduates for a degree in biochemistry or for post graduate studies in the subject.

After completing the course, the students will be able to:

  • explain biomolecular structure and dynamics
  • be familiar with modern biophysics and biomolecular structure research
  • critically assess the potential and limitations of different experimental methods
  • have a deeper understanding of protein structure-function relationship.
  • have knowledge about and be able to apply the methods of crystallization, X-ray diffraction data collection of both soluble and membrane-bound proteins
  • be informed about, and to some extent able to apply NMR and vibration spectroscopic methods for characterization of proteins and their interactions
  • possess the practical knowledge necessary for the characterization of proteins and determine their three-dimensional structure
  • describe different analysis tools such as molecular graphics and Fourier transformation
  • interpret and discuss laboratory results and draw reasonable conclusions
  • critically, independently and creatively analyze the structure and function of a protein, implementing these advanced tasks within specified time frames
  • demonstrate an ability to both national and international contexts, orally and in writing present and discuss their conclusions

Content

The course will consist of lectures and laboratory assignments. Lectures will cover crystal symmetry; X-ray diffraction theory; electron and nuclear magnetic resonance spectroscopy theory; electron microscopy theory; vibrational spectroscopy theory. These experimental methods will be discussed in the context of specific protein examples. Laboratory exercises are an extremely valuable part of the course and will consist of X-ray crystallization, model building and analysis of crystal structures. The students will be able to perform NMR signal assignments and analyze NMR structures.

Organisation

This course consists of up to 20 two hour lectures and seven laboratory assignments. Lectures will run for two hours almost every day, and the laboratory exercises will run for one afternoon each.

Literature

Two useful (but not compulsory) texts are:

Wilson, K. (Ed.). (2010). "Principles and techniques of biochemistry and molecular biology." (7. ed.). Cambridge: Cambridge University Press.
Rhodes "Crystallography made crystal clear: a guide for users of macromolecular models"

The course schedule and lecture notes will be placed on the homepage
http://www.csb.gu.se/index.php/courses/protein-structure-and-function 

Examination including compulsory elements

Course grades will be awarded upon the performance in a written exam. Laboratory exercises must also be performed to a suitable level to receive credit.

The course syllabus contains changes

  • Changes to course rounds:
    • 2020-10-12: Examinator Examinator changed from Gergely Katona (mbtkgek) to Richard Neutze (mbtkrn) by UOL
      [Course round 1]