Search course

Use the search function to find more information about the study programmes and courses available at Chalmers. When there is a course homepage, a house symbol is shown that leads to this page.

Graduate courses

Departments' graduate courses for PhD-students.

​​​​
​​

Syllabus for

Academic year
KBB058 - Structure and dynamics of biomolecules
Biomolekylär struktur och dynamik
 
Syllabus adopted 2019-02-12 by Head of Programme (or corresponding)
Owner: MPBIO
7,5 Credits
Grading: TH - Five, Four, Three, Fail
Education cycle: Second-cycle
Major subject: Bioengineering, Chemical Engineering
Department: 0114 - KEMI OCH MOLEKYLÄRBIOLOGI GU


Teaching language: English
Application code: 08124
Open for exchange students: No
Maximum participants: 20

Module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 Summer course No Sp
0118 Laboratory 1,5c Grading: UG   1,5c    
0218 Examination 6,0c Grading: TH   6,0c   Contact examiner,  Contact examiner,  Contact examiner

In programs

MPBIO BIOTECHNOLOGY, MSC PROGR, Year 1 (compulsory elective)
MPBIO BIOTECHNOLOGY, MSC PROGR, Year 2 (elective)

Examiner:

Gergely Katona

  Go to Course Homepage


Eligibility:


In order to be eligible for a second cycle course the applicant needs to fulfil the general and specific entry requirements of the programme that owns the course. (If the second cycle course is owned by a first cycle programme, second cycle entry requirements apply.)
Exemption from the eligibility requirement: Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling these requirements.

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.


Published: Wed 26 Feb 2020.