BMB534: Experimental protein chemistry (5 ECTS)

STADS: 01011401

Level
Bachelor course

Teaching period
The course is offered in the autumn semester.

Teacher responsible
Email: php@bmb.sdu.dk

Timetable
Show entire timetable
Show personal time table for this course.

Comment:
Max 12 stk

Prerequisites:
None

Academic preconditions:
Students participating in the course are expected to:

• Have a knowledge of basic molecular biology, protein chemical concepts, and biochemical processes (the content of BMB533 is expected to be known)
• The ability to apply common IT tools
• The course requires active participation, including oral presentations made by the students in groups
• Knowledge of general laboratory safety is expected.

Course introduction
The course aims to give the students an introduction to basic protein chemical techniques used for the characterization of protein primary structure and identification of proteins. During the course, the students will use these techniques to solve two relevant issues; 1) identification of gel-separated placental proteins and 2) determination of the primary structure of a known protein, containing four unknown amino acids and a substitution.

The course builds on the knowledge acquired in the program's second year, in particular molecular biology and protein chemistry (BMB533).

In relation to the competence profile, the course explicitly focus on:

• Obtain knowledge of theory and experimental methods in protein chemistry.
• Apply protein chemical analysis methods.
• Manage the complexity of the interaction between the results which illustrates a problem from several angles.
• Provide a presentation and pass the knowledge gained during the course
• Critically evaluate the results obtained by the methods used for the course
• The course includes laboratory-based projects, which provides personal competence in the organization of work.
• Laboratory projects will be carried out as group work, so skills in interaction will be strengthened.

Expected learning outcome
The learning objectives of the course are that the student demonstrates the ability to:

• Describe the primary structure of a protein and explain the principles of the most important methods for analysis of protein primary structure
• Explain the principles of separation of polypeptides using HPLC
• Describe the principles of gel electrophoresis
• Explain the principles of the amino acid analysis and mass spectrometry of polypeptides, to process data from it and integrate these into the solution of protein primary structure
• Explain the principle of a MALDI mass spectrometer
• Explain the principles of mass spectrometric protein identification and be able to analyze the data obtained
• Explain the principles in mass spectrometric sequencing of peptides and to analyze ms/ms data
• Being able to combine and evaluate techniques for the analysis of protein structures used during the course.
• To be able to use the programs used during the course

Subject overview
The following topics will be treated during the course:

1. Primary structure of proteins
2. Chemical characteristics of amino acids
3. The principles of amino acid analysis and its use for
1. Protein / peptide characterization
2. Quantitation
4. Protein sequencing in the form of mass spectrometric sequencing
5. SDS gel electrophoresis of proteins
6. Liquid chromatography
1. Reverses phase for peptide separation
2. Ion exchange
3. Solid phase extraction
7. Basic mass spectrometry (MALDI)
1. Intact mass analysis
2. Peptide mass fingerprinting
3. MS/MS for identification
8. Bioinformatical protein analysi

Most of the methods listed above will be used and/or demonstrated in the laboratory exercises.

NB: The training course is conducted according to legal safety instructions, but using experimental protocols and chemicals that are suspected to be potentially harmful to pregnant / lactating women. Pregnant / nursing students should therefore contact the course coordinator in good time before course registration or as soon as possible.

Literature
There isn't any litterature for the course at the moment.

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
Active participation in the exercises and oral group presentation. Pass/fail, internal marking by teacher.

Assessment and marking:
Project assignment, has to be handed in three weeks after the end of the course. Pass/fail, internal marking. (01011402)

If failed, the report can be resubmitted after two weeks.

Expected working hours
The teaching method is based on three phase model.
Intro phase: 8 hours
Skills training phase: 40 hours, hereof:
 - Tutorials: 4 hours
 - Laboratory exercises: 36 hours

Educational activities

Educational form
Activities during the study phase: Reading of text book, articles and course compendium. Preparation for laboratory work.

As the course is an intense summer course, the course days will consist of element both from the intro- and training phase, whereas the study phase will take place both prior to and during the course.

Language
This course is taught in English, if international students participate. Otherwise the course is taught in Danish.

Remarks
If failed, the report can be resubmitted after two weeks

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.