Protein Research Lab

Course content

This is an experimental laboratory course based on a seven weeks teaching period with 2 x 8 hours/week of student directed research on protein expression and purification, followed by experimentally addressing a self-defined testable hypothesis through biophysical studies.

The course totals 100 hours of obligatory laboratory work.

One week is reserved for oral presentations of scientific data in a seminar format and through a scientific poster session. 

Experimental part
Follows the concept of student-directed research. The student can choose between different projects that includes recombinant expression of proteins and engineered variants, design of purification strategies, purification and characterisation. Methods include fractionation methods, electrophoresis, chromatography (size exclusion, affinity, ion exchange, reversed phase etc.), Western blot (antibody based) analysis, pull-down and immune precipitation assays, peptide mass finger printing, protein crystallization, applied bioinformatics, chemical modification, and mass spectrometry. It also includes CD-, fluorescence-, and NMR-spectroscopy, isothermal titration calorimetry, molecular graphics and modelling, ligand binding, pKa determination and data processing and presentation. The laboratory course of 100 hours is distributed over seven weeks and students work in research teams of 3-4 student researchers

At the end of the laboratory course, each group presents its data by an oral presentation with discussion and at a scientific poster session of 3 hours where they present their own poster. A scientific board consisting of lecturers on the course and/or of external evaluators will discuss the poster make poster evaulations.

Learning outcome

Knowledge:

  • Describe and understand details of the chemical and physical properties, reactivity and experimental analysis of amino acids, both in isolation and in the context of protein structures
  • Describe the basic methods and principles of application of NMR for protein characterization
  • Understand and describe intrinsically disordered proteins in terms of biophysical properties and functional advantages
  • Explain mechanism of folding, and describe and apply methods for studies of protein folding and stability in vitro
  • Describe physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
  • Describe and understand the principle of SDS-PAGE including the stacking effect
  • Describe and understand basic chromatographic theory
  • Describe thermodynamically the underlying physical chemistry in protein interactions and calculate thermodynamic parameters from selected graphical presentations
  • Participate in a seminar on latest topics in protein science

 

Skills:

  • Evaluate the relative advantages and disadvantages of NMR approaches for protein structure analysis
  • Evaluate qualities of experimental protein structures
  • Demonstrate a thorough understanding of a selection of modern protein biophysical, spectroscopic and chemical experimental and analytical methods and assessment of when to use which method for solving a specific problem
  • Understand and evaluate thermodynamics of protein folding and stability for two-state folders and understand protein folding intermediates
  • Describe and evaluate methods for protein quantification
  • Design purification procedures based on predefined protein properties
  • Evaluate and conclude on protein purity from appropriate methods
  • Analyse experimental data from protein purification protocols
  • Quantitatively analyse and evaluate protein-ligand and protein-protein interactions
  • Describe and understand the use of methods applied in protein-ligand interactions including ITC, surface plasmon resonance, fluorescence and NMR spectroscopy
  • Evaluate methods and theoretical approaches to address questions in relation to this research topic
  • Execute protein purification and characterization experiments
  • Define testable hypotheses in relation to experimental protein science

 

Competences:

  • Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
  • Differentiate between physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
  • Critically evaluate advantages and disadvantages of different procedures used for proteins purification and characterization
  • Cite, evaluate and understand various heterologous protein expression systems
  • Critically evaluate experimental biophysical results
  • Critically evaluate experimental data on enzyme mechanisms, function, and control
  • Analyze, evaluate and condense experimental data in protein science from combinations of all possible areas of curriculum to solve relevant protein science problems
  • Demonstrate written- and oral communication in a protein scientific language
  • Defining, attacking and presenting a scientific problem in protein chemistry (oral presentation)
  • Communicate verbally in a scientific language and present published scientific results in power points in a clear and informative way
  • Design strategies to test scientific hypotheses experimentally
  • Design, execute, critically evaluate, and present experiments in protein chemistry
  • Design a scientific poster of the students own scientific results and present this in front of an audience

An 80 hours obligatory lab-course disseminated over 7 weeks. A total of 14 hours of obligatory oral presentations and scientific discussions.

See Absalon

It is recommended that the student has passed a basic course in protein science such as Protein Videnskab og Enzymology (PVEt) (biochemistry), Protein structure and function (chemistry), Protein Chemistry and Enzymology I and II (Molecular Biomedicine) or Protein Chemistry and Enzymology for Biologists (Biology). We do not recommend that the student has only passed a basic biochemistry course, and a prior course in biophysics/physical chemistry is highly recommended.

Students who have passed all first-year courses and half of the second year courses (corresponding to a total of 90 ECTS) of their curriculum would have obtained competencies that would enable them to follow the course, including the recommendations for basic courses listed above.

Academic qualifications equivalent to a BSc degree is recommended.

If you have passed or followed Protein Science A, you are not eligible for attending this course.

Oral
Individual
Collective

Oral feedback both individually and in groups on oral presentations and written presentations in the form of a scientific poster presenting the results of the laboratory work.

ECTS
7,5 ECTS
Type of assessment
Continuous assessment
80% attendance in laboratory exercises.
In the end of the course you have to make an oral presentation of your results in a powerpoint and a written presentation in the form of a poster. The poster must also be orally presented.
Aid
All aids allowed
Marking scale
passed/not passed
Censorship form
No external censorship
Several internal examiners.
Criteria for exam assessment

See Learning Outcome.

Single subject courses (day)

  • Category
  • Hours
  • Exam
  • 0
  • Preparation
  • 80
  • Lectures
  • 6
  • Practical exercises
  • 100
  • Project work
  • 20
  • English
  • 206