NBIA06017U Protein Science A (ProtSciA)
BSc Programme in Biochemistry
Six weeks teaching period with 4 x 2 hours theoretical teaching
a week and 80 hours of obligatory laboratory work distributed
over six weeks. Teaching will be in a colloquium format with a
total of 9-12 subjects covered. Each subject is assigned either 2x2
hours or 1x2 hours. Each session will consist of one or more
of: lecturing, problem solving, student seminars, concepts,
case-based teaching, computer assignments, and scientific
One week is reserved for oral presentations of scientific data in a seminar format.
The course consists of two parts:
- Theoretical part: this is very similar to the
course "Protein Science C". The theoretical part focuses
on the physics, chemistry, structure and function of proteins in
their biological environments. A generel part is complemented by a
more specific part. General subjects include: protein chemistry
methods and strategies, protein structures and structure
determination, folding and misfolding, proteome
analysis. Specific subjects include protein physics,
thermodynamics, protein-protein interactions, protein design and
engineering, protein dynamics, misfolding and disease.
- Experimental part (cannot be followed
separately): 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, yeast-2-hybrid analysis, peptide mass finger printing,
protein crystallization, applied bioinformatics, chemical
modification, and mass spectrometry. It includes also 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 80 hours is distributed over six weeks and
students work in research teams of 3-4 student
At the end of the laboratory course, each group present its data by an oral presentation and at a scientific poster session of 3 hours where they present their own poster. A scientific board consisting of lecturers on the course or of external evaluators evaluates the posters.
- 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
- Explain and describe methods for the determination of protein topology and fold
- Describe the basic methods and principles of NMR for protein structure determination and other applications of NMR regarding applications for protein characterization
- Describe and understand basic principles in small-angle X-ray scattering
- Understand relative advantages and disadvantages of NMR approaches for protein structure analysis
- Understand the principles for cryo-electron microscopy for protein structure analysis
- 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 and understand mechanisms for protein misfolding
- 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 and understand membrane protein structure
- Describe the concepts of hydropathy plots in relation to membrane protein structure
- Describe thermodynamically the underlying physical chemistry in protein interactions and calculate thermodynamic parameters from selected graphical presentations
- Describe and understand the following terms: protein sequence, homology, ortologous and paralogous proteins, domain swapping, protein annotation, phylogenetic reconstruction, distance matrix, phylogenetic tree
- Describe and understand concepts, strategies, and methods in proteomics and functional genomics
- Describe and understand basic concepts in protein engineering especially in relation to enzymes
- Describe selected methods for high-throughput protein science
- Participate in a seminar on latest topics in protein science
- Integrate amino acid properties and modifications in relation to chemistry, disease and enzyme design
- Explain the practical matters of small angle x-ray scattering in relation to protein stuctures
- Evaluate data from small angle x-ray scattering
- Evaluate Kratky plots and distribution functions
- 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
- Evaluate free energy landscapes and folding funnels
- Analyse phi-values in relation to transition states for protein folding
- Relate the effect of protein stability in disease
- 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
- Understand and differentiate between agonism, antagonism and inverse antagonism
- Evaluate principles of protein regulation, active site chemistry and binding
- Diagnose binding reactions qualitatively and quantitatively and analyse these
- Describe and understand the use of methods applied in protein-ligand interactions including ITC, surface plasmon resonance, fluorescence and NMR spectroscopy
- Cite and understand the use of methods applied in proteomics and functional genomics including mass spectrometry, SILAC, MS/MS, 2-D gel electrophoresis, protein and DNA arrays, fluorescence resonance energy transfer, yeast two-hybrid, pull-down assays
- Cite and understand the use of applied protein bioinformatics (BLAST homology searches)
- Describe simple protein structures
- 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
- Describe and understand the concept of hygrogen exchange in protein
- Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
- Integrate and evaluate protein structure-function relationships
- 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
- Demonstrate insight into membrane protein purification problems and procedures
- Demonstrate a thorough understanding of the structure/function relationship of various membrane protein families
- Integrate experimental and theoretical data in membrane protein structure analysis and integrate these in relation to pharmaceutical science
- Understand and differentiate between negative and positive cooperativity in binding
- Demonstrate insight into isotope labelling, sequential assignments and evaluate the quality of NMR spectra
- Critically evaluate experimental results from proteome analysis
- 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
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, most preferably including the recommendations for basic courses listed above.
Theoretical teaching mostly Tuesday and Thursday mornings. The remaining teaching is distributed as laboratory hours and oral presentations over the rest of the week.
Colloquium: A mixture of lecturing, problem solving, student seminars, computer assignments, scientific discussions and student presentations.
- Class Instruction
- Practical exercises
- Project work
Oral feedback both individually on and in groups on oral presentations and written presentations in the form of a scientific poster presenting the results of the laboratory work.
- 15 ECTS
- Type of assessment
- Written examination, 2 hours under invigilationOral examination, 20 minutesOral examination initiated from a set of predefined questions without preparation time.
One overall grade will be given with 50% weight on each exam.
The course has been selected for ITX exam on Peter Bangs Vej.
Both the oral and the written part of the exam must be passed individually.
- Exam registration requirements
80% attendance in laboratory exercises and at the oral and poster presentations. Has presented the data obtained in the laboratory course in an oral and written poster presentation. Has participated actively in the oral science presentation and presented experimental data from primary paper in an oral presentation.
- Only certain aids allowed
Calculator and Maple
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
- Exam period
Several internal examiners.
The same as the ordinary exam.
If less than 10 students for Protein Science A and C put together have signed up, the reexam will be held as a 20-min. oral exam without preparation and without aids.
If the requirement of 80% attendance at exercises is not fulfilled, the student must take the course again the next year.
If the other exam registration requirements is not fulfilled, it can be fulfilled no later than three weeks before the reexamination by agreement with the teacher.
If the student do not pass the ordinary exam, the student has to take both exams again.
Criteria for exam assesment
In order to obtain the grade 12 the student should convincingly
and accurately demonstrate the knowledge, skills and competencies
described under "Learning Outcome".
The student should also:
- Have participated actively in the laboratory course.
- Provide a critical and detailed oral and poster presentation of the practical part of the lab course.
- Give an oral presentation regarding experimental data from a primary paper.
- Have participated actively in the oral- and poster presentations from the lab course and in the oral science presentations.