Engelsk   Dansk
Velkommen til Københavns Universitets kursuskatalog

NBIA06017U  Protein Science A (ProtSciA) Volume 2017/2018

Course information

LanguageEnglish
Credit15 ECTS
LevelBachelor
Duration1 block
Placement
Block 1
Schedule
Uden for skemastruktur. Eksperimentelt kursus, hvor alle skemagrupper kan blive brugt til undervisning.
Course capacity33
Continuing and further education
Study boardStudy Board for the Biological Area
Contracting department
  • Department of Biology
Course responsible
  • Birthe Brandt Kragelund (3-6969724769707635727c356b72)
Saved on the 08-03-2017
Education

BSc Programme in Biochemistry
BSc Programme in Molecular Biomedicine
BSc Programme in Biology
BSc Programme in Nanoscience

Content

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 discussions.

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 researchers.
    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.
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
  • 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


Skills:

  • 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
  • Explain spin-spin coupling, J-coupling, and relaxation with respect to NMR
  • 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


Competences:

  • 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
  • Understand and integrate different regulatory aspects of enzymes such as those found in the blood coagulation system and the apoptotic system (programmed cell death)
  • 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
Literature

See Absalon

Teaching and learning methods
4x 2-hours theoretical teaching sessions – colloquia – a week (9-12 in total, divided into 2x 2 hours and 1x 2 hours sessions) and 80 hours obligatory lab-course disseminated over 6 weeks. A total of 14 hours of obligatory oral presentations and scientific discussions.
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.
Feedback form
Oral
Individual
Collective

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.

Academic qualifications
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), Nanobio1+2 (nanoscience), Protein Chemistry and Enzymology I and II (Molecular Biomedicine) or General Biochemistry 2 - Protein Chemistry and Enzymology for Biologists (Biology). We do not recommend that the student has only passed a basic biochemistry course.

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.
Remarks
A second team will be made only when a minimum of 48 students are signed up for the course.
Sign up
Self Service at KUnet
Exam
Credit15 ECTS
Type of assessment
Written examination, 2 hours under invigilation
Oral examination, 20 minutes
Oral examination initiated from a set of predefined questions without preparation time.

One overall grade will be given with 50% weight on each exam.

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 presented a primary paper in an oral presentation.

AidWithout aids
Marking scale7-point grading scale
Censorship formNo external censorship
Exam period

Several internal examiners.

Re-exam

As ordinary.

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.

In case the requirement of oral and written presentations has not been fulfilled, this should be done no later than two weeks prior to the reexamination by agreement with the course responsible.

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 an assigned paper.
  • Have participated actively in the oral- and poster presentation sessions.
Workload
CategoryHours
Exam2,5
Preparation261,5
Lectures14
Colloquia34
Practical exercises80
Project work20
Total 412,0
Saved on the 08-03-2017