NBIA06017U Protein Science A (ProtSciA)

Volume 2013/2014
Education
BSc Programme in Biochemistry
BSc Programme in Nanoscience
Content
Six weeks teaching period with 4 x 2 hours theoretical teaching a week and 70 hours of obligatory laboratory work distributed over five weeks. Teaching will be in colloquium form with a total of 11 subjects covered. Each subject is assigned 2+2 hours. Each 2-hour session will be a mixture of lecturing, problem solving, student seminars, computer assignments, and scientific discussions.
One week is reserved for oral presentations of scientific data.

The two parts of the course are:
  • the 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 fundamental part is complemented by a subject-oriented part. General subjects include: protein chemistry methods and strategies, protein structures and structure determination, folding and misfolding, proteome analysis, enzyme mechanisms and engineering. Specific subjects include protein physics, thermodynamics, protein-protein interactions, protein design and engineering, protein dynamics, misfolding and disease.
  • the experimental part (cannot be followed separately): focuses on the purification and characterization of proteins from natural sources and of recombinant proteins. Methods include fractionation methods, electrophoresis, chromatography, Western blot (antibody based) analysis, pull-down and immune precipatation assays, peptide mass finger printing, protein crystallization, applied bioinformatics, chemical modification, and mass spectrometry. It includes also CD-, fluorescence-, and NMR-spectroscopy, molecular graphics and modeling, ligand binding, pKa values and data processing. The laboratory course of 70 hours is distributed over six weeks.
    The first part (40h) weeks 36, 37, 38 is a basic protein characterization part, the last part (30h), weeks 39, 40 and 41 is differentiated into a biophysical part.
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 protein structural context
  • Explain and describe methods for topology and fold determination of proteins
  • Describe the basic methods and principles of NMR for protein structure determination and other applications of NMR spectroscopy relevant for protein characterization
  • Describe and understand basic principles in small-angle X-ray scattering
  • Understand relative advantages and disadvantages of crystallographic and NMR approaches for protein structure analysis
  • Explain mechanism of folding and analyze methods for studies of protein folding and stability in vitro
  • Describe and understand current protein misfolding mechanisms
  • 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 selected theoretical aspects of enzyme catalysis and mechanism
  • Describe and understand basic concepts in protein engineering especially in relation to enzymes
  • 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 principles of protein crystallization theoreticaly and practically
  • Evaluate protein structures determined by X-ray crystallography
  • Evaluate Kratky plots and distribution ensembles
  • Evaluate the relative advantages and disadvantages of crystallographic and NMR approaches for protein structure analysis
  • Evaluate qualities of 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 protein folding intermediates and thermodynamics of protein folding and stability
  • Evaluate free energy landscapes and folding funnels
  • Analyse phi-values in relation to protein folding and transition states
  • Relate protein stability to diseased states
  • Describe and evaluate methods for protein quantification
  • Design purification procedures based on predefined protein properties
  • Evaluate and conclude on protein purity from appropriate methods
  • Analyze experimental data from protein purification protocols
  • Quantitatively analyze 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 analyze these
  • Describe and understand the use of methods applied in protein-ligand interactions including ITC, surface Plasmon resonance, fluorescence and NMR spectroscopy
  • Understand and explain spin-spin coupling, J-coupling, and relaxation with respect to NMR
  • Understand and evaluate chemical and conformational exchange, hydrogen-to-deuterium exchange in relation to effects in NMR spectra
  • 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)
  • Understand and evaluate kinetics and/vs. thermodynamics in enzymolgy
  • Evaluate kinetic and thermodynamic studies, based on steady-state kinetics and linear free energy relationships (LFER), of enzymes
  • Describe and design simple protein structures
  • Evaluate methods and theoretical approaches to address questions in relation to this research topic
  • Execute protein purification and characterization experiments

 

Competencies:

  • 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 labeling, 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 results in power points in a clear and informative way
  • Design, execute, critically evaluate, and present experiments in protein chemistry
See Absalon
It is a requirement that the student has passed a basic course in protein science such as Biokemi2 (biochemistry), Proteiners struktur og funktion (chemistry), Nanobio1 (nanoscience).

Open to students of Biochemistry, Nanotechnology and Chemistry who have passed all first year courses and half of the second year courses (corresponding to a total of 90 ECTS-points) of their curriculum.
4-hour theoretical teaching sessions - colloguia (11 in total, divided into 2+2 hours) and 70 hours lab-course.
Theoretical teaching mostly Tuesdays and Fridays in Copenhagen Biocenter. The remaining teaching is distributed as laboratory hours and oral presentations.
Laboratorie courses.
Colloquium: A mixture of lecturing, problem solving, student seminars, computer assignments, scientific discussions and student presentations. (A total of 22x2 hours, 4 hours per subject). A total of 70 hours of obligatory laboratory work are disseminated over 6 weeks. A total of 11 hours of obligatory oral presentations and scientific discussions.
A second team will be made only when a minimum of 48 students are signed up for the course. Priority is given to biochemistry students.

Credit for this course will not be given to students that have passed the former courses "Experimental and Theoretical Protein Chemitry" or "Proteiner. Struktur og funktion”.
  • Category
  • Hours
  • Colloquia
  • 33
  • Exam
  • 4
  • Lectures
  • 11
  • Practical exercises
  • 70
  • Preparation
  • 274
  • Project work
  • 20
  • Total
  • 412
Credit
15 ECTS
Type of assessment
Written examination, 4 hours under invigilation
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Exam registration requirements
Written reports of the practical work should be approved one week before the exam at the latest. It will appear from the critique, what parts require revision.

80% attendance with participation in exercises and oral presentations
Aid
Without aids
Marking scale
7-point grading scale
Censorship form
External censorship
Re-exam
Same as ordinary. However, if less than 10 students for Protein Science A and Protein Science C put together have signed up, the exam will be held as a 20-minute oral exam without preparation and without aids
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
  • Hand-in a written report covering the practical part of the basic section including: 1) description and critical evaluation of the methods used; 2) explanation of the protocols and strategies used; 3) data evaluation; 4) presentation of the results including graphs, gels, chromatograms, analyses, and calculated results; 5) estimation of experimental errors and an explanation of these; 6) answers to the questions included with exercise I and II
  • Provided a critical and detailed oral presentation of the practical part of the biophysical section covering data evaluation; presentation of the results including graphs, fits, chromatograms, analyses, and calculated results
  • Given two oral presentations, one regarding protein structure analyses and one of an assigned paper.
  • Participated in two oral presenation sessions.