Protein Science C (ProtSciC)

Course content

Six weeks teaching period with 4x 2 hours theoretical teaching a week. Teaching will be in colloquium form with a total of 9-12 subjects covered. Each subject is assigned either 2x 2 hours or 1x 2 hours. Each session will consist of one or more of: lecturing, problem solving, concepts, case-based teaching, student seminars, computer assignments, and scientific discussions. 

One week is reserved for mandatory oral presentations of scientific data in a seminar format.

The content is very similar to the theoretical part of the course "Protein Science A". The course focuses on the physics, chemistry, structure and function of proteins in their biological environments. A general 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.

Education

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

MSc Programme in Biology with a minor subject

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 structure
  • Explain and describe methods for the determination of protein topology and fold
  • Describe the basic methods and principles of NMR regarding application 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
  • 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 mechanism 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 selected theoretical aspects of enzyme catalysis and mechanism
  • 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 structures
  • Evaluate data from small angle x-ray scattering
  • Evaluate Kratky plots and distribution ensembles
  • Evaluate the relative advantages and disadvantages of crystallographic and 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
  • Analyze phi-values in relation 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
  • 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 agonism
  • 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
  • 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


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 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 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

4x 2-hours theoretical teaching sessions – in colloquia – a week (9-12 in total, divided into 2x 2 hours and 1x 2 hours sessions). A total of 11 hours of mandatory oral presentations and scientific discussions.
Theoretical teaching Tuesdays and Thursday mornings.
Colloquium: A mixture of lecturing, problem solving, student seminars, computer assignments, scientific discussions and student presentations.

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), 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.

ECTS
7,5 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.

The course has been selected for ITX exam at Peter Bangs Vej.
Aid
Without aids
Marking scale
7-point grading scale
Censorship form
No external censorship
Criteria for exam assessment

In order to obtain the grade 12 the student should convincingly and accurately demonstrate the knowledge, skills and competences described under "Learning Outcome".
 

Single subject courses (day)

  • Category
  • Hours
  • Exam
  • 2,5
  • Preparation
  • 134,5
  • Lectures
  • 14
  • Colloquia
  • 35
  • Project work
  • 20
  • English
  • 206,0