|
| Udgave: |
Efterår 2012 NAT |
| Point: |
15,0 |
| Blokstruktur: |
1. blok |
| Fagområde: |
andet |
| Varighed: |
7 uger |
| Institutter: |
Biologisk Institut |
| Uddannelsesdel: |
Bachelor niveau |
| Kontaktpersoner: |
Birthe B. Kragelund, bbk@bio.ku.dk 3532 2081 |
| Skema- oplysninger: |
4-hour theoretical teaching sessions (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.
Introduction and course kick-off Monday 3 September, 12:15 - 13:00.
Oral presentation week: Week 43.
Laboratory course:
General part (40 h) week 36, 37 and 38, in Copenhagen Biocenter.
Biophysical part (30 h) weeks 39, 40 and 41 in Copenhagen Biocenter. |
| Skema- oplysninger: |
 Vis skema for kurset
Samlet oversigt over tid og sted for alle kurser inden for Lektionsplan for Det Naturvidenskabelige Fakultet Efterår 2012 NAT |
| Undervisnings- form: |
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. |
| Formål: |
The course is open for Biochemistry, Chemistry and Nanotechnology students and includes the chemistry, physics, structure, function and biology of proteins. Students will obtain a solid practical and a theoretical understanding of protein biology, structure and function and the physical and chemical properties of proteins. |
| Indhold: |
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.
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| Målbeskrivelse: |
In order to obtain the grade 12 the student should convincingly and accurately:
Composition and structure of proteins
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
Integrate amino acid properties and modifications in relation to chemistry, disease and enzyme design
Critically evaluate experimental results from studies of protein primary and secondary structure using protein chemistry
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
Explain the principles of protein crystallization theoreticaly and practically
Evaluate protein structures determined by X-ray crystallography
Describe and understand basic principles in small-angle X-ray scattering
Evaluate Kratky plots and distribution ensembles
Understand and evaluate the relative advantages and disadvantages of crystallographic and NMR approaches for protein structure analysis
Evaluate qualities of protein structures
Integrate and evaluate protein structure-function relationships
Physical and chemical properties of proteins
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
Describe and differentiate between physical forces in terms of energy, range and dependence on geometry, environments and other parameters of importance
Explain mechanism of folding and analyze methods for studies of protein folding and stability in vitro and evaluate free energy landscapes and folding funnels
Understand and evaluate protein folding intermediates and thermodynamics of protein folding and stability
Analyse phi-values in relation to protein folding and transition states
Relate protein stability to diseased states
Describe and understand current protein misfolding mechanisms
Protein purification and identification
Describe and understand the principle of SDS-PAGE including the stacking effect
Describe and evaluate methods for protein quantification
Describe and understand basic chromatographic theory
Critically evaluate advantages and disadvantages of different procedures used for proteins purification and characterization
Design purification procedures based on predefined protein properties
Evaluate and conclude on protein purity from appropriate methods
Analyze experimental data from protein purification protocols
Cite, evaluate and understand various heterologous protein expression systems
Membrane protein properties
Demonstrate insight into membrane protein purification problems and procedures
Describe and understand membrane protein structure
Describe the concepts of hydropathy plots in relation to membrane protein structure
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
Interactions and conformational properties of proteins
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
Understand and differentiate between negative and positive cooperativity in binding
Describe thermodynamically the underlying physical chemistry in protein interactions and calculate thermodynamic parameters from selected graphical presentations
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 effexcts in NMR spectra
Demonstrate insight into isotope labelling, sequential assignments and evaluate the quality of NMR spectra
From gene to function – from genomics to proteomics
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
Critically evaluate experimental results from proteome analysis
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)
Enzyme mechanism: engineering and design
Describe and understand selected theoretical aspects of enzyme catalysis and mechanism
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
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)
Describe and understand basic concepts in protein engineering especially in relation to enzymes
Describe and design simple protein structures
Defining, attacking and presenting a scientific problem in protein chemistry (oral presentation)
Select and define a simple scientific research topic in protein chemistry based on a selected set (1-3) of scientific papers
Evaluate methods and theoretical approaches to address questions in relation to this research topic
Communicate verbally in a scientific language and present results in power points in a clear and informative way
Others
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
Participate in a seminar on latest topics in protein science
Specific competence goals for the practical part of the course
To pass the practical part of the Protein Science A course the students must be able to design, execute, critically evaluate, and present experiments in protein chemistry. The students should have performed the following at a satisfactory level:
Participated in the practical course by designing and executing experiments
Written a report covering the practical part of the basic section. The report should cover: 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
Written two minor reports covering the practical part of the biophysical section. These include a) report of the NMR exercise and b) report of the spectroscopic and chromatographic part and should cover data evaluation; presentation of the results including graphs, fits, chromatograms, analyses, and calculated results; and answers to specific questions.
Given two oral presentations, one for each section of the practical course. The presentations should include an introduction, a presentation of the results, and conclusions
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| Lærebøger: |
The course material will be a collection of original papers, extracts from textbooks and notes and laboratory manuals and can be downloaded from the course website. |
| Tilmelding: |
Via KUnet during the period 15 May - 1 June. |
| Faglige forudsætninger: |
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. |
| Formelle krav: |
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). Students of Biochemistry are given priority. |
| Eksamensform: |
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. A four- hours written exam without books and notes and with external examiner. Grading is according to the Danish 7-point scale.
Reexamination will be 20 minutes of oral examination if less than 10 students are signed up. Otherwise, same form as the ordinary examination. |
| Eksamen: |
Skriftlig prøve den 6. november 2012.
Reeksamen: BEMÆRK reeksamensformen er ændret! Mundtlig prøve den 29. januar 2013. Såfremt der 10 eller færre tilmeldte til reeksamen ændres eksamensformen til mundtlig prøve. |
| Kursus hjemmeside: |
 |
| Kursus hjemmeside: |
Absalon via KUnet |
| Bemærkninger: |
Antallet af studerende på kurset er begrænset til 33. Der vil blive oprettet et ekstra hold ved minimum 48 tilmeldte. Biokemistuderende har fortrinsret.
Teaching language will be English if non-Danish speaking students are accepted.
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”. |
| Undervisnings- sprog: |
Engelsk
|
| Sidst redigeret: |
4/1-2013 |