|
| 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: |
2- and 4-hour teaching sessions
mostly Tuesday and Thursday in Copenhagen Biocenter
Introduction and course kick-off: Monday 3 September, 12:15-13:00.
Oral presentations: Week 43.
Laboratory course: (50 h) Weeks 38, 39 and 40 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: |
Lectures, problem solving, computer assignments, and scientific discussions and student presentations. |
| Formål: |
The course is open for Biology, Chemistry, Nanotechnology, and Bioinformatics students and includes the chemistry, structure, function and biology of proteins. Students will obtain both a practical and a theoretical understanding of protein biology, structure and function and chemical properties of proteins |
| Indhold: |
The course is composed of two parts: a theoretical part, and an experimental part. The theoretical part focuses on the physics, chemistry, structure and function of proteins in their biological environments.The experimental part focuses on the purification and characterization of proteins from natural sources and of recombinant proteins. Methods include fractionation methods, electrophoresis, chromatography, peptide-mapping, applied bioinformatics, chemical modification, and mass spectrometry.
The theoretical part is in large parts common to Protein Science B and D but a more detailed description is provided for PSB for certain methodlogies.
General subjects include: protein chemistry methods and strategies, protein structures and structure determination, folding and misfolding, proteome analysis, enzyme mechanisms.
Teaching is distributed as follows: Six weeks theoretical teaching period with 3 x 2 hours teaching a week.
Each week will consist of a 2 x 1-hour lectures followed by 2 x 2-hour problem solving, computer assignments, scientific discussions and student presentations.
One week is reserved for essay writing. The essay is an obligatory written assignment in the format of a scientific project proposal.
The laboratory course of 50 hours is distributed over three weeks.
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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 the structure and functional properties of the 20 common amino acids
Describe protein structure elements (helix, sheet, coil), primary, secondary tertiary structure
Describe and understand the peptide bond and its implication for protein structure
Describe and understand the structure and functional properties of amino acids in relation to protein structure and function
Cite the most common posttranslational modifications and describe their features in broad terms
Combine the understanding of amino acids, modifications and structural elements and to apply this to a general understanding of proteins structure and function
Physical and chemical properties of proteins
Describe and understand methods of protein stability determination
Determine the stability of proteins from urea or guanidinium unfolding/refolding curves
Describe and understand how molecular chaperones function in relation to protein folding in vivo
Describe and understand the significance of folding off-pathways such as protein aggregation
Combine the understanding of protein folding and stability to a general understanding of the relationship between in vivo and in vitro protein folding
Protein purification and preparation
Cite and understand the common methods in protein purification including the most common types of column chromatography, protein precipitation, dialysis, electrophoresis, isoelectric focusing, mass spectrometry, protein quantification, and chemical modification of proteins
Critically evaluate advantages and disadvantages of different procedures used for proteins purification and characterization
Analyze experimental data from protein purification protocols
Design simple purification procedures based on predefined protein properties
Evaluate and conclude on protein purity from appropriate methods
Cite and understand the basic concepts of heterologous protein expression
Methods in analysis of structure and dynamics of proteins
Describe methodologies for protein structure determination (NMR and X-ray)
Describe and understand the basic principles of protein crystallization
Describe the use of CD spectroscopy for structural analysis of proteins
Describe the use of fluorescence spectroscopy for analysis of protein
Describe the basic concepts of fluorescence resonance energy transfer
Understand the relative advantages of the above methods for protein structure and functional analysis
Membrane protein properties
Describe the basic properties of biological membranes
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
Interactions and conformational properties of proteins
Describe and evaluate protein-ligand and protein-protein interactions
Describe and evaluate allosteric properties
Apply the knowledge on protein interactions and conformation to biological systems and protein function regulations
Diagnose binding reactions qualitatively and quantitatively and analyze these
Understand the underlying physical chemistry in protein interactions and calculate binding parameters from selected graphical presentations
Protein turnover: concepts and techniques
Describe mechanisms of intracellular protein turnover in relation to proteasome structure and function
Describe and understand the use of immunological techniques in protein chemistry
Apply the understanding of immunological techniques to practical problems in cellular protein chemistry
Understand and apply the use of pulse labeling techniques to practical problems in cellular protein chemistry
From gene to function – bioinformatics and proteomics
Describe and understand the following terms: protein sequence convergence and divergence, ortologous and paralogous proteins, domain swapping, homology, sequence alignments, structural alignments, phylogenetic reconstruction, distance matrix, phylogenetic tree
Describe and understand concepts, strategies and methods in proteomics and functional genomics
Critically evaluate experimental results from proteomic analysis
Cite and understand the use of methods applied in proteomics and functional genomics including mass spectrometry, MS/MS, 2-D gel electrophoresis, protein and DNA micro array, fluorescence resonance energy transfer, yeast two-hybrid assay
Cite and understand the use of applied protein bioinformatics (BLAST homology searches)
Enzyme mechanism, regulation and kinetics
Describe and understand selected theoretical aspects of enzyme catalysis and mechanism
Understand and integrate different regulatory aspects of enzymes
Critically evaluate experimental data on enzyme mechanisms, function, and regulation
Have an insight in apoptosis (programmed cell death)
Combine the knowledge on regulation and kinetics to biological systems
Describe and understand the basic concepts of enzyme engineering
Fluorescent proteins as tools
Describe and understand the application of fluorescent proteins
Design experiments based on this knowledge
Defining, attacking and presenting a scientific problem in protein chemistry (oral presentation)
Select and define a simple scientific research proposal in protein chemistry based on a selected set (1-3) of scientific papers
Evaluate methods and theoretical approaches to address specific 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 contemporary topics in protein science
Specific competence goals for the practical part of the course
To pass the practical part of the Protein Science B 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, by designing and executing experiments, in the practical course
Prepared a written a report covering the practical part of the basic section. The report should answer the questions included with exercise. The report will include: 1) description and critical evaluation of the methods used; 2) rationalization 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
Given an oral presentation in connection with the practical course. The presentation should include an introduction, a presentation of the results, and conclusions
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| Lærebøger: |
David Nelson and Michael Cox: Principles of Biochemistry. Freeman (2008). Additional course material will be available at the course website |
| Tilmelding: |
Via KUnet in the period 15 May - 1 June. |
| Faglige forudsætninger: |
Open to students of Biology, Chemistry, and Bioinformatics. It is recommended that students have passed all first year courses and half of the second year courses (corresponding to a recommended total of 90 ECTS-points) of the biology or chemistry bachelor curriculum. |
| 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: |
Maximum number of students: 30.
All teaching material is in English.
Teaching language will be English if non-Danish speaking students are present.
Credit for this course will not be given to students that have passed the former courses "Experimental and Theoretical Protein Chemistry" or "Proteiner, Struktur og function”.
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| Undervisnings- sprog: |
Engelsk
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| Sidst redigeret: |
4/1-2013 |