NBIA07005U Protein Science F (ProtSciF)

Volume 2013/2014
Education
BSc Programme in Molecular Biomedicine
Content
Four weeks of theoretical teaching period with 2 x 3 hours teaching a week. Each 3-hours teaching session will be a mixture of lecturing, problem solving, student seminars, computer assignments, and scientific discussions.

One week is reserved for essay writing where the student writes a grant proposal covering a self-defined project within an assigned subject. The essay is presented orally with feed-back and forms the starting point for the oral examination.

This course is theoretical and covers the biology, chemistry, structure and function of proteins in their biological environments. Subjects include: protein chemistry methods and strategies, fluorescent proteins as tools, redox potentials, intrisic disorder in protein science, proteome analysis, and enzyme mechanisms, protein metabolism in living cells, including in vivo folding, processing, enzyme systems and regulation, systems biology and proteomics. A basic knowledge of protein chemistry is required for admission to the (F) line.
Learning Outcome
Knowledge:
  • Describe and understand basic methods in protein science such as SDS-PAGE, NATIVE-PAGE, ion-exchange chromatography, and
  • gelfiltration
  • Describe and understand advanced methods in protein science in relation to interactions covering application of ITC, SPR and NMR
  • spectroscopy in interaction analyses
  • 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
  • Understand and describe basic concepts of thiol-disulphide reactions in disulphide exchange reactions and disulphide bond formation
  • Understand and describe the function and mechanism of selected antioxidant redox enzymes and systems
  • Understand and describe basic concepts of oxidation damage and reactive oxygen species
  • Describe mechanisms of protein degradation in relation to proteasome structure and function
  • Describe and understand the proteolysis in the light of antigen presentation and immunological aspects
  • Demonstrate insight into intrisic disorder of proteins
  • Describe and understand disorder characteristics
  • Describe the concepts of intrisic disorder in relation to membrane proteins and evaluate and analyses outputs
  • Knowledge on post translational modifications in relation to protein disorder
  • Describe thermodynamically the underlying physical chemistry in protein interactions and discuss these in terms of conformer selection
  • mechanism of protein-protein interactions
  • Describe and understand the following terms: protein sequence convergence and divergence, orthologous 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
  • Describe and understand structure, function and application of fluorescent proteins
  • Participate in a seminar on latest topics in protein science

Skills
:
  • Demonstrate a general understanding of a selection of biophysical, spectroscopic, chemical and analytical methods
  • Demonstrate the ability to assess when to use which methods for solving a specific problem
  • Calculate redox and reaction rate of thiols and disulfide equilibria
  • Apply the understanding of immunological techniques to practical problems in cellular protein chemistry
  • Demonstrate a thorough understanding of the structure/function relationship of disordered proteins
  • Evaluate protein stability and flexibility in relation to function
  • 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)
  • Design experiments based knowledge on structure, function and application of fluorescent proteins
  • Evaluate methods and theoretical approaches to address specific questions in relation to this research topic
  • Write a grant proposal in relation to a pre-defined subject provided by the lecturers of the course
  • Demonstrate written- and oral communication in a protein scientific language

Competencies
:
  • Integrate experimental and theoretical data in membrane protein structure analysis and integrate these in relation to pharmaceutical
  • Science
  • Critically evaluate experimental results from proteomic analysis
  • 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 subjects
  • Communicate verbally in a scientific language and present results in power points in a clear and informative way
  • Analyze, evaluate and condense experimental data in protein science from combinations of all possible areas of curriculum to solve relevant
  • protein science problems
See Absalon.
It is a requirement that a basic course in protein chemistry or protein biology has been passed, such as Biokemi2 (Biochemistry), Proteinkemi og Enzymology I (Molecular biomedicine), Almen biokemi 2 (Biology), Nanobio 2 (Nanoscience).

Open to students of Biochemistry, Biology, Nanascoence, and Molecular Biomedicine 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.
Subject-oriented teaching. A mixture of lecturing, problem solving, student seminars, computer assignments, and scientific discussions. A written essay is handed in based on an assigned subject and presented orally with feed-back. The essay forms the initiation point for the exam.
Credit for this course will not be given to students that have passed the former courses "Theoretical Protein Chemistry" or "Proteiner. Struktur og funktion".
  • Category
  • Hours
  • Exam
  • 0,5
  • Lectures
  • 3
  • Preparation
  • 138,5
  • Project work
  • 40
  • Theory exercises
  • 24
  • Total
  • 206,0
Credit
7,5 ECTS
Type of assessment
Oral examination, 30 minutes
The exam is without preparation and is initiated from the essay.
Exam registration requirements
To be able to attend the exam the students should have performed the following at a satisfactory level:

1) Written a grant proposal relating to a subject presented at the course after guidelines provided at the course

2) Presented the proposal orally in a 10 minutes presentations and discussed the content satisfactorily with the assigned lecturer
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners
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".