NBIA06018U Protein Science B (ProtSciB)

• 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
• Describe and understand methods of protein stability determination
• 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
• 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
• 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
• Understand the underlying physical chemistry in protein interactions and calculate binding parameters from selected graphical presentations
• Describe mechanisms of intracellular protein turnover in relation to proteasome structure and function
• Describe and understand the use of immunological techniques in protein chemistry
• Describe and understand selected theoretical aspects of enzyme catalysis and mechanism
• Understand and integrate different regulatory aspects of enzymes
• Have an insight in apoptosis (programmed cell death)
• Describe and understand the basic concepts of enzyme engineering
• Describe and understand the application of fluorescent proteins
• Participate in a seminar on contemporary topics in protein scienc

Skills:

• Cite the most common posttranslational modifications and describe their features in broad terms
• Determine the stability of proteins from urea or guanidinium unfolding/refolding curves
• 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
• 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
• Understand the relative advantages of the above methods for protein structure and functional analysis
• 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
• 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
• 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
• 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)
• Evaluate methods and theoretical approaches to address specific questions in relation to this research
• Demonstrate written- and oral communication in a protein scientific language

Competencies:

Combine the understanding of amino acids, modifications and structural elements and to apply this to a general understanding of proteins structure and function
Combine the understanding of protein folding and stability to a general understanding of the relationship between in vivo and in vitro protein folding
Critically evaluate advantages and disadvantages of different procedures used for proteins purification and characterization
Demonstrate a thorough understanding of the structure/function relationship of various membrane protein families
Critically evaluate experimental results from proteomic analysis
Critically evaluate experimental data on enzyme mechanisms, function, and regulation
Combine the knowledge on regulation and kinetics to biological systems
Design, execute, critically evaluate, and present experiments in protein chemistry