ATTENTION: This page is kept as a record of Dr Verlinde's teaching activities. Obviously, since retirement Dr Verlinde has no teaching duties anymore.

• Organizers: Christophe Verlinde and Keri Lewis
• Credits: 4
• Offered: Twice a year: Fall and Spring ( max: 56 students)
  WARNING: This lab fills very early.

Syllabus:

I.	Protein isolation
(a)	Basis of affinity chromatography
(b)	Dissociation constants, relative affinities
(c)	Isozymes
(d)	Native gel electrophoresis
(e)	SDS-PAGE analysis of purity
(f)	Quantitative protein determination
(g)	Enzymatic reactions, specific activity, reaction mechanisms
(h)	Kinetic analysis of two-substrate reactions

II.	Immunological techniques
(a)	The antibody response, B cells, T cells, antigen presentation
(b)	Structure and function of IgG
(c)	Isolation of IgY from egg yolk
(d)	Monoclonal and polyclonal antibodies
(e)	Salt precipitation of proteins
(f)	Biotinylation of proteins
(g)	Streptavidin-biotin interaction
(h)	Principles of ELISA
(i)	Principles of Western blot

III.	Recombinant DNA techniques
(a)	Gene structure, exons, introns, mutations
(b)	DsRed fluorescent protein
(c)	Polymerase chain reaction, amplification of DNA
(d)	DNA sequencing based on fluorescent dye terminator
(e)	Sequence analysis with BLAST through NCBI website
(f)	Preparation of a cloning vector
(g)	Cloning of PCR fragment
(h)	Transformation of E. coli, blue/white colony selection
(i)	Mini-prep of plasmid DNA
(j)	Restriction enzyme digestion of amplimers and plasmid DNA
(k)	Agarose gel electrophoresis

• Grading:

  Students will be graded on lab participation (10%), 3 quizes (40%), and 3 written reports (50%).
  
  Grade history: median 3.2 out of 4.0

• Organizer: Christophe Verlinde


• Description:
  
  This course aims to provide a basic understanding of the various forces governing molecular interactions in biology,
  with a focus on medicine. In addition, students will be introduced to the principles of computer modeling techniques
  that are in use for predicting the molecular behaviour of proteins, ligands and their complexes. The power of these
  techniques will then be illustrated in terms of in computro ligand discovery, drug design, and the understanding at the
  atomic level of some genetic diseases. Practical experience will be gained during one computer lab session.

  Note that this is NOT a training course in using a particular molecular software package.

• Contents
  1. Lecture: Forces and Energies
  2. Lecture: HBonds and Salt Bridges
  3. Lecture: Electrostatics
  4. Lecture: Molecular simulations
  5. Lecture: Solvation
  6. Lecture: Membrane protein folding and stability
  7. Molecular modeling session: ligand docking
  
  
• Background and prerequisites

  The course will assume knowledge at the level of an advanced undergraduate level of biochemistry, math and physics.
  Be aware that principles of physical chemistry and equations will not be eschewed.
  

• Grading

  Students will be graded on in-class participation and a final written exam. Participation includes in-class
  assignments and the demonstration of familiarity with assigned reading during in-class discussions.
  
  Grade history: median 3.5 out of 4.0
  

• Recommended reading

  Andrew R. Leach. "Molecular Modelling: Principles and Applications". Prentice Hall, 2nd edition, 2001.

• Credits: 1.5
• Offered: Spring weeks 6-10. (quorum: 7; max: 20 students)

• PABIO 536 lecture from the 90ies (not updated): 3-D Modeling of Proteins
  

• Computational Chemistry by Chris Cramer
• HHMI Biointeractive
• Solvation of macromolecules
• UW BIOC530