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Advanced Methods in Biochemistry

The course provides a thorough overview of modern biochemical and molecular biological methods, as well as available resources for gaining knowledge about these methods.


‘Advanced Methods in Biochemistry’ will introduce you to the fundamental principles behind several basic and more advanced techniques commonly used in biochemical research. During the course, the strengths and weaknesses of each technique will be covered to explain which techniques are suitable for particular applications.

Upon establishing this foundation, you will be taught how to combine different methods to overcome problems associated with the individual techniques. The theoretical aspect of the course will be supplemented with a lab practical where you will apply a number of these techniques yourself. In the end, you should be able to design strategies to address complex biological questions using the techniques you have been exposed to from a theoretical and practical perspective.

Upon completion of the course you should be able to:

  • Describe the principles behind a number of common biochemical techniques.
  • Explain the strengths and weaknesses of a technique for particular applications.
  • Combine different biochemical methods to address a complex biological question.  
  • Troubleshoot biochemical methods based on their scientific principles. 
  • Analyze generated data and communicate them in writing and orally.
  • Read, communicate and critically evaluate course-related scientific literature.

You will be expected to:

  • Attend and actively participate in the lectures and tutorials.
  • Participate in discussions with other students and the faculty.
  • Read the assigned literature and complete the assignments and the lab report on time.
  • Present the lab practical results in writing and make the appropriate corrections.
  • Course structure

    Materials on how to make buffers and solutions (including sterilization), pH, the metric system, statistics and making lab notes are provided at the beginning of the course.

    These are some of the topics that will be covered:

    - Cell homogenization and fractionation
    The organization and chemical composition of pro- and eukaryotic cells will be discussed in relationship to different homogenization methods, which are used to enrich for particular fractions from these cells.

    - History of molecular biology 
    Students will be taught the history behind the main organisms used for molecular biology and how these are handled, genotyped, cultured and stored.

    - Centrifugation
    The theoretical basis for multiple centrifugation techniques will be explained as well as their applications. These include: differential centrifugation, density gradient centrifugation and analytical ultracentrifugation.

    - Recombinant DNA techniques
    Several modern DNA analysis methods will be covered, ranging from DNA isolation and sequencing to PCR and a variety of molecular biology techniques for DNA manipulation. Significant time will be spent on: restriction enzyme digests and other reactions that modify DNA, PCR, primer design, sequencing methods, homology cloning, Gibson cloning, recombineering, Cas9-based genome editing, forwarded evolution et c.

    - Protein production
    Several different eukaryotic and prokaryotic protein production platforms are available. These will be thoroughly explained from both a theoretical and need perspective based on the current protein production bottlenecks. Specifically, we will address how to choose an organism, the expression system, and the design of the target gene.

    - Protein isolation using physiochemical properties
    The biochemical principles for a number of basic protein purification techniques will be covered. This will include the buffer systems and resins that support: affinity chromatography, ion exchange chromatography, hydrophobic interaction chromatography, and gel-filtration. We will also go over which of these are suitable for HPLC and why.

    - Antibodies and their applications
    We will discuss the factors to consider for generating a polyclonal/monoclonal antibody, alternative binding approaches that can replace antibodies, and several applications such as: immuno-blotting, immuno-precipitations, and ELISAs.

    - Mass spectrometry
    Basics of mass spectrometry, MALDI-TOF, MS/MS (including sequencing proteins), quantitative proteomics (e.g. iTRAQ, iCAT and spectral counting) and characterization of post-translational modifications using MS et c.

    - Gel-electrophoresis and detection methods
    Different gel-electrophoresis techniques for DNA and protein will be explained as well as a number of methods for staining and detection.

    - Microarrays
    DNA + protein arrays, RNA-seq, ribosome profiling et c.


    Teaching format

    Lectures and tutorials

    All the lectures are linked to tutorials, which are a significant part of the course. For the tutorials you get assignments (‘homework’), i.e., you have to answer questions based on the lectures and articles you have to read.

    The assignments are handed in, checked (feedback is given) and graded (fail, good, very good). In case the tutorial is graded with a ‘fail’, the tutorial has to be corrected until it is graded with at least a ‘good’.

    To be able to finish the course all tutorials should have been graded with a ‘good’ or ‘very good’.

    There is one ‘special’ tutorial: the cloning tutorial. In the cloning tutorial you design constructs (primer design, plasmid design, and you learn how to use different computer programs to facilitate this).


    -Protein production practical
    Primer design, PCR, cloning, overexpression screening, monitoring, protein production, cell breakage, centrifugation, protein characterization (SDS-PAGE, immuno-blotting).

    You write a lab report, feedback will be given and report is updated until the level of the report is acceptable.



    Written exam, and the student have to complete all tutorials and lab reports on time.


    Jan-Willem de Gier


  • Schedule

    The schedule will be available no later than one month before the start of the course. We do not recommend print-outs as changes can occur. At the start of the course, your department will advise where you can find your schedule during the course.
  • Course literature

    Note that the course literature can be changed up to two months before the start of the course.

    • "Principles  and  Techniques  of  Biochemistry  and  Molecular  Biology" (8th editon). Edited by Andreas Hofmannn and Samuel Clokie (Cambridge University Press).
    • Hand-outs, articles et c. in electronic form will be provided.
  • Course reports

  • Contact

    Course coordinator and examiner
    Chemistry Section & Student Affairs Office