NBIB16001U  Molecular Microbiology

Volume 2016/2017

BSc Programme in Biochemistry

BSc Programme in Biology


Molecular Microbiology is a discipline that combines genetics, physiology, biochemistry, molecular biology and cytology with microbiology. These fields have undergone dramatic, in some cases almost explosive, developments during the last decade. In particular, the genetics of microorganisms has become very efficient with rapid methods of gene mutation and replacement and rapid whole genome sequencing; biochemistry has been revolutionized by methods for rapid protein purification and crystallization and high-throughput protein-protein interaction methods whereas cytology has been revolutionized by the introduction of fluorescent protein tags and a number of high-end methods to visualize the fluorescently tagged proteins within living cells. Last but not least, the genomics era has spawned a genuine revolution in microbiology, transforming it into an exact discipline. There are now more than 8,000 fully sequenced and annotated prokaryotic genomes available. Making use of this vast biological information it is now possible to classify prokaryotes numerically and thereby chose model systems of general importance.   

The present course in Molecular Microbiology is held by researchers belonging to the Centre for Bacterial Stress Response and Persistence that was generated by funding from the Danish National Research Foundation, the Novo Nordisk Foundation and the European Research Foundation. It is our aim with the course to give a broad overview of rapidly developing and exciting topics in Molecular Microbiology, with an emphasis on molecular mechanisms underlying bacterial stress physiology and survival. Each lecture will give an overview of a separate topic as described below. These topics will then be discussed in depth via recent research articles presented by the students and the teachers. Finally, in the laboratory part, relevant cutting edge techniques will be used to investigate research problems that we currently studying. This comprehensive course will thus provide a strong platform for those students who wish to pursue or already is pursuing a research career in Molecular Microbiology and related fields.           

The theoretical part (lectures and colloquia) will contain an in-depth discussion of the following topics:

  • Basic bacterial physiology analysed with cutting edge technologies such as microarrays, deep RNA sequencing and ribosome profiling. The connection between growth rate, ribosome synthesis and translation
  • How bacteria under stress uses intracellular second messengers (ppGpp and cyclic-di-GMP) to reprogram their physiology
  • How bacteria under stress reprogram their transcription patterns using alternative RNA polymerase sigma factors
  • Molecular mechanisms underlying bacterial survival duringstationary phase
  • Heterogeneity (stochasticity) in bacterial populations: sporulation, competence and persistence
  • Molecular mechanisms underlying bacterial persistence
  • How bacterial toxin – antitoxins contribute to survival during stress
  • Bacterial cell division and DNA segregation. Presentation of high-end cytological methods to study cell division in bacterial model organisms
  • Bacterial cell wall synthesis and its control
  • The coupling between stress response and cell wall synthesis
Learning Outcome


  • Ability to describing and understanding genetics of model organisms
  • Understanding how whole genome sequences forwards rapid genetic analysis
  • Understanding how phylogeny and genomics allow for the design of projects aiming at answering important questions of general biological significance 
  • Describing and understanding how the use of fluorescent proteins has transformed cell biology
  • Describing and understanding cell division and DNA segregation in bacteria
  • Describing and understanding the biology and function of bacterial cell walls
  • Describing and understanding the transcription machinery in bacteria
  • Understanding and describing the translation machinery in bacteria.


  • Evaluate the stringent response in relation to bacterial physiology and pathogenesis
  • Know how to use phylogeny and genomics to design projects aiming at answering important questions of general microbiological significance 
  • Know how to use fluorescent reporter fusion proteins to obtain knowledge about the cellular dynamics of particular proteins.


  • Be able to read, understand and present cutting edge literature in the field of molecular microbiology
  • Be able to use standard phylogenetic analyses and web based databases to understand the biological importance of specific genes, proteins and metabolites.

See Absalon.

Curriculum in 1. and 2. year courses are considered known.
Lectures, colloquia and lab exercises.
Type of assessment
Written examination, 4 hours under invigilation
All aids allowed

NB: If the exam is held at the ITX, the ITX will provide computers. Private computers, tablets or mobile phones CANNOT be brought along to the exam. Books and notes should be brought on paper or saved on a USB key.

Marking scale
7-point grading scale
Censorship form
External censorship

As ordinary exam.

If ten or fewer students have signed up for re-exam, the type of assessment will be changed to an 30 minutes oral exam (1 hour preparation, all aids allowed).

Criteria for exam assesment

In order to obtain the grade 12 the student should convincingly and accurately demonstrate the knowledge, skills and competences described under "Learning Outcome".

  • Category
  • Hours
  • Lectures
  • 20
  • Colloquia
  • 20
  • Practical exercises
  • 90
  • Exam
  • 4
  • Preparation
  • 278
  • Total
  • 412