Molecular Microbiology

Course content

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, genetic engineering 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 detection 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 is now possible to classify prokaryotes numerically and thereby choose model systems of general importance.

The present course in Molecular Microbiology is taught by researchers belonging to the Sections of Functional Genomics and of Biomolecular Science. It is our aim with the course to give a broad overview of both the fundamental knowledge and the rapidly developing and exciting topics in Molecular Microbiology. Emphasis is placed on the molecular mechanisms underlying bacterial stress physiology, which is essential for bacterial survival in the environment, and thereby tolerance and resistance to antibiotics. The topics will be discussed in lectures given by researchers and also in theoretical excises(i.e. colloquium) where in-depth discussion of recent research articles will be presented by the students with guidance from the instructors. Finally, in the laboratory exercise part, relevant critical and cutting-edge techniques will be used to investigate research problems that we currently study in the laboratory. This comprehensive course will thus provide a strong platform for those students who wish to pursue or already are pursuing a research career in molecular microbiology and also in areas connected with general microbiology.

The theoretical part (lectures and colloquia) will contain an in-depth discussion of molecular topics such as:

  • Techniques used to study molecular microbiology
  • Basic bacterial physiological processes, such as DNA replication, gene transcription, protein translation
  • How bacteria under stress reprogram their physiology by using e.g. intracellular second messengers ppGpp
  • How bacteria under stress reprogram their transcription patterns using alternative RNA polymerase sigma factors
  • How bacteriophages interactwith and hijack bacterial cells 
  • Molecular mechanisms of bacterial translation and its dynamic regulation in response to stresses
  • Bacterial ribonucleases and small regulatory RNA molecules
  • Molecular mechanisms underlying bacterial survival during stationary phase
  • The connection between growth rate, ribosome synthesis and translation

The practical part (lab exercises):

The practical part of the course will consist of a full-time two-week lab course. During that time the students will be introduced to several techniques within the field of molecular microbiology, including:

  • Basic methods for propagation of bacteria in the laboratory
  • Purification of DNA (plasmid, genome) from bacterial cells 
  • Using reporter genes to analyze gene expression
  • PCR and genetic construction of site-directed mutant genes and proteins
  • Molecular cloning techniques
  • DNA sequencing and sequence analysis
  • Study of protein-protein interactions by using a two-hybrid system
  • Analyzing protein structure using Pymol
  • Strategies for proper documentation of laboratory experiments and results
  • Discussion of the obtained results 

BSc Programme in Biochemistry
BSc Programme in Biology
BSc Programme in Molecular Biomedicine

Learning outcome



Describe and understand the following: 

  • The genetics of model bacterial organisms
  • The molecular processes of DNA replication 
  • Transcription in bacteria 
  • How bacteria reprogram the physiology upon stresses by using sigma factors and the stringent response messenger ppGpp



  • Evaluate the stringent response in relation to bacterial physiology
  • Know how to construct and express mutant genes and proteins
  • Know how to study protein-protein, protein-DNA and protein -small ligand interactions



  • Ability to combine knowledgeand skills to solve problems 
  • Be able to read, understand and present cutting edge literatures in the field of molecular microbiology
  • Be able to pinpoint inconsistent data or explanations in literatures by using one’s knowledge obtained and logic reasoning
  • Having a mindset to apply ceitical thinking on the project or litteratures andformulate your own hypothesis regarding open questions in molecular microbiology and design experiments to test them

Lectures, colloquia and lab exercises

See Absalon.


Teaching and learning materials and methods:




  • An eBook will be used to give an overview and provide some reading materials of the related topics.  But, the teachers will make presentation slides containing more materials beyond the eBook and from other sources (such as other textbooks, review articles), to better cover the topics.  A detailed teaching plan with this information will be provided before the course starts.
  • The different teachers may use varied teaching methods and activities to teach these topics. For instance, some teachers will use in-class presentations and/or following quizzes, whereas others may provide recorded videos of some lectures, and ask you to do corresponding quizzes before an in-class discussion of your learning outcome. For the latter, the teachers will remind you beforehand what to do.




  • Recent and/or classic research articles will be used to give a chance to read and understand how research is done. You will also learn how to logically think about and address a scientific question through this theoretical exercise.
  • You will form several study groups voluntarily, and each group will be assigned a portion of a research article. Each group presents the assigned results and answer relevant questions from the other groups and the teachers.


Lab exercises


  • A lab manual will be prepared for you to read up on the theoretical background and the scientific questions to be addressed. The techniques to be used will be explained as well. Besides, detailed daily plan and procedures will be provided inside the manual.
  • You will form groups of 2-3 to perform the experiments each day. The teachers will explain and discuss the principles each day with you before you actually perform the experiments. Other experiment related questions will be discussed as well. You will also need to write a detailed lab notebook to record precisely what you did and how you did, and the result you obtained. At the end of the exercise, all data will be pooled together and discussed with relevant questions.

Curriculum in 1. and 2. year courses (BSc Programme in Biochemistry, BSc Programme in Biology or BSc Programme in Molecular Biomedicine) are considered known.

Type of assessment
Written examination, 4 hours under invigilation
Type of assessment details
The course has been selected for ITX exam
See important information about ITX-exams at Study Information, menu point: Exams -> Exam types and rules -> Written on-site exams (ITX)
Written aids allowed




Marking scale
7-point grading scale
Censorship form
External censorship

The same as the ordinary exam.

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

All written aids allowed

Criteria for exam assessment

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

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 20
  • Class Instruction
  • 10
  • Preparation
  • 288
  • Practical exercises
  • 90
  • Exam
  • 4
  • English
  • 412


Course number
Programme level

1 block

Block 1
Uden for skemastruktur
The number of seats may be reduced in the late registration period
Study Board for the Biological Area
Contracting department
  • Department of Biology
Contracting faculty
  • Faculty of Science
Course Coordinator
  • YONG ZHANG   (10-7d73726b327e6c65726b44666d73326f7932686f)
Saved on the 15-05-2023

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