BI2MM2: Molecular Microbiology

Module code: BI2MM2

Module provider: School of Biological Sciences

Credits: 20

Level: 5

When you’ll be taught: Semester 2

Module convenor: Professor Simon Andrews , email: s.c.andrews@reading.ac.uk

Module co-convenor: Dr Glyn Barrett, email: glyn.barrett@reading.ac.uk

Pre-requisite module(s): BEFORE TAKING THIS MODULE YOU MUST ( TAKE BI1FM1 AND TAKE BI1CMP1 ) (Compulsory)

Co-requisite module(s):

Pre-requisite or Co-requisite module(s):

Module(s) excluded:

Placement information: NA

Academic year: 2025/6

Available to visiting students: Yes

Talis reading list: Yes

Last updated: 3 April 2025

Overview

Module aims and purpose

Although microscopic and relatively simple, microbes impact our lives and the planet profoundly, and they use remarkably complex mechanisms to replicate, survive, evolve, and interact with their environment and other host organisms. The purpose of this module is to deliver a detailed understanding of the mechanisms that microbes use to thrive and adapt to the multiple challenges that they face.  

In this module you will learn about microbial genetics and evolution including the mechanisms of horizontal gene transfer that enable bacteria to rapidly evolve and adapt to challenge and opportunity. You will also learn how bacteria protect the integrity of their genomes against DNA damage, discover how bacteria sense and respond to environmental stress, how they regulate their cell cycle and control the replication of their genomes. You will also explore mechanisms of bacterial motility and taxis, and how bacteria assemble their cellular membranes, transport solutes across their membranes and how they inject effector macromolecules directly into host cells to manipulate host-cell function. 

We will consider how bacteria and their viruses (“bacteriophages”) engage in a continuous evolutionary battle (“arms race”) by studying the infection strategies of bacteriophages and the molecular mechanisms bacteria use to defend themselves against bacteriophage infection, and the counter strategies bacteriophages evolve in response to these bacterial defences.  

You will also learn about the various replication strategies used by different viruses focussing in detail on viruses of major significance, including Poliovirus, SARS-CoV-2, Ebola virus, Variola virus (smallpox) and HIV. You’ll discover how these viruses regulate production of viral proteins to ensure successful infection, replication, and dissemination, and how they evolve to overcome immune responses and can adapt to infect new hosts to cause an outbreak of an emerging infectious disease. 

You will engage in a series of microbiology laboratory-based practical classes that will introduce and reinforce microbiology technical skills including aseptic technique, bacterial culture and phage propagation/infection.  You will learn to perform bacterial transposon mutagenesis and transduction experiments, and to reproduce the seminal bacteriophage one step growth curve experiment in a team.  You will also develop skills in genetic problem solving through tutorials.  

After completing this module, you could apply the knowledge you have gained to benefit human society and/or the planet through development of medical, food, environmental and/or biotechnological applications of microbiology in your future studies and career.

Module learning outcomes

By the end of the module, it is expected that students will be able to:

1. Describe and explain molecular details of microbial genome, structure, function and evolution, and solve genetics problems.
2. Describe and explain key bacterial structures and explain cellular processes including molecular mechanisms of solute and protein transport, stress and regulatory responses, motility and taxis.
3. Compare and contrast replication cycles of selected viruses belonging to different Baltimore groups, explaining how they regulate production of viral proteins and avoid / overcome host defence mechanisms.
4. Safely and competently perform molecular microbiology laboratory techniques to generate robust datasets and analyse the functional significance of the results, both independently and collaboratively as part of a team.

Module content

Lecture materials will cover the following topics:

• Bacterial genetics and evolution, including chromosomes, DNA damage and repair, homologous recombination, mobile genetic elements (plasmids, integrons) and mechanisms of horizontal gene transfer (transposition, transformation, transduction, conjugation)
• Bacterial cell cycle, control of DNA replication, bacterial growth regulation
• Bacterial cell structure, physiology, and regulation: cell membrane, solute transport and macromolecule secretion systems, two-component sensor-regulators, stress response systems, quorum sensing, motility and taxis, and sporulation
• Bacteriophage structure and diversity, replication cycles and the mechanism of their multiplication, counter strategies to overcome bacterial defence mechanisms
• Viral genetics and evolution: viral genomes and Baltimore classification, concept of quasispecies, genetic drift and shift, viral tropism and host switching
• Viral genome replication mechanisms, regulation of protein production and immune evasion
• Yeast genetics and replication; cell cycle and control of DNA replication, asexual and sexual reproduction

Practical classes include the following training / activities:

• Good microbiological laboratory practice (GMLP) including aseptic technique and containment
• Transposon Tn5 mutagenesis, mutant selection, mutant screening, gene fusion analysis, transduction experiments
• A large group experiment to recreate the seminal one step bacteriophage growth curve experiment performed by Ellis and Delbrück

Tutorials:

• Guided tutorial exercises support development of microbial genetics problem solving skills
• Effective group work and data handling in Excel

Structure

Teaching and learning methods

The learning outcomes will be met through a mixture of lectures, group work, tutorials, laboratory-based practical classes, self-directed learning and directed independent study. Appropriate supplementary information and reading lists will be provided on Blackboard.

Tutorial sessions will prepare students for an assessed genetics problem solving exercise.

Study hours

At least 45 hours of scheduled teaching and learning activities will be delivered in person, with the remaining hours for scheduled and self-scheduled teaching and learning activities delivered either in person or online. You will receive further details about how these hours will be delivered before the start of the module.

Please note the independent study hours above are notional numbers of hours; each student will approach studying in different ways. We would advise you to reflect on your learning and the number of hours you are allocating to these tasks.

Semester 1 The hours in this column may include hours during the Christmas holiday period.

Semester 2 The hours in this column may include hours during the Easter holiday period.

Summer The hours in this column will take place during the summer holidays and may be at the start and/or end of the module.

Assessment

Requirements for a pass

Students need to achieve an overall module mark of 40% to pass this module.

Summative assessment

Penalties for late submission of summative assessment

The Support Centres will apply the following penalties for work submitted late:

Assessments with numerical marks

• where the piece of work is submitted after the original deadline (or any formally agreed extension to the deadline): 10% of the total marks available for that piece of work will be deducted from the mark for each working day (or part thereof) following the deadline up to a total of three working days;
• the mark awarded due to the imposition of the penalty shall not fall below the threshold pass mark, namely 40% in the case of modules at Levels 4-6 (i.e. undergraduate modules for Parts 1-3) and 50% in the case of Level 7 modules offered as part of an Integrated Masters or taught postgraduate degree programme;
• where the piece of work is awarded a mark below the threshold pass mark prior to any penalty being imposed, and is submitted up to three working days after the original deadline (or any formally agreed extension to the deadline), no penalty shall be imposed;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension to the deadline): a mark of zero will be recorded.

Assessments marked Pass/Fail

• where the piece of work is submitted within three working days of the deadline (or any formally agreed extension of the deadline): no penalty will be applied;
• where the piece of work is submitted more than three working days after the original deadline (or any formally agreed extension of the deadline): a grade of Fail will be awarded.

The University policy statement on penalties for late submission can be found at: /cqsd/-/media/project/functions/cqsd/documents/qap/penaltiesforlatesubmission.pdf

You are strongly advised to ensure that coursework is submitted by the relevant deadline. You should note that it is advisable to submit work in an unfinished state rather than to fail to submit any work.

Formative assessment

Formative assessment is any task or activity which creates feedback (or feedforward) for you about your learning, but which does not contribute towards your overall module mark.

Students will be able to reflect on their progress in understanding lecture material by completing weekly formative quizzes (Blackboard tests and Kahoot! games) 

Students will be encouraged to participate in peer marking of formative genetics problems and essay plans in tutorials to prepare for the summative exam. 

Students will be given the opportunity to reflect on their results and encouraged to seek 1:1 feedback from practical class leaders / demonstrators during laboratory classes to help improve their practical and analytical skills. 

Reassessment

Additional costs