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Study information

Secondary Metabolites

Module titleSecondary Metabolites
Module codeBIO3090
Academic year2024/5
Module staff

Dr Alison Hill (Convenor)

Duration: Term123
Duration: Weeks


Number students taking module (anticipated)


Module description

In this module, you will learn about how microorganisms make structurally complex metabolites, such as nicotine, the antibacterial drug erythromycin and cholesterol, from simple basic building blocks. We will explore the pathways that are used to build up these molecules and the enzymes that catalyse the reactions. We will also discuss the shikimic acid pathway.  The structure and chemistry of amino acids and monosaccharides will also be examined and you will gain an understanding of their typical reactions and how they are used in synthesis.

Module aims - intentions of the module

This module aims to study the applications of organic compounds in the natural world with particular reference to biological systems. It further aims to rationalise the properties and reactivity of the principal classes of natural products and to demonstrate the fundamental chemistry behind biochemical reactions in biosynthetic pathways.

Intended Learning Outcomes (ILOs)

ILO: Module-specific skills

On successfully completing the module you will be able to...

  • 1. Recognise and draw complex natural products and biomolecules in three dimensions and perform retrobiosynthetic analysis in order to devise multi-step biosynthetic routes
  • 2. Summarise and critically evaluate the organic chemistry aspects of chemical processes important in biology
  • 3. Illustrate and critically discuss the structure and function of important biomolecules
  • 4. Discuss the chemical reactivity and physical properties of important biomolecules

ILO: Discipline-specific skills

On successfully completing the module you will be able to...

  • 5. Analyse and evaluate independently a range of research-informed literature, and synthesise research-informed examples from the literature into written work
  • 6. Deploy established techniques of analysis and enquiry

ILO: Personal and key skills

On successfully completing the module you will be able to...

  • 7. Communicate effectively arguments, evidence and conclusions using written and oral means in a manner appropriate to the intended audience
  • 8. Develop logical and reasoned argument with sound, convincing conclusions
  • 9. Analyse and evaluate appropriate data with very limited guidance

Syllabus plan

Interaction of functional groups to produce molecules with unusual reactivity is exemplified by the polyketide-derived metabolites, the amino acids (acid-base properties, peptides and hormones), the carbohydrates (acetals, hemi-acetals and mutarotation, stereochemistry both configurational and conformational), certain heterocyclic bases, terpenes and organyl phosphates, shikimic-acid derived metabolites.

Description of natural product biosynthetic pathways based on acetate, amino acids and mevalonate and how they are investigated using labelled compounds

Comparison of biochemical reactions with the basic organic chemistry covered in previous modules.

Learning activities and teaching methods (given in hours of study time)

Scheduled Learning and Teaching ActivitiesGuided independent studyPlacement / study abroad

Details of learning activities and teaching methods

CategoryHours of study timeDescription
Scheduled Learning and Teaching14Lectures
Scheduled Learning and Teaching3Small group tutorials
Scheduled Learning and Teaching1Journal club
Scheduled Learning and Teaching1Revision tutorial
Guided Independent Study6Tutorial work
Guided Independent Study45Lecture consolidation and associated reading
Guided Independent Study20Preparation of coursework
Guided Independent Study20Problem-based learning
Guided Independent Study38Exam revision
Guided Independent Study2Journal club preparation

Formative assessment

Form of assessmentSize of the assessment (eg length / duration)ILOs assessedFeedback method
Lecturer feedback during small group tutorialsAd hocAllOral
Journal club1 x 1 hour5-9Oral
Lecturer Feedback through PadletAd hocAllWritten

Summative assessment (% of credit)

CourseworkWritten examsPractical exams

Details of summative assessment

Form of assessment% of creditSize of the assessment (eg length / duration)ILOs assessedFeedback method
Problem and essay-based examination602 hoursAllWritten on request
Problem sheet 1153 hours1-7Written and model answers
Problem sheet 2254.5 hoursAllWritten and model answers

Details of re-assessment (where required by referral or deferral)

Original form of assessmentForm of re-assessmentILOs re-assessedTimescale for re-assessment
Problem and essay-based examinationProblem and essay-based examination (60%)AllAugust Ref/Def
Problem sheet 1Problem sheet 1 (15%)1-7August Ref/Def
Problem sheet 2Problem sheet 2 (25%)AllAugust Ref/Def

Re-assessment notes

Deferral – if you miss an assessment for certificated reasons that are approved by the Mitigation Committee, you will normally be either deferred in the assessment or an extension may be granted. If deferred, the format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). The mark given for a deferred assessment will not be capped and will be treated as it would be if it were your first attempt at the assessment.

Referral - if you have failed the module (i.e. a final overall module mark of less than 40%) and the module cannot be condoned, you will be required to complete a re-assessment for each of the failed components on the module. The format and timing of the re-assessment for each of the summative assessments is detailed in the table above ('Details of re-assessment'). If you pass the module following re-assessment, your module mark will be capped at 40%.

Indicative learning resources - Basic reading

  • Mann J., Chemical Aspects of Biosynthesis, Oxford Primer, Oxford University Press, 1994, ISBN 0-19- 855676-4
  • Dewick, PM, Medicinal Natural Products – A Biosynthetic Approach, Wiley-Blackwell, 2009, ISBN 0470741678
  • J. H. Jones, Amino acids and Peptide Synthesis, Oxford Primer, Oxford University Press, 2002 ISBN 0-19-925738-8
  • B. G. Davis and A. J. Fairbanks, Carbohydrate Chemistry, Oxford Primer, Oxford University Press, 2002 ISBN 0-19-855833-3

Indicative learning resources - Web based and electronic resources

  • ELE page

Key words search

Microorganisms, amino acids, monosaccharides, biosynthesis, secondary metabolism, polyketides, terpenes, shikimate, alkaloids

Credit value15
Module ECTS


Module pre-requisites

BIO2085 Structure and Reactivity of Organic Compounds II (BIO2086 is useful)

Module co-requisites


NQF level (module)


Available as distance learning?


Origin date


Last revision date