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The University of Southampton

CHEM3038 Advanced Organic Chemistry (Bioorganic)

Module Overview

Aims and Objectives

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

  • Detail the structure of DNA and RNA, including the structure of the bases.
  • Explain and detail the mechanism of the reactions used in solid-phase DNA synthesis.
  • Discuss and describe the structure and synthesis of carbohydrates.
  • Detail the structure of amino acids, and how they assemble to form peptides and proteins.
  • Design the chemical synthesis of a short peptide, including the mechanisms of the proposed steps.
  • Understand the chemical basis and mechanisms of the cellular pathways in glycolysis.
  • Determine the biochemical origin of terpene and polyketide natural products. Understand the role of chemical mechanisms in the biosynthetic reactions leading to terpene and polyketide natural products
  • Explain the role of enzymes in natural product biosynthesis.
  • Understand the importance of natural products in the modern world.


Fundamentals of Bio-organic Chemistry Nucleic Acids Chemistry • Chemical structure and properties of nucleosides, nucleotides, nucleic acids. • Structure and properties of DNA – A, B, and Z-DNA structures, Watson-Crick base pairing. • The biological and biochemical mechanisms of DNA replication and transcription. • Synthesis of nucleosides as drugs and for oligonucleotide synthesis, involving protecting group chemistry. • Automated solid-phase DNA synthesis using phosphoramidite chemistry with emphasis on the reaction mechanisms of each step. Carbohydrate Chemistry An Introduction to Carbohydrates, their classification, structure and representation, Mutarotation, anomeric effect, conformational equilibria, death-taxes-protecting groups, Glycosyl donors/acceptors, polysaccharides and nucleosides. Enzymology and Protein Chemistry • The structure of amino acids and the primary, secondary and tertiary structure of peptides and proteins. • Mechanism of the serine proteases – the Asp-His-Ser catalytic triad and stabilisation of the tetrahedral oxyanion intermediate by hydrogen bonding. • Molecular basis for the selectivity of the serine proteases – trypsin as compared to chymotrypsin. • Mechanism of the methyltransferases • Michaelis-Menten enzyme kinetics. • The chemical reactions of glycolysis. • .The chemistry of amino acid biosynthesis. Natural Product Biosynthesis • Thioesters of co-enzyme A as acyl group carriers in biosynthesis. • Chemical structure of terpenes (including monoterpenes, sesquiterpenes, diterpenes and polymers) and their derivation from isoprene units. • The biosynthetic pathway to isoprenoids - Claisen-like, Aldol and decarboxylation mechanisms and the subsequent formation of isoprene equivalents illustrated by dimethyl allyl pyrophosphate (DMAPP). • Terpene biosynthesis: The reaction steps fall into three classes: i) initiation: formation of the carbocation ii) propagation: rearrangement/reaction of the carbocation iii) termination: quenching of the carbocation. Formation of a wide variety of monoterpenes by quenching of the α-terpinyl cation. • Biosynthesis of sequiterpenes, diterpenes and triterpenes. • Fatty acid biosynthesis. Six key steps: i) thioester formation ii) C-C bond formation iii) ketone reduction iv) dehydration v) enoyl reduction vi) thioesterase. • Polyketide and aliphatic polyketide biosynthesis. Aromatic Polyketide biosynthesis. • Biosynthesis of 6-methylsalicylic acid, tetracylins. Modular polyketide synthases, erythromycin biosynthesis, engineering novel polyketide antibiotics.

Learning and Teaching

Teaching and learning methods

Lectures, workshops

Practical classes and workshops8
Wider reading or practice53
Preparation for scheduled sessions30
Follow-up work25
Total study time150

Resources & Reading list

J. McMurry and T. Begley. The Organic Chemistry of Biological Pathways. 



MethodPercentage contribution
Final Assessment   (2 hours) 100%


MethodPercentage contribution
Final Assessment   (2 hours) 100%

Repeat Information

Repeat type: Internal & External

Linked modules

Pre-requisites: CHEM2001 AND CHEM2005

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