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CHEM6095 Advanced Organic Chemistry (Bioorganic)

Module Overview

Aims and Objectives

Module Aims

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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, amino acid biosynthesis and nucleotide biosynthesis.
  • 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.

Syllabus

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. • The chemistry of nucleotide biosynthesis. 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. 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. 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

TypeHours
Wider reading or practice53
Lecture24
Follow-up work25
Practical classes and workshops8
Revision10
Preparation for scheduled sessions30
Total study time150

Resources & Reading list

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

Assessment

Summative

MethodPercentage contribution
Coursework 30%
Examination  (2 hours) 70%

Referral

MethodPercentage contribution
Coursework 30%
Examination  (2 hours) 70%

Repeat Information

Repeat type: Internal & External

Linked modules

Pre-requisites

To study this module, you will need to have studied the following module(s):

CodeModule
CHEM2005Aspects of Organic Synthesis
CHEM2001Organic Reaction Mechanisms
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