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CHEM2010 Organic Chemistry in the Environment

Module Overview

Aims and Objectives

Module Aims

To develop an understanding of how molecules in the environment are made and degraded. The course includes some examples from the natural world (such as proteins, lipid and carbohydrates), and other examples that are manmade (including pesticides and pollutants). To provide an overview of the organic chemistry of the terrestrial environment and the techniques of analysis employed in its study. The course focuses on the chemical and biochemical processes involved in the synthesis and breakdown of both natural and man-made organic chemicals and how they can be investigated. With the objective of establishing a common level of understanding of natural product chemistry, the course starts by providing information of the basic chemicals of life and how they are biosynthesised. The main body of the course then moves to focus on the degradation of natural organic matter in the environment (leading to coal, oil and natural gas formation) together with a discussion of manmade chemicals (pesticides – insecticides and herbicides), their synthesis, applications, biological mechanisms, environmental degradation and impact. Our current understanding of the behavior of organic pollutants in the environment comes from the application of modern methods of organic trace analysis and this topic is therefore introduced in the context of typical applications drawn from the fields of oil exploration and environmental pollution.

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

  • Explain concepts of major biomolecules.
  • Describe methods for extraction, separation, purification and analysis of organic environmental pollutants, using crude oil and pesticides as key examples.
  • Describe the biosynthesis of major biomolecules.
  • Describe the degradation of biomolecules.
  • Apply organic chemistry principles to explain chemistry of biomolecules.
  • Discuss the need for and environmental impact of common pesticides (insecticides and herbicides).
  • Describe the composition and environmental impact of crude oil spills.
  • Describe the biological mechanisms of action of common pesticides.
  • Explain the chemical synthesis of common pesticides, with detailed reaction mechanisms where appropriate.
  • Discuss the mechanisms of chemical and biochemical degradation of common pesticides.


Introduction to Organic Molecules in the Environment. The course begins by describing the chemical structure and properties of several important families of organic compounds that occur in the natural enviroment. These include carbohydrates, proteins (including enzymes), fatty acids, terpenes and lignins. Aspects covered will include the naming and chemical structure, functional groups and biochemical roles and their biosynthesis. The following biosynthetic transformations will be covered: polysaccharides from monosaccharides; D-glucose from carbon dioxide; the plant polymer lignin from cinnamic acids Fate of Organic Molecules in the Environment The second section describes the degradation of organic molecules in the environment. The chemical stability of organic molecules and the chemistry of their breakdown is discussed. The biochemical mechansims that degrade organic molecules and recycle them, including glycosidases, protease and lipases and fatty acid catabolism are discussed. The chemistry of biological oxidations in mammalian and microbial systems is described. The carbon cycle and the formation of coal oil and gas is discussed. Man’s discovery of oil and gas reserves depends on our ability to determine their presence and quality in geological formations. Man-made Materials in the Environment The third section of the course includes a discussion of man-made environmental pollution, including concepts of chemical toxicity, biomagnification and persistence. Six classes of compounds will be studied: organophosphorus and carbamate insecticides, organochlorine insecticides, polychlorinated biphenyls, dioxins and herbicides. The chemistry, biological activity and environmental consequences of use of each class will be described including the structures, chemical synthesis, mode of action, enviromental impact and associated problems, mechanisms of dispersal and highlighting some solutions to environmental problems. Pollution in the Environment and Modern Analytical Methods The final section of the course will show how extraction methods and modern trace analysis (gas and liquid chromatography), when used in combination with mass spectrometry, can be employed to investigate the persistence and breakdown of organic pollutants in the environment. Examples and case studies used will draw on the topics covered in the earlier sections of the course.

Learning and Teaching

Teaching and learning methods

Lectures, problem-solving Seminars with group working and tutor support

Follow-up work70
Preparation for scheduled sessions38
Total study time150

Resources & Reading list

S D Killops and V J Killops (2004). An Introduction to Organic Geochemistry. 

G W van Loon and S J Duffy (2000). Environmental Chemistry: A Global Perspective. 

Clayden, Greeves, Warren and Wothers. Organic Chemistry. 

J Mann (1987). Secondary Metabolism. 

R P Schwarzenbach, P M Gschwend and D M Imboden (2002). Environmental Organic Chemistry. 



MethodPercentage contribution
Examination 100%


MethodPercentage contribution
Examination 100%

Repeat Information

Repeat type: Internal & External

Linked modules

Pre-requisites: CHEM1031 AND CHEM1032

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