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Synthetic Logic for Biochemistry - CHE00027I

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  • Department: Chemistry
  • Module co-ordinator: Dr. Martin Fascione
  • Credit value: 20 credits
  • Credit level: I
  • Academic year of delivery: 2020-21
    • See module specification for other years: 2019-20

Module will run

Occurrence Teaching cycle
A Autumn Term 2020-21 to Summer Term 2020-21

Module aims

Organic chemistry and the synthetic logic which underpins it is essential for the study of modern chemical and cell biology. Of particular importance is the ability to synthesise molecules capable of intervening in biological pathways - as such in lectures during this course you will explore retrosynthesis - a key strategic approach to modern synthetic chemistry. Additionally, you will also begin to understand how organic chemists can differentiate between different mechanistic pathways. This is important in biological processes as it enables biochemists to deconvolute the way in which enzymes work. Advanced organic chemistry practicals held throughout the duration of the module will serve to reinforce the synthetic and mechanistic chemistry principles discussed in these lectures. Through a combination of lectures and workshops you will also learn how organic chemists can use their underpinning knowledge to: i) recapitulate Nature’s chemical logic in the lab in the in vitro organic synthesis of key biomolecules such as peptides and sugars, this will introduce key concepts such as protecting group methodology, coupling chemistry and control of stereochemical outcomes during reactions; and also iii) combine chemical and biological understanding to enzymology, leading to enhanced and new reactivity facilitating the study of dynamic biological processes.

Module learning outcomes

This module builds directly on your Year 1 organic chemistry, providing you with a greater depth of understanding, some hands on practical work, and an understanding of how strategy, mechanism and synthesis begin to work together in advanced organic chemistry. You will also learn how an understanding of organic reaction mechanisms has allowed chemists to design and synthesise chemical probes which have been deployed for the study of biochemical processes in vivo.

Module content

Retrosynthetic Analysis (AFP, 6 lectures, 1 x 2h unassessed workshop)

Strategy of organic synthesis, synthons, planning and designing the synthesis of organic targets.


Synthesis of Biological Molecules (LIW, 6 lectures, 1 x 2h unassessed workshop)

Synthesis of peptides including coupling chemistry and protecting group methodologies. Synthesis of sugars including protecting groups, the anomeric effect and stereochemistry/conformation.


Chemical tools for biology (MAF, 6 lectures, 1 x 2h unassessed workshop)

Showcasing how synthetic logic applied to enzymology can deliver enhanced or novel reactivity for chemical and cell biology. Including in vivo/ in vitro labelling of proteins.


Physical Organic Chemistry (IJSF, 8 lectures, 1 x 2h unassessed workshop)

Determining the mechanism of organic reactions. Hammett relationship, electronic and steric effects on reactions, thermodynamics and kinetics of reaction processes, solvent effects.

Practical Chemistry (MAF, 6 1-day practicals)

Advanced organic synthesis practicals focussing on development of key skills including, air sensitive chemistry technique, flash column chromatography, and NMR spectroscopy.



Task Length % of module mark
Online Exam
Synthetic logic for biochemistry 1
N/A 35
Online Exam
Synthetic logic for biochemistry 2
N/A 35
N/A 30

Special assessment rules


Additional assessment information

Closed examination 70%

Spring exam (35%, 1.5 h), 2 compulsory 20 mark questions (1 from AFP, 1 from MAF)

Summer exam (35%, 1.5 h), 2 compulsory 20 mark questions (1 from IJSF, 1 from LIW)

Assessed practicals    30%

Practical experiments 1 and 2 (autumn week 4 and 7) will be formatively assessed.

Practicals 3 (autumn week 10), 4, 5, and 6 (Spring week 2, 5 and 8)  assessed through post and in-lab write up, sample quality, and characterisation, with equal weighting for each experiment.

The submission deadlines for all practical scripts is on the same day of the following week.


Task Length % of module mark
Online Exam
Synthetic logic for biochemistry 1
N/A 35
Online Exam
Synthetic logic for biochemistry 2
N/A 35

Module feedback

Workshops: Written and/or oral feedback for workshops will be given either during the sessions or within a week.

Practicals: Written feedback will be provided on all summative practical work within 20 working days

Exams: Closed exam results with per-question breakdown are returned to the students via supervisors within 5 weeks (as per special approval by the University Teaching Committee). Outline answers are made available via the Chemistry web pages when the students receive their marks, so that they can assess their own detailed progress/achievement. The examiners’ reports for each question are made available to the students via the Chemistry web pages.

Indicative reading

Retrosynthesic Analysis:

Organic Synthesis, C. Willis and M. Wills, Oxford (Primer)

Organic Chemistry, J. Clayden, N. Greeves, S. Warren & P. Wothers, Oxford (briefly in Chapter 30)

Organic Synthesis: The Disconnection Approach, S. Warren (1st  ed) or S. Warren & P. Wyatt (2nd  ed), Wiley

Keynotes in Organic Chemistry, A.F. Parsons, Blackwell (for revising year 1 reactions)

Synthesis of biological molecules: 

Amino Acid and Peptide Synthesis, J. Jones

Carbohydrate Chemistry, B.G. Davis and A.J. Fairbanks

The information on this page is indicative of the module that is currently on offer. The University is constantly exploring ways to enhance and improve its degree programmes and therefore reserves the right to make variations to the content and method of delivery of modules, and to discontinue modules, if such action is reasonably considered to be necessary by the University. Where appropriate, the University will notify and consult with affected students in advance about any changes that are required in line with the University's policy on the Approval of Modifications to Existing Taught Programmes of Study.

Coronavirus (COVID-19): changes to courses

The 2020/21 academic year will start in September. We aim to deliver as much face-to-face teaching as we can, supported by high quality online alternatives where we must.

Find details of the measures we're planning to protect our community.

Course changes for new students