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Chemical and Structural Biology - CHE00036I

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  • Department: Chemistry
  • Module co-ordinator: Dr. Martin Fascione
  • Credit value: 20 credits
  • Credit level: I
  • Academic year of delivery: 2023-24

Module will run

Occurrence Teaching cycle
A Semester 2 2023-24

Module aims

This module builds directly on Stage 1 organic and biological chemistry. In the first half of the module students will be provided with an understanding of how an underpinning knowledge of organic reaction mechanisms can allow biochemists to design and synthesise biomolecules and chemical probes which can be used to elucidate biochemical processes in vivo. Focussing on how to recapitulate Nature’s syntheses of key biomolecules such as peptides and sugars using modern synthetic methods, introducing key concepts such as protecting group methodology, coupling chemistry and control of stereochemical outcomes during reactions In the second half students will then explore aspects of protein structure and function, including methods for determination of structure, which will highlight how elucidating the structural basis of protein function has had major impact on our understanding of biological function. There will a strong emphasis on case studies and how the techniques are deployed to address specific biological and biomolecular questions.

Module learning outcomes

To reinforce knowledge of key organic reaction mechanisms including substitution reactions, amide bond formation, and carbonyl chemistry.

To describe how synthetic modification of proteins can be used to i) explore biological mechanisms and ii) construct ‘protein-small molecule’ conjugate therapeutics

Be able to design chemical routes to the synthesis of key biological molecules, including peptides and sugars

To describe how protein structure relates to protein mechanism and thus to biological function

To evaluate how the relationship between sequence, structure and function can be exploited and to model the structure of homologous proteins

Describe the basic principles of how protein structures are determined using the methods of X-ray crystallography, electron microscopy and NMR spectroscopy

Engage with case studies to cement their understanding of the key topics.

Module content

Chemical Tools for Biology (6 lectures, 1 x 2 h unassessed workshop, MAF)

  • 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.

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

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

Protein Structure and Diversity (2 lectures, JA (2))

  • From sequence to structure, and from structure to function. Relations between proteins. Creation of in silico protein models.
  • Factors involved in protein folding and assembly. Essential features of protein structure.

Determining Protein Structure and Stability (9 lectures, JNB (3), AAA (2) MJP (4))

Techniques of Structure Determination

  • Protein Crystallography
  • Cryo-Electron Microscopy
  • NMR Spectroscopy and its Applications

The function of proteins in biological systems (6 lectures, JNB (3) AAA (3))

  • Advanced imaging strategies in CryoEM and heterogeneity of dynamic targets.
  • The structural enzymology of the oxidative phosphorylation system.
  • DNA translocating motors
  • Viruses - Structure and Assembly

1 x 2 h unassessed workshop (structural basis of enzyme action, protein graphics)

Assessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed exam : CSB exam		 2 hours 100

Special assessment rules

None

Reassessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed exam : CSB exam		 2 hours 100

Module feedback

Results and feedback within 5 weeks. Exams are returned with question level marks and access to outline answers and markers' reports.

Indicative reading

Amino Acid and Peptide Synthesis, J. Jones

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

Other recommended reading is provided by the individual lectures in the form of suggested textbooks and review articles listed on hand-out material and as citations on slides.


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.