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Proteins Architecture & Action - CHE00022I

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  • Department: Chemistry
  • Module co-ordinator: Prof. Tony Wilkinson
  • Credit value: 10 credits
  • Credit level: I
  • Academic year of delivery: 2022-23
    • See module specification for other years: 2021-22

Module summary

This module concerns the most versatile class of biological molecules - proteins. The first parts of the module cover protein structure, stability and folding including consideration of techniques used to study proteins. The second half of the module concerns the diverse activities of proteins and how structure gives rise to function including detailed case studies.

Module will run

Occurrence Teaching period
A Spring Term 2022-23 to Summer Term 2022-23

Module aims

This module explores advanced aspects of protein science – including protein structure and function, determination of structure and protein engineering. Our appreciation of almost all aspects of biochemistry and molecular biology has been enhanced by the elucidation of atomic resolution structures that reveal the underlying chemical mechanisms responsible for biological function. In addition, our ability to exploit this understanding through the use of genetic approaches to engineer proteins, is leading to the generation of improved proteins for therapeutic and biotechnology applications. Students studying this module will be equipped to go on to further studies in biochemistry/molecular biology related fields of study, as well as having valuable insight into the growing biotechnology sector of industry.

Module learning outcomes

Students will:

  • understand the basic principles of how protein structures are determined using the methods of X-ray crystallography, NMR spectroscopy and cryo-electron microscopy
  • appreciate how protein structure relates to protein mechanism and thus to biological function.
  • understand how the relationship between sequence, structure and function can be exploited to model the structure of homologous proteins
  • learn about the wide range of functions which can be performed by proteins – such as enzymes, membrane bound electron transport proteins and structural proteins. Students will be expected to rationalise and understand the behaviour of different proteins based on their structural features.
  • engage with case studies to cement their understanding of the key topics.

Module content

The module focuses on proteins, the most versatile of all molecules. After a discussion of the main features of protein structure, the patterns that emerge and how these can be exploited to predict unkown protein structures will be treated. The course goes on to cover the determination of 3D structure through X-ray diffraction, electron microscopy and NMR spectroscopy. The course concludes with some examples of proteins in action featuring oxidative phosphorylation systems, DNA translocating motor systems and viruses.

Introduction: 1 lecture KSW (1)

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 KSW (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

The course contains 2 Workshops in which Molecular Graphics will be used. The first will feature Electron Density Map Fitting and the second will explore the Structural Basis of Enzyme Action

Assessment: Workshop assessment: 1 x 3.5 hour Assessed Computational Workshop on Structural Basis of Enzyme Action. Closed examination: students answer one compulsory question.

Assessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed Exam: PAA Exam		 1 hours 80
Essay/coursework
Assessed Workshop: Structural Basis of Enzyme Action		 3.5 hours 20

Special assessment rules

Non-reassessable

Additional assessment information

Assessed Computational Workshop on Structural Basis of Enzyme Action. This workshop takes the form of an extended session in which the students are introduced to relevant software and databases as they explore the structure of a specified glycosyl hydrolase. After the workshop, the students have up to a week to complete and hand in answers to a set of questions on the enzyme which can be addressed using the skills they have learnt. Due to the linked workshop component, this is a non-reassessable activity (though it can be rescheduled with a degree of flexibility during term time).

Reassessment

Task Length % of module mark
Closed/in-person Exam (Centrally scheduled)
Closed Exam: PAA Exam		 1 hours 80

Module feedback

Students will receive feedback on their performance in the workshop assessments. They will receive verbal feedback on their progress in the formative workshops, which support lectures.

The closed examinations held in the Summer term are marked typically within 4 weeks with mark slips (with per-question break-down) being returned to students via supervisors in week 10 of the Summer Term. 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

This 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.