Biochemical reactions & interactions - BIO00054I

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  • Department: Biology
  • Module co-ordinator: Dr. Christoph Baumann
  • Credit value: 20 credits
  • Credit level: I
  • Academic year of delivery: 2018-19
    • See module specification for other years: 2019-20

Module summary

This course builds on preliminary studies of mechanistic organic and inorganic chemistry and enzyme-catalysed reactions, and an introduction to common biochemical and biophysical methods, provided in Stage 1. In this module, the scope of chemical catalysis observed in biochemical reactions will be explored, with an emphasis on the molecular mechanisms by which they are achieved. In parallel, students will be introduced to the advanced approaches used to characterise biological molecules and molecular complexes using exemplar protein-protein, protein-nucleic acid and protein-small molecule (enzyme-substrate) interactions. This will include a discussion of the challenges and limitations of these approaches using literature-based examples. After an introduction and revision of the basic principles of enzymatic catalysis (transition state theory, general acid/base, covalent and electrostatic catalysis, kinetics), the major types of enzyme-catalysed reaction mechanism will be illustrated with reference to examples of physiological, medicinal and biotechnological relevance. Students will also be provided with examples of how advanced biochemical and biophysical methods can be used to probe enzyme mechanism and the functional oligomeric state of an enzyme. Module content will be delivered in both one-hour lecture format and as longer interactive problem-solving workshops where students will apply what they have learned through structured independent study. Students will have access to online learning materials covering the following: liquid chromatography and mass spectrometry of biological molecules, calorimetry, analytical ultracentrifugation and molecular weight determination, detection and characterisation of protein-ligand interactions, ultraviolet–visible spectroscopy, fluorescence spectroscopy and techniques for studying molecular interactions at the single-molecule level. This is a core module for Biochemistry and Natural Science Biophysical Science students.

Module will run

Occurrence Teaching cycle
A Summer Vacation 2017-18 to Spring Term 2018-19

Module aims

This module will equip the student with a basic knowledge of the molecular chemistry that underpins enzymatic reactions, and an understanding of the advanced methods used to identify and characterise bio-molecular interactions.

Module learning outcomes

1. Describe and differentiate common chemical reactions catalysed by enzymes, and explain the core chemical principles and characteristics of these reactions

2. Understand the theoretical principles underlying the following techniques: analytical ultracentrifugation, ultraviolet–visible spectroscopy, calorimetry, mass spectrometry and fluorescence spectroscopy

3. Understand and apply advanced approaches used to characterise protein-protein, protein-nucleic acid and protein-small molecule (enzyme-substrate) interactions in modern biochemical research

4. Integrate general knowledge of chemistry and protein biochemistry, and apply this to the description of unseen enzyme mechanism(s) and the identification of unknown binding partner(s).

5. Select and apply appropriate quantitative data analysis procedures to extract parameters describing binding equilibria and unseen enzyme mechanisms

6. Integrate critical reading of the literature into experimental design, problem solving and quantitative data analysis as relates to enzyme mechanism and bio-molecular interactions.

Module content

The module builds on concepts in visible/UV spectroscopy and AUC from 8C Biochemical Skills module, concepts in thermodynamics and reaction kinetics from Physical Chemistry section of 'Foundation Chemistry for Biochemists' and 'Chemistry for Natural Sciences' modules.

It provides core knowledge in biophysical techniques which is important for Molecular Recognition and Biological Macromolecules and Machines modules in stage 3, and for students interested in biophysical techniques and research projects in stage 3/4.

Assessment

Task Length % of module mark
Open Examination
Open examination
N/A 40
University - closed examination
Biochemical Reactions & Interactions
1.5 hours 60

Special assessment rules

None

Reassessment

Task Length % of module mark
Open Examination
Open examination
N/A 40
University - closed examination
Biochemical Reactions & Interactions
1.5 hours 60

Module feedback

Feedback on your progress is important to your learning process and we return all first and second year work to you after marking for feedback purposes via Biology Student Services in week 9 or 10 of the spring and summer terms. You will be notified by e-mail when your work is ready for collection.

Module marks are made available to both you and your supervisor via your eVision account as soon as the marks are available, by week 6 of the spring term and week 8 of the summer term. You are expected to discuss your performance and progress with your supervisor in your mid-spring term and end of summer term supervisory meetings.

A histogram of all module marks is produced and posted on the examinations notice board outside Biology Student Services.

Specimen answers are posted on the web: by comparing the specimen answers with your own, you should obtain a clear idea of what was expected of you. For each module the markers will also give general feedback on how well the questions were answered and point out any standard errors that students may have made.

Indicative reading

These are accessible through the VLE module site.



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.