Studying at York
Biochemical reactions & interactions - BIO00054I
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 period |
|---|---|
| A | Autumn Term 2022-23 to Summer Term 2022-23 |
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.
Indicative assessment
| Task | % of module mark |
|---|---|
| Essay/coursework | 40 |
| Online Exam -less than 24hrs (Centrally scheduled) | 60 |
Special assessment rules
None
Indicative reassessment
| Task | % of module mark |
|---|---|
| Essay/coursework | 40 |
| Online Exam -less than 24hrs (Centrally scheduled) | 60 |
Module feedback
Cohort-level feedback will be provided on performance in closed exams and made available via the VLE. Marks for open assessments will be made available to you and your supervisor via e:vision. Individual comments will be added to your script and/or on separate summary feedback document. Histograms of module marks will be posted on the notice boards outside the Biology Student Services office. Individual marks will be made available to you and your supervisor via e:vision. Exam scripts will be made available at the end of either the Spring or Summer terms. You should take the opportunity to discuss your marks and feedback with your supervisor.
During the teaching of the module you will receive feedback that may be at a whole class or individual level. Forms of feedback may include: model answers and discussion of workshop questions, summaries of performance in practicals, VLE-based quizzes, individual spoken comments during workshops, individual written comments on formative work.
Indicative reading
These are accessible through the VLE module site.