BIOC30090 Proteins and Enzymes

Academic Year 2023/2024

This module builds on material covered in stage 2 to further understand the structure and function of proteins and enzymes .The use of NMR and X-ray crystallography to determine the structure of peptides and proteins is explained. Selected structures resulting in Nobel prizes are described. The use of electron microscopy in determining the structures of viruses and ribosomes is described. The relative merits of these approaches are assessed. Biochemical methods for examining protein-protein, protein-ligand and protein-DNA interactions are explained. These include immunological approaches, fluorescence energy transfer, surface plasmon resonance, isothermal titration calorimetry, DNA footprinting, microarrays and whole genome analysis. Post-translational processing of proteins, signal sequences and protein trafficking pathways are described. Protein degradation via lysosomal and proteasome pathways are explained. An introduction to chemical kinetics is given and the application of the Michaelis-Menten and Briggs-Haldane models to enzyme kinetics is explained. Methods for determining catalytic constants and inhibition constants are described. Other topics covered include Catalytic antibodies, Ribozymes, pH effects in enzyme catalysed reactions and the mechanism of action of enzymes. Site directed and random mutagenesis and their applications are explained. Other topics include chimeric fusion proteins, directed evolution, protein design and industrial applications.

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Curricular information is subject to change

Learning Outcomes:

On completion of this module students should be able to: 1. Understand how NMR, X-ray crystallography and electron microscopy can be used to determine biological strucures. 2. Utilise a range of biological techniques for examining protein-protein, protein-ligand and protein-DNA interactions. 3. Acquire a detailed understanding of how antibody-antigen, receptor-ligand and protein-protein interactions and can be applied to combat disease. 4. Understand how data on protein-DNA interactions are applied to understand biological functions at the genome level. 5. Understand the post translational processing of proteins and protein trafficking. 3. Determine catalytic constants kcat, KM, kcat/KM and the values of the inhibition constants Ki and IC50. 6. Measure pKa values in free enzymes and enzyme-substrate complexes. 7. Understand how enzymes can utilise transition state stabilisation, ground state stabilisation, nucleophilic, catalysis, electophilic catalysis, general acid-base calysis and binding/entropic catalysis to catalyse reactions. 8. Be aware of some of the ways ribozymes and catalytic antibodies can be used in medicine. 9. Utilise site directed mutagenesis to identify essential amino acids. 10. Protein design and industrial applications of mutagenesis experiments.

Student Effort Hours: 
Student Effort Type Hours
Lectures

24
Practical

15
Specified Learning Activities

8
Autonomous Student Learning

64
Total

111
Approaches to Teaching and Learning:
This modules uses problem solving skills by understanding the methods and techniques used in a laboratory experiment. It also improves the writing skills by generating several laboratory reports. Feedback will be available from the instructors and coordinators for further improvements. 
Requirements, Exclusions and Recommendations
Learning Recommendations:

It is recommended that students taking this module have successfully completed BIOC20050 or other modules with equivalent learning outcomes.


Module Requisites and Incompatibles
Not applicable to this module.
 
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Continuous Assessment: Laboratory write ups Throughout the Trimester n/a Graded No

15
Class Test: Class test Throughout the Trimester n/a Graded No

15
Examination: Answer four questions in total, one question each from four sections 2 hour End of Trimester Exam No Graded No

70

Carry forward of passed components
No
 
Resit In Terminal Exam
Spring Yes - 2 Hour
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment
• Group/class feedback, post-assessment
• Online automated feedback

How will my Feedback be Delivered?

Feedback will be available for all laboratory classes and their write ups. Calculations will also be conducted during the laboratory classes. This will help to answer the laboratory test at the end of the semester. This will further enhance the writing skills and calculations for the end semester exam.

Name Role
Assoc Professor Gerard Cagney Lecturer / Co-Lecturer
Assoc Professor Margaret Worrall Lecturer / Co-Lecturer
Ms Maeve Boyce Tutor
Ms Caoimbhe Burke Tutor
Ms Niamh Duggan Tutor
Miss Ella Fouhy Tutor
Ms Manushak Hovsepyan Tutor
Yanqiu Ye Tutor
Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.
 
Autumn
      
Practical Offering 1 Week(s) - 10 Mon 10:00 - 12:50
Practical Offering 1 Week(s) - 12 Mon 10:00 - 12:50
Practical Offering 1 Week(s) - 3, 5 Mon 10:00 - 12:50
Practical Offering 1 Week(s) - 9 Mon 10:00 - 12:50
Lecture Offering 1 Week(s) - Autumn: All Weeks Thurs 15:00 - 15:50
Lecture Offering 1 Week(s) - Autumn: All Weeks Tues 16:00 - 16:50
Autumn