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BIOC30090

Academic Year 2024/2025

Proteins and Enzymes (BIOC30090)

Subject:
Biochemistry
College:
Science
School:
Biomolecular & Biomed Science
Level:
3 (Degree)
Credits:
5
Module Coordinator:
Assoc Professor Chandralal Hewage
Trimester:
Autumn
Mode of Delivery:
Blended
Internship Module:
No
How will I be graded?
Letter grades

Curricular information is subject to change.

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.

About this Module

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
Specified Learning Activities

8
Autonomous Student Learning

64
Lectures

24
Practical

15
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 and analytical 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 Component Scale Must Pass Component % of Final Grade In Module Component Repeat Offered
Report(s): Online submission of the Laboratory class report Week 4 Standard conversion grade scale 40% No
3.75
 No
Report(s): Online submission of the Laboratory class report Week 6 Standard conversion grade scale 40% No
3.75
 No
Report(s): Online submission of the Laboratory class report Week 10 Standard conversion grade scale 40% No
3.75
 No
Report(s): Online submission of the Laboratory class report Week 11 Standard conversion grade scale 40% No
3.75
 No
Practical Skills Assessment: Practical exam based on laboratory classes Week 12 Standard conversion grade scale 40% No
15
 No
Exam (In-person): End trimester exam covering all aspects of the teaching End of trimester
Duration:
2 hr(s)
 Standard conversion grade scale 40% No
70
 No

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
Master Ciaran Carey Tutor
Ms Manushak Hovsepyan Tutor
Ms Kate Lawless Tutor
Ellen Purcell Tutor
Mr Mikhail Romanov Tutor
Xia Xiao 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
Autumn Practical Offering 1 Week(s) - 12 Mon 10:00 - 12:50
Autumn Practical Offering 1 Week(s) - 3, 5 Mon 10:00 - 12:50
Autumn Practical Offering 1 Week(s) - 9 Mon 10:00 - 12:50
Autumn Lecture Offering 1 Week(s) - Autumn: All Weeks Thurs 15:00 - 15:50
Autumn Lecture Offering 1 Week(s) - Autumn: All Weeks Tues 16:00 - 16:50
Autumn Lecture Offering 1 Week(s) - 1 Tues 17:00 - 17:50
Autumn Lecture Offering 1 Week(s) - 1 Wed 17:00 - 17:50
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