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Module Code - Title:

BY4223 - PROTEIN CHEMISTRY AND BIOLOGICS

Year Last Offered:

N/A

Hours Per Week:

Lecture

0

Lab

20

Tutorial

0

Other

10

Private

10

Credits

24

Grading Type:

N

Prerequisite Modules:

Rationale and Purpose of the Module:

The module will provide knowledge, understanding and practical skills in recombinant protein production, protein isolation techniques, protein modification and characterization. The module will provide a theoretical basis for experimental methods to support troubleshooting and design of experiment. Skills for problem solving related to genetic engineering of recombinant proteins will be established and methods used to immobilize, chemically tag and stabilize proteins presented. The theoretical and practical aspects of the module will be enhanced by complementary understanding of the industry regulatory framework required for production of recombinant proteins for use as active ingredients in biological medicaments. Data handling will be supported by extension of coding skills and analytic tools. Characterization of proteins will include structure analysis, drug docking, and development of understanding of Structure-Activity-Relationships (SAR), which is fundamental to design of new biotherapeutics.

Syllabus:

Tutorials, workshops and self-directed team learning will support development of understanding and knowledge of the following topics: 1. Cell biology of protein production - gene expression, transcription and translation 2. Expression systems - mammalian, plant, yeast and bacterial 3. Molecular biology of protein engineering - codon optimization, point mutations 4. Growth methods - batch and continuous 5. The basis of chromatography - FPLC & HPLC 6. First stage protein harvest methods - Filtration, precipitation 7. Affinity chromatographic methods - IMAC, GST & other tags 8. Charge based chromatographic methods 9. Hydrophobic based chromatographic methods 10. Size Exclusion Chromatography 11. Specialized affinity methods SPA (Staphylococcal Protein A), Proteins G, H & L & MAbs 12. Residual tests - host protein, LPS 13. Critical Quality Attributes (CQA) tests 14. Structure determination and analysis 15. Structure Activity Relationship (SAR) studies 16. Strategies to immobilize proteins 17. Strategies to chemically modify proteins 18. Working in a regulated environment - the European Medicines Agency (EMA) and the Food and Drug Administration (FDA) and other governance organizations Acquisition and understanding of knowledge will be supported by completion of practical laboratories covering the following topics. 1. Protein Structure analysis and molecular docking 2. Molecular cloning 3. Design of synthetic DNA 4. Point mutagenesis testing SAR in proteins 5. DNA sequence determination and analysis 6. Expression of a recombinant protein in a Bacterial expression system 7. Optimization of expression of a recombinant protein in a Bacterial expression system 8. Production of recombinant protein using Bioreactors 9. Use of FPLC chromatographic methods to purify a recombinant protein 10. Production of a recombinant protein in a Mammalian expression system 11. Purification of Immunoglobulin G by Protein A affinity chromatography 12. Determination of protein concentration and purity 13. Test for residual host protein and endotoxin by ELISA 14. Coupling protein to solid supports - CNBr Sepharose coupling - making Protein A Sepharose. 15. Chemical modification of proteins - biotin tagging

Learning Outcomes:

Cognitive (Knowledge, Understanding, Application, Analysis, Evaluation, Synthesis)

On successful completion of this module, students will be able to: 1. Describe processes used by cells to produce proteins 2. Explain the molecular basis of regulation of protein expression 3. Describe how a recombinant protein is produced 4. Describe 3 different expression systems for production of recombinant proteins 5. Explain the basis of different key separation technologies 6. Discuss affinity chromatography in the context of Monoclonal Antibody (MAb) purification 7. Describe CQA testing 8. Design a testing regime to evaluate protein purity 9. Use knowledge of the regulations pertaining to protein production to evaluate risk in a protein production workflow 10. Demonstrate and distinguish between three distinct chromatographic techniques 11. Analyse chromatographic data and evaluate reproducibility 12. Critique data from chromatographic experiments 13. Design, defend and execute a protein purification regime for a recombinant protein 14. Discuss Structure Activity Relationships 15. Analyse and compare protein structures 16. Describe how to immobilize proteins to solid supports and discuss the importance of this technology 17. Describe methods to chemically modify proteins and discuss the importance of these techniques

Affective (Attitudes and Values)

On successful completion of this module, students will be able to: 1. Demonstrate a comprehensive appreciation of the regulatory framework which guides production of proteins and other biotherapeutics for use as active ingredients. 2. Demonstrate a comprehensive appreciation for record keeping and data integrity. 3. Work in a professional manner akin to GMP (Good Manufacturing Principles).

Psychomotor (Physical Skills)

On successful completion of this module, students will be able to: 1. Perform experimentation using a range of instrumentation associated with protein production, isolation and testing. 2. Conduct themselves in an organized and calm manner consistent with a professional laboratory environment.

How the Module will be Taught and what will be the Learning Experiences of the Students:

The module will be taught through a series of workshops, flipped classrooms, demonstrations and lab practice sessions employing techniques in active learning (Bloom's Taxonomy levels). The module will use group learning focused on problem-based learning. The students will work in teams to extract information on syllabus topics, design experimentation, investigate methodologies, critique data and incorporate information into presentations for peer-learning. Workshop-style delivery of new material to the student will be used in conjunction with supervised and non-supervised group work encouraging independence and agility. Use will be made of computer-based learning tools and self-testing. Laboratory practice will focus on mastery of core skills in protein chemistry and recombinant protein production and purification which will be taught by small group demonstration and practice generating knowledgeable graduates. Self-directed practical learning will be supported generating independent, curious and courageous graduates. Student agency will be achieved through integrating aspects of theory, practice, coding, analytics and professional skills. Analysis of real world data and design of experiment challenges will form part of the learning experience generating knowledgeable graduates.

Research Findings Incorporated in to the Syllabus (If Relevant):

Prime Texts:

Rob Reed, Jonathan Weyers, David A Holmes and Allan Jones (2021) Practical Skills in Biomolecular Science. 6th Edition , Pearson
rvey Lodish; Arnold Berk; Chris A. Kaiser; Monty Krieger; Anthony Bretscher; Hidde Ploegh; Kelsey C. Martin; Michael Yaffe; Angelika Amon (2021) Molecular Cell Biology. 9th Edition , Macmillan

Other Relevant Texts:

Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, and Rebecca Orr (2021) Campbell Biology. 12th Edition , Pearson

Programme(s) in which this Module is Offered:

Semester(s) Module is Offered:

Summer

Module Leader:

Jakki.Cooney@ul.ie